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Gentoo's Bugzilla – Attachment 452742 Details for
Bug 599232
sci-biology/arb-5.3 - respect EPREFIX
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build.log
build.log (text/plain), 677.03 KB, created by
Martin Mokrejš
on 2016-11-08 19:31:40 UTC
(
hide
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Description:
build.log
Filename:
MIME Type:
Creator:
Martin Mokrejš
Created:
2016-11-08 19:31:40 UTC
Size:
677.03 KB
patch
obsolete
>[32;01m * [39;49;00mPackage: sci-biology/arb-5.3 >[32;01m * [39;49;00mRepository: gentoo >[32;01m * [39;49;00mMaintainer: sci-biology@gentoo.org >[32;01m * [39;49;00mUSE: abi_x86_64 amd64 elibc_glibc kernel_linux prefix userland_GNU >[32;01m * [39;49;00mFEATURES: nostrip preserve-libs splitdebug >>>> Unpacking source... >>>> Unpacking arb-5.3.tgz to /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work >>>> Unpacking arb-5.3-linker.patch.xz to /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work >>>> Source unpacked in /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work >>>> Preparing source in /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3 ... > [32;01m*[0m Applying arb-5.3-linker.patch ... >[A[311C [34;01m[ [32;01mok[34;01m ][0m > [32;01m*[0m Applying 5.1-libs.patch ... >[A[311C [34;01m[ [32;01mok[34;01m ][0m > [32;01m*[0m Applying 5.1-bfr-overflow.patch ... >[A[311C [34;01m[ [32;01mok[34;01m ][0m > [32;01m*[0m Applying 5.2-libpng15.patch ... >[A[311C [34;01m[ [32;01mok[34;01m ][0m > [32;01m*[0m Applying arb-5.2-gcc-47.patch ... >[A[311C [34;01m[ [32;01mok[34;01m ][0m >make -j8 ARBHOME=/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3 links >SOURCE_TOOLS/generate_all_links.sh >make[1]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. >make[1]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin' >find . -type l -exec rm {} \; >ln -s -f `find ../SH ../PERL_SCRIPTS -perm -100 ! -type d ! -name 'config*' -print` . >make[1]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin' >generate_all_links.sh done. >touch SOURCE_TOOLS/generate_all_links.stamp >>>> Source prepared. >>>> Configuring source in /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3 ... >>>> Source configured. >>>> Compiling source in /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3 ... >make -j8 ARBHOME=/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3 PATH=/scratch/mmokrejs/gentoo_rap/usr/lib/portage/python2.7/ebuild-helpers/unprivileged:/scratch/mmokrejs/gentoo_rap/usr/lib/portage/python2.7/ebuild-helpers:/scratch/mmokrejs/gentoo_rap/usr/local/sbin:/scratch/mmokrejs/gentoo_rap/usr/local/bin:/scratch/mmokrejs/gentoo_rap/usr/sbin:/scratch/mmokrejs/gentoo_rap/usr/bin:/scratch/mmokrejs/gentoo_rap/sbin:/scratch/mmokrejs/gentoo_rap/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/scratch/mmokrejs/gentoo_rap/opt/bin:/scratch/mmokrejs/gentoo_rap/usr/x86_64-pc-linux-gnu/gcc-bin/5.4.0:/scratch/mmokrejs/gentoo_rap/opt/intel/compilers_and_libraries_2016.2.181/linux/bin/intel64:/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin LD_LIBRARY_PATH=:/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/lib tarfile >make clean2 >make[1]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3' >make[2]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PROBE' >rm -f PT_new_design.o PT_family.o PT_prefixtree.o PT_main.o PT_io.o PT_etc.o PT_secundaer.o PT_buildtree.o PT_match.o PT_findEx.o *.a >make[2]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/AISC' >rm -f aisc.o aisc_commands.o aisc_var_ref.o aisc_mix.o aisc >make[2]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/AISC_MKPTPS' >rm -f mkptypes.o aisc_mkpt >make[2]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/ALIV3' >rm -f a3.o a3_seq.o a3_ptree1.o a3_ptree2.o a3_helix.o a3_darray.o a3_ali.o a3_matrix.o a3_arbdb.o a3_basen.o *.a >make[2]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/ARBDB' >rm -f adsort.o adlang1.o adstring.o admatch.o arbdb.o ad_core.o admath.o adoptimize.o adsystem.o adindex.o adperl.o adlink.o adsocket.o adcomm.o adhash.o adquery.o ad_save_load.o adcompr.o admalloc.o ad_load.o admap.o adTest.o adtune.o adGene.o adtcp.o adhashtools.o adExperiment.o adtools.o adseqcompr.o adtables.o adRevCompl.o adChangeKey.o adali.o adcolumns.o adtree.o adname.o aditem.o arbdbpp.o ad_config.o *.a *.so >make[2]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/ARBDBPP' >rm -f adtsequence.o adt_edit.o adtali.o adextended.o adseq.o adspecies.o admain.o adali.o liste.o *.a *.so >make[2]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/ARBDB2' >rm -f adsort.o adlang1.o adstring.o admatch.o arbdb.o ad_core.o admath.o adoptimize.o adsystem.o adindex.o adperl.o adlink.o adsocket.o adcomm.o adhash.o adquery.o ad_save_load.o adcompr.o admalloc.o ad_load.o admap.o adTest.o adtune.o adGene.o adtcp.o adhashtools.o adExperiment.o adtools.o adseqcompr.o adtables.o adRevCompl.o adChangeKey.o adali.o adcolumns.o adtree.o adname.o aditem.o ad_config.o *.a *.so >make[2]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/AISC' >make[2]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/ARBDBS' >rm -f adsort.o adlang1.o adstring.o admatch.o arbdb.o ad_core.o admath.o adoptimize.o adsystem.o adindex.o adperl.o adlink.o adsocket.o adcomm.o adhash.o adquery.o ad_save_load.o adcompr.o admalloc.o ad_load.o admap.o adTest.o adtune.o adGene.o adtcp.o adhashtools.o adExperiment.o adtools.o adseqcompr.o adtables.o adRevCompl.o adChangeKey.o adali.o adcolumns.o adtree.o adname.o aditem.o arbdbpp.o ad_config.o *.a >make[2]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/AISC_MKPTPS' >make[2]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PROBE' >make[2]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/ALIV3' >make[2]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/ARBDBPP' >make[2]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/ARBDB' >make[2]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/ARBDB2' >make[2]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/ARBDBS' >make[2]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/ARB_GDE' >rm -f GDE_ParseMenu.o GDE.o GDE_event.o GDE_arbdb_io.o GDE_HGLfile.o GDE_Genbank.o GDE_FileIO.o *.a >make[2]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/AWT' >rm -f AWT_input_mask.o AWT_hotkeys.o AWT_www.o AWT_tables.o AWT_irstree.o AWT_asciiprint.o AWT_map_key.o AWT_tree_cmp.o AWT_seq_colors.o AWT_pro_a_nucs.o AWT_csp.o AWT_canvas.o AWT_dtree.o AWT_tree.o AWT_tree_cb.o AWT_nei.o AWT_filter.o AWT_sel_boxes.o AWT_canio.o AWT_nds.o AWT_query_and_functions.o AWT_file_selection.o AWT_preset.o AWT_seq_dna.o AWT_seq_protein.o AWT_seq_simple_pro.o AWT_codon_table.o AWT_iupac.o AWT_config_manager.o AWT_advice.o AWT_db_browser.o AWT_attributes.o AWT_changekey.o AWT_item_sel_list.o AWT_macro.o AWT_translate.o *.a *.so >make[2]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/AWTC' >rm -f AWTC_next_neighbours.o AWTC_constructSequence.o AWTC_seq_search.o AWTC_submission.o *.a >make[2]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/AWTI' >rm -f AWTI_import.o AWTI_export.o *.a >make[2]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/CONSENSUS_TREE' >rm -f CT_part.o CT_hash.o CT_ntree.o CT_rbtree.o CT_dtree.o CT_ctree.o CT_mem.o *.a >make[2]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/CONVERTALN' >rm -f main.o fconv.o mg.o genbank.o macke.o phylip.o paup.o util.o date.o embl.o gcg.o printable.o alma.o routines.o convert.o /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/arb_convert_aln >make[2]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/ARB_GDE' >make[2]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/DBSERVER' >rm -f db_server.o *.a >make[2]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/DIST' >rm -f DI_mldist.o DI_protdist.o DI_compress_matrix.o DI_view_matrix.o DI_save_matr.o DI_main.o DI_matr.o distanalyse.o *.a >make[2]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/AWT' >make[2]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/CONVERTALN' >make[2]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/AWTC' >make[2]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/AWTI' >make[2]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/CONSENSUS_TREE' >make[2]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/DBSERVER' >make[2]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/EDIT' >rm -f edit.o edit_naligner.o edit_tools.o ed_conf.o *.a >make[2]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/DIST' >make[2]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/EDIT4' >rm -f ED4_protein_2nd_structure.o ED4_ProteinViewer.o ED4_search.o ED4_cursor.o ED4_dump.o ED4_nds.o ED4_secedit.o ED4_RNA3D.o ED4_main.o ED4_mini_classes.o ED4_edit_string.o ED4_base.o ED4_manager.o ED4_terminal.o ED4_root.o EDB_root_bact.o ED4_window.o ED4_members.o ED4_no_class.o ED4_list.o ED4_text_terminals.o ED4_tools.o ED4_block.o ED4_visualizeSAI.o edit_naligner.o graph_aligner_gui.o ED4_dots.o *.a >make[2]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/EISPACK' >rm -f eispack.o d_sign.o *.a >make[2]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDE' >make[2]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GENOM' >rm -f GEN_interface.o GEN_map.o GEN_graphic.o GEN_gene.o GEN_nds.o GEN_color_groups.o GEN_translations.o EXP_interface.o EXP_main.o *.a >make[2]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GENOM_IMPORT' >rm *.o >make[2]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/EDIT' >make[2]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GL' >make[2]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/ISLAND_HOPPING' >rm -f island_hopping.o i-hopper.o align.o memory.o trnsprob.o *.a >make[2]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/EISPACK' >make[2]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/EDIT4' >make[3]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GL/glpng' >rm -f glpng.o *.a >make[2]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GENOM' >rm: cannot remove '*.o': No such file or directory >make[2]: [Makefile:33: clean] Error 1 (ignored) >rm *.a >make[3]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDE/CLUSTAL' >rm -f clustalv.o amenu.o myers.o sequence.o showpair.o upgma.o util.o trees.o gcgcheck.o /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/clustalv >make[3]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GL/glAW' >rm -f GLwMDrawA.o AW_window_ogl.o *.a >make[3]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDE/SUPPORT' >rm -f /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/CAP2 /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/Restriction /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/Zuk_to_gen /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/count /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/findall /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/lsadt /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/sho_helix /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/varpos >make[2]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/ISLAND_HOPPING' >make[3]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDE/CLUSTAL' >make[3]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDE/SUPPORT' >make[3]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GL/glpng' >make[3]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDE/AxML' >rm -f axml.o /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/axml >rm: cannot remove '*.a': No such file or directory >make[2]: [Makefile:34: clean] Error 1 (ignored) >rm *.bak >make[3]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDE/RAxML' >rm -f axml.o raxmlParsimony.o rev_functions.o optimizeModel.o multiple.o searchAlgo.o topologies.o parsePartitions.o treeIO.o models.o bipartitionList.o rapidBootstrap.o evaluatePartialGeneric.o evaluateGeneric.o newviewGeneric.o makenewzGeneric.o evaluateGenericVector.o categorizeGeneric.o /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/raxmlHPC >make[3]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GL/glAW' >make[2]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GL' >make[3]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDE/AxML' >make[3]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDE/RAxML' >make[3]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDE/PHYML' >rm -f main.o utilities.o optimiz.o lk.o bionj.o models.o free.o options.o simu.o eigen.o /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/phyml >make[2]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/MERGE' >rm -f MG_checkfield.o MG_main.o MG_trees.o MG_alignment.o MG_species.o MG_extendeds.o MG_names.o MG_gene_species.o MG_configs.o MG_preserves.o *.a >make[2]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/MULTI_PROBE' >rm -f MP_main.o MP_Window.o MP_noclass.o MP_sonde.o MP_sondentopf.o MP_mo_liste.o MP_probe.o MP_GenerationDuplicates.o MP_Generation.o MP_probe_combi_statistic.o MP_probe_tabs.o MP_permute.o *.a >rm: cannot remove '*.bak': No such file or directory >make[2]: [Makefile:35: clean] Error 1 (ignored) >rm *~ >make[2]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/NALIGNER' >rm -f ali_aligner.o ali_arbdb.o ali_global.o ali_main.o ali_pathmap.o ali_prealigner.o ali_profile.o ali_pt.o ali_sequence.o ali_solution.o *.a >make[3]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDE/PHYML' >make[2]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/NAMES' >rm -f names.o *.a >make[3]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDE/CLUSTALW' >rm -f *.o /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/clustalw >make[2]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/MERGE' >rm: cannot remove '*~'make[2]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/NAMES_COM' >: No such file or directory >make[2]: [Makefile:36: clean] Error 1 (ignored) >rm *# >make[2]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/MULTI_PROBE' >make[2]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/NALIGNER' >make[2]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/NTREE' >rm -f AP_consensus.o AP_conservProfile2Gnuplot.o AP_cprofile.o AP_csp_2_gnuplot.o AP_pos_var_pars.o NT_cb.o NT_concatenate.o NT_dbrepair.o NT_edconf.o NT_extern.o NT_import.o NT_ins_col.o NT_join.o NT_main.o NT_sort.o NT_trackAliChanges.o NT_validManual.o NT_validNameParser.o NT_validNames.o ad_ali.o ad_ext.o ad_spec.o ad_transpro.o ad_trees.o *.a >make[2]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/NAMES' >make[3]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/NAMES_COM' >rm -f *.[ao] >make[3]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDE/CLUSTALW' >rm: cannot remove '*#': No such file or directory >make[2]: [Makefile:37: clean] Error 1 (ignored) >rm *\% >make[3]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDE/PHYLIP' >rm -f /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/clique /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/consense /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/contml /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/contrast /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/dnacomp /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/dnadist /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/dnainvar /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/dnaml /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/dnamlk /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/dnamove /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/dnapars /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/dnapenny /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/dolmove /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/dollop /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/dolpenny /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/factor /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/fitch /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/gendist /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/kitsch /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/mix /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/move /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/neighbor /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/pars /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/penny /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/proml /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/promlk /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/protdist /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/protpars /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/restdist /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/restml /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/retree /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/seqboot /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/treedist /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/drawgram /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/drawtree *.o >make[3]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDE/TREEPUZZLE' >rm -f src/gamma.o src/ml1.o src/ml2.o src/ml3.o src/model1.o src/model2.o src/puzzle1.o src/puzzle2.o src/sched.o src/util.o /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/puzzle >make[3]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDE/FASTDNAML' >rm -f fastDNAml.o /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/fastdnaml >make[2]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/NTREE' >rm -f */*.[ao] >make[3]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDE/TREEPUZZLE' >make[2]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PARSIMONY' >rm -f PARS_main.o PARS_dtree.o PARS_debug.o PARS_klprops.o AP_buffer.o AP_main.o AP_tree_nlen.o AP_tree_edge.o *.a >make[3]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDE/FASTDNAML' >make[2]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PGT' >rm -f main.o dialog.o arb_interface.o main_dialog.o import_dialog.o selection_dialog.o file_import.o tiff_image.o image_dialog.o plot.o analyze_window.o entry_sel_dialog.o config_dialog.o help_dialog.o msgbox.o *.a >rm: cannot remove '*%': No such file or directory >make[2]: [Makefile:38: clean] Error 1 (ignored) >make[2]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GENOM_IMPORT' >make[3]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDE/PHYLIP' >make[2]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDE' >make[2]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PHYLO' >rm -f PH_data.o PH_root.o PH_main.o PH_filt.o PH_display.o PH_matr.o *.a >make[2]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PARSIMONY' >rm -f GENH/* >make[2]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PRIMER_DESIGN' >rm -f PRD_Pair.o PRD_Item.o PRD_Node.o PRD_Range.o PRD_SequenceIterator.o PRD_SearchFIFO.o PRD_Design.o primer_design.o *.a >make[2]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PGT' >make[2]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PROBE_COM' >make[2]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PROBE_DESIGN' >rm -f probe_design.o SaiProbeVisualization.o probe_match_parser.o *.a >make[2]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PROBE_SET' >rm -f ps_node.o ps_filebuffer.o ps_database.o ps_tools.o fb_test.o ps_convert_db.o ps_merge_my_dbs.o ps_detect_weak_differences.o ps_find_probes.o ps_eval_candidates.o ps_get_probes.o ps_my2ascii.o ps_my2asciipaths.o ps_arb2asciipaths.o ps_show_result.o >make[3]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PROBE_COM' >rm -f *.[ao] >rm -f GENC/* >make[2]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PHYLO' >make[2]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/READSEQ' >rm -f readseq.o ureadseq.o /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/arb_readseq >make[2]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PRIMER_DESIGN' >rm -f /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PROBE_SET/bin/ps_show_result /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PROBE_SET/bin/ps_arb2asciipaths /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PROBE_SET/bin/ps_my2asciipaths /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PROBE_SET/bin/ps_my2ascii /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PROBE_SET/bin/ps_get_probes /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PROBE_SET/bin/ps_eval /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PROBE_SET/bin/ps_find /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PROBE_SET/bin/ps_detect /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PROBE_SET/bin/ps_merge /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PROBE_SET/bin/ps_convert /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PROBE_SET/bin/fb_test >make[2]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PROBE_DESIGN' >make[2]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/RNA3D' >rm -f RNA3D_Main.o RNA3D_Interface.o RNA3D_Graphics.o RNA3D_OpenGLEngine.o RNA3D_OpenGLGraphics.o RNA3D_Textures.o RNA3D_StructureData.o RNA3D_Renderer.o *.a >make[2]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/READSEQ' >make[2]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PROBE_SET' >rm -f */*.[ao] >rm -f .depends >make[2]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SECEDIT' >rm -f SEC_toggle.o SEC_bonddef.o SEC_db.o SEC_helix.o SEC_graphic.o SEC_structure.o SEC_read.o SEC_io.o SEC_paint.o SEC_layout.o SEC_split.o SEC_abspos.o SEC_main.o *.a >make[3]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/NAMES_COM' >make[2]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/NAMES_COM' >make[2]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SEQ_QUALITY' >rm -f SQ_main.o SQ_functions.o SQ_GroupData.o *.a >make[2]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/RNA3D' >make[2]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SERVERCNTRL' >rm -f servercntrl.o *.a >make[2]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/STAT' >rm -f ST_quality.o ST_ml.o ST_window.o *.a >make[2]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL' >rm -f GENH/* >make[2]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SECEDIT' >make[3]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/TREE_READ' >rm -f TreeRead.o TreeTools.o *.a >make[2]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SEQ_QUALITY' >make[2]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/TOOLS' >rm -f /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/arb_2_ascii /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/arb_2_bin /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/arb_a2ps /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/arb_count_chars /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/arb_dnarates /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/arb_export_rates /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/arb_export_tree /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/arb_gene_probe /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/arb_message /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/arb_notify /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/arb_primer /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/arb_probe /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/arb_proto_2_xsub /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/arb_read_tree /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/arb_replace /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/arb_swap_rnastr >make[2]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SERVERCNTRL' >make[2]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/TREEGEN' >rm -f base.o defines.o frand.o readcfg.o rns.o sim.o simcfg.o spreadin.o *.a >make[2]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/STAT' >make[3]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/TREE_WRITE' >rm -f TreeWrite.o *.a >rm -f arb_2_ascii.o arb_2_bin.o arb_a2ps.o arb_count_chars.o arb_dnarates.o arb_export_rates.o arb_export_tree.o arb_gene_probe.o arb_message.o arb_notify.o arb_primer.o arb_probe.o arb_proto_2_xsub.o arb_read_tree.o arb_replace.o arb_swap_rnastr.o >rm -f GENC/* >make[3]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/HELIX' >rm -f BI_helix.o *.a >make[3]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/AW_HELIX' >rm -f AW_helix.o *.a >make[3]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/TREE_READ' >make[2]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/TOOLS' >make[2]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/WETC' >rm -f WETC_main.o *.a >make[2]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/TREEGEN' >make[3]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/TREE_WRITE' >make[3]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/AW_NAME' >rm -f AW_rename.o AW_names_admin.o *.a >rm -f .depends >make[3]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/HELIX' >make[3]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/DB_SCANNER' >rm -f db_scanner.o *.a >make[3]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/AW_HELIX' >make[3]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PROBE_COM' >make[2]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PROBE_COM' >make[2]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/WINDOW' >rm -f AW_position.o AW_Xm.o AW_at.o AW_button.o AW_click.o AW_debug.o AW_device.o AW_font_group.o AW_global_awars.o AW_nawar.o AW_preset.o AW_print.o AW_question.o AW_size.o AW_status.o AW_window.o AW_xfig.o AW_xfigfont.o AW_xfont.o AW_xkey.o AW_window_Xm_interface.o *.a *.so >make[2]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/WETC' >make[3]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/FILE_BUFFER' >rm -f FileBuffer.o *.a >make[3]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/AW_NAME' >make[2]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/XML' >rm -f xml.o *.a >make[3]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/REGEXPR' >rm -f RegExpr.o *.a >make[3]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/DB_SCANNER' >make[2]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDEHELP' >rm -f MENUS/dnamlrates.genmenu MENUS/fastdnaml.genmenu MENUS/pretty_print.genmenu MENUS/phylip_dist_org.genmenu MENUS/puzzle.genmenu MENUS/align.genmenu MENUS/warning.genmenu MENUS/phylip_ml.genmenu MENUS/raxml.genmenu MENUS/desoete.genmenu MENUS/phylip_help.genmenu MENUS/export.genmenu MENUS/phylip_dist.genmenu MENUS/inc_fastdnaml.genmenu MENUS/import.genmenu MENUS/start_arb.genmenu MENUS/phylip_pars.genmenu ARB_GDEmenus helpfiles.lst >make[2]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/WINDOW' >make[3]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/FILE_BUFFER' >make[2]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/XML' >make[2]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SOURCE_TOOLS' >rm -f generate_all_links.stamp >make[3]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/REGEXPR' >make[3]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/FAST_ALIGNER' >rm -f fast_aligner.o ClustalV.o *.a >make[2]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin' >find . -type l -exec rm {} \; >make[2]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SOURCE_TOOLS' >make[3]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDEHELP' >make[2]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PERL2ARB' >test -f Makefile && make clean >make[3]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/FAST_ALIGNER' >make[2]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL' >cat: helpfiles.lst: No such file or directory >rm -f ./HELP_GEN/*.help >make[2]: [Makefile.main:99: clean] Error 1 (ignored) >rm -f Makefile.old proto.h debug.h ARB.c ARB.xs .depends depends.stamp Makefile.PL /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/lib/ARB.pm /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/lib/ARB.so >make[2]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PERL2ARB' >rm -f ./HELP_DOC_GEN/*.doc >make[3]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDEHELP' >make[2]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDEHELP' >make[2]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/HELP_SOURCE' >rm -f arb_help2xml.o /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/arb_help2xml >rm -f `find ../lib/help -name "*.hlp"` >rm -f `find ../lib/help_html -name "*.html"` >find: '../lib/help_html': No such file or directory >rm -f xml.stamp dummy _index.html >rm -f `find Xml -name "*.xml"` >find: 'Xml': No such file or directory >make -C genhelp clean >make[3]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/HELP_SOURCE/genhelp' >rm -f *.hlp >make[3]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/HELP_SOURCE/genhelp' >make[2]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/HELP_SOURCE' >find . -type f -perm -100 -exec rm {} \; >make[2]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin' >rm -f *.last_gcc >make[1]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3' >make all >make[1]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3' >make links >make[2]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3' >SOURCE_TOOLS/generate_all_links.sh >make[3]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin' >make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. >find . -type l -exec rm {} \; >ln -s -f `find ../SH ../PERL_SCRIPTS -perm -100 ! -type d ! -name 'config*' -print` . >make[3]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin' >generate_all_links.sh done. >touch SOURCE_TOOLS/generate_all_links.stamp >make[2]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3' >make com >make[2]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3' >-------------------------------------------------------------------------------- Make everything in AISC_MKPTPS >make[3]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/AISC_MKPTPS' >cc -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AISC_MKPTPS -c mkptypes.c >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -Wl,-O1 -Wl,--as-needed -Wl,--export-dynamic -rdynamic -o aisc_mkpt mkptypes.o >make[3]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/AISC_MKPTPS' >-------------------------------------------------------------------------------- Make everything in AISC >make[3]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/AISC' >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AISC -c aisc.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AISC -c aisc_commands.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AISC -c aisc_var_ref.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AISC -c aisc_mix.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >aisc_commands.c: In function 'int do_com_next(const char*)': >aisc_commands.c:906:21: warning: variable 'p' set but not used [-Wunused-but-set-variable] > char *p; > ^ >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -Wl,-O1 -Wl,--as-needed -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AISC -o aisc aisc.o aisc_commands.o aisc_var_ref.o aisc_mix.o >make[3]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/AISC' >-------------------------------------------------------------------------------- Make everything in NAMES_COM >make[3]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/NAMES_COM' >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/NAMES_COM' >umask 002;makedepend C/*.c GENC/*.c -I GENH -I C -f- -w1 | grep -v ' /usr' | sed -e 's/^C/O/ig' > .depends_new >/scratch/mmokrejs/gentoo_rap/bin/sh: makedepend: command not found >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SOURCE_TOOLS/mv_if_diff .depends_new .depends >.depends created. >../MAKEBIN/aisc AISC/aisc.pa names.aisc GENH/aisc.h >../MAKEBIN/aisc AISC/aisc_com.pa names.aisc GENH/aisc_com.h >rm -f GENH/aisc_server_extern.aisc >rm -f GENH/aisc_server_extern.h >../MAKEBIN/aisc_mkpt -a C/aisc_extern.c names_extern.c >GENH/aisc_server_extern.aisc >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NAMES_COM -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -fno-strict-aliasing -Wno-unused -c -o O/client.o C/client.c -IGENH -I. -IC >../MAKEBIN/aisc_mkpt -C C/aisc_extern.c names_extern.c >GENH/aisc_server_extern.h >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NAMES_COM -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -fno-strict-aliasing -Wno-unused -c -o O/debug.o C/debug.c -IGENH -I. -IC >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NAMES_COM -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -fno-strict-aliasing -Wno-unused -c -o O/server.o C/server.c -IGENH -I. -IC >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NAMES_COM -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -fno-strict-aliasing -Wno-unused -c -o O/struct_man.o C/struct_man.c -IGENH -I. -IC >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NAMES_COM -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -fno-strict-aliasing -Wno-unused -c -o O/aisc_extern.o C/aisc_extern.c -IGENH -I. -IC >../MAKEBIN/aisc AISC/aisc_server.pa names.aisc GENC/aisc_server.c GENH/aisc_server_extern.aisc GENH/import_proto.h >../MAKEBIN/aisc AISC/aisc_global.pa names.aisc GENC/aisc_global.c GENH/aisc_server_extern.aisc GENH/import_proto.h >../MAKEBIN/aisc AISC/aisc_debug_globals.pa names.aisc GENC/aisc_debug_globals.c GENH/aisc_server_extern.aisc GENH/import_proto.h >rm -f GENH/aisc_server_proto.h >../MAKEBIN/aisc_mkpt -C GENC/aisc_server.c >GENH/aisc_server_proto.h >echo GENH/import_proto.h >GENH/import_proto.h >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NAMES_COM -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -fno-strict-aliasing -Wno-unused -c -o GENC/aisc_debug_globals.o GENC/aisc_debug_globals.c -IGENH -I. -IC >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NAMES_COM -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -fno-strict-aliasing -Wno-unused -c -o GENC/aisc_global.o GENC/aisc_global.c -IGENH -I. -IC -DAISC_SAVE_YES >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NAMES_COM -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -fno-strict-aliasing -Wno-unused -c -o GENC/aisc_server.o GENC/aisc_server.c -IGENH -I. -IC -DAISC_SAVE_YES >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NAMES_COM -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -fno-strict-aliasing -Wno-unused -c -o names_extern.o names_extern.c -IGENH -I. -IC -DAISC_SAVE_YES >ld -r -o client.a O/client.o O/debug.o GENC/aisc_debug_globals.o >ld -r -o server.a O/server.o O/struct_man.o O/aisc_extern.o GENC/aisc_global.o GENC/aisc_server.o names_extern.o >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/NAMES_COM' >make[3]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/NAMES_COM' >-------------------------------------------------------------------------------- Make everything in PROBE_COM >make[3]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PROBE_COM' >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PROBE_COM' >umask 002;makedepend C/*.c GENC/*.c -I GENH -I C -f- -w1 | grep -v ' /usr' | sed -e 's/^C/O/ig' > .depends_new >/scratch/mmokrejs/gentoo_rap/bin/sh: makedepend: command not found >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SOURCE_TOOLS/mv_if_diff .depends_new .depends >.depends created. >../MAKEBIN/aisc AISC/aisc.pa PT.aisc GENH/aisc.h >../MAKEBIN/aisc AISC/aisc_com.pa PT.aisc GENH/aisc_com.h >rm -f GENH/aisc_server_extern.aisc >rm -f GENH/aisc_server_extern.h >../MAKEBIN/aisc_mkpt -a C/aisc_extern.c PT_extern.c >GENH/aisc_server_extern.aisc >../MAKEBIN/aisc_mkpt -C C/aisc_extern.c PT_extern.c >GENH/aisc_server_extern.h >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PROBE_COM -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -fno-strict-aliasing -Wno-unused -c -o O/client.o C/client.c -IGENH -I. -IC >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PROBE_COM -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -fno-strict-aliasing -Wno-unused -c -o O/debug.o C/debug.c -IGENH -I. -IC >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PROBE_COM -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -fno-strict-aliasing -Wno-unused -c -o O/server.o C/server.c -IGENH -I. -IC >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PROBE_COM -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -fno-strict-aliasing -Wno-unused -c -o O/struct_man.o C/struct_man.c -IGENH -I. -IC >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PROBE_COM -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -fno-strict-aliasing -Wno-unused -c -o O/aisc_extern.o C/aisc_extern.c -IGENH -I. -IC >../MAKEBIN/aisc AISC/aisc_server.pa PT.aisc GENC/aisc_server.c GENH/aisc_server_extern.aisc GENH/import_proto.h >../MAKEBIN/aisc AISC/aisc_global.pa PT.aisc GENC/aisc_global.c GENH/aisc_server_extern.aisc GENH/import_proto.h >../MAKEBIN/aisc AISC/aisc_debug_globals.pa PT.aisc GENC/aisc_debug_globals.c GENH/aisc_server_extern.aisc GENH/import_proto.h >rm -f GENH/aisc_server_proto.h >echo GENH/import_proto.h >../MAKEBIN/aisc_mkpt -C GENC/aisc_server.c >GENH/aisc_server_proto.h >GENH/import_proto.h >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PROBE_COM -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -fno-strict-aliasing -Wno-unused -c -o GENC/aisc_debug_globals.o GENC/aisc_debug_globals.c -IGENH -I. -IC >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PROBE_COM -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -fno-strict-aliasing -Wno-unused -c -o GENC/aisc_global.o GENC/aisc_global.c -IGENH -I. -IC -DAISC_SAVE_NO >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PROBE_COM -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -fno-strict-aliasing -Wno-unused -c -o GENC/aisc_server.o GENC/aisc_server.c -IGENH -I. -IC -DAISC_SAVE_NO >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PROBE_COM -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -fno-strict-aliasing -Wno-unused -c -o PT_extern.o PT_extern.c -IGENH -I. -IC -DAISC_SAVE_NO >ld -r -o client.a O/client.o O/debug.o GENC/aisc_debug_globals.o >ld -r -o server.a O/server.o O/struct_man.o O/aisc_extern.o GENC/aisc_global.o GENC/aisc_server.o PT_extern.o >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PROBE_COM' >make[3]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PROBE_COM' >make[2]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3' >make arb >make[2]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3' >(cd lib;make all) >make[3]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/lib' >test -e arb_tcp.dat || cp -p arb_tcp_org.dat arb_tcp.dat >test -L nas && echo "lib/nas is a link - skipped" || \ > (cd nas;make all) >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/lib/nas' >rm -f names.dat >cp names.dat.template names.dat >rm -f *% >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/lib/nas' >make[3]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/lib' >make arbbasic2 >make[3]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3' >-------------------------------------------------------------------------------- Make everything in AISC_MKPTPS >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/AISC_MKPTPS' >make[4]: Nothing to be done for 'dummy.a'. >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/AISC_MKPTPS' >-------------------------------------------------------------------------------- Make everything in AISC >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/AISC' >make[4]: Nothing to be done for 'dummy.a'. >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/AISC' >-------------------------------------------------------------------------------- Make everything in TEMPLATES >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/TEMPLATES' >../SOURCE_TOOLS/build_info.pl >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/TEMPLATES' >-------------------------------------------------------------------------------- Make everything in NAMES_COM >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/NAMES_COM' >make[4]: 'server.a' is up to date. >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/NAMES_COM' >-------------------------------------------------------------------------------- Make everything in NAMES_COM >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/NAMES_COM' >make[4]: 'server.a' is up to date. >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/NAMES_COM' >-------------------------------------------------------------------------------- Make everything in PROBE_COM >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PROBE_COM' >make[4]: 'server.a' is up to date. >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PROBE_COM' >make SL/SL.dummy >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3' >-------------------------------------------------------------------------------- Make everything in SL >make[5]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL' >make[6]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/HELIX' >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_SL -DIN_ARB_HELIX -c BI_helix.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >ld -r -o HELIX.a BI_helix.o >make[6]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/HELIX' >make[6]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/AW_HELIX' >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_SL -DIN_ARB_AW_HELIX -c AW_helix.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >ld -r -o AW_HELIX.a AW_helix.o >make[6]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/AW_HELIX' >make[6]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/REGEXPR' >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_SL -DIN_ARB_REGEXPR -c RegExpr.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >ld -r -o REGEXPR.a RegExpr.o >make[6]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/REGEXPR' >make[6]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/FILE_BUFFER' >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_SL -DIN_ARB_FILE_BUFFER -c FileBuffer.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >ld -r -o FILE_BUFFER.a FileBuffer.o >make[6]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/FILE_BUFFER' >make[6]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/DB_SCANNER' >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_SL -DIN_ARB_DB_SCANNER -c db_scanner.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >ld -r -o DB_SCANNER.a db_scanner.o >make[6]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/DB_SCANNER' >make[6]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/TREE_READ' >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_SL -DIN_ARB_TREE_READ -c TreeRead.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_SL -DIN_ARB_TREE_READ -c TreeTools.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >ld -r -o TREE_READ.a TreeRead.o TreeTools.o >make[6]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/TREE_READ' >make[6]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/TREE_WRITE' >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_SL -DIN_ARB_TREE_WRITE -c TreeWrite.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >ld -r -o TREE_WRITE.a TreeWrite.o >make[6]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/TREE_WRITE' >make[6]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/AW_NAME' >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_SL -DIN_ARB_AW_NAME -c AW_rename.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_SL -DIN_ARB_AW_NAME -c AW_names_admin.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >ld -r -o AW_NAME.a AW_rename.o AW_names_admin.o >make[6]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/AW_NAME' >make[6]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/FAST_ALIGNER' >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_SL -DIN_ARB_FAST_ALIGNER -c fast_aligner.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_SL -DIN_ARB_FAST_ALIGNER -c ClustalV.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >fast_aligner.cxx: In function 'const char* alignCompactedTo(AWTC_CompactedSubSequence*, const AWTC_FastSearchSequence*, int, GB_CSTR, long int, GBDATA*, GBDATA*, const AlignParams&)': >fast_aligner.cxx:1254:31: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated [-Wdeprecated-declarations] > GBDATA *gbd = GBT_add_data(gb_toAlign, alignment, "data", GB_STRING); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from fast_aligner.cxx:19: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_t_prot.h:108:9: note: declared here > GBDATA *GBT_add_data P_((GBDATA *species, const char *ali_name, const char *key, GB_TYPES type)) __ATTR__DEPRECATED; > ^ >fast_aligner.cxx:1254:31: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated [-Wdeprecated-declarations] > GBDATA *gbd = GBT_add_data(gb_toAlign, alignment, "data", GB_STRING); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from fast_aligner.cxx:19: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_t_prot.h:108:9: note: declared here > GBDATA *GBT_add_data P_((GBDATA *species, const char *ali_name, const char *key, GB_TYPES type)) __ATTR__DEPRECATED; > ^ >fast_aligner.cxx:1254:84: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated [-Wdeprecated-declarations] > GBDATA *gbd = GBT_add_data(gb_toAlign, alignment, "data", GB_STRING); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from fast_aligner.cxx:19: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_t_prot.h:108:9: note: declared here > GBDATA *GBT_add_data P_((GBDATA *species, const char *ali_name, const char *key, GB_TYPES type)) __ATTR__DEPRECATED; > ^ >fast_aligner.cxx: In function 'void AWTC_start_faligning(AW_window*, AW_CL)': >fast_aligner.cxx:2368:57: warning: narrowing conversion of 'root->AW_root::awar(((const char*)"faligner/next_relatives"))->AW_awar::read_int()' from 'long int' to 'int' inside { } is ill-formed in C++11 [-Wnarrowing] > root->awar(FA_AWAR_NEXT_RELATIVES)->read_int(), > ^ >fast_aligner.cxx:2369:52: warning: narrowing conversion of 'root->AW_root::awar(((const char*)"next_neighbours/oligo_len"))->AW_awar::read_int()' from 'long int' to 'int' inside { } is ill-formed in C++11 [-Wnarrowing] > root->awar(AWAR_NN_OLIGO_LEN)->read_int(), > ^ >fast_aligner.cxx:2370:53: warning: narrowing conversion of 'root->AW_root::awar(((const char*)"next_neighbours/mismatches"))->AW_awar::read_int()' from 'long int' to 'int' inside { } is ill-formed in C++11 [-Wnarrowing] > root->awar(AWAR_NN_MISMATCHES)->read_int(), > ^ >ld -r -o FAST_ALIGNER.a fast_aligner.o ClustalV.o >make[6]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/FAST_ALIGNER' >make[5]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL' >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3' >make[3]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3' >make arbshared arbapplications help >make[3]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3' >make -C bin all >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin' >find . -type l -exec rm {} \; >-------------------------------------------------------------------------------- Make everything in AISC_MKPTPS >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/AISC_MKPTPS' >make[4]: Nothing to be done for 'dummy.a'. >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/AISC_MKPTPS' >ln -s -f `find ../SH ../PERL_SCRIPTS -perm -100 ! -type d ! -name 'config*' -print` . >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin' >-------------------------------------------------------------------------------- Make everything in AISC >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/AISC' >make[4]: Nothing to be done for 'dummy.a'. >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/AISC' >-------------------------------------------------------------------------------- Building prototyper >make AISC_MKPTPS/AISC_MKPTPS.dummy >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3' >-------------------------------------------------------------------------------- Make everything in AISC_MKPTPS >make[5]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/AISC_MKPTPS' >make[5]: Nothing to be done for 'AISC_MKPTPS.a'. >make[5]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/AISC_MKPTPS' >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3' >-------------------------------------------------------------------------------- Make everything in AWTI >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/AWTI' >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWTI -c AWTI_import.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWTI -c AWTI_export.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >ld -r -o AWTI.a AWTI_import.o AWTI_export.o >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/AWTI' >-------------------------------------------------------------------------------- Make everything in ARBDBPP >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/ARBDBPP' >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBPP -c adtsequence.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBPP -c adt_edit.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >adt_edit.cxx: In member function 'AD_ERR* ADT_SEQUENCE::show_edit_search(ADT_SEARCH*, ADT_EDIT*)': >adt_edit.cxx:581:13: warning: variable 'seq_empty_var' set but not used [-Wunused-but-set-variable] > long seq_empty_var; > ^ >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBPP -c adtali.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBPP -c adextended.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBPP -c adseq.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >adseq.cxx: In member function 'AD_ERR* AD_CONT::create(AD_SPECIES*, AD_ALI*)': >adseq.cxx:1012:20: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated [-Wdeprecated-declarations] > GBDATA *erg = GBT_add_data(adptr1->gb_species,adptr2->name(),"data", GB_STRING); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from adseq.cxx:16: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_t_prot.h:108:9: note: declared here > GBDATA *GBT_add_data P_((GBDATA *species, const char *ali_name, const char *key, GB_TYPES type)) __ATTR__DEPRECATED; > ^ >adseq.cxx:1012:20: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated [-Wdeprecated-declarations] > GBDATA *erg = GBT_add_data(adptr1->gb_species,adptr2->name(),"data", GB_STRING); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from adseq.cxx:16: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_t_prot.h:108:9: note: declared here > GBDATA *GBT_add_data P_((GBDATA *species, const char *ali_name, const char *key, GB_TYPES type)) __ATTR__DEPRECATED; > ^ >adseq.cxx:1012:84: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated [-Wdeprecated-declarations] > GBDATA *erg = GBT_add_data(adptr1->gb_species,adptr2->name(),"data", GB_STRING); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from adseq.cxx:16: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_t_prot.h:108:9: note: declared here > GBDATA *GBT_add_data P_((GBDATA *species, const char *ali_name, const char *key, GB_TYPES type)) __ATTR__DEPRECATED; > ^ >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBPP -c adspecies.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBPP -c admain.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBPP -c adali.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBPP -c liste.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -Wl,-O1 -Wl,--as-needed -Wl,--export-dynamic -shared -o libARBDBPP.so adtsequence.o adt_edit.o adtali.o adextended.o adseq.o adspecies.o admain.o adali.o liste.o >touch libARBDBPP.a >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/ARBDBPP' >-------------------------------------------------------------------------------- Make everything in WINDOW >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/WINDOW' >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_WINDOW -c AW_position.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_WINDOW -c AW_Xm.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_WINDOW -c AW_at.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_WINDOW -c AW_button.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >AW_button.cxx: In function 'void AW_variable_update_callback(Widget, XtPointer, XtPointer)': >AW_button.cxx:199:37: warning: variable 'found' set but not used [-Wunused-but-set-variable] > bool found; > ^ >AW_button.cxx: In member function 'int AW_window::get_index_of_element(AW_selection_list*, const char*)': >AW_button.cxx:1617:17: warning: variable 'found_index' set but not used [-Wunused-but-set-variable] > int found_index = -1; > ^ >AW_button.cxx: In function 'const char* detect_bitmap_size(const char*, int*, int*)': >AW_button.cxx:398:47: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] > fgets(buffer, MAX_LINE_LENGTH, in); > ^ >AW_button.cxx:417:51: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] > fgets(buffer, MAX_LINE_LENGTH, in); > ^ >AW_button.cxx:418:51: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] > fgets(buffer, MAX_LINE_LENGTH, in); > ^ >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_WINDOW -c AW_click.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_WINDOW -c AW_debug.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_WINDOW -c AW_device.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >AW_device.cxx: In member function 'int AW_device::text_overlay(int, const char*, long int, AW_pos, AW_pos, AW_pos, AW_bitset, AW_CL, AW_CL, AW_CL, AW_pos, AW_pos, int (*)(AW_device*, int, const char*, size_t, size_t, size_t, AW_pos, AW_pos, AW_pos, AW_pos, AW_CL, AW_CL, AW_CL))': >AW_device.cxx:721:22: warning: variable 'yi' set but not used [-Wunused-but-set-variable] > int xi, yi; > ^ >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_WINDOW -c AW_font_group.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_WINDOW -c AW_global_awars.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_WINDOW -c AW_nawar.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_WINDOW -c AW_preset.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >AW_nawar.cxx: In member function 'AW_awar* AW_root::awar_pointer(const char*, void*, AW_default)': >AW_nawar.cxx:193:111: warning: passing NULL to non-pointer argument 4 of 'AW_awar::AW_awar(AW_VARIABLE_TYPE, const char*, const char*, double, AW_default, AW_root*)' [-Wconversion-null] > vs = new AW_awar(AW_POINTER, var_name, (const char *)default_value, NULL, default_file, this); > ^ >AW_preset.cxx: In function 'void* AW_manage_GC(AW_window*, AW_device*, int, int, AW_GCM_AREA, void (*)(AW_window*, AW_CL, AW_CL), AW_CL, AW_CL, bool, const char*, ...)': >AW_preset.cxx:613:18: warning: variable 'flag_no_color_selector' set but not used [-Wunused-but-set-variable] > bool flag_no_color_selector = false; > ^ >AW_preset.cxx:614:18: warning: variable 'flag_append_in_same_line' set but not used [-Wunused-but-set-variable] > bool flag_append_in_same_line = false; > ^ >AW_preset.cxx: In function 'bool aw_insert_gcs(AW_root*, AW_window_simple*, aw_gc_manager*, bool)': >AW_preset.cxx:786:17: warning: variable 'first' set but not used [-Wunused-but-set-variable] > bool first = true; > ^ >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_WINDOW -c AW_print.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_WINDOW -c AW_question.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_WINDOW -c AW_size.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_WINDOW -c AW_status.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >AW_status.cxx: In function 'int aw_status_read_int(int, int)': >AW_status.cxx:281:19: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] > return *(int*)buffer; > ^ >AW_status.cxx: In function 'void aw_status_timer_event(AW_root*, AW_CL, AW_CL)': >AW_status.cxx:419:28: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] > system(buf); > ^ >AW_status.cxx: In function 'void aw_help_edit_help(AW_window*)': >AW_status.cxx:1746:25: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] > system(copy_cmd); > ^ >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_WINDOW -c AW_window.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >AW_window.cxx: In member function 'void AW_window::insert_separator()': >AW_window.cxx:3002:12: warning: variable 'separator' set but not used [-Wunused-but-set-variable] > Widget separator; > ^ >AW_window.cxx: In member function 'void AW_window::insert_separator_help()': >AW_window.cxx:3011:12: warning: variable 'separator' set but not used [-Wunused-but-set-variable] > Widget separator; > ^ >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_WINDOW -c AW_xfig.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_WINDOW -c AW_xfigfont.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_WINDOW -c AW_xfont.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_WINDOW -c AW_xkey.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_WINDOW -c AW_window_Xm_interface.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -Wl,-O1 -Wl,--as-needed -Wl,--export-dynamic -shared -o libAW.so AW_position.o AW_Xm.o AW_at.o AW_button.o AW_click.o AW_debug.o AW_device.o AW_font_group.o AW_global_awars.o AW_nawar.o AW_preset.o AW_print.o AW_question.o AW_size.o AW_status.o AW_window.o AW_xfig.o AW_xfigfont.o AW_xfont.o AW_xkey.o AW_window_Xm_interface.o >touch libAW.a >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/WINDOW' >-------------------------------------------------------------------------------- Make everything in ARBDB >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/ARBDB' >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c adsort.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c adlang1.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c adstring.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c admatch.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >admatch.c: In function 'GBS_string_eval': >admatch.c:763:13: warning: ignoring return value of 'gbs_build_replace_string', declared with attribute warn_unused_result [-Wunused-result] > gbs_build_replace_string(strstruct,bar,wildcard, max_wildcard, mwildcard, max_mwildcard,gb_container); > ^ >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c arbdb.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >arbdb.c: In function 'GB_copy_with_protection': >arbdb.c:1469:13: warning: null argument where non-null required (argument 2) [-Wnonnull] > GB_SETSMDMALLOC(dest, GB_GETSIZE(source), > ^ >arbdb.c:1469:13: warning: null argument where non-null required (argument 2) [-Wnonnull] >arbdb.c: In function 'gb_remove_callback': >arbdb.c:2239:13: warning: variable 'removed' set but not used [-Wunused-but-set-variable] > GB_BOOL removed = GB_FALSE; > ^ >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c ad_core.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c admath.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >ad_core.c: In function 'ad_use': >ad_core.c:11:17: warning: parameter 'dummy' set but not used [-Wunused-but-set-parameter] > void ad_use(int dummy, ...) { > ^ >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c adoptimize.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c adsystem.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >adsystem.c: In function 'gb_load_single_key_data': >adsystem.c:141:101: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] > GB_ensure_callback(gb_key,(GB_CB_TYPE)(GB_CB_CHANGED|GB_CB_DELETE),gb_system_key_changed_cb,(int *)q); > ^ >adsystem.c:159:123: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] > GB_remove_callback(ks->gb_master_ali,(GB_CB_TYPE)(GB_CB_CHANGED|GB_CB_DELETE),gb_system_master_changed_cb,(int *)q); > ^ >adsystem.c:160:123: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] > GB_add_callback (ks->gb_master_ali,(GB_CB_TYPE)(GB_CB_CHANGED|GB_CB_DELETE),gb_system_master_changed_cb,(int *)q); > ^ >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c adindex.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c adperl.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c adlink.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c adsocket.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c adcomm.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >adcomm.c: In function 'gbcms_write_updated': >adcomm.c:303:23: warning: variable 'hs' set but not used [-Wunused-but-set-variable] > struct Hs_struct *hs; > ^ >adcomm.c: In function 'gbcms_talking_init_transaction': >adcomm.c:533:14: warning: variable 'buffer' set but not used [-Wunused-but-set-variable] > long *buffer; > ^ >adcomm.c: In function 'gbcm_read_bin': >adcomm.c:1231:27: warning: variable 'flags3' set but not used [-Wunused-but-set-variable] > struct gb_flag_types3 flags3; > ^ >adsocket.c: In function 'GB_get_full_path': >adsocket.c:1256:13: warning: ignoring return value of 'realpath', declared with attribute warn_unused_result [-Wunused-result] > realpath(newpath, path_buf[path_toggle]); > ^ >adsocket.c:1260:13: warning: ignoring return value of 'realpath', declared with attribute warn_unused_result [-Wunused-result] > realpath(anypath, path_buf[path_toggle]); > ^ >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c adhash.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c adquery.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >adquery.c: In function 'gb_search': >adquery.c:449:28: warning: comparison between 'GB_TYPES {aka enum gb_key_types}' and 'enum gb_search_enum' [-Wenum-compare] > if (create == GB_CREATE_CONTAINER) { > ^ >adquery.c:455:28: warning: comparison between 'GB_TYPES {aka enum gb_key_types}' and 'enum gb_search_enum' [-Wenum-compare] > if (create == GB_CREATE_CONTAINER) { > ^ >adquery.c:526:31: warning: comparison between 'GB_TYPES {aka enum gb_key_types}' and 'enum gb_search_enum' [-Wenum-compare] > if (s2 || (create == GB_CREATE_CONTAINER)) { > ^ >adquery.c: In function 'GB_command_interpreter': >adquery.c:861:19: warning: variable 'len' set but not used [-Wunused-but-set-variable] > int len; > ^ >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c ad_save_load.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >ad_save_load.c: In function 'gb_write_bin_rek': >ad_save_load.c:799:13: warning: null argument where non-null required (argument 1) [-Wnonnull] > i = fwrite(GB_GETDATA(gbd),(size_t)memsize,1,out); > ^ >ad_save_load.c: In function 'GB_save_as': >ad_save_load.c:1079:5: warning: 'GB_get_error' is deprecated [-Wdeprecated-declarations] > return GB_get_error(); > ^ >In file included from arbdb.h:268:0, > from adlocal.h:573, > from ad_save_load.c:13: >./ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >ad_save_load.c: In function 'GB_save_quick_as': >ad_save_load.c:1126:5: warning: 'GB_get_error' is deprecated [-Wdeprecated-declarations] > if (gb_check_saveable(gb_main,path,"bn")) return GB_get_error(); > ^ >In file included from arbdb.h:268:0, > from adlocal.h:573, > from ad_save_load.c:13: >./ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >ad_save_load.c:1148:9: warning: 'GB_get_error' is deprecated [-Wdeprecated-declarations] > return GB_get_error(); > ^ >In file included from arbdb.h:268:0, > from adlocal.h:573, > from ad_save_load.c:13: >./ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >ad_save_load.c:1173:9: warning: 'GB_get_error' is deprecated [-Wdeprecated-declarations] > return GB_get_error(); > ^ >In file included from arbdb.h:268:0, > from adlocal.h:573, > from ad_save_load.c:13: >./ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >ad_save_load.c:1184:9: warning: 'GB_get_error' is deprecated [-Wdeprecated-declarations] > GB_warning(GB_get_error()); > ^ >In file included from arbdb.h:268:0, > from adlocal.h:573, > from ad_save_load.c:13: >./ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >ad_save_load.c: In function 'GB_save_quick': >ad_save_load.c:1213:5: warning: 'GB_get_error' is deprecated [-Wdeprecated-declarations] > if (gb_check_saveable(gb,refpath,"q")) return GB_get_error(); > ^ >In file included from arbdb.h:268:0, > from adlocal.h:573, > from ad_save_load.c:13: >./ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >ad_save_load.c:1234:9: warning: 'GB_get_error' is deprecated [-Wdeprecated-declarations] > return GB_get_error(); > ^ >In file included from arbdb.h:268:0, > from adlocal.h:573, > from ad_save_load.c:13: >./ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >ad_save_load.c:1267:5: warning: 'GB_get_error' is deprecated [-Wdeprecated-declarations] > if (GB_rename_file(sec_path,path)) return GB_get_error(); > ^ >In file included from arbdb.h:268:0, > from adlocal.h:573, > from ad_save_load.c:13: >./ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >ad_save_load.c: In function 'gb_check_saveable': >ad_save_load.c:1307:9: warning: 'GB_get_error' is deprecated [-Wdeprecated-declarations] > return GB_get_error(); > ^ >In file included from arbdb.h:268:0, > from adlocal.h:573, > from ad_save_load.c:13: >./ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >ad_save_load.c:1312:9: warning: 'GB_get_error' is deprecated [-Wdeprecated-declarations] > return GB_get_error(); > ^ >In file included from arbdb.h:268:0, > from adlocal.h:573, > from ad_save_load.c:13: >./ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c adcompr.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c admalloc.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c ad_load.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c admap.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >admap.c: In function 'gb_save_mapfile': >admap.c:636:9: warning: variable 'writeOffset' set but not used [-Wunused-but-set-variable] > writeOffset; > ^ >admap.c:635:10: warning: variable 'calcOffset' set but not used [-Wunused-but-set-variable] > long calcOffset, > ^ >admap.c: In function 'gb_is_valid_mapfile': >admap.c:722:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] > fread((char *)mheader, sizeof(*mheader),1,in); > ^ >ad_load.c: In function 'GB_login': >ad_load.c:1380:17: warning: ignoring return value of 'gb_scan_directory', declared with attribute warn_unused_result [-Wunused-result] > gb_scan_directory(base,&dir); > ^ >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c adTest.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c adtune.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >adTest.c: In function 'testData': >adTest.c:36:9: warning: variable 'err' set but not used [-Wunused-but-set-variable] > int err = 0; > ^ >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c adGene.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c adtcp.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c adhashtools.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c adExperiment.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c adtools.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >adtools.c: In function 'GBT_check_arb_file': >adtools.c:74:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] > fgets(buffer,50,in); > ^ >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c adseqcompr.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c adtables.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c adRevCompl.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c adChangeKey.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c adali.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c adcolumns.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >adali.c: In function 'GBT_create_sequence_data': >adali.c:597:5: warning: 'GBT_add_data' is deprecated [-Wdeprecated-declarations] > GBDATA *gb_data = GBT_add_data(species, ali_name, key, type); > ^ >adali.c:568:9: note: declared here > GBDATA *GBT_add_data(GBDATA *species,const char *ali_name, const char *key, GB_TYPES type) { > ^ >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c adtree.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c adname.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c aditem.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c arbdbpp.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c ad_config.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -Wl,-O1 -Wl,--as-needed -Wl,--export-dynamic -shared -o libARBDB.so adsort.o adlang1.o adstring.o admatch.o arbdb.o ad_core.o admath.o adoptimize.o adsystem.o adindex.o adperl.o adlink.o adsocket.o adcomm.o adhash.o adquery.o ad_save_load.o adcompr.o admalloc.o ad_load.o admap.o adTest.o adtune.o adGene.o adtcp.o adhashtools.o adExperiment.o adtools.o adseqcompr.o adtables.o adRevCompl.o adChangeKey.o adali.o adcolumns.o adtree.o adname.o aditem.o arbdbpp.o ad_config.o >touch libARBDB.a >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/ARBDB' >-------------------------------------------------------------------------------- Make everything in AWT >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/AWT' >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_input_mask.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >AWT_input_mask.cxx: In function 'void create_new_mask_cb(AW_window*)': >AWT_input_mask.cxx:2242:18: warning: variable 'closeWindow' set but not used [-Wunused-but-set-variable] > bool closeWindow = false; > ^ >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_hotkeys.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_www.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >In file included from AWT_www.cxx:16:0: >AWT_www.cxx: In function 'void awt_create_aww_vars(AW_root*, AW_default)': >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/static_assert.h:25:19: warning: typedef '_arb_compile_assertion_typedef___LINE__' locally defined but not used [-Wunused-local-typedefs] > CA_UNIQUETYPE(_arb_compile_assertion_typedef_) > ^ >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/static_assert.h:20:26: note: in definition of macro 'CA_JOINTYPE' > #define CA_JOINTYPE(X,Y) X##Y > ^ >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/static_assert.h:25:5: note: in expansion of macro 'CA_UNIQUETYPE' > CA_UNIQUETYPE(_arb_compile_assertion_typedef_) > ^ >AWT_www.cxx:61:5: note: in expansion of macro 'COMPILE_ASSERT' > COMPILE_ASSERT(EXAMPLE_COUNT <= WWW_COUNT); > ^ >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_tables.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_irstree.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >AWT_tables.cxx: In function 'void ad_table_field_reorder_cb(AW_window*, awt_table*)': >AWT_tables.cxx:25:14: warning: variable 'warning' set but not used [-Wunused-but-set-variable] > GB_ERROR warning = 0; > ^ >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_asciiprint.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_map_key.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_tree_cmp.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_seq_colors.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_pro_a_nucs.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_csp.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_canvas.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_dtree.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_tree.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_tree_cb.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_nei.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_filter.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_sel_boxes.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_canio.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_nds.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >AWT_canio.cxx: In function 'void AWT_print_tree_to_file_xfig(AW_window*, AW_CL)': >AWT_canio.cxx:268:53: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] > system(GBS_global_string("xfig %s &", dest)); > ^ >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_query_and_functions.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_file_selection.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_preset.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_seq_dna.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_seq_protein.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_seq_simple_pro.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_codon_table.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_iupac.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >AWT_codon_table.cxx: In function 'bool AWT_is_codon(char, const char*, const AWT_allowedCode&, AWT_allowedCode&, const char**)': >AWT_codon_table.cxx:518:18: warning: variable 'correct_disallowed_translation' set but not used [-Wunused-but-set-variable] > bool correct_disallowed_translation = false; > ^ >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_config_manager.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_advice.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >AWT_config_manager.cxx: In function 'void AWT_start_config_manager(AW_window*, AW_CL)': >AWT_config_manager.cxx:119:24: warning: variable 'reopen' set but not used [-Wunused-but-set-variable] > bool reopen = false; > ^ >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_db_browser.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_attributes.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_changekey.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_item_sel_list.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_macro.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_translate.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -Wl,-O1 -Wl,--as-needed -Wl,--export-dynamic -shared -o libAWT.so AWT_input_mask.o AWT_hotkeys.o AWT_www.o AWT_tables.o AWT_irstree.o AWT_asciiprint.o AWT_map_key.o AWT_tree_cmp.o AWT_seq_colors.o AWT_pro_a_nucs.o AWT_csp.o AWT_canvas.o AWT_dtree.o AWT_tree.o AWT_tree_cb.o AWT_nei.o AWT_filter.o AWT_sel_boxes.o AWT_canio.o AWT_nds.o AWT_query_and_functions.o AWT_file_selection.o AWT_preset.o AWT_seq_dna.o AWT_seq_protein.o AWT_seq_simple_pro.o AWT_codon_table.o AWT_iupac.o AWT_config_manager.o AWT_advice.o AWT_db_browser.o AWT_attributes.o AWT_changekey.o AWT_item_sel_list.o AWT_macro.o AWT_translate.o >touch libAWT.a >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/AWT' >-------------------------------------------------------------------------------- Make everything in GENOM >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GENOM' >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GENOM -c GEN_interface.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GENOM -c GEN_map.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >GEN_map.cxx: In function 'void gen_extract_gene_2_pseudoSpecies(GBDATA*, GBDATA*, EG2PS_data*)': >GEN_map.cxx:882:39: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated [-Wdeprecated-declarations] > GBDATA *gb_data = GBT_add_data(gb_exist_geneSpec, ali, "data", GB_STRING); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from GEN_map.cxx:14: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_t_prot.h:108:9: note: declared here > GBDATA *GBT_add_data P_((GBDATA *species, const char *ali_name, const char *key, GB_TYPES type)) __ATTR__DEPRECATED; > ^ >GEN_map.cxx:882:39: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated [-Wdeprecated-declarations] > GBDATA *gb_data = GBT_add_data(gb_exist_geneSpec, ali, "data", GB_STRING); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from GEN_map.cxx:14: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_t_prot.h:108:9: note: declared here > GBDATA *GBT_add_data P_((GBDATA *species, const char *ali_name, const char *key, GB_TYPES type)) __ATTR__DEPRECATED; > ^ >GEN_map.cxx:882:93: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated [-Wdeprecated-declarations] > GBDATA *gb_data = GBT_add_data(gb_exist_geneSpec, ali, "data", GB_STRING); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from GEN_map.cxx:14: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_t_prot.h:108:9: note: declared here > GBDATA *GBT_add_data P_((GBDATA *species, const char *ali_name, const char *key, GB_TYPES type)) __ATTR__DEPRECATED; > ^ >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GENOM -c GEN_graphic.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >GEN_graphic.cxx:158:33: warning: unused parameter 'selected_range' [-Wunused-parameter] > inline int smart_text(AW_world& selected_range, AW_device *device, int gc, const char *str,AW_pos x,AW_pos y, AW_pos alignment, AW_bitset filteri, AW_CL cd1, AW_CL cd2,long opt_strlen) { > ^ >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GENOM -c GEN_gene.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GENOM -c GEN_nds.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GENOM -c GEN_color_groups.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >GEN_nds.cxx:307:2: warning: #warning make this function more general like AWT_popup_select_species_field_window [-Wcpp] > #warning make this function more general like AWT_popup_select_species_field_window > ^ >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GENOM -c GEN_translations.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GENOM -c EXP_interface.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GENOM -c EXP_main.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >ld -r -o GENOM.a GEN_interface.o GEN_map.o GEN_graphic.o GEN_gene.o GEN_nds.o GEN_color_groups.o GEN_translations.o EXP_interface.o EXP_main.o >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GENOM' >-------------------------------------------------------------------------------- Make everything in GENOM_IMPORT >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GENOM_IMPORT' >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GENOM_IMPORT -c GenomeImport.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GENOM_IMPORT -c Importer.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GENOM_IMPORT -c DBwriter.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GENOM_IMPORT -c SequenceBuffer.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >SequenceBuffer.cxx: In member function 'void BaseCounter::checkOverallCounter() const': >SequenceBuffer.cxx:55:67: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'size_t {aka long unsigned int}' [-Wformat=] > count[BC_ALL], all, source.c_str()); > ^ >SequenceBuffer.cxx:55:67: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'size_t {aka long unsigned int}' [-Wformat=] >SequenceBuffer.cxx: In member function 'void BaseCounter::expectEqual(const BaseCounter&) const': >SequenceBuffer.cxx:116:114: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'size_t {aka long unsigned int}' [-Wformat=] > error = error+"\n "+whichCounter+": "+GBS_global_string("%u <> %u", count[i], other.count[i]); > ^ >SequenceBuffer.cxx:116:114: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'size_t {aka long unsigned int}' [-Wformat=] >DBwriter.cxx: In member function 'void DBwriter::writeSequence(const SequenceBuffer&)': >DBwriter.cxx:226:23: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated [-Wdeprecated-declarations] > GBDATA *gb_data = GBT_add_data(gb_organism, ali_name, "data", GB_STRING); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from DBwriter.cxx:16: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_t_prot.h:108:9: note: declared here > GBDATA *GBT_add_data P_((GBDATA *species, const char *ali_name, const char *key, GB_TYPES type)) __ATTR__DEPRECATED; > ^ >DBwriter.cxx:226:23: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated [-Wdeprecated-declarations] > GBDATA *gb_data = GBT_add_data(gb_organism, ali_name, "data", GB_STRING); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from DBwriter.cxx:16: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_t_prot.h:108:9: note: declared here > GBDATA *GBT_add_data P_((GBDATA *species, const char *ali_name, const char *key, GB_TYPES type)) __ATTR__DEPRECATED; > ^ >DBwriter.cxx:226:76: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated [-Wdeprecated-declarations] > GBDATA *gb_data = GBT_add_data(gb_organism, ali_name, "data", GB_STRING); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from DBwriter.cxx:16: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_t_prot.h:108:9: note: declared here > GBDATA *GBT_add_data P_((GBDATA *species, const char *ali_name, const char *key, GB_TYPES type)) __ATTR__DEPRECATED; > ^ >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GENOM_IMPORT -c MetaInfo.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GENOM_IMPORT -c Feature.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GENOM_IMPORT -c Location.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GENOM_IMPORT -c tools.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >-------------------- Checking GENOM_IMPORT.a >Target 'GENOM_IMPORT.a' not found >-> rebuilding GENOM_IMPORT.a (Thu Jan 1 00:59:59 1970) >ld -r -o GENOM_IMPORT.a GenomeImport.o Importer.o DBwriter.o SequenceBuffer.o MetaInfo.o Feature.o Location.o tools.o >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GENOM_IMPORT' >-------------------------------------------------------------------------------- Make everything in MERGE >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/MERGE' >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_MERGE -c MG_checkfield.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_MERGE -c MG_main.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_MERGE -c MG_trees.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_MERGE -c MG_alignment.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_MERGE -c MG_species.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_MERGE -c MG_extendeds.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_MERGE -c MG_names.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_MERGE -c MG_gene_species.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_MERGE -c MG_configs.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_MERGE -c MG_preserves.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >ld -r -o MERGE.a MG_checkfield.o MG_main.o MG_trees.o MG_alignment.o MG_species.o MG_extendeds.o MG_names.o MG_gene_species.o MG_configs.o MG_preserves.o >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/MERGE' >-------------------------------------------------------------------------------- Make everything in ARBDB2 >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/ARBDB2' >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c adsort.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c adlang1.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c adstring.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c admatch.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >admatch.c: In function 'GBS_string_eval': >admatch.c:763:13: warning: ignoring return value of 'gbs_build_replace_string', declared with attribute warn_unused_result [-Wunused-result] > gbs_build_replace_string(strstruct,bar,wildcard, max_wildcard, mwildcard, max_mwildcard,gb_container); > ^ >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c arbdb.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >arbdb.c: In function 'GB_copy_with_protection': >arbdb.c:1469:13: warning: null argument where non-null required (argument 2) [-Wnonnull] > GB_SETSMDMALLOC(dest, GB_GETSIZE(source), > ^ >arbdb.c:1469:13: warning: null argument where non-null required (argument 2) [-Wnonnull] >arbdb.c: In function 'gb_remove_callback': >arbdb.c:2239:13: warning: variable 'removed' set but not used [-Wunused-but-set-variable] > GB_BOOL removed = GB_FALSE; > ^ >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c ad_core.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >ad_core.c: In function 'ad_use': >ad_core.c:11:17: warning: parameter 'dummy' set but not used [-Wunused-but-set-parameter] > void ad_use(int dummy, ...) { > ^ >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c admath.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c adoptimize.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c adsystem.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >adsystem.c: In function 'gb_load_single_key_data': >adsystem.c:141:101: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] > GB_ensure_callback(gb_key,(GB_CB_TYPE)(GB_CB_CHANGED|GB_CB_DELETE),gb_system_key_changed_cb,(int *)q); > ^ >adsystem.c:159:123: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] > GB_remove_callback(ks->gb_master_ali,(GB_CB_TYPE)(GB_CB_CHANGED|GB_CB_DELETE),gb_system_master_changed_cb,(int *)q); > ^ >adsystem.c:160:123: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] > GB_add_callback (ks->gb_master_ali,(GB_CB_TYPE)(GB_CB_CHANGED|GB_CB_DELETE),gb_system_master_changed_cb,(int *)q); > ^ >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c adindex.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c adperl.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c adlink.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c adsocket.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c adcomm.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >adsocket.c: In function 'GB_get_full_path': >adsocket.c:1256:13: warning: ignoring return value of 'realpath', declared with attribute warn_unused_result [-Wunused-result] > realpath(newpath, path_buf[path_toggle]); > ^ >adsocket.c:1260:13: warning: ignoring return value of 'realpath', declared with attribute warn_unused_result [-Wunused-result] > realpath(anypath, path_buf[path_toggle]); > ^ >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c adhash.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >adcomm.c: In function 'gbcms_write_updated': >adcomm.c:303:23: warning: variable 'hs' set but not used [-Wunused-but-set-variable] > struct Hs_struct *hs; > ^ >adcomm.c: In function 'gbcms_talking_init_transaction': >adcomm.c:533:14: warning: variable 'buffer' set but not used [-Wunused-but-set-variable] > long *buffer; > ^ >adcomm.c: In function 'gbcm_read_bin': >adcomm.c:1231:27: warning: variable 'flags3' set but not used [-Wunused-but-set-variable] > struct gb_flag_types3 flags3; > ^ >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c adquery.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >adquery.c: In function 'gb_search': >adquery.c:449:28: warning: comparison between 'GB_TYPES {aka enum gb_key_types}' and 'enum gb_search_enum' [-Wenum-compare] > if (create == GB_CREATE_CONTAINER) { > ^ >adquery.c:455:28: warning: comparison between 'GB_TYPES {aka enum gb_key_types}' and 'enum gb_search_enum' [-Wenum-compare] > if (create == GB_CREATE_CONTAINER) { > ^ >adquery.c:526:31: warning: comparison between 'GB_TYPES {aka enum gb_key_types}' and 'enum gb_search_enum' [-Wenum-compare] > if (s2 || (create == GB_CREATE_CONTAINER)) { > ^ >adquery.c: In function 'GB_command_interpreter': >adquery.c:861:19: warning: variable 'len' set but not used [-Wunused-but-set-variable] > int len; > ^ >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c ad_save_load.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >ad_save_load.c: In function 'gb_write_bin_rek': >ad_save_load.c:799:13: warning: null argument where non-null required (argument 1) [-Wnonnull] > i = fwrite(GB_GETDATA(gbd),(size_t)memsize,1,out); > ^ >ad_save_load.c: In function 'GB_save_as': >ad_save_load.c:1079:5: warning: 'GB_get_error' is deprecated [-Wdeprecated-declarations] > return GB_get_error(); > ^ >In file included from arbdb.h:268:0, > from adlocal.h:573, > from ad_save_load.c:13: >./ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >ad_save_load.c: In function 'GB_save_quick_as': >ad_save_load.c:1126:5: warning: 'GB_get_error' is deprecated [-Wdeprecated-declarations] > if (gb_check_saveable(gb_main,path,"bn")) return GB_get_error(); > ^ >In file included from arbdb.h:268:0, > from adlocal.h:573, > from ad_save_load.c:13: >./ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >ad_save_load.c:1148:9: warning: 'GB_get_error' is deprecated [-Wdeprecated-declarations] > return GB_get_error(); > ^ >In file included from arbdb.h:268:0, > from adlocal.h:573, > from ad_save_load.c:13: >./ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >ad_save_load.c:1173:9: warning: 'GB_get_error' is deprecated [-Wdeprecated-declarations] > return GB_get_error(); > ^ >In file included from arbdb.h:268:0, > from adlocal.h:573, > from ad_save_load.c:13: >./ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >ad_save_load.c:1184:9: warning: 'GB_get_error' is deprecated [-Wdeprecated-declarations] > GB_warning(GB_get_error()); > ^ >In file included from arbdb.h:268:0, > from adlocal.h:573, > from ad_save_load.c:13: >./ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >ad_save_load.c: In function 'GB_save_quick': >ad_save_load.c:1213:5: warning: 'GB_get_error' is deprecated [-Wdeprecated-declarations] > if (gb_check_saveable(gb,refpath,"q")) return GB_get_error(); > ^ >In file included from arbdb.h:268:0, > from adlocal.h:573, > from ad_save_load.c:13: >./ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >ad_save_load.c:1234:9: warning: 'GB_get_error' is deprecated [-Wdeprecated-declarations] > return GB_get_error(); > ^ >In file included from arbdb.h:268:0, > from adlocal.h:573, > from ad_save_load.c:13: >./ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >ad_save_load.c:1267:5: warning: 'GB_get_error' is deprecated [-Wdeprecated-declarations] > if (GB_rename_file(sec_path,path)) return GB_get_error(); > ^ >In file included from arbdb.h:268:0, > from adlocal.h:573, > from ad_save_load.c:13: >./ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >ad_save_load.c: In function 'gb_check_saveable': >ad_save_load.c:1307:9: warning: 'GB_get_error' is deprecated [-Wdeprecated-declarations] > return GB_get_error(); > ^ >In file included from arbdb.h:268:0, > from adlocal.h:573, > from ad_save_load.c:13: >./ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >ad_save_load.c:1312:9: warning: 'GB_get_error' is deprecated [-Wdeprecated-declarations] > return GB_get_error(); > ^ >In file included from arbdb.h:268:0, > from adlocal.h:573, > from ad_save_load.c:13: >./ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c adcompr.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c admalloc.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c ad_load.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >ad_load.c: In function 'GB_login': >ad_load.c:1380:17: warning: ignoring return value of 'gb_scan_directory', declared with attribute warn_unused_result [-Wunused-result] > gb_scan_directory(base,&dir); > ^ >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c admap.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >admap.c: In function 'gb_save_mapfile': >admap.c:636:9: warning: variable 'writeOffset' set but not used [-Wunused-but-set-variable] > writeOffset; > ^ >admap.c:635:10: warning: variable 'calcOffset' set but not used [-Wunused-but-set-variable] > long calcOffset, > ^ >admap.c: In function 'gb_is_valid_mapfile': >admap.c:722:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] > fread((char *)mheader, sizeof(*mheader),1,in); > ^ >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c adTest.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >adTest.c: In function 'testData': >adTest.c:36:9: warning: variable 'err' set but not used [-Wunused-but-set-variable] > int err = 0; > ^ >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c adtune.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c adGene.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c adtcp.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c adhashtools.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c adExperiment.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c adtools.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c adseqcompr.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >adtools.c: In function 'GBT_check_arb_file': >adtools.c:74:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] > fgets(buffer,50,in); > ^ >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c adtables.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c adRevCompl.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c adChangeKey.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c adali.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >adali.c: In function 'GBT_create_sequence_data': >adali.c:597:5: warning: 'GBT_add_data' is deprecated [-Wdeprecated-declarations] > GBDATA *gb_data = GBT_add_data(species, ali_name, key, type); > ^ >adali.c:568:9: note: declared here > GBDATA *GBT_add_data(GBDATA *species,const char *ali_name, const char *key, GB_TYPES type) { > ^ >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c adcolumns.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c adtree.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c adname.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c aditem.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fPIC -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c ad_config.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -Wl,-O1 -Wl,--as-needed -Wl,--export-dynamic -shared -o libARBDB.so adsort.o adlang1.o adstring.o admatch.o arbdb.o ad_core.o admath.o adoptimize.o adsystem.o adindex.o adperl.o adlink.o adsocket.o adcomm.o adhash.o adquery.o ad_save_load.o adcompr.o admalloc.o ad_load.o admap.o adTest.o adtune.o adGene.o adtcp.o adhashtools.o adExperiment.o adtools.o adseqcompr.o adtables.o adRevCompl.o adChangeKey.o adali.o adcolumns.o adtree.o adname.o aditem.o ad_config.o >touch libARBDB.a >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/ARBDB2' >-------------------------------------------------------------------------------- Make everything in ARBDBS >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/ARBDBS' >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c adsort.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c adlang1.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c adstring.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c admatch.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >admatch.c: In function 'GBS_string_eval': >admatch.c:763:13: warning: ignoring return value of 'gbs_build_replace_string', declared with attribute warn_unused_result [-Wunused-result] > gbs_build_replace_string(strstruct,bar,wildcard, max_wildcard, mwildcard, max_mwildcard,gb_container); > ^ >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c arbdb.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c ad_core.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >arbdb.c: In function 'GB_copy_with_protection': >arbdb.c:1469:13: warning: null argument where non-null required (argument 2) [-Wnonnull] > GB_SETSMDMALLOC(dest, GB_GETSIZE(source), > ^ >arbdb.c:1469:13: warning: null argument where non-null required (argument 2) [-Wnonnull] >arbdb.c: In function 'gb_remove_callback': >arbdb.c:2239:13: warning: variable 'removed' set but not used [-Wunused-but-set-variable] > GB_BOOL removed = GB_FALSE; > ^ >ad_core.c: In function 'ad_use': >ad_core.c:11:17: warning: parameter 'dummy' set but not used [-Wunused-but-set-parameter] > void ad_use(int dummy, ...) { > ^ >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c admath.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c adoptimize.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c adsystem.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >adsystem.c: In function 'gb_load_single_key_data': >adsystem.c:141:101: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] > GB_ensure_callback(gb_key,(GB_CB_TYPE)(GB_CB_CHANGED|GB_CB_DELETE),gb_system_key_changed_cb,(int *)q); > ^ >adsystem.c:159:123: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] > GB_remove_callback(ks->gb_master_ali,(GB_CB_TYPE)(GB_CB_CHANGED|GB_CB_DELETE),gb_system_master_changed_cb,(int *)q); > ^ >adsystem.c:160:123: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] > GB_add_callback (ks->gb_master_ali,(GB_CB_TYPE)(GB_CB_CHANGED|GB_CB_DELETE),gb_system_master_changed_cb,(int *)q); > ^ >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c adindex.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c adperl.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c adlink.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c adsocket.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >adsocket.c: In function 'GB_get_full_path': >adsocket.c:1256:13: warning: ignoring return value of 'realpath', declared with attribute warn_unused_result [-Wunused-result] > realpath(newpath, path_buf[path_toggle]); > ^ >adsocket.c:1260:13: warning: ignoring return value of 'realpath', declared with attribute warn_unused_result [-Wunused-result] > realpath(anypath, path_buf[path_toggle]); > ^ >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c adcomm.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c adhash.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >adcomm.c: In function 'gbcms_write_updated': >adcomm.c:303:23: warning: variable 'hs' set but not used [-Wunused-but-set-variable] > struct Hs_struct *hs; > ^ >adcomm.c: In function 'gbcms_talking_init_transaction': >adcomm.c:533:14: warning: variable 'buffer' set but not used [-Wunused-but-set-variable] > long *buffer; > ^ >adcomm.c: In function 'gbcm_read_bin': >adcomm.c:1231:27: warning: variable 'flags3' set but not used [-Wunused-but-set-variable] > struct gb_flag_types3 flags3; > ^ >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c adquery.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >adquery.c: In function 'gb_search': >adquery.c:449:28: warning: comparison between 'GB_TYPES {aka enum gb_key_types}' and 'enum gb_search_enum' [-Wenum-compare] > if (create == GB_CREATE_CONTAINER) { > ^ >adquery.c:455:28: warning: comparison between 'GB_TYPES {aka enum gb_key_types}' and 'enum gb_search_enum' [-Wenum-compare] > if (create == GB_CREATE_CONTAINER) { > ^ >adquery.c:526:31: warning: comparison between 'GB_TYPES {aka enum gb_key_types}' and 'enum gb_search_enum' [-Wenum-compare] > if (s2 || (create == GB_CREATE_CONTAINER)) { > ^ >adquery.c: In function 'GB_command_interpreter': >adquery.c:861:19: warning: variable 'len' set but not used [-Wunused-but-set-variable] > int len; > ^ >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c ad_save_load.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c adcompr.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >ad_save_load.c: In function 'gb_write_bin_rek': >ad_save_load.c:799:13: warning: null argument where non-null required (argument 1) [-Wnonnull] > i = fwrite(GB_GETDATA(gbd),(size_t)memsize,1,out); > ^ >ad_save_load.c: In function 'GB_save_as': >ad_save_load.c:1079:5: warning: 'GB_get_error' is deprecated [-Wdeprecated-declarations] > return GB_get_error(); > ^ >In file included from arbdb.h:268:0, > from adlocal.h:573, > from ad_save_load.c:13: >./ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >ad_save_load.c: In function 'GB_save_quick_as': >ad_save_load.c:1126:5: warning: 'GB_get_error' is deprecated [-Wdeprecated-declarations] > if (gb_check_saveable(gb_main,path,"bn")) return GB_get_error(); > ^ >In file included from arbdb.h:268:0, > from adlocal.h:573, > from ad_save_load.c:13: >./ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >ad_save_load.c:1148:9: warning: 'GB_get_error' is deprecated [-Wdeprecated-declarations] > return GB_get_error(); > ^ >In file included from arbdb.h:268:0, > from adlocal.h:573, > from ad_save_load.c:13: >./ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >ad_save_load.c:1173:9: warning: 'GB_get_error' is deprecated [-Wdeprecated-declarations] > return GB_get_error(); > ^ >In file included from arbdb.h:268:0, > from adlocal.h:573, > from ad_save_load.c:13: >./ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >ad_save_load.c:1184:9: warning: 'GB_get_error' is deprecated [-Wdeprecated-declarations] > GB_warning(GB_get_error()); > ^ >In file included from arbdb.h:268:0, > from adlocal.h:573, > from ad_save_load.c:13: >./ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >ad_save_load.c: In function 'GB_save_quick': >ad_save_load.c:1213:5: warning: 'GB_get_error' is deprecated [-Wdeprecated-declarations] > if (gb_check_saveable(gb,refpath,"q")) return GB_get_error(); > ^ >In file included from arbdb.h:268:0, > from adlocal.h:573, > from ad_save_load.c:13: >./ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >ad_save_load.c:1234:9: warning: 'GB_get_error' is deprecated [-Wdeprecated-declarations] > return GB_get_error(); > ^ >In file included from arbdb.h:268:0, > from adlocal.h:573, > from ad_save_load.c:13: >./ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >ad_save_load.c:1267:5: warning: 'GB_get_error' is deprecated [-Wdeprecated-declarations] > if (GB_rename_file(sec_path,path)) return GB_get_error(); > ^ >In file included from arbdb.h:268:0, > from adlocal.h:573, > from ad_save_load.c:13: >./ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >ad_save_load.c: In function 'gb_check_saveable': >ad_save_load.c:1307:9: warning: 'GB_get_error' is deprecated [-Wdeprecated-declarations] > return GB_get_error(); > ^ >In file included from arbdb.h:268:0, > from adlocal.h:573, > from ad_save_load.c:13: >./ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >ad_save_load.c:1312:9: warning: 'GB_get_error' is deprecated [-Wdeprecated-declarations] > return GB_get_error(); > ^ >In file included from arbdb.h:268:0, > from adlocal.h:573, > from ad_save_load.c:13: >./ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c admalloc.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c ad_load.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >ad_load.c: In function 'GB_login': >ad_load.c:1380:17: warning: ignoring return value of 'gb_scan_directory', declared with attribute warn_unused_result [-Wunused-result] > gb_scan_directory(base,&dir); > ^ >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c admap.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >admap.c: In function 'gb_save_mapfile': >admap.c:636:9: warning: variable 'writeOffset' set but not used [-Wunused-but-set-variable] > writeOffset; > ^ >admap.c:635:10: warning: variable 'calcOffset' set but not used [-Wunused-but-set-variable] > long calcOffset, > ^ >admap.c: In function 'gb_is_valid_mapfile': >admap.c:722:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] > fread((char *)mheader, sizeof(*mheader),1,in); > ^ >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c adTest.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c adtune.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >adTest.c: In function 'testData': >adTest.c:36:9: warning: variable 'err' set but not used [-Wunused-but-set-variable] > int err = 0; > ^ >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c adGene.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c adtcp.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c adhashtools.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c adExperiment.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c adtools.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >adtools.c: In function 'GBT_check_arb_file': >adtools.c:74:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] > fgets(buffer,50,in); > ^ >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c adseqcompr.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c adtables.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c adRevCompl.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c adChangeKey.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c adali.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >adali.c: In function 'GBT_create_sequence_data': >adali.c:597:5: warning: 'GBT_add_data' is deprecated [-Wdeprecated-declarations] > GBDATA *gb_data = GBT_add_data(species, ali_name, key, type); > ^ >adali.c:568:9: note: declared here > GBDATA *GBT_add_data(GBDATA *species,const char *ali_name, const char *key, GB_TYPES type) { > ^ >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c adcolumns.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c adtree.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c adname.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c aditem.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c arbdbpp.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c ad_config.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >ld -r -o libARBDB.a adsort.o adlang1.o adstring.o admatch.o arbdb.o ad_core.o admath.o adoptimize.o adsystem.o adindex.o adperl.o adlink.o adsocket.o adcomm.o adhash.o adquery.o ad_save_load.o adcompr.o admalloc.o ad_load.o admap.o adTest.o adtune.o adGene.o adtcp.o adhashtools.o adExperiment.o adtools.o adseqcompr.o adtables.o adRevCompl.o adChangeKey.o adali.o adcolumns.o adtree.o adname.o aditem.o arbdbpp.o ad_config.o >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/ARBDBS' >-------------------------------------------------------------------------------- Make everything in SL/DB_SCANNER >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/DB_SCANNER' >make[4]: 'DB_SCANNER.a' is up to date. >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/DB_SCANNER' >-------------------------------------------------------------------------------- Make everything in SL/FILE_BUFFER >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/FILE_BUFFER' >make[4]: 'FILE_BUFFER.a' is up to date. >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/FILE_BUFFER' >-------------------------------------------------------------------------------- Make everything in SL/HELIX >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/HELIX' >make[4]: 'HELIX.a' is up to date. >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/HELIX' >-------------------------------------------------------------------------------- Make everything in SL/REGEXPR >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/REGEXPR' >make[4]: 'REGEXPR.a' is up to date. >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/REGEXPR' >-------------------------------------------------------------------------------- Make everything in SL/TREE_READ >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/TREE_READ' >make[4]: 'TREE_READ.a' is up to date. >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/TREE_READ' >-------------------------------------------------------------------------------- Make everything in SL/TREE_WRITE >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/TREE_WRITE' >make[4]: 'TREE_WRITE.a' is up to date. >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/TREE_WRITE' >-------------------------------------------------------------------------------- Make everything in SERVERCNTRL >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SERVERCNTRL' >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_SERVERCNTRL -c servercntrl.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >servercntrl.c: In function 'arb_start_server': >servercntrl.c:145:62: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] > if (!gbmain || GBCMC_system(gbmain,command)) system(command); > ^ >servercntrl.c: In function 'arb_look_and_start_server': >servercntrl.c:202:29: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] > system(copy_cmd); > ^ >ld -r -o SERVERCNTRL.a servercntrl.o >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SERVERCNTRL' >-------------------------------------------------------------------------------- Make everything in STAT >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/STAT' >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_STAT -c ST_quality.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_STAT -c ST_ml.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_STAT -c ST_window.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >ST_quality.cxx: In function 'void st_ml_add_quality_string_to_species(GBDATA*, const char*, const char*, int, int, GB_HASH*, st_report_enum, const char*)': >ST_quality.cxx:168:33: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated [-Wdeprecated-declarations] > GBDATA *gb_report = GBT_add_data(gb_species, alignment_name, "quality", GB_STRING); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from ST_quality.cxx:9: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_t_prot.h:108:9: note: declared here > GBDATA *GBT_add_data P_((GBDATA *species, const char *ali_name, const char *key, GB_TYPES type)) __ATTR__DEPRECATED; > ^ >ST_quality.cxx:168:33: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated [-Wdeprecated-declarations] > GBDATA *gb_report = GBT_add_data(gb_species, alignment_name, "quality", GB_STRING); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from ST_quality.cxx:9: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_t_prot.h:108:9: note: declared here > GBDATA *GBT_add_data P_((GBDATA *species, const char *ali_name, const char *key, GB_TYPES type)) __ATTR__DEPRECATED; > ^ >ST_quality.cxx:168:94: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated [-Wdeprecated-declarations] > GBDATA *gb_report = GBT_add_data(gb_species, alignment_name, "quality", GB_STRING); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from ST_quality.cxx:9: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_t_prot.h:108:9: note: declared here > GBDATA *GBT_add_data P_((GBDATA *species, const char *ali_name, const char *key, GB_TYPES type)) __ATTR__DEPRECATED; > ^ >ST_ml.cxx: In member function 'ST_ML_Color* ST_ML::get_color_string(char*, AP_tree*, int, int)': >ST_ml.cxx:820:9: warning: variable 'source_sequence_len' set but not used [-Wunused-but-set-variable] > int source_sequence_len = 0; > ^ >ld -r -o STAT.a ST_quality.o ST_ml.o ST_window.o >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/STAT' >-------------------------------------------------------------------------------- Make everything in XML >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/XML' >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_XML -c xml.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >xml.cxx:40:67: warning: unused parameter 'quotedText' [-Wunused-parameter] > static string encodeEntities(const string& str, bool quotedText = false) { > ^ >ld -r -o XML.a xml.o >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/XML' >-------------------------------------------------------------------------------- Make everything in SEQ_QUALITY >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SEQ_QUALITY' >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_SEQ_QUALITY -c SQ_main.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_SEQ_QUALITY -c SQ_functions.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_SEQ_QUALITY -c SQ_GroupData.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >SQ_functions.cxx: In function 'const char* SQ_reset_quality_calcstate(GBDATA*)': >SQ_functions.cxx:82:21: warning: 'const char* GB_get_error()' is deprecated [-Wdeprecated-declarations] > error = GB_get_error(); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdb.h:268:0, > from SQ_functions.cxx:21: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >SQ_functions.cxx:82:21: warning: 'const char* GB_get_error()' is deprecated [-Wdeprecated-declarations] > error = GB_get_error(); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdb.h:268:0, > from SQ_functions.cxx:21: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >SQ_functions.cxx:82:34: warning: 'const char* GB_get_error()' is deprecated [-Wdeprecated-declarations] > error = GB_get_error(); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdb.h:268:0, > from SQ_functions.cxx:21: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >SQ_functions.cxx:92:29: warning: 'const char* GB_get_error()' is deprecated [-Wdeprecated-declarations] > error = GB_get_error(); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdb.h:268:0, > from SQ_functions.cxx:21: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >SQ_functions.cxx:92:29: warning: 'const char* GB_get_error()' is deprecated [-Wdeprecated-declarations] > error = GB_get_error(); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdb.h:268:0, > from SQ_functions.cxx:21: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >SQ_functions.cxx:92:42: warning: 'const char* GB_get_error()' is deprecated [-Wdeprecated-declarations] > error = GB_get_error(); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdb.h:268:0, > from SQ_functions.cxx:21: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >SQ_functions.cxx: In function 'int SQ_get_value(GBDATA*, const char*)': >SQ_functions.cxx:131:13: warning: variable 'gb_species_data' set but not used [-Wunused-but-set-variable] > GBDATA *gb_species_data; > ^ >SQ_functions.cxx: In function 'int SQ_get_value_no_tree(GBDATA*, const char*)': >SQ_functions.cxx:171:13: warning: variable 'gb_species_data' set but not used [-Wunused-but-set-variable] > GBDATA *gb_species_data; > ^ >SQ_functions.cxx: In function 'const char* SQ_evaluate(GBDATA*, const SQ_weights&, bool)': >SQ_functions.cxx:239:21: warning: 'const char* GB_get_error()' is deprecated [-Wdeprecated-declarations] > error = GB_get_error(); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdb.h:268:0, > from SQ_functions.cxx:21: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >SQ_functions.cxx:239:21: warning: 'const char* GB_get_error()' is deprecated [-Wdeprecated-declarations] > error = GB_get_error(); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdb.h:268:0, > from SQ_functions.cxx:21: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >SQ_functions.cxx:239:34: warning: 'const char* GB_get_error()' is deprecated [-Wdeprecated-declarations] > error = GB_get_error(); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdb.h:268:0, > from SQ_functions.cxx:21: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >SQ_functions.cxx:216:13: warning: variable 'gb_species_data' set but not used [-Wunused-but-set-variable] > GBDATA *gb_species_data; > ^ >SQ_functions.cxx: In function 'const char* SQ_pass1(SQ_GroupData*, GBDATA*, GBT_TREE*, AP_filter*)': >SQ_functions.cxx:450:17: warning: 'const char* GB_get_error()' is deprecated [-Wdeprecated-declarations] > error = GB_get_error(); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdb.h:268:0, > from SQ_functions.cxx:21: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >SQ_functions.cxx:450:17: warning: 'const char* GB_get_error()' is deprecated [-Wdeprecated-declarations] > error = GB_get_error(); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdb.h:268:0, > from SQ_functions.cxx:21: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >SQ_functions.cxx:450:30: warning: 'const char* GB_get_error()' is deprecated [-Wdeprecated-declarations] > error = GB_get_error(); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdb.h:268:0, > from SQ_functions.cxx:21: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >SQ_functions.cxx:461:25: warning: 'const char* GB_get_error()' is deprecated [-Wdeprecated-declarations] > error = GB_get_error(); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdb.h:268:0, > from SQ_functions.cxx:21: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >SQ_functions.cxx:461:25: warning: 'const char* GB_get_error()' is deprecated [-Wdeprecated-declarations] > error = GB_get_error(); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdb.h:268:0, > from SQ_functions.cxx:21: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >SQ_functions.cxx:461:38: warning: 'const char* GB_get_error()' is deprecated [-Wdeprecated-declarations] > error = GB_get_error(); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdb.h:268:0, > from SQ_functions.cxx:21: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >SQ_functions.cxx:469:25: warning: 'const char* GB_get_error()' is deprecated [-Wdeprecated-declarations] > error = GB_get_error(); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdb.h:268:0, > from SQ_functions.cxx:21: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >SQ_functions.cxx:469:25: warning: 'const char* GB_get_error()' is deprecated [-Wdeprecated-declarations] > error = GB_get_error(); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdb.h:268:0, > from SQ_functions.cxx:21: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >SQ_functions.cxx:469:38: warning: 'const char* GB_get_error()' is deprecated [-Wdeprecated-declarations] > error = GB_get_error(); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdb.h:268:0, > from SQ_functions.cxx:21: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >SQ_functions.cxx:439:13: warning: variable 'gb_species_data' set but not used [-Wunused-but-set-variable] > GBDATA *gb_species_data; > ^ >SQ_functions.cxx: In function 'const char* SQ_pass1_no_tree(SQ_GroupData*, GBDATA*, AP_filter*)': >SQ_functions.cxx:554:21: warning: 'const char* GB_get_error()' is deprecated [-Wdeprecated-declarations] > error = GB_get_error(); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdb.h:268:0, > from SQ_functions.cxx:21: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >SQ_functions.cxx:554:21: warning: 'const char* GB_get_error()' is deprecated [-Wdeprecated-declarations] > error = GB_get_error(); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdb.h:268:0, > from SQ_functions.cxx:21: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >SQ_functions.cxx:554:34: warning: 'const char* GB_get_error()' is deprecated [-Wdeprecated-declarations] > error = GB_get_error(); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdb.h:268:0, > from SQ_functions.cxx:21: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >SQ_functions.cxx:564:29: warning: 'const char* GB_get_error()' is deprecated [-Wdeprecated-declarations] > error = GB_get_error(); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdb.h:268:0, > from SQ_functions.cxx:21: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >SQ_functions.cxx:564:29: warning: 'const char* GB_get_error()' is deprecated [-Wdeprecated-declarations] > error = GB_get_error(); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdb.h:268:0, > from SQ_functions.cxx:21: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >SQ_functions.cxx:564:42: warning: 'const char* GB_get_error()' is deprecated [-Wdeprecated-declarations] > error = GB_get_error(); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdb.h:268:0, > from SQ_functions.cxx:21: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >SQ_functions.cxx:572:29: warning: 'const char* GB_get_error()' is deprecated [-Wdeprecated-declarations] > error = GB_get_error(); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdb.h:268:0, > from SQ_functions.cxx:21: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >SQ_functions.cxx:572:29: warning: 'const char* GB_get_error()' is deprecated [-Wdeprecated-declarations] > error = GB_get_error(); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdb.h:268:0, > from SQ_functions.cxx:21: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >SQ_functions.cxx:572:42: warning: 'const char* GB_get_error()' is deprecated [-Wdeprecated-declarations] > error = GB_get_error(); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdb.h:268:0, > from SQ_functions.cxx:21: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >SQ_functions.cxx:534:13: warning: variable 'gb_species_data' set but not used [-Wunused-but-set-variable] > GBDATA *gb_species_data; > ^ >SQ_functions.cxx: In function 'const char* SQ_pass2(const SQ_GroupData*, GBDATA*, GBT_TREE*, AP_filter*)': >SQ_functions.cxx:649:17: warning: 'const char* GB_get_error()' is deprecated [-Wdeprecated-declarations] > error = GB_get_error(); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdb.h:268:0, > from SQ_functions.cxx:21: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >SQ_functions.cxx:649:17: warning: 'const char* GB_get_error()' is deprecated [-Wdeprecated-declarations] > error = GB_get_error(); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdb.h:268:0, > from SQ_functions.cxx:21: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >SQ_functions.cxx:649:30: warning: 'const char* GB_get_error()' is deprecated [-Wdeprecated-declarations] > error = GB_get_error(); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdb.h:268:0, > from SQ_functions.cxx:21: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >SQ_functions.cxx:659:25: warning: 'const char* GB_get_error()' is deprecated [-Wdeprecated-declarations] > error = GB_get_error(); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdb.h:268:0, > from SQ_functions.cxx:21: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >SQ_functions.cxx:659:25: warning: 'const char* GB_get_error()' is deprecated [-Wdeprecated-declarations] > error = GB_get_error(); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdb.h:268:0, > from SQ_functions.cxx:21: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >SQ_functions.cxx:659:38: warning: 'const char* GB_get_error()' is deprecated [-Wdeprecated-declarations] > error = GB_get_error(); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdb.h:268:0, > from SQ_functions.cxx:21: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >SQ_functions.cxx:664:25: warning: 'const char* GB_get_error()' is deprecated [-Wdeprecated-declarations] > error = GB_get_error(); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdb.h:268:0, > from SQ_functions.cxx:21: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >SQ_functions.cxx:664:25: warning: 'const char* GB_get_error()' is deprecated [-Wdeprecated-declarations] > error = GB_get_error(); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdb.h:268:0, > from SQ_functions.cxx:21: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >SQ_functions.cxx:664:38: warning: 'const char* GB_get_error()' is deprecated [-Wdeprecated-declarations] > error = GB_get_error(); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdb.h:268:0, > from SQ_functions.cxx:21: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >SQ_functions.cxx:733:29: warning: 'const char* GB_get_error()' is deprecated [-Wdeprecated-declarations] > error = GB_get_error(); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdb.h:268:0, > from SQ_functions.cxx:21: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >SQ_functions.cxx:733:29: warning: 'const char* GB_get_error()' is deprecated [-Wdeprecated-declarations] > error = GB_get_error(); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdb.h:268:0, > from SQ_functions.cxx:21: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >SQ_functions.cxx:733:42: warning: 'const char* GB_get_error()' is deprecated [-Wdeprecated-declarations] > error = GB_get_error(); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdb.h:268:0, > from SQ_functions.cxx:21: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >SQ_functions.cxx:737:29: warning: 'const char* GB_get_error()' is deprecated [-Wdeprecated-declarations] > error = GB_get_error(); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdb.h:268:0, > from SQ_functions.cxx:21: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >SQ_functions.cxx:737:29: warning: 'const char* GB_get_error()' is deprecated [-Wdeprecated-declarations] > error = GB_get_error(); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdb.h:268:0, > from SQ_functions.cxx:21: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >SQ_functions.cxx:737:42: warning: 'const char* GB_get_error()' is deprecated [-Wdeprecated-declarations] > error = GB_get_error(); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdb.h:268:0, > from SQ_functions.cxx:21: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >SQ_functions.cxx:638:13: warning: variable 'gb_species_data' set but not used [-Wunused-but-set-variable] > GBDATA *gb_species_data; > ^ >SQ_functions.cxx: In function 'const char* SQ_pass2_no_tree(const SQ_GroupData*, GBDATA*, AP_filter*)': >SQ_functions.cxx:889:21: warning: 'const char* GB_get_error()' is deprecated [-Wdeprecated-declarations] > error = GB_get_error(); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdb.h:268:0, > from SQ_functions.cxx:21: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >SQ_functions.cxx:889:21: warning: 'const char* GB_get_error()' is deprecated [-Wdeprecated-declarations] > error = GB_get_error(); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdb.h:268:0, > from SQ_functions.cxx:21: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >SQ_functions.cxx:889:34: warning: 'const char* GB_get_error()' is deprecated [-Wdeprecated-declarations] > error = GB_get_error(); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdb.h:268:0, > from SQ_functions.cxx:21: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >SQ_functions.cxx:898:29: warning: 'const char* GB_get_error()' is deprecated [-Wdeprecated-declarations] > error = GB_get_error(); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdb.h:268:0, > from SQ_functions.cxx:21: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >SQ_functions.cxx:898:29: warning: 'const char* GB_get_error()' is deprecated [-Wdeprecated-declarations] > error = GB_get_error(); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdb.h:268:0, > from SQ_functions.cxx:21: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >SQ_functions.cxx:898:42: warning: 'const char* GB_get_error()' is deprecated [-Wdeprecated-declarations] > error = GB_get_error(); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdb.h:268:0, > from SQ_functions.cxx:21: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >SQ_functions.cxx:903:29: warning: 'const char* GB_get_error()' is deprecated [-Wdeprecated-declarations] > error = GB_get_error(); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdb.h:268:0, > from SQ_functions.cxx:21: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >SQ_functions.cxx:903:29: warning: 'const char* GB_get_error()' is deprecated [-Wdeprecated-declarations] > error = GB_get_error(); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdb.h:268:0, > from SQ_functions.cxx:21: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >SQ_functions.cxx:903:42: warning: 'const char* GB_get_error()' is deprecated [-Wdeprecated-declarations] > error = GB_get_error(); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdb.h:268:0, > from SQ_functions.cxx:21: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >SQ_functions.cxx:972:33: warning: 'const char* GB_get_error()' is deprecated [-Wdeprecated-declarations] > error = GB_get_error(); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdb.h:268:0, > from SQ_functions.cxx:21: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >SQ_functions.cxx:972:33: warning: 'const char* GB_get_error()' is deprecated [-Wdeprecated-declarations] > error = GB_get_error(); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdb.h:268:0, > from SQ_functions.cxx:21: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >SQ_functions.cxx:972:46: warning: 'const char* GB_get_error()' is deprecated [-Wdeprecated-declarations] > error = GB_get_error(); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdb.h:268:0, > from SQ_functions.cxx:21: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >SQ_functions.cxx:976:33: warning: 'const char* GB_get_error()' is deprecated [-Wdeprecated-declarations] > error = GB_get_error(); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdb.h:268:0, > from SQ_functions.cxx:21: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >SQ_functions.cxx:976:33: warning: 'const char* GB_get_error()' is deprecated [-Wdeprecated-declarations] > error = GB_get_error(); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdb.h:268:0, > from SQ_functions.cxx:21: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >SQ_functions.cxx:976:46: warning: 'const char* GB_get_error()' is deprecated [-Wdeprecated-declarations] > error = GB_get_error(); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdb.h:268:0, > from SQ_functions.cxx:21: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >SQ_functions.cxx:871:13: warning: variable 'gb_species_data' set but not used [-Wunused-but-set-variable] > GBDATA *gb_species_data; > ^ >SQ_functions.cxx: In function 'const char* SQ_count_nr_of_species(GBDATA*)': >SQ_functions.cxx:1120:21: warning: 'const char* GB_get_error()' is deprecated [-Wdeprecated-declarations] > error = GB_get_error(); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdb.h:268:0, > from SQ_functions.cxx:21: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >SQ_functions.cxx:1120:21: warning: 'const char* GB_get_error()' is deprecated [-Wdeprecated-declarations] > error = GB_get_error(); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdb.h:268:0, > from SQ_functions.cxx:21: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >SQ_functions.cxx:1120:34: warning: 'const char* GB_get_error()' is deprecated [-Wdeprecated-declarations] > error = GB_get_error(); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdb.h:268:0, > from SQ_functions.cxx:21: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >SQ_functions.cxx:1130:29: warning: 'const char* GB_get_error()' is deprecated [-Wdeprecated-declarations] > error = GB_get_error(); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdb.h:268:0, > from SQ_functions.cxx:21: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >SQ_functions.cxx:1130:29: warning: 'const char* GB_get_error()' is deprecated [-Wdeprecated-declarations] > error = GB_get_error(); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdb.h:268:0, > from SQ_functions.cxx:21: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >SQ_functions.cxx:1130:42: warning: 'const char* GB_get_error()' is deprecated [-Wdeprecated-declarations] > error = GB_get_error(); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdb.h:268:0, > from SQ_functions.cxx:21: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >SQ_functions.cxx:1102:13: warning: variable 'gb_species_data' set but not used [-Wunused-but-set-variable] > GBDATA *gb_species_data; > ^ >SQ_functions.cxx: In function 'const char* SQ_mark_species(GBDATA*, int, bool)': >SQ_functions.cxx:1239:13: warning: variable 'gb_species_data' set but not used [-Wunused-but-set-variable] > GBDATA *gb_species_data; > ^ >ld -r -o SEQ_QUALITY.a SQ_main.o SQ_functions.o SQ_GroupData.o >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SEQ_QUALITY' >-------------------------------------------------------------------------------- Make everything in PRIMER_DESIGN >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PRIMER_DESIGN' >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PRIMER_DESIGN -c PRD_Pair.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PRIMER_DESIGN -c PRD_Item.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PRIMER_DESIGN -c PRD_Node.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PRIMER_DESIGN -c PRD_Range.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >PRD_Node.cxx: In member function 'void Node::print()': >PRD_Node.cxx:64:28: warning: array subscript is above array bounds [-Warray-bounds] > if ( child[3] ) { child[4]->print(); } > ^ >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PRIMER_DESIGN -c PRD_SequenceIterator.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PRIMER_DESIGN -c PRD_SearchFIFO.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PRIMER_DESIGN -c PRD_Design.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PRIMER_DESIGN -c primer_design.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >ld -r -o PRIMER_DESIGN.a PRD_Pair.o PRD_Item.o PRD_Node.o PRD_Range.o PRD_SequenceIterator.o PRD_SearchFIFO.o PRD_Design.o primer_design.o >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PRIMER_DESIGN' >-------------------------------------------------------------------------------- Make everything in SL/AW_HELIX >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/AW_HELIX' >make[4]: 'AW_HELIX.a' is up to date. >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/AW_HELIX' >-------------------------------------------------------------------------------- Make everything in NTREE >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/NTREE' >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NTREE -c AP_consensus.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >AP_consensus.cxx: In function 'const char* CON_export(char*, char*, int**, char*, int*, char*, int, long int, long int, int, int, int, double, double, int, int)': >AP_consensus.cxx:409:23: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated [-Wdeprecated-declarations] > GBDATA *gb_data = GBT_add_data(gb_extended, align,"data", GB_STRING); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from AP_consensus.cxx:52: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_t_prot.h:108:9: note: declared here > GBDATA *GBT_add_data P_((GBDATA *species, const char *ali_name, const char *key, GB_TYPES type)) __ATTR__DEPRECATED; > ^ >AP_consensus.cxx:409:23: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated [-Wdeprecated-declarations] > GBDATA *gb_data = GBT_add_data(gb_extended, align,"data", GB_STRING); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from AP_consensus.cxx:52: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_t_prot.h:108:9: note: declared here > GBDATA *GBT_add_data P_((GBDATA *species, const char *ali_name, const char *key, GB_TYPES type)) __ATTR__DEPRECATED; > ^ >AP_consensus.cxx:409:72: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated [-Wdeprecated-declarations] > GBDATA *gb_data = GBT_add_data(gb_extended, align,"data", GB_STRING); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from AP_consensus.cxx:52: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_t_prot.h:108:9: note: declared here > GBDATA *GBT_add_data P_((GBDATA *species, const char *ali_name, const char *key, GB_TYPES type)) __ATTR__DEPRECATED; > ^ >AP_consensus.cxx:411:25: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated [-Wdeprecated-declarations] > GBDATA *gb_options= GBT_add_data(gb_extended, align,"_TYPE", GB_STRING); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from AP_consensus.cxx:52: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_t_prot.h:108:9: note: declared here > GBDATA *GBT_add_data P_((GBDATA *species, const char *ali_name, const char *key, GB_TYPES type)) __ATTR__DEPRECATED; > ^ >AP_consensus.cxx:411:25: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated [-Wdeprecated-declarations] > GBDATA *gb_options= GBT_add_data(gb_extended, align,"_TYPE", GB_STRING); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from AP_consensus.cxx:52: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_t_prot.h:108:9: note: declared here > GBDATA *GBT_add_data P_((GBDATA *species, const char *ali_name, const char *key, GB_TYPES type)) __ATTR__DEPRECATED; > ^ >AP_consensus.cxx:411:75: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated [-Wdeprecated-declarations] > GBDATA *gb_options= GBT_add_data(gb_extended, align,"_TYPE", GB_STRING); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from AP_consensus.cxx:52: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_t_prot.h:108:9: note: declared here > GBDATA *GBT_add_data P_((GBDATA *species, const char *ali_name, const char *key, GB_TYPES type)) __ATTR__DEPRECATED; > ^ >AP_consensus.cxx:465:28: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated [-Wdeprecated-declarations] > GBDATA *gb_graph = GBT_add_data(gb_extended, align,"FREQUENCIES", GB_DB); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from AP_consensus.cxx:52: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_t_prot.h:108:9: note: declared here > GBDATA *GBT_add_data P_((GBDATA *species, const char *ali_name, const char *key, GB_TYPES type)) __ATTR__DEPRECATED; > ^ >AP_consensus.cxx:465:28: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated [-Wdeprecated-declarations] > GBDATA *gb_graph = GBT_add_data(gb_extended, align,"FREQUENCIES", GB_DB); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from AP_consensus.cxx:52: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_t_prot.h:108:9: note: declared here > GBDATA *GBT_add_data P_((GBDATA *species, const char *ali_name, const char *key, GB_TYPES type)) __ATTR__DEPRECATED; > ^ >AP_consensus.cxx:465:80: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated [-Wdeprecated-declarations] > GBDATA *gb_graph = GBT_add_data(gb_extended, align,"FREQUENCIES", GB_DB); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from AP_consensus.cxx:52: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_t_prot.h:108:9: note: declared here > GBDATA *GBT_add_data P_((GBDATA *species, const char *ali_name, const char *key, GB_TYPES type)) __ATTR__DEPRECATED; > ^ >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NTREE -c AP_conservProfile2Gnuplot.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >AP_consensus.cxx: In function 'void CON_calc_max_freq_cb(AW_window*)': >AP_consensus.cxx:962:27: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated [-Wdeprecated-declarations] > GBDATA *gb_data = GBT_add_data(gb_extended, align,"data", GB_STRING); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from AP_consensus.cxx:52: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_t_prot.h:108:9: note: declared here > GBDATA *GBT_add_data P_((GBDATA *species, const char *ali_name, const char *key, GB_TYPES type)) __ATTR__DEPRECATED; > ^ >AP_consensus.cxx:962:27: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated [-Wdeprecated-declarations] > GBDATA *gb_data = GBT_add_data(gb_extended, align,"data", GB_STRING); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from AP_consensus.cxx:52: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_t_prot.h:108:9: note: declared here > GBDATA *GBT_add_data P_((GBDATA *species, const char *ali_name, const char *key, GB_TYPES type)) __ATTR__DEPRECATED; > ^ >AP_consensus.cxx:962:76: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated [-Wdeprecated-declarations] > GBDATA *gb_data = GBT_add_data(gb_extended, align,"data", GB_STRING); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from AP_consensus.cxx:52: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_t_prot.h:108:9: note: declared here > GBDATA *GBT_add_data P_((GBDATA *species, const char *ali_name, const char *key, GB_TYPES type)) __ATTR__DEPRECATED; > ^ >AP_consensus.cxx:963:27: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated [-Wdeprecated-declarations] > GBDATA *gb_data2 = GBT_add_data(gb_extended, align,"dat2", GB_STRING); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from AP_consensus.cxx:52: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_t_prot.h:108:9: note: declared here > GBDATA *GBT_add_data P_((GBDATA *species, const char *ali_name, const char *key, GB_TYPES type)) __ATTR__DEPRECATED; > ^ >AP_consensus.cxx:963:27: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated [-Wdeprecated-declarations] > GBDATA *gb_data2 = GBT_add_data(gb_extended, align,"dat2", GB_STRING); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from AP_consensus.cxx:52: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_t_prot.h:108:9: note: declared here > GBDATA *GBT_add_data P_((GBDATA *species, const char *ali_name, const char *key, GB_TYPES type)) __ATTR__DEPRECATED; > ^ >AP_consensus.cxx:963:76: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated [-Wdeprecated-declarations] > GBDATA *gb_data2 = GBT_add_data(gb_extended, align,"dat2", GB_STRING); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from AP_consensus.cxx:52: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_t_prot.h:108:9: note: declared here > GBDATA *GBT_add_data P_((GBDATA *species, const char *ali_name, const char *key, GB_TYPES type)) __ATTR__DEPRECATED; > ^ >AP_consensus.cxx:966:27: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated [-Wdeprecated-declarations] > GBDATA *gb_options = GBT_add_data(gb_extended, align,"_TYPE", GB_STRING); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from AP_consensus.cxx:52: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_t_prot.h:108:9: note: declared here > GBDATA *GBT_add_data P_((GBDATA *species, const char *ali_name, const char *key, GB_TYPES type)) __ATTR__DEPRECATED; > ^ >AP_consensus.cxx:966:27: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated [-Wdeprecated-declarations] > GBDATA *gb_options = GBT_add_data(gb_extended, align,"_TYPE", GB_STRING); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from AP_consensus.cxx:52: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_t_prot.h:108:9: note: declared here > GBDATA *GBT_add_data P_((GBDATA *species, const char *ali_name, const char *key, GB_TYPES type)) __ATTR__DEPRECATED; > ^ >AP_consensus.cxx:966:77: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated [-Wdeprecated-declarations] > GBDATA *gb_options = GBT_add_data(gb_extended, align,"_TYPE", GB_STRING); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from AP_consensus.cxx:52: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_t_prot.h:108:9: note: declared here > GBDATA *GBT_add_data P_((GBDATA *species, const char *ali_name, const char *key, GB_TYPES type)) __ATTR__DEPRECATED; > ^ >AP_conservProfile2Gnuplot.cxx: In function 'void AP_conservProfile2Gnuplot_callback(AW_window*)': >AP_conservProfile2Gnuplot.cxx:58:42: warning: ignoring return value of 'const char* GB_xcmd(const char*, GB_BOOL, GB_BOOL)', declared with attribute warn_unused_result [-Wunused-result] > GB_xcmd(script, GB_TRUE, GB_TRUE); // execute GNUPLOT using command_file > ^ >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NTREE -c AP_cprofile.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NTREE -c AP_csp_2_gnuplot.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NTREE -c AP_pos_var_pars.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >AP_cprofile.cxx: In function 'void CPRO_workupstatistic(unsigned char)': >AP_cprofile.cxx:234:17: warning: variable 'colmax' set but not used [-Wunused-but-set-variable] > long column,colmax,memneeded=0; > ^ >AP_cprofile.cxx: In function 'void CPRO_memrequirement_cb(AW_root*)': >AP_cprofile.cxx:663:10: warning: variable 'versus' set but not used [-Wunused-but-set-variable] > char versus=0; /* all vs all */ > ^ >AP_cprofile.cxx: In function 'void CPRO_condense_cb(AW_window*, AW_CL)': >AP_cprofile.cxx:1420:14: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated [-Wdeprecated-declarations] > gb_param=GBT_add_data(gb_extended,align,"_TYPE",GB_STRING); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from AP_cprofile.cxx:51: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_t_prot.h:108:9: note: declared here > GBDATA *GBT_add_data P_((GBDATA *species, const char *ali_name, const char *key, GB_TYPES type)) __ATTR__DEPRECATED; > ^ >AP_cprofile.cxx:1420:14: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated [-Wdeprecated-declarations] > gb_param=GBT_add_data(gb_extended,align,"_TYPE",GB_STRING); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from AP_cprofile.cxx:51: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_t_prot.h:108:9: note: declared here > GBDATA *GBT_add_data P_((GBDATA *species, const char *ali_name, const char *key, GB_TYPES type)) __ATTR__DEPRECATED; > ^ >AP_cprofile.cxx:1420:62: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated [-Wdeprecated-declarations] > gb_param=GBT_add_data(gb_extended,align,"_TYPE",GB_STRING); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from AP_cprofile.cxx:51: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_t_prot.h:108:9: note: declared here > GBDATA *GBT_add_data P_((GBDATA *species, const char *ali_name, const char *key, GB_TYPES type)) __ATTR__DEPRECATED; > ^ >AP_cprofile.cxx:1423:23: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated [-Wdeprecated-declarations] > GBDATA *gb_data = GBT_add_data(gb_extended, align,"data", GB_STRING); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from AP_cprofile.cxx:51: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_t_prot.h:108:9: note: declared here > GBDATA *GBT_add_data P_((GBDATA *species, const char *ali_name, const char *key, GB_TYPES type)) __ATTR__DEPRECATED; > ^ >AP_cprofile.cxx:1423:23: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated [-Wdeprecated-declarations] > GBDATA *gb_data = GBT_add_data(gb_extended, align,"data", GB_STRING); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from AP_cprofile.cxx:51: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_t_prot.h:108:9: note: declared here > GBDATA *GBT_add_data P_((GBDATA *species, const char *ali_name, const char *key, GB_TYPES type)) __ATTR__DEPRECATED; > ^ >AP_cprofile.cxx:1423:72: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated [-Wdeprecated-declarations] > GBDATA *gb_data = GBT_add_data(gb_extended, align,"data", GB_STRING); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from AP_cprofile.cxx:51: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_t_prot.h:108:9: note: declared here > GBDATA *GBT_add_data P_((GBDATA *species, const char *ali_name, const char *key, GB_TYPES type)) __ATTR__DEPRECATED; > ^ >AP_csp_2_gnuplot.cxx: In function 'char* get_overlay_files(AW_root*, const char*, const char*&)': >AP_csp_2_gnuplot.cxx:92:50: warning: 'const char* GB_get_error()' is deprecated [-Wdeprecated-declarations] > if (!found_prefix_files) error = GB_get_error(); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdb.h:268:0, > from AP_csp_2_gnuplot.cxx:8: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >AP_csp_2_gnuplot.cxx:92:50: warning: 'const char* GB_get_error()' is deprecated [-Wdeprecated-declarations] > if (!found_prefix_files) error = GB_get_error(); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdb.h:268:0, > from AP_csp_2_gnuplot.cxx:8: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >AP_csp_2_gnuplot.cxx:92:63: warning: 'const char* GB_get_error()' is deprecated [-Wdeprecated-declarations] > if (!found_prefix_files) error = GB_get_error(); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdb.h:268:0, > from AP_csp_2_gnuplot.cxx:8: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >AP_csp_2_gnuplot.cxx:100:55: warning: 'const char* GB_get_error()' is deprecated [-Wdeprecated-declarations] > if (!found_postfix_files) error = GB_get_error(); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdb.h:268:0, > from AP_csp_2_gnuplot.cxx:8: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >AP_csp_2_gnuplot.cxx:100:55: warning: 'const char* GB_get_error()' is deprecated [-Wdeprecated-declarations] > if (!found_postfix_files) error = GB_get_error(); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdb.h:268:0, > from AP_csp_2_gnuplot.cxx:8: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >AP_csp_2_gnuplot.cxx:100:68: warning: 'const char* GB_get_error()' is deprecated [-Wdeprecated-declarations] > if (!found_postfix_files) error = GB_get_error(); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdb.h:268:0, > from AP_csp_2_gnuplot.cxx:8: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_prot.h:43:10: note: declared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; > ^ >AP_csp_2_gnuplot.cxx: In function 'void AP_csp_2_gnuplot_cb(AW_window*, AW_CL, AW_CL)': >AP_csp_2_gnuplot.cxx:388:62: warning: ignoring return value of 'const char* GB_xcmd(const char*, GB_BOOL, GB_BOOL)', declared with attribute warn_unused_result [-Wunused-result] > GB_xcmd(script, GB_TRUE, GB_TRUE); > ^ >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NTREE -c NT_cb.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NTREE -c NT_concatenate.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NTREE -c NT_dbrepair.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >NT_cb.cxx: In function 'void NT_system_cb2(AW_window*, AW_CL, AW_CL)': >NT_cb.cxx:128:35: warning: ignoring return value of 'const char* GB_xcmd(const char*, GB_BOOL, GB_BOOL)', declared with attribute warn_unused_result [-Wunused-result] > GB_xcmd(sys,GB_TRUE, GB_FALSE); > ^ >NT_concatenate.cxx: In function 'const char* displayAlignmentInfo(GBDATA*, GB_ERROR, char*, char*)': >NT_concatenate.cxx:310:37: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated [-Wdeprecated-declarations] > GBDATA *gb_data = GBT_add_data(gb_extended, new_ali_name,"data", GB_STRING); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from NT_concatenate.cxx:22: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_t_prot.h:108:9: note: declared here > GBDATA *GBT_add_data P_((GBDATA *species, const char *ali_name, const char *key, GB_TYPES type)) __ATTR__DEPRECATED; > ^ >NT_concatenate.cxx:310:37: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated [-Wdeprecated-declarations] > GBDATA *gb_data = GBT_add_data(gb_extended, new_ali_name,"data", GB_STRING); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from NT_concatenate.cxx:22: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_t_prot.h:108:9: note: declared here > GBDATA *GBT_add_data P_((GBDATA *species, const char *ali_name, const char *key, GB_TYPES type)) __ATTR__DEPRECATED; > ^ >NT_concatenate.cxx:310:93: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated [-Wdeprecated-declarations] > GBDATA *gb_data = GBT_add_data(gb_extended, new_ali_name,"data", GB_STRING); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from NT_concatenate.cxx:22: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_t_prot.h:108:9: note: declared here > GBDATA *GBT_add_data P_((GBDATA *species, const char *ali_name, const char *key, GB_TYPES type)) __ATTR__DEPRECATED; > ^ >NT_concatenate.cxx: In function 'void concatenateAlignments(AW_window*)': >NT_concatenate.cxx:415:39: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated [-Wdeprecated-declarations] > GBDATA *gb_data = GBT_add_data(gb_species, new_ali_name, "data", GB_STRING); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from NT_concatenate.cxx:22: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_t_prot.h:108:9: note: declared here > GBDATA *GBT_add_data P_((GBDATA *species, const char *ali_name, const char *key, GB_TYPES type)) __ATTR__DEPRECATED; > ^ >NT_concatenate.cxx:415:39: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated [-Wdeprecated-declarations] > GBDATA *gb_data = GBT_add_data(gb_species, new_ali_name, "data", GB_STRING); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from NT_concatenate.cxx:22: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_t_prot.h:108:9: note: declared here > GBDATA *GBT_add_data P_((GBDATA *species, const char *ali_name, const char *key, GB_TYPES type)) __ATTR__DEPRECATED; > ^ >NT_concatenate.cxx:415:95: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated [-Wdeprecated-declarations] > GBDATA *gb_data = GBT_add_data(gb_species, new_ali_name, "data", GB_STRING); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from NT_concatenate.cxx:22: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_t_prot.h:108:9: note: declared here > GBDATA *GBT_add_data P_((GBDATA *species, const char *ali_name, const char *key, GB_TYPES type)) __ATTR__DEPRECATED; > ^ >NT_concatenate.cxx: In function 'GBDATA* concatenateFieldsCreateNewSpecies(AW_window*, GBDATA*, speciesConcatenateList)': >NT_concatenate.cxx:664:39: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated [-Wdeprecated-declarations] > GBDATA *gb_data = GBT_add_data(gb_new_species, ali_names[no_of_alignments], "data", GB_STRING); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from NT_concatenate.cxx:22: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_t_prot.h:108:9: note: declared here > GBDATA *GBT_add_data P_((GBDATA *species, const char *ali_name, const char *key, GB_TYPES type)) __ATTR__DEPRECATED; > ^ >NT_concatenate.cxx:664:39: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated [-Wdeprecated-declarations] > GBDATA *gb_data = GBT_add_data(gb_new_species, ali_names[no_of_alignments], "data", GB_STRING); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from NT_concatenate.cxx:22: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_t_prot.h:108:9: note: declared here > GBDATA *GBT_add_data P_((GBDATA *species, const char *ali_name, const char *key, GB_TYPES type)) __ATTR__DEPRECATED; > ^ >NT_concatenate.cxx:664:114: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated [-Wdeprecated-declarations] > GBDATA *gb_data = GBT_add_data(gb_new_species, ali_names[no_of_alignments], "data", GB_STRING); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from NT_concatenate.cxx:22: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_t_prot.h:108:9: note: declared here > GBDATA *GBT_add_data P_((GBDATA *species, const char *ali_name, const char *key, GB_TYPES type)) __ATTR__DEPRECATED; > ^ >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NTREE -c NT_edconf.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NTREE -c NT_extern.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NTREE -c NT_import.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NTREE -c NT_ins_col.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >NT_import.cxx: In function 'void NT_import_sequences(AW_window*, AW_CL, AW_CL)': >NT_import.cxx:52:30: warning: variable 'gb_merge_is_genom_db' set but not used [-Wunused-but-set-variable] > int gb_main_is_genom_db, gb_merge_is_genom_db; > ^ >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NTREE -c NT_join.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NTREE -c NT_main.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NTREE -c NT_sort.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NTREE -c NT_trackAliChanges.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >NT_main.cxx: In function 'int main(int, char**)': >NT_main.cxx:399:50: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] > system("touch ${HOME}/.arb_prop/msgtime"); > ^ >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NTREE -c NT_validManual.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NTREE -c NT_validNameParser.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >NT_validNameParser.cxx: In function 'validNames::Desco validNames::determineType(const string&)': >NT_validNameParser.cxx:89:14: warning: variable 'isSee' set but not used [-Wunused-but-set-variable] > bool isSee = false; > ^ >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NTREE -c NT_validNames.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NTREE -c ad_ali.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NTREE -c ad_ext.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NTREE -c ad_spec.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NTREE -c ad_transpro.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NTREE -c ad_trees.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >ad_spec.cxx: In function 'void ad_field_convert_commit_cb(AW_window*, AW_CL)': >ad_spec.cxx:729:29: warning: unused variable 'selector' [-Wunused-variable] > const ad_item_selector *selector = (const ad_item_selector*) cl_item_selector; > ^ >ad_transpro.cxx: In function 'const char* arb_r2a(GBDATA*, bool, bool, int, bool, const char*, const char*)': >ad_transpro.cxx:159:48: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated [-Wdeprecated-declarations] > GBDATA *gb_dest_data = GBT_add_data(gb_species, ali_dest, "data", GB_STRING); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from ad_transpro.cxx:7: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_t_prot.h:108:9: note: declared here > GBDATA *GBT_add_data P_((GBDATA *species, const char *ali_name, const char *key, GB_TYPES type)) __ATTR__DEPRECATED; > ^ >ad_transpro.cxx:159:48: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated [-Wdeprecated-declarations] > GBDATA *gb_dest_data = GBT_add_data(gb_species, ali_dest, "data", GB_STRING); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from ad_transpro.cxx:7: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_t_prot.h:108:9: note: declared here > GBDATA *GBT_add_data P_((GBDATA *species, const char *ali_name, const char *key, GB_TYPES type)) __ATTR__DEPRECATED; > ^ >ad_transpro.cxx:159:100: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated [-Wdeprecated-declarations] > GBDATA *gb_dest_data = GBT_add_data(gb_species, ali_dest, "data", GB_STRING); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from ad_transpro.cxx:7: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_t_prot.h:108:9: note: declared here > GBDATA *GBT_add_data P_((GBDATA *species, const char *ali_name, const char *key, GB_TYPES type)) __ATTR__DEPRECATED; > ^ >ad_trees.cxx: In function 'char* readXmlTree(char*)': >ad_trees.cxx:418:44: warning: ignoring return value of 'const char* GB_xcmd(const char*, GB_BOOL, GB_BOOL)', declared with attribute warn_unused_result [-Wunused-result] > GB_xcmd(command, GB_FALSE, GB_TRUE); > ^ >ad_trees.cxx:422:44: warning: ignoring return value of 'const char* GB_xcmd(const char*, GB_BOOL, GB_BOOL)', declared with attribute warn_unused_result [-Wunused-result] > GB_xcmd(command, GB_FALSE, GB_TRUE); > ^ >-------------------- Checking NTREE.a >Target 'NTREE.a' not found >-> rebuilding NTREE.a (Thu Jan 1 00:59:59 1970) >ld -r -o NTREE.a AP_consensus.o AP_conservProfile2Gnuplot.o AP_cprofile.o AP_csp_2_gnuplot.o AP_pos_var_pars.o NT_cb.o NT_concatenate.o NT_dbrepair.o NT_edconf.o NT_extern.o NT_import.o NT_ins_col.o NT_join.o NT_main.o NT_sort.o NT_trackAliChanges.o NT_validManual.o NT_validNameParser.o NT_validNames.o ad_ali.o ad_ext.o ad_spec.o ad_transpro.o ad_trees.o >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/NTREE' >-------------------------------------------------------------------------------- Make everything in WETC >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/WETC' >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_WETC -c -o WETC_main.o WETC_main.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >ld -r -o WETC.a WETC_main.o >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/WETC' >-------------------------------------------------------------------------------- Make everything in SL/FAST_ALIGNER >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/FAST_ALIGNER' >make[4]: 'FAST_ALIGNER.a' is up to date. >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/FAST_ALIGNER' >-------------------------------------------------------------------------------- Make everything in READSEQ >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/READSEQ' >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_READSEQ -c readseq.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_READSEQ -c ureadseq.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -Wl,-O1 -Wl,--as-needed -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_READSEQ -o /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/arb_readseq readseq.o ureadseq.o >readseq.o: In function `main': >readseq.c:(.text.startup+0x631): warning: the use of `tmpnam' is dangerous, better use `mkstemp' >readseq.o: In function `chooseFormat': >readseq.c:(.text+0x848): warning: the `gets' function is dangerous and should not be used. >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/READSEQ' >-------------------------------------------------------------------------------- Make everything in ISLAND_HOPPING >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/ISLAND_HOPPING' >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ISLAND_HOPPING -c island_hopping.cpp -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ISLAND_HOPPING -DARB -c i-hopper.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ISLAND_HOPPING -DARB -c align.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >align.c: In function 'Align': >align.c:343:49: warning: 'jjj' may be used uninitialized in this function [-Wmaybe-uninitialized] > f->beginX=iii-l+1; f->beginY=jjj-l+1; f->length=l; > ^ >align.c:312:53: note: 'jjj' was declared here > Island *p; Fragment *f,**ff,*L; int k,ii,jj,iii,jjj,l; double s; > ^ >align.c:343:30: warning: 'iii' may be used uninitialized in this function [-Wmaybe-uninitialized] > f->beginX=iii-l+1; f->beginY=jjj-l+1; f->length=l; > ^ >align.c:312:49: note: 'iii' was declared here > Island *p; Fragment *f,**ff,*L; int k,ii,jj,iii,jjj,l; double s; > ^ >align.c:326:41: warning: 'jjj' may be used uninitialized in this function [-Wmaybe-uninitialized] > f->beginX=iii; f->beginY=jjj; f->length=l; > ^ >align.c:312:53: note: 'jjj' was declared here > Island *p; Fragment *f,**ff,*L; int k,ii,jj,iii,jjj,l; double s; > ^ >align.c:326:26: warning: 'iii' may be used uninitialized in this function [-Wmaybe-uninitialized] > f->beginX=iii; f->beginY=jjj; f->length=l; > ^ >align.c:312:49: note: 'iii' was declared here > Island *p; Fragment *f,**ff,*L; int k,ii,jj,iii,jjj,l; double s; > ^ >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ISLAND_HOPPING -DARB -c memory.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ISLAND_HOPPING -DARB -c trnsprob.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >trnsprob.c: In function 'updateTrnsprob': >trnsprob.c:236:68: warning: 'f' may be used uninitialized in this function [-Wmaybe-uninitialized] > Q[A][T]=b*F[T]*s; Q[A][C]=d*F[C]*s; Q[A][G]=f*F[G]*s; > ^ >trnsprob.c:235:68: warning: 'e' may be used uninitialized in this function [-Wmaybe-uninitialized] > Q[C][T]=a*F[T]*s; Q[C][A]=d*F[A]*s; Q[C][G]=e*F[G]*s; > ^ >trnsprob.c:235:50: warning: 'd' may be used uninitialized in this function [-Wmaybe-uninitialized] > Q[C][T]=a*F[T]*s; Q[C][A]=d*F[A]*s; Q[C][G]=e*F[G]*s; > ^ >trnsprob.c:234:50: warning: 'c' may be used uninitialized in this function [-Wmaybe-uninitialized] > Q[T][C]=a*F[C]*s; Q[T][A]=b*F[A]*s; Q[T][G]=c*F[G]*s; > ^ >trnsprob.c:234:32: warning: 'b' may be used uninitialized in this function [-Wmaybe-uninitialized] > Q[T][C]=a*F[C]*s; Q[T][A]=b*F[A]*s; Q[T][G]=c*F[G]*s; > ^ >trnsprob.c:234:14: warning: 'a' may be used uninitialized in this function [-Wmaybe-uninitialized] > Q[T][C]=a*F[C]*s; Q[T][A]=b*F[A]*s; Q[T][G]=c*F[G]*s; > ^ >ld -r -o ISLAND_HOPPING.a island_hopping.o i-hopper.o align.o memory.o trnsprob.o >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/ISLAND_HOPPING' >-------------------------------------------------------------------------------- Make everything in EDIT >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/EDIT' >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_EDIT -c edit.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_EDIT -c edit_naligner.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >edit_naligner.cxx: In function 'void aed_start_naligning(AW_window*)': >edit_naligner.cxx:102:19: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] > system(buffer); > ^ >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_EDIT -c edit_tools.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_EDIT -c ed_conf.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >ld -r -o EDIT.a edit.o edit_naligner.o edit_tools.o ed_conf.o >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/EDIT' >-------------------------------------------------------------------------------- Make everything in CONSENSUS_TREE >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/CONSENSUS_TREE' >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_CONSENSUS_TREE -c CT_part.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_CONSENSUS_TREE -c CT_hash.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_CONSENSUS_TREE -c CT_ntree.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_CONSENSUS_TREE -c CT_rbtree.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_CONSENSUS_TREE -c CT_dtree.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_CONSENSUS_TREE -c CT_ctree.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_CONSENSUS_TREE -c CT_mem.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >ld -r -o CONSENSUS_TREE.a CT_part.o CT_hash.o CT_ntree.o CT_rbtree.o CT_dtree.o CT_ctree.o CT_mem.o >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/CONSENSUS_TREE' >-------------------------------------------------------------------------------- Make everything in DIST >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/DIST' >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_DIST -c DI_mldist.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_DIST -c DI_protdist.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_DIST -c DI_compress_matrix.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_DIST -c DI_view_matrix.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_DIST -c DI_save_matr.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_DIST -c DI_main.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_DIST -c DI_matr.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >DI_main.cxx: In function 'int main(int, char**)': >DI_main.cxx:40:18: warning: variable 'awd' set but not used [-Wunused-but-set-variable] > AWT_graphic *awd; > ^ >DI_main.cxx:71:63: warning: ignoring return value of 'const char* ARB_init_global_awars(AW_root*, AW_default, GBDATA*)', declared with attribute warn_unused_result [-Wunused-result] > ARB_init_global_awars(aw_root, aw_default, GLOBAL_gb_main); > ^ >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_DIST -c distanalyse.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >DI_matr.cxx: In function 'void di_autodetect_callback(AW_window*)': >DI_matr.cxx:1426:23: warning: variable 'trans' set but not used [-Wunused-but-set-variable] > DI_TRANSFORMATION trans; > ^ >distanalyse.cxx: In member function 'char* DI_MATRIX::analyse(AW_root*)': >distanalyse.cxx:30:21: warning: variable 'mean_gc' set but not used [-Wunused-but-set-variable] > float act_gc, mean_gc, min_gc=9999.9, max_gc=0.0; > ^ >DI_matr.cxx: In member function 'char* DI_MATRIX::load(char*, AP_filter*, AP_weights*, LoadWhat, GB_CSTR, bool, GBDATA**)': >DI_matr.cxx:345:9: warning: 'no_of_species' may be used uninitialized in this function [-Wmaybe-uninitialized] > if (out_tree_species) { > ^ >DI_matr.cxx:402:86: warning: 'gb_species' may be used uninitialized in this function [-Wmaybe-uninitialized] > case DI_LOAD_MARKED: gb_species = GBT_next_marked_species(gb_species); break; > ^ >ld -r -o DIST.a DI_mldist.o DI_protdist.o DI_compress_matrix.o DI_view_matrix.o DI_save_matr.o DI_main.o DI_matr.o distanalyse.o >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/DIST' >-------------------------------------------------------------------------------- Make everything in SECEDIT >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SECEDIT' >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_SECEDIT -c SEC_toggle.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_SECEDIT -c SEC_bonddef.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_SECEDIT -c SEC_db.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >SEC_db.cxx:328:2: warning: #warning @@@reread alilen [-Wcpp] > #warning @@@reread alilen > ^ >SEC_db.cxx:329:2: warning: #warning test changing ali length! [-Wcpp] > #warning test changing ali length! > ^ >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_SECEDIT -c SEC_helix.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_SECEDIT -c SEC_graphic.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_SECEDIT -c SEC_structure.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_SECEDIT -c SEC_read.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_SECEDIT -c SEC_io.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_SECEDIT -c SEC_paint.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >SEC_paint.cxx:368:2: warning: #warning move to SEC_db_interface [-Wcpp] > #warning move to SEC_db_interface > ^ >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_SECEDIT -c SEC_layout.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_SECEDIT -c SEC_split.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_SECEDIT -c SEC_abspos.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_SECEDIT -c SEC_main.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >SEC_main.cxx:88:2: warning: #warning make the refresh invisible [-Wcpp] > #warning make the refresh invisible > ^ >SEC_main.cxx:702:30: warning: unused parameter 'gb_main' [-Wunused-parameter] > static void SEC_exit(GBDATA *gb_main, void *cl_sec_root) { > ^ >ld -r -o SECEDIT.a SEC_toggle.o SEC_bonddef.o SEC_db.o SEC_helix.o SEC_graphic.o SEC_structure.o SEC_read.o SEC_io.o SEC_paint.o SEC_layout.o SEC_split.o SEC_abspos.o SEC_main.o >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SECEDIT' >-------------------------------------------------------------------------------- Make everything in DBSERVER >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/DBSERVER' >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_DBSERVER -c db_server.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >ld -r -o DBSERVER.a db_server.o >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/DBSERVER' >-------------------------------------------------------------------------------- Make everything in PARSIMONY >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PARSIMONY' >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PARSIMONY -c PARS_main.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PARSIMONY -c PARS_dtree.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PARSIMONY -c PARS_debug.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PARSIMONY -c PARS_klprops.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PARSIMONY -c AP_buffer.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PARSIMONY -c AP_main.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PARSIMONY -c AP_tree_nlen.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PARSIMONY -c AP_tree_edge.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >AP_tree_nlen.cxx: In member function 'virtual AP_BOOL AP_tree_nlen::clear(long unsigned int, long unsigned int)': >AP_tree_nlen.cxx:662:28: warning: logical not is only applied to the left hand side of comparison [-Wlogical-not-parentheses] > if (!this->stack_level == datum) > ^ >AP_tree_nlen.cxx: In member function 'void AP_tree_nlen::kernighan_rek(int, int*, int, int, double (*)(double, double*, int), double*, int, AP_FLOAT, AP_FLOAT, AP_FLOAT, AP_KL_FLAG, AP_BOOL*)': >AP_tree_nlen.cxx:964:41: warning: logical not is only applied to the left hand side of comparison [-Wlogical-not-parentheses] > if (!pars_refpntr[i]->kernighan == AP_NONE) continue; > ^ >AP_tree_nlen.cxx:964:41: warning: comparison of constant '5' with boolean expression is always false [-Wbool-compare] >ld -r -o PARSIMONY.a PARS_main.o PARS_dtree.o PARS_debug.o PARS_klprops.o AP_buffer.o AP_main.o AP_tree_nlen.o AP_tree_edge.o >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PARSIMONY' >-------------------------------------------------------------------------------- Make everything in PHYLO >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PHYLO' >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PHYLO -c PH_data.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PHYLO -c PH_root.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PHYLO -c PH_main.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >PH_data.cxx: In member function 'const char* PHDATA::calculate_matrix(const char*, double, PH_TRANSFORMATION)': >PH_data.cxx:201:5: warning: 'options_vector[0]' may be used uninitialized in this function [-Wmaybe-uninitialized] > switch(options_vector[0]) // '.' in column > ^ >PH_data.cxx:210:5: warning: 'options_vector[1]' may be used uninitialized in this function [-Wmaybe-uninitialized] > switch(options_vector[1]) // '-' in column > ^ >PH_data.cxx:219:5: warning: 'options_vector[2]' may be used uninitialized in this function [-Wmaybe-uninitialized] > switch(options_vector[2]) // '.' in column > ^ >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PHYLO -c PH_filt.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PHYLO -c PH_display.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >PH_main.cxx: In function 'void startup_sequence_cb(AW_window*, AW_CL, AW_CL)': >PH_main.cxx:50:16: warning: variable 'load_what' set but not used [-Wunused-but-set-variable] > char *use,*load_what; > ^ >PH_main.cxx: In function 'const char* PH_create_ml_multiline_SAI(GB_CSTR, int, GBDATA**)': >PH_main.cxx:157:31: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated [-Wdeprecated-declarations] > gb_data = GBT_add_data(gb_sai,PHDATA::ROOT->use,"data",GB_STRING); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from phylo.hxx:23, > from PH_main.cxx:1: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_t_prot.h:108:9: note: declared here > GBDATA *GBT_add_data P_((GBDATA *species, const char *ali_name, const char *key, GB_TYPES type)) __ATTR__DEPRECATED; > ^ >PH_main.cxx:157:31: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated [-Wdeprecated-declarations] > gb_data = GBT_add_data(gb_sai,PHDATA::ROOT->use,"data",GB_STRING); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from phylo.hxx:23, > from PH_main.cxx:1: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_t_prot.h:108:9: note: declared here > GBDATA *GBT_add_data P_((GBDATA *species, const char *ali_name, const char *key, GB_TYPES type)) __ATTR__DEPRECATED; > ^ >PH_main.cxx:157:85: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated [-Wdeprecated-declarations] > gb_data = GBT_add_data(gb_sai,PHDATA::ROOT->use,"data",GB_STRING); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from phylo.hxx:23, > from PH_main.cxx:1: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_t_prot.h:108:9: note: declared here > GBDATA *GBT_add_data P_((GBDATA *species, const char *ali_name, const char *key, GB_TYPES type)) __ATTR__DEPRECATED; > ^ >PH_main.cxx:162:31: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated [-Wdeprecated-declarations] > gb_TYPE = GBT_add_data(gb_sai,PHDATA::ROOT->use,"_TYPE",GB_STRING); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from phylo.hxx:23, > from PH_main.cxx:1: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_t_prot.h:108:9: note: declared here > GBDATA *GBT_add_data P_((GBDATA *species, const char *ali_name, const char *key, GB_TYPES type)) __ATTR__DEPRECATED; > ^ >PH_main.cxx:162:31: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated [-Wdeprecated-declarations] > gb_TYPE = GBT_add_data(gb_sai,PHDATA::ROOT->use,"_TYPE",GB_STRING); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from phylo.hxx:23, > from PH_main.cxx:1: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_t_prot.h:108:9: note: declared here > GBDATA *GBT_add_data P_((GBDATA *species, const char *ali_name, const char *key, GB_TYPES type)) __ATTR__DEPRECATED; > ^ >PH_main.cxx:162:86: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated [-Wdeprecated-declarations] > gb_TYPE = GBT_add_data(gb_sai,PHDATA::ROOT->use,"_TYPE",GB_STRING); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from phylo.hxx:23, > from PH_main.cxx:1: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_t_prot.h:108:9: note: declared here > GBDATA *GBT_add_data P_((GBDATA *species, const char *ali_name, const char *key, GB_TYPES type)) __ATTR__DEPRECATED; > ^ >PH_main.cxx: In function 'void PH_save_ml_cb(AW_window*)': >PH_main.cxx:330:31: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated [-Wdeprecated-declarations] > gb_bits = GBT_add_data(gb_sai,PHDATA::ROOT->use,"bits",GB_BITS); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from phylo.hxx:23, > from PH_main.cxx:1: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_t_prot.h:108:9: note: declared here > GBDATA *GBT_add_data P_((GBDATA *species, const char *ali_name, const char *key, GB_TYPES type)) __ATTR__DEPRECATED; > ^ >PH_main.cxx:330:31: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated [-Wdeprecated-declarations] > gb_bits = GBT_add_data(gb_sai,PHDATA::ROOT->use,"bits",GB_BITS); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from phylo.hxx:23, > from PH_main.cxx:1: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_t_prot.h:108:9: note: declared here > GBDATA *GBT_add_data P_((GBDATA *species, const char *ali_name, const char *key, GB_TYPES type)) __ATTR__DEPRECATED; > ^ >PH_main.cxx:330:83: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated [-Wdeprecated-declarations] > gb_bits = GBT_add_data(gb_sai,PHDATA::ROOT->use,"bits",GB_BITS); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from phylo.hxx:23, > from PH_main.cxx:1: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_t_prot.h:108:9: note: declared here > GBDATA *GBT_add_data P_((GBDATA *species, const char *ali_name, const char *key, GB_TYPES type)) __ATTR__DEPRECATED; > ^ >PH_main.cxx:335:31: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated [-Wdeprecated-declarations] > gb_TYPE = GBT_add_data(gb_sai,PHDATA::ROOT->use,"_TYPE",GB_STRING); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from phylo.hxx:23, > from PH_main.cxx:1: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_t_prot.h:108:9: note: declared here > GBDATA *GBT_add_data P_((GBDATA *species, const char *ali_name, const char *key, GB_TYPES type)) __ATTR__DEPRECATED; > ^ >PH_main.cxx:335:31: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated [-Wdeprecated-declarations] > gb_TYPE = GBT_add_data(gb_sai,PHDATA::ROOT->use,"_TYPE",GB_STRING); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from phylo.hxx:23, > from PH_main.cxx:1: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_t_prot.h:108:9: note: declared here > GBDATA *GBT_add_data P_((GBDATA *species, const char *ali_name, const char *key, GB_TYPES type)) __ATTR__DEPRECATED; > ^ >PH_main.cxx:335:86: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated [-Wdeprecated-declarations] > gb_TYPE = GBT_add_data(gb_sai,PHDATA::ROOT->use,"_TYPE",GB_STRING); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from phylo.hxx:23, > from PH_main.cxx:1: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_t_prot.h:108:9: note: declared here > GBDATA *GBT_add_data P_((GBDATA *species, const char *ali_name, const char *key, GB_TYPES type)) __ATTR__DEPRECATED; > ^ >PH_main.cxx: In function 'int main(int, char**)': >PH_main.cxx:576:63: warning: ignoring return value of 'const char* ARB_init_global_awars(AW_root*, AW_default, GBDATA*)', declared with attribute warn_unused_result [-Wunused-result] > ARB_init_global_awars(aw_root, aw_default, GLOBAL_gb_main); > ^ >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PHYLO -c PH_matr.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >PH_matr.cxx:9:2: warning: #warning module completely unused [-Wcpp] > #warning module completely unused > ^ >ld -r -o PHYLO.a PH_data.o PH_root.o PH_main.o PH_filt.o PH_display.o PH_matr.o >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PHYLO' >-------------------------------------------------------------------------------- Make everything in PROBE_COM >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PROBE_COM' >make[4]: 'server.a' is up to date. >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PROBE_COM' >-------------------------------------------------------------------------------- Make everything in EDIT4 >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/EDIT4' >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_EDIT4 -c -o ED4_protein_2nd_structure.o ED4_protein_2nd_structure.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_EDIT4 -c -o ED4_ProteinViewer.o ED4_ProteinViewer.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >ED4_ProteinViewer.cxx: In function 'void PV_WriteTranslatedSequenceToDB(ED4_AA_sequence_terminal*, char*)': >ED4_ProteinViewer.cxx:498:44: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated [-Wdeprecated-declarations] > gb_ProSeqData = GBT_add_data(gb_species,newAlignmentName,"data", GB_STRING); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from ED4_ProteinViewer.cxx:23: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_t_prot.h:108:9: note: declared here > GBDATA *GBT_add_data P_((GBDATA *species, const char *ali_name, const char *key, GB_TYPES type)) __ATTR__DEPRECATED; > ^ >ED4_ProteinViewer.cxx:498:44: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated [-Wdeprecated-declarations] > gb_ProSeqData = GBT_add_data(gb_species,newAlignmentName,"data", GB_STRING); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from ED4_ProteinViewer.cxx:23: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_t_prot.h:108:9: note: declared here > GBDATA *GBT_add_data P_((GBDATA *species, const char *ali_name, const char *key, GB_TYPES type)) __ATTR__DEPRECATED; > ^ >ED4_ProteinViewer.cxx:498:102: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated [-Wdeprecated-declarations] > gb_ProSeqData = GBT_add_data(gb_species,newAlignmentName,"data", GB_STRING); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from ED4_ProteinViewer.cxx:23: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_t_prot.h:108:9: note: declared here > GBDATA *GBT_add_data P_((GBDATA *species, const char *ali_name, const char *key, GB_TYPES type)) __ATTR__DEPRECATED; > ^ >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_EDIT4 -c -o ED4_search.o ED4_search.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >ED4_search.cxx: In function 'void load_search_paras_from_file(AW_window*, AW_CL)': >ED4_search.cxx:1616:38: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] > fgets(buffer, BUFFERSIZE, in); > ^ >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_EDIT4 -c -o ED4_cursor.o ED4_cursor.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_EDIT4 -c -o ED4_dump.o ED4_dump.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_EDIT4 -c -o ED4_nds.o ED4_nds.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_EDIT4 -c -o ED4_secedit.o ED4_secedit.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_EDIT4 -c -o ED4_RNA3D.o ED4_RNA3D.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_EDIT4 -c -o ED4_main.o ED4_main.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_EDIT4 -c -o ED4_mini_classes.o ED4_mini_classes.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_EDIT4 -c -o ED4_edit_string.o ED4_edit_string.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_EDIT4 -c -o ED4_base.o ED4_base.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >ED4_mini_classes.cxx: In function 'void ED4_consensus_display_changed(AW_root*, AW_CL, AW_CL)': >ED4_mini_classes.cxx:447:60: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] > ED4_ROOT->root_group_man->route_down_hierarchy((void**)show, 0, toggle_consensus_display); > ^ >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_EDIT4 -c -o ED4_manager.o ED4_manager.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_EDIT4 -c -o ED4_terminal.o ED4_terminal.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >ED4_manager.cxx: In member function 'virtual ED4_returncode ED4_manager::handle_move(ED4_move_info*)': >ED4_manager.cxx:512:26: warning: variable 'level' set but not used [-Wunused-but-set-variable] > ED4_AREA_LEVEL level; > ^ >ED4_manager.cxx: In member function 'virtual ED4_returncode ED4_main_manager::resize_requested_by_parent()': >ED4_manager.cxx:952:20: warning: variable 'result' set but not used [-Wunused-but-set-variable] > ED4_returncode result = ED4_R_OK; > ^ >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_EDIT4 -c -o ED4_root.o ED4_root.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >ED4_terminal.cxx:164:2: warning: #warning temporary workaround - gb_type GB_INT and GB_FLOAT in the switch directive must not be displayed but ignored [-Wcpp] > #warning temporary workaround - gb_type GB_INT and GB_FLOAT in the switch directive must not be displayed but ignored > ^ >ED4_terminal.cxx:1422:2: warning: #warning test drawing of ED4_columnStat_terminal [-Wcpp] > #warning test drawing of ED4_columnStat_terminal > ^ >ED4_terminal.cxx: In member function 'virtual ED4_returncode ED4_terminal::draw_drag_box(AW_pos, AW_pos, GB_CSTR, int)': >ED4_terminal.cxx:408:21: warning: variable 'width' set but not used [-Wunused-but-set-variable] > AW_pos width, height, drag_x, drag_y; > ^ >ED4_terminal.cxx:408:28: warning: variable 'height' set but not used [-Wunused-but-set-variable] > AW_pos width, height, drag_x, drag_y; > ^ >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_EDIT4 -c -o EDB_root_bact.o EDB_root_bact.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_EDIT4 -c -o ED4_window.o ED4_window.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_EDIT4 -c -o ED4_members.o ED4_members.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_EDIT4 -c -o ED4_no_class.o ED4_no_class.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_EDIT4 -c -o ED4_list.o ED4_list.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_EDIT4 -c -o ED4_text_terminals.o ED4_text_terminals.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_EDIT4 -c -o ED4_tools.o ED4_tools.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_EDIT4 -c -o ED4_block.o ED4_block.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >ED4_no_class.cxx: In function 'ED4_returncode call_edit(void**, void**, ED4_base*)': >ED4_no_class.cxx:177:17: warning: variable 'gb_type' set but not used [-Wunused-but-set-variable] > GB_TYPES gb_type; > ^ >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_EDIT4 -c -o ED4_visualizeSAI.o ED4_visualizeSAI.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >ED4_block.cxx: In function 'void ED4_with_whole_block(ED4_blockoperation, int)': >ED4_block.cxx:179:28: warning: variable 'err_term' set but not used [-Wunused-but-set-variable] > ED4_sequence_terminal *err_term = 0; > ^ >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_EDIT4 -c -o edit_naligner.o edit_naligner.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_EDIT4 -c -o graph_aligner_gui.o graph_aligner_gui.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_EDIT4 -c -o ED4_dots.o ED4_dots.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >edit_naligner.cxx: In function 'void aed_start_naligning(AW_window*)': >edit_naligner.cxx:102:19: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] > system(buffer); > ^ >ED4_dots.cxx: In function 'void dot_missing_bases(AW_window*)': >ED4_dots.cxx:181:54: warning: 'sai_len' may be used uninitialized in this function [-Wmaybe-uninitialized] > for (p = 0; p<stat.pos_count && stat.position[p]<sai_len; p++) { > ^ >ld -r -o EDIT4.a ED4_protein_2nd_structure.o ED4_ProteinViewer.o ED4_search.o ED4_cursor.o ED4_dump.o ED4_nds.o ED4_secedit.o ED4_RNA3D.o ED4_main.o ED4_mini_classes.o ED4_edit_string.o ED4_base.o ED4_manager.o ED4_terminal.o ED4_root.o EDB_root_bact.o ED4_window.o ED4_members.o ED4_no_class.o ED4_list.o ED4_text_terminals.o ED4_tools.o ED4_block.o ED4_visualizeSAI.o edit_naligner.o graph_aligner_gui.o ED4_dots.o >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/EDIT4' >-------------------------------------------------------------------------------- Make everything in NAMES_COM >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/NAMES_COM' >make[4]: 'server.a' is up to date. >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/NAMES_COM' >-------------------------------------------------------------------------------- Make everything in PROBE_COM >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PROBE_COM' >make[4]: 'server.a' is up to date. >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PROBE_COM' >-------------------------------------------------------------------------------- Make everything in NAMES_COM >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/NAMES_COM' >make[4]: 'server.a' is up to date. >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/NAMES_COM' >-------------------- Updating shared libraries >make libs >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3' >-------------------------------------------------------------------------------- Make everything in NAMES_COM >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/NAMES_COM' >make[4]: 'server.a' is up to date. >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/NAMES_COM' >-------------------------------------------------------------------------------- Make everything in PROBE_COM >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PROBE_COM' >make[4]: 'server.a' is up to date. >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PROBE_COM' >cp LIBLINK/libARBDB.so lib/libARBDB.so >cp LIBLINK/libARBDBPP.so lib/libARBDBPP.so >cp LIBLINK/libARBDO.so lib/libARBDO.so >cp LIBLINK/libAW.so lib/libAW.so >cp LIBLINK/libAWT.so lib/libAWT.so >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3' >-------------------------------------------------------------------------------- Make everything in ARB_GDE >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/ARB_GDE' >../MAKEBIN/aisc_mkpt -G -A -E -w GDE_proto.h GDE_ParseMenu.cxx GDE.cxx GDE_event.cxx GDE_arbdb_io.cxx GDE_HGLfile.cxx GDE_Genbank.cxx GDE_FileIO.cxx > GDE_proto.h.tmp >../SOURCE_TOOLS/mv_if_diff GDE_proto.h.tmp GDE_proto.h >GDE_proto.h did not change. >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARB_GDE -c GDE_ParseMenu.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARB_GDE -c GDE.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARB_GDE -c GDE_event.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARB_GDE -c GDE_arbdb_io.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARB_GDE -c GDE_HGLfile.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARB_GDE -c GDE_Genbank.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >GDE_event.cxx: In function 'void GDE_export(NA_Alignment*, char*, long int)': >GDE_event.cxx:305:39: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated [-Wdeprecated-declarations] > GBDATA *gb_data = GBT_add_data(gb_extended, align, "data", GB_STRING); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from GDE_event.cxx:12: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_t_prot.h:108:9: note: declared here > GBDATA *GBT_add_data P_((GBDATA *species, const char *ali_name, const char *key, GB_TYPES type)) __ATTR__DEPRECATED; > ^ >GDE_event.cxx:305:39: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated [-Wdeprecated-declarations] > GBDATA *gb_data = GBT_add_data(gb_extended, align, "data", GB_STRING); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from GDE_event.cxx:12: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_t_prot.h:108:9: note: declared here > GBDATA *GBT_add_data P_((GBDATA *species, const char *ali_name, const char *key, GB_TYPES type)) __ATTR__DEPRECATED; > ^ >GDE_event.cxx:305:89: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated [-Wdeprecated-declarations] > GBDATA *gb_data = GBT_add_data(gb_extended, align, "data", GB_STRING); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from GDE_event.cxx:12: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_t_prot.h:108:9: note: declared here > GBDATA *GBT_add_data P_((GBDATA *species, const char *ali_name, const char *key, GB_TYPES type)) __ATTR__DEPRECATED; > ^ >GDE_event.cxx:369:43: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated [-Wdeprecated-declarations] > GBDATA *gb_data = GBT_add_data(gb_species, align, "data", GB_STRING); // does only add if not already existing > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from GDE_event.cxx:12: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_t_prot.h:108:9: note: declared here > GBDATA *GBT_add_data P_((GBDATA *species, const char *ali_name, const char *key, GB_TYPES type)) __ATTR__DEPRECATED; > ^ >GDE_event.cxx:369:43: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated [-Wdeprecated-declarations] > GBDATA *gb_data = GBT_add_data(gb_species, align, "data", GB_STRING); // does only add if not already existing > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from GDE_event.cxx:12: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_t_prot.h:108:9: note: declared here > GBDATA *GBT_add_data P_((GBDATA *species, const char *ali_name, const char *key, GB_TYPES type)) __ATTR__DEPRECATED; > ^ >GDE_event.cxx:369:92: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated [-Wdeprecated-declarations] > GBDATA *gb_data = GBT_add_data(gb_species, align, "data", GB_STRING); // does only add if not already existing > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from GDE_event.cxx:12: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_t_prot.h:108:9: note: declared here > GBDATA *GBT_add_data P_((GBDATA *species, const char *ali_name, const char *key, GB_TYPES type)) __ATTR__DEPRECATED; > ^ >GDE_event.cxx:428:36: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated [-Wdeprecated-declarations] > GBDATA *gb_color = GBT_add_data(gb_extended, align, "colmask", GB_BYTES); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from GDE_event.cxx:12: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_t_prot.h:108:9: note: declared here > GBDATA *GBT_add_data P_((GBDATA *species, const char *ali_name, const char *key, GB_TYPES type)) __ATTR__DEPRECATED; > ^ >GDE_event.cxx:428:36: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated [-Wdeprecated-declarations] > GBDATA *gb_color = GBT_add_data(gb_extended, align, "colmask", GB_BYTES); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from GDE_event.cxx:12: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_t_prot.h:108:9: note: declared here > GBDATA *GBT_add_data P_((GBDATA *species, const char *ali_name, const char *key, GB_TYPES type)) __ATTR__DEPRECATED; > ^ >GDE_event.cxx:428:88: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated [-Wdeprecated-declarations] > GBDATA *gb_color = GBT_add_data(gb_extended, align, "colmask", GB_BYTES); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from GDE_event.cxx:12: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_t_prot.h:108:9: note: declared here > GBDATA *GBT_add_data P_((GBDATA *species, const char *ali_name, const char *key, GB_TYPES type)) __ATTR__DEPRECATED; > ^ >GDE_event.cxx: In function 'void GDE_startaction_cb(AW_window*, GmenuItem*, AW_CL)': >GDE_event.cxx:557:23: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] > system(Action); > ^ >GDE_HGLfile.cxx: In function 'void StripSpecial(char*)': >GDE_HGLfile.cxx:69:9: warning: variable 'i' set but not used [-Wunused-but-set-variable] > int i,j,len; > ^ >GDE_HGLfile.cxx: In function 'void ReadGDE(char*, NA_Alignment*, int)': >GDE_HGLfile.cxx:199:26: warning: variable 'count' set but not used [-Wunused-but-set-variable] > int success,count,temp = 0; > ^ >GDE_HGLfile.cxx:200:35: warning: variable 'c' set but not used [-Wunused-but-set-variable] > char in_line[GBUFSIZ],c; > ^ >GDE_HGLfile.cxx:203:18: warning: variable 'genclen' set but not used [-Wunused-but-set-variable] > int genclen = 0,curelem = 0; > ^ >GDE_HGLfile.cxx:195:55: warning: parameter 'type' set but not used [-Wunused-but-set-parameter] > void ReadGDE(char *filename,NA_Alignment *dataset,int type) > ^ >GDE_Genbank.cxx: In function 'void ReadGen(char*, NA_Alignment*, int)': >GDE_Genbank.cxx:94:13: warning: variable 'count' set but not used [-Wunused-but-set-variable] > int count,IS_REALLY_AA = FALSE; > ^ >GDE_Genbank.cxx:89:55: warning: parameter 'type' set but not used [-Wunused-but-set-parameter] > void ReadGen(char *filename,NA_Alignment *dataset,int type) > ^ >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARB_GDE -c GDE_FileIO.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >GDE_FileIO.cxx: In function 'void ReadNA_Flat(char*, char*, int)': >GDE_FileIO.cxx:125:9: warning: variable 'i' set but not used [-Wunused-but-set-variable] > int i, jj, c, curelem=0,offset; > ^ >GDE_FileIO.cxx:125:16: warning: variable 'c' set but not used [-Wunused-but-set-variable] > int i, jj, c, curelem=0,offset; > ^ >GDE_FileIO.cxx:128:10: warning: variable 'curname' set but not used [-Wunused-but-set-variable] > char curname[GBUFSIZ]; > ^ >GDE_FileIO.cxx:122:58: warning: parameter 'type' set but not used [-Wunused-but-set-parameter] > static void ReadNA_Flat(char *filename,char *dataset,int type) > ^ >GDE_FileIO.cxx: In function 'void AppendNA(NA_Base*, int, NA_Sequence*)': >GDE_FileIO.cxx:422:14: warning: variable 'temp' set but not used [-Wunused-but-set-variable] > NA_Base *temp; > ^ >GDE_FileIO.cxx: In function 'void ReadCMask(const char*)': >GDE_FileIO.cxx:710:24: warning: variable 'orig_ctype' set but not used [-Wunused-but-set-variable] > int *colors = 0,orig_ctype,jj,indx = 0; > ^ >GDE_FileIO.cxx: In function 'int WriteStatus(NA_Alignment*, char*, int)': >GDE_FileIO.cxx:860:54: warning: parameter 'method' set but not used [-Wunused-but-set-parameter] > int WriteStatus(NA_Alignment *aln,char *filename,int method) > ^ >GDE_FileIO.cxx: In function 'void ReadStatus(char*)': >GDE_FileIO.cxx:927:23: warning: parameter 'filename' set but not used [-Wunused-but-set-parameter] > void ReadStatus(char *filename) > ^ >GDE_FileIO.cxx: In function 'void NormalizeOffset(NA_Alignment*)': >GDE_FileIO.cxx:962:9: warning: variable 'i' set but not used [-Wunused-but-set-variable] > int i; > ^ >GDE_FileIO.cxx: In function 'void ReadCMask(const char*)': >GDE_FileIO.cxx:837:48: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] > fgets(in_line,GBUFSIZ,file); > ^ >ld -r -o ARB_GDE.a GDE_ParseMenu.o GDE.o GDE_event.o GDE_arbdb_io.o GDE_HGLfile.o GDE_Genbank.o GDE_FileIO.o >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/ARB_GDE' >-------------------------------------------------------------------------------- Make everything in EISPACK >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/EISPACK' >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_EISPACK -c eispack.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_EISPACK -c d_sign.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >ld -r -o EISPACK.a eispack.o d_sign.o >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/EISPACK' >-------------------------------------------------------------------------------- Make everything in GDEHELP >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDEHELP' >( cat genmenu.header; sed -e "s/^[ ]*//" ) < MENUS/dnamlrates.menu > MENUS/dnamlrates.genmenu >( cat genmenu.header; sed -e "s/^[ ]*//" ) < MENUS/fastdnaml.menu > MENUS/fastdnaml.genmenu >( cat genmenu.header; sed -e "s/^[ ]*//" ) < MENUS/pretty_print.menu > MENUS/pretty_print.genmenu >( cat genmenu.header; sed -e "s/^[ ]*//" ) < MENUS/phylip_dist_org.menu > MENUS/phylip_dist_org.genmenu >( cat genmenu.header; sed -e "s/^[ ]*//" ) < MENUS/puzzle.menu > MENUS/puzzle.genmenu >( cat genmenu.header; sed -e "s/^[ ]*//" ) < MENUS/align.menu > MENUS/align.genmenu >( cat genmenu.header; sed -e "s/^[ ]*//" ) < MENUS/warning.menu > MENUS/warning.genmenu >( cat genmenu.header; sed -e "s/^[ ]*//" ) < MENUS/phylip_ml.menu > MENUS/phylip_ml.genmenu >( cat genmenu.header; sed -e "s/^[ ]*//" ) < MENUS/raxml.menu > MENUS/raxml.genmenu >( cat genmenu.header; sed -e "s/^[ ]*//" ) < MENUS/desoete.menu > MENUS/desoete.genmenu >( cat genmenu.header; sed -e "s/^[ ]*//" ) < MENUS/phylip_help.menu > MENUS/phylip_help.genmenu >( cat genmenu.header; sed -e "s/^[ ]*//" ) < MENUS/export.menu > MENUS/export.genmenu >( cat genmenu.header; sed -e "s/^[ ]*//" ) < MENUS/phylip_dist.menu > MENUS/phylip_dist.genmenu >( cat genmenu.header; sed -e "s/^[ ]*//" ) < MENUS/inc_fastdnaml.menu > MENUS/inc_fastdnaml.genmenu >( cat genmenu.header; sed -e "s/^[ ]*//" ) < MENUS/import.menu > MENUS/import.genmenu >( cat genmenu.header; sed -e "s/^[ ]*//" ) < MENUS/start_arb.menu > MENUS/start_arb.genmenu >( cat genmenu.header; sed -e "s/^[ ]*//" ) < MENUS/phylip_pars.menu > MENUS/phylip_pars.genmenu >chmod a+w ARB_GDEmenus >chmod: cannot access 'ARB_GDEmenus': No such file or directory >make[4]: [Makefile:19: ARB_GDEmenus] Error 1 (ignored) >cpp -IMENUS ARB_GDEmenus.source >ARB_GDEmenus >chmod a-w ARB_GDEmenus >grep -i '^itemhelp:' < ARB_GDEmenus | sed -e 's/^itemhelp://' | sort | uniq > helpfiles.lst >make[5]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDEHELP' >---------------------------------------------------------------- >lynx -dump -nolist -display_charset=iso-8859-1 ../GDE/PHYLIP/doc/proml.html | sed -e 's/©/(C)/' > HELP_DOC_GEN/proml.doc >Collecting documentation for external programs used in GDE menus >lynx -dump -nolist -display_charset=iso-8859-1 ../GDE/PHYLIP/doc/dnapars.html | sed -e 's/©/(C)/' > HELP_DOC_GEN/dnapars.doc >test -s HELP_DOC_GEN/proml.doc || (echo HELP_DOC_GEN/proml.doc not generated or empty && rm HELP_DOC_GEN/proml.doc && false) >test -s HELP_DOC_GEN/dnapars.doc || (echo HELP_DOC_GEN/dnapars.doc not generated or empty && rm HELP_DOC_GEN/dnapars.doc && false) >lynx -dump -nolist -display_charset=iso-8859-1 ../GDE/PHYLIP/doc/protpars.html | sed -e 's/©/(C)/' > HELP_DOC_GEN/protpars.doc >test -s HELP_DOC_GEN/protpars.doc || (echo HELP_DOC_GEN/protpars.doc not generated or empty && rm HELP_DOC_GEN/protpars.doc && false) >lynx -dump -nolist -display_charset=iso-8859-1 ../GDE/PHYML/usersguide_phyliplike.html | sed -e 's/©/(C)/' > HELP_DOC_GEN/phyml.doc >./genhelp.sh HELP_GEN/CAP2.help "CAP2" arb_help.head HELP_PLAIN/CAP2.help >test -s HELP_DOC_GEN/phyml.doc || (echo HELP_DOC_GEN/phyml.doc not generated or empty && rm HELP_DOC_GEN/phyml.doc && false) >./genhelp.sh HELP_GEN/DNAml_rates.help "DNAml_rates" arb_help.head HELP_PLAIN/DNAml_rates.help >./genhelptree.sh HELP_GEN/clustalw.help "clustalw" arb_help.head /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDE/CLUSTALW/clustalw_help /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDE/CLUSTALW/clustalw.doc >BASE='clustalw' PREFIX='HELP_GEN' >./genhelptree.sh HELP_GEN/dnaml.help "dnaml" arb_help.head /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDE/AxML/AxML.doc /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDE/FASTDNAML/fastDNAml.doc >BASE='dnaml' PREFIX='HELP_GEN' >./genhelp.sh HELP_GEN/dnapars.help "dnapars" arb_help.head HELP_DOC_GEN/dnapars.doc >./genhelp.sh HELP_GEN/lsadt.help "lsadt" arb_help.head HELP_PLAIN/lsadt.help >lynx -dump -nolist -display_charset=iso-8859-1 ../GDE/PHYLIP/doc/fitch.html | sed -e 's/©/(C)/' > HELP_DOC_GEN/fitch.doc >lynx -dump -nolist -display_charset=iso-8859-1 ../GDE/PHYLIP/doc/kitsch.html | sed -e 's/©/(C)/' > HELP_DOC_GEN/kitsch.doc >lynx -dump -nolist -display_charset=iso-8859-1 ../GDE/PHYLIP/doc/neighbor.html | sed -e 's/©/(C)/' > HELP_DOC_GEN/neighbor.doc >test -s HELP_DOC_GEN/fitch.doc || (echo HELP_DOC_GEN/fitch.doc not generated or empty && rm HELP_DOC_GEN/fitch.doc && false) >test -s HELP_DOC_GEN/kitsch.doc || (echo HELP_DOC_GEN/kitsch.doc not generated or empty && rm HELP_DOC_GEN/kitsch.doc && false) >test -s HELP_DOC_GEN/neighbor.doc || (echo HELP_DOC_GEN/neighbor.doc not generated or empty && rm HELP_DOC_GEN/neighbor.doc && false) >lynx -dump -nolist -display_charset=iso-8859-1 ../GDE/PHYLIP/doc/dnadist.html | sed -e 's/©/(C)/' > HELP_DOC_GEN/dnadist.doc >test -s HELP_DOC_GEN/dnadist.doc || (echo HELP_DOC_GEN/dnadist.doc not generated or empty && rm HELP_DOC_GEN/dnadist.doc && false) >lynx -dump -nolist -display_charset=iso-8859-1 ../GDE/PHYLIP/doc/protdist.html | sed -e 's/©/(C)/' > HELP_DOC_GEN/protdist.doc >./genhelp.sh HELP_GEN/phyml.help "phyml" arb_help.head HELP_DOC_GEN/phyml.doc >test -s HELP_DOC_GEN/protdist.doc || (echo HELP_DOC_GEN/protdist.doc not generated or empty && rm HELP_DOC_GEN/protdist.doc && false) >./genhelp.sh HELP_GEN/proml.help "proml" arb_help.head HELP_DOC_GEN/proml.doc >./genhelp.sh HELP_GEN/protpars.help "protpars" arb_help.head HELP_DOC_GEN/protpars.doc >./genhelptree.sh HELP_GEN/readseq.help "readseq" arb_help.head /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/READSEQ/Readme /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/READSEQ/Formats /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/READSEQ/Readseq.help >BASE='readseq' PREFIX='HELP_GEN' >lynx -dump -nolist -display_charset=iso-8859-1 ../GDE/TREEPUZZLE/doc/manual.html | sed -e 's/©/(C)/' > HELP_DOC_GEN/treepuzzle.doc >test -s HELP_DOC_GEN/treepuzzle.doc || (echo HELP_DOC_GEN/treepuzzle.doc not generated or empty && rm HELP_DOC_GEN/treepuzzle.doc && false) >./genhelptree.sh HELP_GEN/phylip_distance.help "phylip_distance" arb_help.head HELP_DOC_GEN/fitch.doc HELP_DOC_GEN/kitsch.doc HELP_DOC_GEN/neighbor.doc HELP_DOC_GEN/dnadist.doc HELP_DOC_GEN/protdist.doc >BASE='phylip_distance' PREFIX='HELP_GEN' >./genhelp.sh HELP_GEN/treepuzzle.help "treepuzzle" arb_help.head HELP_DOC_GEN/treepuzzle.doc >make[5]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDEHELP' >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDEHELP' >-------------------------------------------------------------------------------- Make everything in SL/AW_NAME >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/AW_NAME' >make[4]: 'AW_NAME.a' is up to date. >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/AW_NAME' >-------------------------------------------------------------------------------- Make everything in AWTC >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/AWTC' >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWTC -c AWTC_next_neighbours.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWTC -c AWTC_constructSequence.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >AWTC_constructSequence.cxx: In function 'char* AWTC_constructSequence(int, const char**, int, char**)': >AWTC_constructSequence.cxx:507:11: warning: unused variable 'resultSeq' [-Wunused-variable] > char *resultSeq = new char[sequenceLength+1]; > ^ >AWTC_constructSequence.cxx:509:9: warning: unused variable 'off' [-Wunused-variable] > int off = 0; > ^ >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWTC -c AWTC_seq_search.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWTC -c AWTC_submission.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >ld -r -o AWTC.a AWTC_next_neighbours.o AWTC_constructSequence.o AWTC_seq_search.o AWTC_submission.o >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/AWTC' >-------------------- Checking bin/arb_wetc >Target 'bin/arb_wetc' not found >-> rebuilding bin/arb_wetc (Thu Jan 1 00:59:59 1970) >Link bin/arb_wetc >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -Wl,-O1 -Wl,--as-needed -Wl,--export-dynamic -rdynamic -o bin/arb_wetc -L/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/LIBLINK WETC/WETC.a SL/HELIX/HELIX.a XML/XML.a -lARBDB -lm -lAW -lAWT -L/usr/X11R6/lib64 -lXm -lXpm -lXt -lXext -lX11 >-------------------------------------------------------------------------------- Make everything in PGT >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PGT' >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PGT -c -o main.o main.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PGT -c -o dialog.o dialog.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PGT -c -o arb_interface.o arb_interface.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PGT -c -o main_dialog.o main_dialog.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >arb_interface.cxx: In function 'void set_AWAR(const char*, char*)': >arb_interface.cxx:722:18: warning: unused variable 'error' [-Wunused-variable] > GB_ERROR error = GB_write_string(gb_awar, content); > ^ >arb_interface.cxx: In function 'void set_CONFIG(const char*, const char*)': >arb_interface.cxx:764:18: warning: unused variable 'error' [-Wunused-variable] > GB_ERROR error = GB_write_string(gb_awar, content); > ^ >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PGT -c -o import_dialog.o import_dialog.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PGT -c -o selection_dialog.o selection_dialog.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PGT -c -o file_import.o file_import.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PGT -c -o tiff_image.o tiff_image.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >file_import.cxx: In function 'int importCSV(importTable*, importData*)': >file_import.cxx:259:14: warning: variable 'error' set but not used [-Wunused-but-set-variable] > GB_ERROR error = GBT_write_string(gb_proteom, "name", data->proteome); > ^ >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PGT -c -o image_dialog.o image_dialog.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PGT -c -o plot.o plot.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PGT -c -o analyze_window.o analyze_window.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >image_dialog.cxx: In member function 'void imageDialog::set_ARB_image_path(const char*)': >image_dialog.cxx:1189:18: warning: unused variable 'error' [-Wunused-variable] > GB_ERROR error = GBT_write_string(gb_proteom, "image_path", path); > ^ >image_dialog.cxx: In member function 'int imageDialog::fillBlankImage()': >image_dialog.cxx:1347:56: warning: narrowing conversion of '255' from 'int' to 'char' inside { } is ill-formed in C++11 [-Wnarrowing] > 0xFF, 0x00, 0xFF, 0x00, 0xFF, 0x00, 0xFF, 0x00}; // 16x16 PIXMAP > ^ >image_dialog.cxx:1347:56: warning: narrowing conversion of '255' from 'int' to 'char' inside { } is ill-formed in C++11 [-Wnarrowing] >image_dialog.cxx:1347:56: warning: narrowing conversion of '255' from 'int' to 'char' inside { } is ill-formed in C++11 [-Wnarrowing] >image_dialog.cxx:1347:56: warning: narrowing conversion of '255' from 'int' to 'char' inside { } is ill-formed in C++11 [-Wnarrowing] >image_dialog.cxx:1347:56: warning: narrowing conversion of '255' from 'int' to 'char' inside { } is ill-formed in C++11 [-Wnarrowing] >image_dialog.cxx:1347:56: warning: narrowing conversion of '255' from 'int' to 'char' inside { } is ill-formed in C++11 [-Wnarrowing] >image_dialog.cxx:1347:56: warning: narrowing conversion of '255' from 'int' to 'char' inside { } is ill-formed in C++11 [-Wnarrowing] >image_dialog.cxx:1347:56: warning: narrowing conversion of '255' from 'int' to 'char' inside { } is ill-formed in C++11 [-Wnarrowing] >image_dialog.cxx:1347:56: warning: narrowing conversion of '255' from 'int' to 'char' inside { } is ill-formed in C++11 [-Wnarrowing] >image_dialog.cxx:1347:56: warning: narrowing conversion of '255' from 'int' to 'char' inside { } is ill-formed in C++11 [-Wnarrowing] >image_dialog.cxx:1347:56: warning: narrowing conversion of '255' from 'int' to 'char' inside { } is ill-formed in C++11 [-Wnarrowing] >image_dialog.cxx:1347:56: warning: narrowing conversion of '255' from 'int' to 'char' inside { } is ill-formed in C++11 [-Wnarrowing] >image_dialog.cxx:1347:56: warning: narrowing conversion of '255' from 'int' to 'char' inside { } is ill-formed in C++11 [-Wnarrowing] >image_dialog.cxx:1347:56: warning: narrowing conversion of '255' from 'int' to 'char' inside { } is ill-formed in C++11 [-Wnarrowing] >image_dialog.cxx:1347:56: warning: narrowing conversion of '255' from 'int' to 'char' inside { } is ill-formed in C++11 [-Wnarrowing] >image_dialog.cxx:1347:56: warning: narrowing conversion of '255' from 'int' to 'char' inside { } is ill-formed in C++11 [-Wnarrowing] >image_dialog.cxx: In member function 'bool imageDialog::updateSelectedGene()': >image_dialog.cxx:2363:35: warning: variable 'awar_gene_id' set but not used [-Wunused-but-set-variable] > char *awar_selected_protein, *awar_gene_id, *name= NULL; > ^ >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PGT -c -o entry_sel_dialog.o entry_sel_dialog.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PGT -c -o config_dialog.o config_dialog.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PGT -c -o help_dialog.o help_dialog.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >help_dialog.cxx: In member function 'void helpDialog::createVisualizationHelp(Widget)': >help_dialog.cxx:83:71: warning: variable 'help_xpm' set but not used [-Wunused-but-set-variable] > markall22_xpm, marknone22_xpm, arb2mark_xpm, mark2arb_xpm, help_xpm, > ^ >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PGT -c -o msgbox.o msgbox.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >ld -r -o PGT.a main.o dialog.o arb_interface.o main_dialog.o import_dialog.o selection_dialog.o file_import.o tiff_image.o image_dialog.o plot.o analyze_window.o entry_sel_dialog.o config_dialog.o help_dialog.o msgbox.o >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PGT' >-------------------- Checking bin/arb_edit4 >Target 'bin/arb_edit4' not found >-> rebuilding bin/arb_edit4 (Thu Jan 1 00:59:59 1970) >Link bin/arb_edit4 >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -Wl,-O1 -Wl,--as-needed -Wl,--export-dynamic -rdynamic -o bin/arb_edit4 -L/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/LIBLINK NAMES_COM/client.a AWTC/AWTC.a EDIT4/EDIT4.a SECEDIT/SECEDIT.a SERVERCNTRL/SERVERCNTRL.a STAT/STAT.a ARB_GDE/ARB_GDE.a ISLAND_HOPPING/ISLAND_HOPPING.a SL/FAST_ALIGNER/FAST_ALIGNER.a SL/HELIX/HELIX.a SL/AW_HELIX/AW_HELIX.a SL/AW_NAME/AW_NAME.a SL/FILE_BUFFER/FILE_BUFFER.a XML/XML.a -lARBDB -lm -lAW -lAWT -L/usr/X11R6/lib64 -lXm -lXpm -lXt -lXext -lX11 -lGLU >-------------------- Checking bin/arb_dist >Target 'bin/arb_dist' not found >-> rebuilding bin/arb_dist (Thu Jan 1 00:59:59 1970) >Link bin/arb_dist >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -Wl,-O1 -Wl,--as-needed -Wl,--export-dynamic -rdynamic -o bin/arb_dist -L/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/LIBLINK PROBE_COM/client.a DIST/DIST.a SERVERCNTRL/SERVERCNTRL.a CONSENSUS_TREE/CONSENSUS_TREE.a EISPACK/EISPACK.a SL/HELIX/HELIX.a XML/XML.a -lARBDB -lm -lAW -lAWT -L/usr/X11R6/lib64 -lXm -lXpm -lXt -lXext -lX11 >-------------------------------------------------------------------------------- Make everything in PROBE_DESIGN >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PROBE_DESIGN' >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PROBE_DESIGN -c -o probe_design.o probe_design.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PROBE_DESIGN -c -o SaiProbeVisualization.o SaiProbeVisualization.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PROBE_DESIGN -c -o probe_match_parser.o probe_match_parser.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >probe_design.cxx: In function 'const char* pd_get_the_gene_names(bytestring&, bytestring&)': >probe_design.cxx:293:21: warning: variable 'sequence' set but not used [-Wunused-but-set-variable] > const char *sequence = 0; > ^ >probe_design.cxx: In function 'void pd_query_pt_server(AW_window*)': >probe_design.cxx:1769:35: warning: ignoring return value of 'const char* GB_xcmd(const char*, GB_BOOL, GB_BOOL)', declared with attribute warn_unused_result [-Wunused-result] > GB_xcmd(sys,GB_TRUE, GB_FALSE); > ^ >ld -r -o PROBE_DESIGN.a probe_design.o SaiProbeVisualization.o probe_match_parser.o >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PROBE_DESIGN' >-------------------- Checking bin/arb_phylo >Target 'bin/arb_phylo' not found >-> rebuilding bin/arb_phylo (Thu Jan 1 00:59:59 1970) >Link bin/arb_phylo >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -Wl,-O1 -Wl,--as-needed -Wl,--export-dynamic -rdynamic -o bin/arb_phylo -L/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/LIBLINK PHYLO/PHYLO.a SL/HELIX/HELIX.a XML/XML.a -lARBDB -lm -lAW -lAWT -L/usr/X11R6/lib64 -lXm -lXpm -lXt -lXext -lX11 >-------------------------------------------------------------------------------- Make everything in NAMES >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/NAMES' >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NAMES -I/opt/gcc.3.4.3/include/c++/3.4.3/include -c names.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >ld -r -o NAMES.a names.o >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/NAMES' >-------------------- Checking bin/arb_db_server >Target 'bin/arb_db_server' not found >-> rebuilding bin/arb_db_server (Thu Jan 1 00:59:59 1970) >Link bin/arb_db_server >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -Wl,-O1 -Wl,--as-needed -Wl,--export-dynamic -rdynamic -o bin/arb_db_server -L/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/LIBLINK DBSERVER/DBSERVER.a SERVERCNTRL/SERVERCNTRL.a -lARBDB -lm >-------------------- Checking bin/arb_pgt >Target 'bin/arb_pgt' not found >-> rebuilding bin/arb_pgt (Thu Jan 1 00:59:59 1970) >Link bin/arb_pgt >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -Wl,-O1 -Wl,--as-needed -Wl,--export-dynamic -rdynamic -o bin/arb_pgt -L/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/LIBLINK PGT/PGT.a -L/usr/X11R6/lib64 -lXm -lXpm -lXt -lXext -lX11 -ltiff -lARBDB -lm >-------------------------------------------------------------------------------- Make everything in MULTI_PROBE >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/MULTI_PROBE' >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_MULTI_PROBE -c MP_main.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_MULTI_PROBE -c MP_Window.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_MULTI_PROBE -c MP_noclass.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_MULTI_PROBE -c MP_sonde.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_MULTI_PROBE -c MP_sondentopf.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_MULTI_PROBE -c MP_mo_liste.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >MP_sondentopf.cxx: In member function 'Sonde* ST_Container::cache_Sonde(char*, int, double)': >MP_sondentopf.cxx:67:13: warning: variable 'hashreturnval' set but not used [-Wunused-but-set-variable] > long hashreturnval; > ^ >MP_mo_liste.cxx: In member function 'long int MO_Liste::put_entry(const char*)': >MP_mo_liste.cxx:184:13: warning: variable 'hashreturnval' set but not used [-Wunused-but-set-variable] > long hashreturnval; > ^ >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_MULTI_PROBE -c MP_probe.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_MULTI_PROBE -c MP_GenerationDuplicates.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >MP_probe.cxx: In member function 'void ProbeValuation::init_valuation()': >MP_probe.cxx:178:22: warning: variable 'stc' set but not used [-Wunused-but-set-variable] > ST_Container *stc; > ^ >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_MULTI_PROBE -c MP_Generation.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_MULTI_PROBE -c MP_probe_combi_statistic.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_MULTI_PROBE -c MP_probe_tabs.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_MULTI_PROBE -c MP_permute.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >ld -r -o MULTI_PROBE.a MP_main.o MP_Window.o MP_noclass.o MP_sonde.o MP_sondentopf.o MP_mo_liste.o MP_probe.o MP_GenerationDuplicates.o MP_Generation.o MP_probe_combi_statistic.o MP_probe_tabs.o MP_permute.o >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/MULTI_PROBE' >-------------------- Checking bin/arb_pars >Target 'bin/arb_pars' not found >-> rebuilding bin/arb_pars (Thu Jan 1 00:59:59 1970) >Link bin/arb_pars >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -Wl,-O1 -Wl,--as-needed -Wl,--export-dynamic -rdynamic -o bin/arb_pars -L/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/LIBLINK NAMES_COM/client.a SERVERCNTRL/SERVERCNTRL.a PARSIMONY/PARSIMONY.a SL/HELIX/HELIX.a SL/AW_NAME/AW_NAME.a XML/XML.a -lARBDB -lm -lAW -lAWT -L/usr/X11R6/lib64 -lXm -lXpm -lXt -lXext -lX11 >-------------------- Checking bin/arb_edit >Target 'bin/arb_edit' not found >-> rebuilding bin/arb_edit (Thu Jan 1 00:59:59 1970) >Link bin/arb_edit >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -Wl,-O1 -Wl,--as-needed -Wl,--export-dynamic -rdynamic -o bin/arb_edit -L/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/LIBLINK NAMES_COM/client.a SERVERCNTRL/SERVERCNTRL.a EDIT/EDIT.a ARB_GDE/ARB_GDE.a STAT/STAT.a XML/XML.a SL/HELIX/HELIX.a SL/AW_HELIX/AW_HELIX.a SL/AW_NAME/AW_NAME.a -lARBDBPP -lARBDB -lm -lAW -lAWT -L/usr/X11R6/lib64 -lXm -lXpm -lXt -lXext -lX11 >-------------------- Checking bin/arb_name_server >Target 'bin/arb_name_server' not found >-> rebuilding bin/arb_name_server (Thu Jan 1 00:59:59 1970) >Link bin/arb_name_server >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -Wl,-O1 -Wl,--as-needed -Wl,--export-dynamic -rdynamic -o bin/arb_name_server -L/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/LIBLINK NAMES_COM/server.a NAMES/NAMES.a SERVERCNTRL/SERVERCNTRL.a -lARBDB NAMES_COM/client.a -lm >-------------------------------------------------------------------------------- Make everything in NALIGNER >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/NALIGNER' >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NALIGNER -c -o ali_aligner.o ali_aligner.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NALIGNER -c -o ali_arbdb.o ali_arbdb.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NALIGNER -c -o ali_global.o ali_global.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NALIGNER -c -o ali_main.o ali_main.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >ali_arbdb.cxx: In member function 'int ALI_ARBDB::put_SAI(const char*, char*)': >ali_arbdb.cxx:157:27: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated [-Wdeprecated-declarations] > GBDATA *gb_data = GBT_add_data(gb_extended,alignment,"data",GB_STRING); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from ali_other_stuff.hxx:12, > from ali_arbdb.hxx:6, > from ali_arbdb.cxx:7: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_t_prot.h:108:9: note: declared here > GBDATA *GBT_add_data P_((GBDATA *species, const char *ali_name, const char *key, GB_TYPES type)) __ATTR__DEPRECATED; > ^ >ali_arbdb.cxx:157:27: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated [-Wdeprecated-declarations] > GBDATA *gb_data = GBT_add_data(gb_extended,alignment,"data",GB_STRING); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from ali_other_stuff.hxx:12, > from ali_arbdb.hxx:6, > from ali_arbdb.cxx:7: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_t_prot.h:108:9: note: declared here > GBDATA *GBT_add_data P_((GBDATA *species, const char *ali_name, const char *key, GB_TYPES type)) __ATTR__DEPRECATED; > ^ >ali_arbdb.cxx:157:78: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated [-Wdeprecated-declarations] > GBDATA *gb_data = GBT_add_data(gb_extended,alignment,"data",GB_STRING); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from ali_other_stuff.hxx:12, > from ali_arbdb.hxx:6, > from ali_arbdb.cxx:7: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_t_prot.h:108:9: note: declared here > GBDATA *GBT_add_data P_((GBDATA *species, const char *ali_name, const char *key, GB_TYPES type)) __ATTR__DEPRECATED; > ^ >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NALIGNER -c -o ali_pathmap.o ali_pathmap.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NALIGNER -c -o ali_prealigner.o ali_prealigner.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NALIGNER -c -o ali_profile.o ali_profile.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NALIGNER -c -o ali_pt.o ali_pt.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >ali_prealigner.cxx: In member function 'void ALI_PREALIGNER::calculate_first_column_first_cell(ali_prealigner_cell*)': >ali_prealigner.cxx:271:29: warning: variable 'v3' set but not used [-Wunused-but-set-variable] > float v1, v2, v3; > ^ >ali_prealigner.cxx: In member function 'void ALI_PREALIGNER::generate_solution(ALI_MAP*)': >ali_prealigner.cxx:616:30: warning: variable 'map_len' set but not used [-Wunused-but-set-variable] > unsigned long map_pos, map_len; > ^ >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NALIGNER -c -o ali_sequence.o ali_sequence.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NALIGNER -c -o ali_solution.o ali_solution.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >ld -r -o NALIGNER.a ali_aligner.o ali_arbdb.o ali_global.o ali_main.o ali_pathmap.o ali_prealigner.o ali_profile.o ali_pt.o ali_sequence.o ali_solution.o >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/NALIGNER' >-------------------- Checking bin/arb_ntree >Target 'bin/arb_ntree' not found >-> rebuilding bin/arb_ntree (Thu Jan 1 00:59:59 1970) >Link bin/arb_ntree >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -Wl,-O1 -Wl,--as-needed -Wl,--export-dynamic -rdynamic -o bin/arb_ntree -L/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/LIBLINK PROBE_COM/client.a ARB_GDE/ARB_GDE.a AWTC/AWTC.a AWTI/AWTI.a GENOM/GENOM.a GENOM_IMPORT/GENOM_IMPORT.a MERGE/MERGE.a MULTI_PROBE/MULTI_PROBE.a NTREE/NTREE.a PRIMER_DESIGN/PRIMER_DESIGN.a PROBE_DESIGN/PROBE_DESIGN.a SEQ_QUALITY/SEQ_QUALITY.a SERVERCNTRL/SERVERCNTRL.a SL/AW_NAME/AW_NAME.a SL/DB_SCANNER/DB_SCANNER.a SL/FILE_BUFFER/FILE_BUFFER.a SL/HELIX/HELIX.a SL/REGEXPR/REGEXPR.a SL/TREE_READ/TREE_READ.a SL/TREE_WRITE/TREE_WRITE.a STAT/STAT.a XML/XML.a -lARBDB -lm -lAW -lAWT -L/usr/X11R6/lib64 -lXm -lXpm -lXt -lXext -lX11 >-------------------- Checking bin/arb_naligner >Target 'bin/arb_naligner' not found >-> rebuilding bin/arb_naligner (Thu Jan 1 00:59:59 1970) >Link bin/arb_naligner >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -Wl,-O1 -Wl,--as-needed -Wl,--export-dynamic -rdynamic -o bin/arb_naligner -L/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/LIBLINK PROBE_COM/client.a NALIGNER/NALIGNER.a SERVERCNTRL/SERVERCNTRL.a SL/HELIX/HELIX.a -lARBDB -lm >-------------------------------------------------------------------------------- Make everything in PROBE >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PROBE' >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PROBE -c PT_new_design.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include -I./../probe_bank/COM >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PROBE -c PT_family.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include -I./../probe_bank/COM >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PROBE -c PT_prefixtree.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include -I./../probe_bank/COM >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PROBE -c PT_main.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include -I./../probe_bank/COM >In file included from probe_tree.hxx:188:0, > from PT_prefixtree.cxx:11: >PT_prefixtree.cxx: In function 'int PTD(POS_TREE*)': >probe_tree.hxx:237:67: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] > (my_int_i) = (unsigned long)bswap_64(*(unsigned long*)(ptr)); \ > ^ >PT_prefixtree.cxx:174:5: note: in expansion of macro 'PT_READ_PNTR' > PT_READ_PNTR(&node->data, i); > ^ >PT_prefixtree.cxx: In function 'POS_TREE* PT_add_to_chain(PTM2*, POS_TREE*, int, int, int)': >PT_prefixtree.cxx:221:9: warning: variable 'mainapos' set but not used [-Wunused-but-set-variable] > int mainapos; // TODO: mainapos isn't used > ^ >In file included from probe_tree.hxx:188:0, > from PT_prefixtree.cxx:11: >PT_prefixtree.cxx: In function 'POS_TREE* PT_change_leaf_to_node(PTM2*, POS_TREE*)': >probe_tree.hxx:237:67: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] > (my_int_i) = (unsigned long)bswap_64(*(unsigned long*)(ptr)); \ > ^ >PT_prefixtree.cxx:252:5: note: in expansion of macro 'PT_READ_PNTR' > PT_READ_PNTR((&node->data),i); > ^ >In file included from PT_prefixtree.cxx:11:0: >probe_tree.hxx:242:30: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] > *(unsigned long*)(ptr)=bswap_64((unsigned long)(my_int_i)); \ > ^ >PT_prefixtree.cxx:258:5: note: in expansion of macro 'PT_WRITE_PNTR' > PT_WRITE_PNTR((&(new_elem->data)),(long)father); > ^ >In file included from probe_tree.hxx:188:0, > from PT_prefixtree.cxx:11: >PT_prefixtree.cxx: In function 'POS_TREE* PT_leaf_to_chain(PTM2*, POS_TREE*)': >probe_tree.hxx:237:67: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] > (my_int_i) = (unsigned long)bswap_64(*(unsigned long*)(ptr)); \ > ^ >PT_prefixtree.cxx:270:5: note: in expansion of macro 'PT_READ_PNTR' > PT_READ_PNTR((&node->data),i); > ^ >In file included from PT_prefixtree.cxx:11:0: >probe_tree.hxx:242:30: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] > *(unsigned long*)(ptr)=bswap_64((unsigned long)(my_int_i)); \ > ^ >PT_prefixtree.cxx:282:5: note: in expansion of macro 'PT_WRITE_PNTR' > PT_WRITE_PNTR((&new_elem->data),(long)father); // father > ^ >In file included from probe_tree.hxx:188:0, > from PT_prefixtree.cxx:11: >PT_prefixtree.cxx: In function 'POS_TREE* PT_create_leaf(PTM2*, POS_TREE**, PT_BASES, int, int, int)': >probe_tree.hxx:237:67: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] > (my_int_i) = (unsigned long)bswap_64(*(unsigned long*)(ptr)); \ > ^ >PT_prefixtree.cxx:317:9: note: in expansion of macro 'PT_READ_PNTR' > PT_READ_PNTR(&father->data,j); > ^ >In file included from PT_prefixtree.cxx:11:0: >probe_tree.hxx:242:30: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] > *(unsigned long*)(ptr)=bswap_64((unsigned long)(my_int_i)); \ > ^ >PT_prefixtree.cxx:321:13: note: in expansion of macro 'PT_WRITE_PNTR' > PT_WRITE_PNTR(&new_elemfather->data,gfather); > ^ >probe_tree.hxx:242:30: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] > *(unsigned long*)(ptr)=bswap_64((unsigned long)(my_int_i)); \ > ^ >PT_prefixtree.cxx:331:21: note: in expansion of macro 'PT_WRITE_PNTR' > PT_WRITE_PNTR((char *) &son->data, new_elemfather); > ^ >probe_tree.hxx:242:30: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] > *(unsigned long*)(ptr)=bswap_64((unsigned long)(my_int_i)); \ > ^ >PT_prefixtree.cxx:340:17: note: in expansion of macro 'PT_WRITE_PNTR' > PT_WRITE_PNTR((&node->data), (PT_PNTR)new_elemfather); > ^ >PT_prefixtree.cxx: In function 'void PTD_clear_fathers(PTM2*, POS_TREE*)': >probe_tree.hxx:242:30: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] > *(unsigned long*)(ptr)=bswap_64((unsigned long)(my_int_i)); \ > ^ >PT_prefixtree.cxx:389:5: note: in expansion of macro 'PT_WRITE_PNTR' > PT_WRITE_PNTR((&node->data), NULL); > ^ >PT_prefixtree.cxx: In function 'void PTD_put_longlong(FILE*, ULONG)': >probe_tree.hxx:242:30: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] > *(unsigned long*)(ptr)=bswap_64((unsigned long)(my_int_i)); \ > ^ >PT_prefixtree.cxx:406:5: note: in expansion of macro 'PT_WRITE_PNTR' > PT_WRITE_PNTR(buf,i); > ^ >PT_prefixtree.cxx: In function 'void PTD_put_int(FILE*, ULONG)': >probe_tree.hxx:211:29: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] > *(unsigned int*)(ptr) = bswap_32((unsigned int)(my_int_i)); \ > ^ >PT_prefixtree.cxx:424:5: note: in expansion of macro 'PT_WRITE_INT' > PT_WRITE_INT(buf,i); > ^ >PT_prefixtree.cxx: In function 'void PTD_put_short(FILE*, ULONG)': >probe_tree.hxx:221:31: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] > *(unsigned short*)(ptr) = bswap_16((unsigned short)(my_int_i)); \ > ^ >PT_prefixtree.cxx:436:5: note: in expansion of macro 'PT_WRITE_SHORT' > PT_WRITE_SHORT(buf,i); > ^ >PT_prefixtree.cxx: In function 'void PTD_set_object_to_saved_status(POS_TREE*, long int, int)': >probe_tree.hxx:242:30: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] > *(unsigned long*)(ptr)=bswap_64((unsigned long)(my_int_i)); \ > ^ >PT_prefixtree.cxx:443:5: note: in expansion of macro 'PT_WRITE_PNTR' > PT_WRITE_PNTR((&node->data),pos); > ^ >PT_prefixtree.cxx: In function 'long int PTD_write_tip_to_disk(FILE*, PTM2*, POS_TREE*, long int)': >PT_prefixtree.cxx:453:14: warning: unused variable 'i' [-Wunused-variable] > int size,i,cnt; > ^ >PT_prefixtree.cxx:454:11: warning: unused variable 'data' [-Wunused-variable] > char *data; > ^ >In file included from probe_tree.hxx:188:0, > from PT_prefixtree.cxx:11: >PT_prefixtree.cxx: In function 'long int PTD_write_leafs_to_disk(FILE*, PTM2*, POS_TREE*, long int, long int*, int*)': >probe_tree.hxx:237:67: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] > (my_int_i) = (unsigned long)bswap_64(*(unsigned long*)(ptr)); \ > ^ >PT_prefixtree.cxx:759:9: note: in expansion of macro 'PT_READ_PNTR' > PT_READ_PNTR((&node->data),father); > ^ >PT_prefixtree.cxx:751:42: warning: variable 'son_size' set but not used [-Wunused-but-set-variable] > long r_pos,r_poss[PT_B_MAX],son_size[PT_B_MAX],o_pos; > ^ >PT_prefixtree.cxx: In function 'void PTD_read_leafs_from_disk(char*, PTM2*, POS_TREE**)': >PT_prefixtree.cxx:815:14: warning: variable 'big_db' set but not used [-Wunused-but-set-variable] > bool big_db = false;; > ^ >PT_prefixtree.cxx:838:14: warning: variable 'info_detected' set but not used [-Wunused-but-set-variable] > bool info_detected = false; > ^ >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PROBE -c PT_io.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include -I./../probe_bank/COM >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PROBE -c PT_etc.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include -I./../probe_bank/COM >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PROBE -c PT_secundaer.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include -I./../probe_bank/COM >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PROBE -c PT_buildtree.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include -I./../probe_bank/COM >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PROBE -c PT_match.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include -I./../probe_bank/COM >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PROBE -c PT_findEx.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include -I./../probe_bank/COM >ld -r -o PROBE.a PT_new_design.o PT_family.o PT_prefixtree.o PT_main.o PT_io.o PT_etc.o PT_secundaer.o PT_buildtree.o PT_match.o PT_findEx.o >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PROBE' >-------------------- Checking bin/arb_pt_server >Target 'bin/arb_pt_server' not found >-> rebuilding bin/arb_pt_server (Thu Jan 1 00:59:59 1970) >Link bin/arb_pt_server >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -Wl,-O1 -Wl,--as-needed -Wl,--export-dynamic -rdynamic -o bin/arb_pt_server -L/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/LIBLINK PROBE_COM/server.a SERVERCNTRL/SERVERCNTRL.a SL/HELIX/HELIX.a PROBE/PROBE.a -lARBDB PROBE_COM/client.a -lm >-------------------------------------------------------------------------------- Make everything in HELP_SOURCE >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/HELP_SOURCE' >make date.xsl.tmp >--------------------------------------------------- >------------ Generating some help files: >(cd genhelp;make all) >make[5]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/HELP_SOURCE/genhelp' >Updating copyright.hlp from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/arb_LICENSE.txt >make[5]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/HELP_SOURCE' >cat date.xsl.header >date.xsl.tmp >bash -c "(export LC_ALL=C;date '+%d. %b %Y')" >>date.xsl.tmp >Updating changes.hlp from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/arb_CHANGES.txt >cat date.xsl.footer >>date.xsl.tmp >make[5]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/HELP_SOURCE' >../SOURCE_TOOLS/mv_if_diff date.xsl.tmp date.xsl >date.xsl created. >mkdir -p Xml >Updating agde_protpars.hlp from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDEHELP/HELP_GEN/protpars.help >mkdir -p Xml/prompt >mkdir -p ../lib/help_html >mkdir -p ../lib/help_html/prompt >mkdir -p ../lib/help >mkdir -p ../lib/help/prompt >Updating agde_readseq_sub_Formats.hlp from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDEHELP/HELP_GEN/readseq_sub_Formats.help >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_HELP_SOURCE -c arb_help2xml.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >cp -p oldhelp/pos_variability.ps.gz ../lib/help/pos_variability.ps.gz >cp -p oldhelp/consensus.ps.gz ../lib/help/consensus.ps.gz >cp -p oldhelp/arb.pdf.gz ../lib/help/arb.pdf.gz >Updating agde_treepuzzle.hlp from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDEHELP/HELP_GEN/treepuzzle.help >Updating agde_dnaml_sub_fastDNAml_doc.hlp from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDEHELP/HELP_GEN/dnaml_sub_fastDNAml_doc.help >Updating agde_phylip_distance_sub_fitch_doc.hlp from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDEHELP/HELP_GEN/phylip_distance_sub_fitch_doc.help >Updating agde_clustalw_sub_clustalw_doc.hlp from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDEHELP/HELP_GEN/clustalw_sub_clustalw_doc.help >Updating agde_proml.hlp from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDEHELP/HELP_GEN/proml.help >Updating agde_phylip_distance.hlp from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDEHELP/HELP_GEN/phylip_distance.help >Updating agde_lsadt.hlp from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDEHELP/HELP_GEN/lsadt.help >Updating agde_dnaml.hlp from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDEHELP/HELP_GEN/dnaml.help >Updating agde_phyml.hlp from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDEHELP/HELP_GEN/phyml.help >Updating agde_phylip_distance_sub_dnadist_doc.hlp from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDEHELP/HELP_GEN/phylip_distance_sub_dnadist_doc.help >Updating agde_CAP2.hlp from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDEHELP/HELP_GEN/CAP2.help >cp -p oldhelp/rna3d_manual.pdf.gz ../lib/help/rna3d_manual.pdf.gz >find ../lib/help_html -name "*.html" -size -1 -exec rm {} \; >Updating agde_phylip_distance_sub_kitsch_doc.hlp from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDEHELP/HELP_GEN/phylip_distance_sub_kitsch_doc.help >Updating agde_readseq.hlp from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDEHELP/HELP_GEN/readseq.help >Updating agde_readseq_sub_Readseq_help.hlp from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDEHELP/HELP_GEN/readseq_sub_Readseq_help.help >Updating agde_phylip_distance_sub_protdist_doc.hlp from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDEHELP/HELP_GEN/phylip_distance_sub_protdist_doc.help >Updating agde_readseq_sub_Readme.hlp from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDEHELP/HELP_GEN/readseq_sub_Readme.help >Updating agde_clustalw.hlp from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDEHELP/HELP_GEN/clustalw.help >Updating agde_phylip_distance_sub_neighbor_doc.hlp from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDEHELP/HELP_GEN/phylip_distance_sub_neighbor_doc.help >Updating agde_DNAml_rates.hlp from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDEHELP/HELP_GEN/DNAml_rates.help >Updating agde_dnapars.hlp from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDEHELP/HELP_GEN/dnapars.help >Updating agde_dnaml_sub_AxML_doc.hlp from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDEHELP/HELP_GEN/dnaml_sub_AxML_doc.help >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -Wl,-O1 -Wl,--as-needed -Wl,--export-dynamic -rdynamic -o /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/arb_help2xml arb_help2xml.o ../XML/XML.a -L/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/LIBLINK -lARBDB >Updating agde_clustalw_sub_clustalw_help.hlp from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDEHELP/HELP_GEN/clustalw_sub_clustalw_help.help >Updating agde_raxml.hlp from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDEHELP/HELP_WRITTEN/raxml.help >Updating GDE overview agde.hlp >make[5]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/HELP_SOURCE/genhelp' >--------------------------------------------------- [old hlp 2 xml] >time make xml >make[5]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/HELP_SOURCE' >touch xml.stamp >oldhelp/treeadm.hlp:6: Warning: Dead link to 'tr_export.hlp' >oldhelp/gde.hlp:6: Warning: Dead link to 'ale.hlp' >./generate_index.pl help_index.xml Xml > Xml/help_index.xml >make[5]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/HELP_SOURCE' >4.89user 19.41system 0:03.77elapsed 643%CPU (0avgtext+0avgdata 3448maxresident)k >0inputs+4368outputs (3major+1026126minor)pagefaults 0swaps >--------------------------------------------------- [xml 2 hlp] >time make help >make[5]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/HELP_SOURCE' >make[5]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/HELP_SOURCE' >4.10user 20.40system 0:03.91elapsed 625%CPU (0avgtext+0avgdata 5060maxresident)k >0inputs+3728outputs (63major+674031minor)pagefaults 0swaps >make ../lib/help/FORM.hlp >make[5]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/HELP_SOURCE' >cp -p oldhelp/FORM.hlp ../lib/help/FORM.hlp >make[5]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/HELP_SOURCE' >--------------------------------------------------- [xml 2 html] >time make html >make[5]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/HELP_SOURCE' >cp -p Logo_25wht.gif ../lib/help_html/Logo_25wht.gif >make[5]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/HELP_SOURCE' >3.45user 21.84system 0:04.08elapsed 618%CPU (0avgtext+0avgdata 31472maxresident)k >0inputs+5592outputs (0major+719752minor)pagefaults 0swaps >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/HELP_SOURCE' >make[3]: Nothing to be done for 'help'. >make[3]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3' >make[2]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3' >make libs >make[2]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3' >make[2]: Nothing to be done for 'libs'. >make[2]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3' >make convert tools gde readseq >make[2]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3' >-------------------------------------------------------------------------------- Make everything in SL/FILE_BUFFER >make[3]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/FILE_BUFFER' >make[3]: 'FILE_BUFFER.a' is up to date. >make[3]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/FILE_BUFFER' >-------------------------------------------------------------------------------- Make everything in ARBDBPP >make[3]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/ARBDBPP' >make[3]: 'libARBDBPP.a' is up to date. >make[3]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/ARBDBPP' >-------------------------------------------------------------------------------- Make everything in ARBDB >make[3]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/ARBDB' >make[3]: 'libARBDB.a' is up to date. >make[3]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/ARBDB' >-------------------------------------------------------------------------------- Make everything in ARBDBS >make[3]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/ARBDBS' >make[3]: 'libARBDB.a' is up to date. >make[3]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/ARBDBS' >-------------------------------------------------------------------------------- Make everything in ARBDB2 >make[3]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/ARBDB2' >make[3]: 'libARBDB.a' is up to date. >make[3]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/ARBDB2' >-------------------------------------------------------------------------------- Make everything in WINDOW >make[3]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/WINDOW' >make[3]: 'libAW.a' is up to date. >make[3]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/WINDOW' >-------------------------------------------------------------------------------- Make everything in AWT >make[3]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/AWT' >make[3]: 'libAWT.a' is up to date. >make[3]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/AWT' >-------------------------------------------------------------------------------- Make everything in AISC_MKPTPS >make[3]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/AISC_MKPTPS' >make[3]: Nothing to be done for 'dummy.a'. >make[3]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/AISC_MKPTPS' >-------------------------------------------------------------------------------- Make everything in SERVERCNTRL >make[3]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SERVERCNTRL' >make[3]: 'SERVERCNTRL.a' is up to date. >make[3]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SERVERCNTRL' >-------------------------------------------------------------------------------- Make everything in AISC >make[3]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/AISC' >make[3]: Nothing to be done for 'dummy.a'. >make[3]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/AISC' >-------------------- Updating shared libraries >make libs >make[3]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3' >-------------------------------------------------------------------------------- Make everything in READSEQ >make[3]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/READSEQ' >make[3]: Nothing to be done for 'all'. >make[3]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/READSEQ' >-------------------------------------------------------------------------------- Make everything in PROBE_COM >make[3]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PROBE_COM' >make[3]: 'server.a' is up to date. >make[3]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PROBE_COM' >-------------------------------------------------------------------------------- Make everything in SL >make[3]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL' >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/TREE_READ' >make[4]: 'TREE_READ.a' is up to date. >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/TREE_READ' >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/TREE_WRITE' >make[4]: 'TREE_WRITE.a' is up to date. >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/TREE_WRITE' >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/HELIX' >make[4]: 'HELIX.a' is up to date. >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/HELIX' >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/AW_HELIX' >make[4]: 'AW_HELIX.a' is up to date. >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/AW_HELIX' >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/AW_NAME' >make[4]: 'AW_NAME.a' is up to date. >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/AW_NAME' >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/FILE_BUFFER' >make[4]: 'FILE_BUFFER.a' is up to date. >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/FILE_BUFFER' >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/DB_SCANNER' >make[4]: 'DB_SCANNER.a' is up to date. >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/DB_SCANNER' >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/REGEXPR' >make[4]: 'REGEXPR.a' is up to date. >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/REGEXPR' >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/FAST_ALIGNER' >make[4]: 'FAST_ALIGNER.a' is up to date. >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/FAST_ALIGNER' >make[3]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL' >make[3]: Nothing to be done for 'libs'. >make[3]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3' >make CONVERTALN/CONVERTALN.dummy >make[3]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3' >-------------------------------------------------------------------------------- Make everything in CONVERTALN >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/CONVERTALN' >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_CONVERTALN -Wstrict-prototypes -c main.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_CONVERTALN -Wstrict-prototypes -c fconv.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_CONVERTALN -Wstrict-prototypes -c mg.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >main.c: In function 'file_type': >main.c:224:5: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] > fscanf(fp, "%s", token); > ^ >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_CONVERTALN -Wstrict-prototypes -c genbank.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >mg.c: In function 'genbank_to_macke': >mg.c:32:24: warning: variable 'total_num' set but not used [-Wunused-but-set-variable] > int indi, total_num; > ^ >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_CONVERTALN -Wstrict-prototypes -c macke.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >mg.c: In function 'macke_to_genbank': >mg.c:658:10: warning: 'IFP2' may be used uninitialized in this function [-Wmaybe-uninitialized] > ifp2 = create_FILE_BUFFER(inf, IFP2); > ^ >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_CONVERTALN -Wstrict-prototypes -c phylip.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_CONVERTALN -Wstrict-prototypes -c paup.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_CONVERTALN -Wstrict-prototypes -c util.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >util.c: In function 'Reallocspace': >util.c:94:9: warning: ignoring return value of 'scanf', declared with attribute warn_unused_result [-Wunused-result] > scanf("%c", &answer); > ^ >util.c: In function 'Dupstr': >util.c:118:13: warning: ignoring return value of 'scanf', declared with attribute warn_unused_result [-Wunused-result] > scanf("%c", &answer); > ^ >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_CONVERTALN -Wstrict-prototypes -c date.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_CONVERTALN -Wstrict-prototypes -c embl.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_CONVERTALN -Wstrict-prototypes -c gcg.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >embl.c: In function 'embl_version': >embl.c:424:9: warning: variable 'index' set but not used [-Wunused-but-set-variable] > int index; > ^ >embl.c: In function 'embl_to_macke': >embl.c:983:15: warning: variable 'total_num' set but not used [-Wunused-but-set-variable] > int indi, total_num; > ^ >gcg.c: In function 'to_gcg': >gcg.c:105:17: warning: 'ofp' may be used uninitialized in this function [-Wmaybe-uninitialized] > fclose(ofp); > ^ >gcg.c:28:14: warning: 'IFP2' may be used uninitialized in this function [-Wmaybe-uninitialized] > ifp2 = create_FILE_BUFFER(inf, IFP2); > ^ >embl.c: In function 'embl_comments': >embl.c:566:11: warning: 'eof' may be used uninitialized in this function [-Wmaybe-uninitialized] > return(eof); > ^ >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_CONVERTALN -Wstrict-prototypes -c printable.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >embl.c: In function 'etog_journal': >embl.c:1373:13: warning: 'index' may be used uninitialized in this function [-Wmaybe-uninitialized] > Append(&new_journal, journal+index); > ^ >embl.c: In function 'macke_to_embl': >embl.c:1788:10: warning: 'IFP2' may be used uninitialized in this function [-Wmaybe-uninitialized] > ifp2 = create_FILE_BUFFER(inf, IFP2); > ^ >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_CONVERTALN -Wstrict-prototypes -c alma.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_CONVERTALN -Wstrict-prototypes -c routines.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >alma.c: In function 'alma_to_macke': >alma.c:35:24: warning: variable 'total_num' set but not used [-Wunused-but-set-variable] > int indi, total_num; > ^ >alma.c: In function 'alma_in_gaps': >alma.c:351:11: warning: function may return address of local variable [-Wreturn-local-addr] > return(eof); > ^ >alma.c:269:13: note: declared here > char line[LINENUM], gap_chars[LINENUM]; > ^ >alma.c:345:7: warning: 'return_num' may be used uninitialized in this function [-Wmaybe-uninitialized] > if(return_num!=0) { > ^ >alma.c: In function 'macke_to_alma': >alma.c:646:10: warning: 'IFP2' may be used uninitialized in this function [-Wmaybe-uninitialized] > ifp2 = create_FILE_BUFFER(inf, IFP2); > ^ >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_CONVERTALN -Wstrict-prototypes -c convert.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -Wl,-O1 -Wl,--as-needed -Wl,--export-dynamic -rdynamic -o /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/arb_convert_aln main.o fconv.o mg.o genbank.o macke.o phylip.o paup.o util.o date.o embl.o gcg.o printable.o alma.o routines.o convert.o ../SL/FILE_BUFFER/FILE_BUFFER.a -L/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/LIBLINK -lARBDB >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/CONVERTALN' >make[3]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3' >-------------------------------------------------------------------------------- Make everything in TOOLS >make[3]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/TOOLS' >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_TOOLS -c arb_2_ascii.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_TOOLS -c arb_2_bin.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_TOOLS -c arb_a2ps.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >arb_2_bin.cxx: In function 'int main(int, char**)': >arb_2_bin.cxx:33:17: warning: variable 'test' set but not used [-Wunused-but-set-variable] > int test = 0; > ^ >arb_a2ps.c: In function 'main': >arb_a2ps.c:1770:9: warning: ignoring return value of 'pipe', declared with attribute warn_unused_result [-Wunused-result] > pipe(fd); > ^ >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_TOOLS -c arb_count_chars.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_TOOLS -c arb_dnarates.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >arb_count_chars.cxx: In function 'int main(int, char**)': >arb_count_chars.cxx:99:27: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated [-Wdeprecated-declarations] > GBDATA *gb_data = GBT_add_data(gb_sai, alignment_name, "data", GB_STRING); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from arb_count_chars.cxx:7: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_t_prot.h:108:9: note: declared here > GBDATA *GBT_add_data P_((GBDATA *species, const char *ali_name, const char *key, GB_TYPES type)) __ATTR__DEPRECATED; > ^ >arb_count_chars.cxx:99:27: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated [-Wdeprecated-declarations] > GBDATA *gb_data = GBT_add_data(gb_sai, alignment_name, "data", GB_STRING); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from arb_count_chars.cxx:7: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_t_prot.h:108:9: note: declared here > GBDATA *GBT_add_data P_((GBDATA *species, const char *ali_name, const char *key, GB_TYPES type)) __ATTR__DEPRECATED; > ^ >arb_count_chars.cxx:99:81: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated [-Wdeprecated-declarations] > GBDATA *gb_data = GBT_add_data(gb_sai, alignment_name, "data", GB_STRING); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from arb_count_chars.cxx:7: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_t_prot.h:108:9: note: declared here > GBDATA *GBT_add_data P_((GBDATA *species, const char *ali_name, const char *key, GB_TYPES type)) __ATTR__DEPRECATED; > ^ >arb_count_chars.cxx:15:17: warning: variable 'db_name' set but not used [-Wunused-but-set-variable] > const char *db_name = ":"; // default name -> link to server > ^ >arb_dnarates.c: In function 'writeToArb': >arb_dnarates.c:1824:9: warning: 'GBT_add_data' is deprecated [-Wdeprecated-declarations] > gb_data = GBT_add_data(gb_sai, alignment_name, "rates", GB_FLOATS); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from arb_dnarates.c:29: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_t_prot.h:108:9: note: declared here > GBDATA *GBT_add_data P_((GBDATA *species, const char *ali_name, const char *key, GB_TYPES type)) __ATTR__DEPRECATED; > ^ >arb_dnarates.c:1826:9: warning: 'GBT_add_data' is deprecated [-Wdeprecated-declarations] > gb_data = GBT_add_data(gb_sai, alignment_name, "data", GB_STRING); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from arb_dnarates.c:29: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_t_prot.h:108:9: note: declared here > GBDATA *GBT_add_data P_((GBDATA *species, const char *ali_name, const char *key, GB_TYPES type)) __ATTR__DEPRECATED; > ^ >arb_dnarates.c:1828:9: warning: 'GBT_add_data' is deprecated [-Wdeprecated-declarations] > gb_data = GBT_add_data(gb_sai, alignment_name, "_CATEGORIES", GB_STRING); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from arb_dnarates.c:29: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_t_prot.h:108:9: note: declared here > GBDATA *GBT_add_data P_((GBDATA *species, const char *ali_name, const char *key, GB_TYPES type)) __ATTR__DEPRECATED; > ^ >arb_dnarates.c:1830:9: warning: 'GBT_add_data' is deprecated [-Wdeprecated-declarations] > gb_data = GBT_add_data(gb_sai, alignment_name, "_TYPE", GB_STRING); > ^ >In file included from /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from arb_dnarates.c:29: >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/ad_t_prot.h:108:9: note: declared here > GBDATA *GBT_add_data P_((GBDATA *species, const char *ali_name, const char *key, GB_TYPES type)) __ATTR__DEPRECATED; > ^ >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_TOOLS -c arb_export_rates.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_TOOLS -c arb_export_tree.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_TOOLS -c arb_gene_probe.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_TOOLS -c arb_message.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_TOOLS -c arb_notify.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_TOOLS -c arb_primer.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_TOOLS -c arb_probe.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >arb_primer.cxx: In function 'void arb_prm_menu()': >arb_primer.cxx:46:46: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] > fgets(aprm.buffer, PRM_BUFFERSIZE, stdin); > ^ >arb_primer.cxx:58:46: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] > fgets(aprm.buffer, PRM_BUFFERSIZE, stdin); > ^ >arb_primer.cxx:63:46: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] > fgets(aprm.buffer, PRM_BUFFERSIZE, stdin); > ^ >arb_primer.cxx:74:46: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] > fgets(aprm.buffer, PRM_BUFFERSIZE, stdin); > ^ >arb_primer.cxx:83:46: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] > fgets(aprm.buffer, PRM_BUFFERSIZE, stdin); > ^ >arb_probe.cxx: In function 'void AP_probe_match_event()': >arb_probe.cxx:253:10: warning: variable 'toksep' set but not used [-Wunused-but-set-variable] > char toksep[2]; > ^ >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_TOOLS -c arb_proto_2_xsub.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_TOOLS -c arb_read_tree.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_TOOLS -c arb_replace.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_TOOLS -c arb_swap_rnastr.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -Wl,-O1 -Wl,--as-needed -Wl,--export-dynamic -rdynamic -o /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/arb_2_ascii arb_2_ascii.o -L/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/LIBLINK -lARBDB >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -Wl,-O1 -Wl,--as-needed -Wl,--export-dynamic -rdynamic -o /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/arb_2_bin arb_2_bin.o -L/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/LIBLINK -lARBDB >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -Wl,-O1 -Wl,--as-needed -Wl,--export-dynamic -rdynamic -o /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/arb_a2ps arb_a2ps.o -L/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/LIBLINK -lARBDB >arb_swap_rnastr.cxx: In function 'void arb_asrs_menu()': >arb_swap_rnastr.cxx:21:47: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] > fgets(asrs.source, ASRS_BUFFERSIZE, stdin); > ^ >arb_swap_rnastr.cxx:23:45: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] > fgets(asrs.dest, ASRS_BUFFERSIZE, stdin); > ^ >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -Wl,-O1 -Wl,--as-needed -Wl,--export-dynamic -rdynamic -o /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/arb_count_chars arb_count_chars.o -L/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/LIBLINK -lARBDB >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -Wl,-O1 -Wl,--as-needed -Wl,--export-dynamic -rdynamic -o /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/arb_dnarates arb_dnarates.o -L/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/LIBLINK -lARBDB >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -Wl,-O1 -Wl,--as-needed -Wl,--export-dynamic -rdynamic -o /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/arb_export_rates arb_export_rates.o -L/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/LIBLINK -lARBDB >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -Wl,-O1 -Wl,--as-needed -Wl,--export-dynamic -rdynamic -o /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/arb_export_tree arb_export_tree.o ../SL/TREE_WRITE/TREE_WRITE.a ../XML/XML.a ../SL/TREE_READ/TREE_READ.a -L/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/LIBLINK -lARBDB >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -Wl,-O1 -Wl,--as-needed -Wl,--export-dynamic -rdynamic -o /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/arb_gene_probe arb_gene_probe.o -L/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/LIBLINK -lARBDB >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -Wl,-O1 -Wl,--as-needed -Wl,--export-dynamic -rdynamic -o /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/arb_message arb_message.o -L/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/LIBLINK -lARBDB >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -Wl,-O1 -Wl,--as-needed -Wl,--export-dynamic -rdynamic -o /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/arb_notify arb_notify.o -L/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/LIBLINK -lARBDB >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -Wl,-O1 -Wl,--as-needed -Wl,--export-dynamic -rdynamic -o /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/arb_primer arb_primer.o -L/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/LIBLINK -lARBDB >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -Wl,-O1 -Wl,--as-needed -Wl,--export-dynamic -rdynamic -o /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/arb_probe arb_probe.o ../SERVERCNTRL/SERVERCNTRL.a ../PROBE_COM/client.a -L/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/LIBLINK -lARBDB >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -Wl,-O1 -Wl,--as-needed -Wl,--export-dynamic -rdynamic -o /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/arb_proto_2_xsub arb_proto_2_xsub.o -L/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/LIBLINK -lARBDB >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -Wl,-O1 -Wl,--as-needed -Wl,--export-dynamic -rdynamic -o /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/arb_read_tree arb_read_tree.o ../SL/TREE_READ/TREE_READ.a -L/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/LIBLINK -lARBDB >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -Wl,-O1 -Wl,--as-needed -Wl,--export-dynamic -rdynamic -o /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/arb_replace arb_replace.o -L/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/LIBLINK -lARBDB >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -Wl,-O1 -Wl,--as-needed -Wl,--export-dynamic -rdynamic -o /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/arb_swap_rnastr arb_swap_rnastr.o -L/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/LIBLINK -lARBDB >rm arb_a2ps.o >make[3]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/TOOLS' >-------------------------------------------------------------------------------- Make everything in GDE >make[3]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDE' >----------------- non-ARB code: warnings disabled >make CLUSTAL/CLUSTAL.dummy SUPPORT/SUPPORT.dummy AxML/AxML.dummy RAxML/RAxML.dummy PHYML/PHYML.dummy CLUSTALW/CLUSTALW.dummy PHYLIP/PHYLIP.dummy TREEPUZZLE/TREEPUZZLE.dummy FASTDNAML/FASTDNAML.dummy >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDE' >make[5]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDE/AxML' >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_AxML -c -o axml.o axml.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -Wl,-O1 -Wl,--as-needed -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_AxML -o /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/axml axml.o -lm >make[5]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDE/AxML' >make[5]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDE/CLUSTAL' >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_CLUSTAL -c -o clustalv.o clustalv.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_CLUSTAL -c -o amenu.o amenu.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_CLUSTAL -c -o myers.o myers.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_CLUSTAL -c -o sequence.o sequence.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_CLUSTAL -c -o showpair.o showpair.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_CLUSTAL -c -o upgma.o upgma.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_CLUSTAL -c -o util.o util.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_CLUSTAL -c -o trees.o trees.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_CLUSTAL -c -o gcgcheck.o gcgcheck.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -Wl,-O1 -Wl,--as-needed -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_CLUSTAL -o /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/clustalv clustalv.o amenu.o myers.o sequence.o showpair.o upgma.o util.o trees.o gcgcheck.o -lm >amenu.o: In function `make_tree': >amenu.c:(.text+0x19c6): warning: the `gets' function is dangerous and should not be used. >make[5]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDE/CLUSTAL' >make[5]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDE/SUPPORT' >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_SUPPORT -Wl,-O1 -Wl,--as-needed -o /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/CAP2 CAP2.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include -lm >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_SUPPORT -Wl,-O1 -Wl,--as-needed -o /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/Restriction Restriction.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include -lm >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_SUPPORT -Wl,-O1 -Wl,--as-needed -o /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/Zuk_to_gen Zuk_to_gen.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include -lm >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_SUPPORT -Wl,-O1 -Wl,--as-needed -o /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/count count.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include -lm >/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/temp/ccx6sDtf.o: In function `main': >Zuk_to_gen.c:(.text.startup+0x5a): warning: the `gets' function is dangerous and should not be used. >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_SUPPORT -Wl,-O1 -Wl,--as-needed -o /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/findall findall.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include -lm >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_SUPPORT -Wl,-O1 -Wl,--as-needed -o /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/lsadt lsadt.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include -lm >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_SUPPORT -Wl,-O1 -Wl,--as-needed -o /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/sho_helix sho_helix.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include -lm >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_SUPPORT -Wl,-O1 -Wl,--as-needed -o /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/varpos varpos.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include -lm >make[5]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDE/SUPPORT' >make[5]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDE/PHYML' >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_PHYML -fomit-frame-pointer -DUNIX -DPHYML -c -o main.o main.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_PHYML -fomit-frame-pointer -DUNIX -DPHYML -c -o utilities.o utilities.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_PHYML -fomit-frame-pointer -DUNIX -DPHYML -c -o optimiz.o optimiz.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_PHYML -fomit-frame-pointer -DUNIX -DPHYML -c -o lk.o lk.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_PHYML -fomit-frame-pointer -DUNIX -DPHYML -c -o bionj.o bionj.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_PHYML -fomit-frame-pointer -DUNIX -DPHYML -c -o models.o models.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_PHYML -fomit-frame-pointer -DUNIX -DPHYML -c -o free.o free.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_PHYML -fomit-frame-pointer -DUNIX -DPHYML -c -o options.o options.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_PHYML -fomit-frame-pointer -DUNIX -DPHYML -c -o simu.o simu.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_PHYML -fomit-frame-pointer -DUNIX -DPHYML -c -o eigen.o eigen.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_PHYML -fomit-frame-pointer -Wl,-O1 -Wl,--as-needed -o /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/phyml main.o utilities.o optimiz.o lk.o bionj.o models.o free.o options.o simu.o eigen.o -lm >make[5]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDE/PHYML' >make[5]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDE/FASTDNAML' >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_FASTDNAML -c -o fastDNAml.o fastDNAml.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -Wl,-O1 -Wl,--as-needed -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_FASTDNAML -o /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/fastdnaml fastDNAml.o -lm >make[5]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDE/FASTDNAML' >make[5]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDE/TREEPUZZLE' >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_TREEPUZZLE -DPACKAGE=\"tree-puzzle\" -DVERSION=\"5.0\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -Isrc -c -o src/gamma.o src/gamma.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_TREEPUZZLE -DPACKAGE=\"tree-puzzle\" -DVERSION=\"5.0\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -Isrc -c -o src/ml1.o src/ml1.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_TREEPUZZLE -DPACKAGE=\"tree-puzzle\" -DVERSION=\"5.0\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -Isrc -c -o src/ml2.o src/ml2.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_TREEPUZZLE -DPACKAGE=\"tree-puzzle\" -DVERSION=\"5.0\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -Isrc -c -o src/ml3.o src/ml3.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_TREEPUZZLE -DPACKAGE=\"tree-puzzle\" -DVERSION=\"5.0\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -Isrc -c -o src/model1.o src/model1.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_TREEPUZZLE -DPACKAGE=\"tree-puzzle\" -DVERSION=\"5.0\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -Isrc -c -o src/model2.o src/model2.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_TREEPUZZLE -DPACKAGE=\"tree-puzzle\" -DVERSION=\"5.0\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -Isrc -c -o src/puzzle1.o src/puzzle1.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_TREEPUZZLE -DPACKAGE=\"tree-puzzle\" -DVERSION=\"5.0\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -Isrc -c -o src/puzzle2.o src/puzzle2.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_TREEPUZZLE -DPACKAGE=\"tree-puzzle\" -DVERSION=\"5.0\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -Isrc -c -o src/sched.o src/sched.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_TREEPUZZLE -DPACKAGE=\"tree-puzzle\" -DVERSION=\"5.0\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -Isrc -c -o src/util.o src/util.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -Wl,-O1 -Wl,--as-needed -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_TREEPUZZLE -DPACKAGE=\"tree-puzzle\" -DVERSION=\"5.0\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -Isrc -o /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/puzzle src/gamma.o src/ml1.o src/ml2.o src/ml3.o src/model1.o src/model2.o src/puzzle1.o src/puzzle2.o src/sched.o src/util.o -lm >make[5]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDE/TREEPUZZLE' >make[5]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDE/CLUSTALW' >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_CLUSTALW -c -o interface.o interface.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_CLUSTALW -c -o gcgcheck.o gcgcheck.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_CLUSTALW -c -o calcprf1.o calcprf1.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_CLUSTALW -c -o prfalign.o prfalign.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_CLUSTALW -c -o calctree.o calctree.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_CLUSTALW -c -o alnscore.o alnscore.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_CLUSTALW -c -o showpair.o showpair.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_CLUSTALW -c -o calcgapcoeff.o calcgapcoeff.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_CLUSTALW -c -o pairalign.o pairalign.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_CLUSTALW -c -o calcprf2.o calcprf2.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_CLUSTALW -c -o amenu.o amenu.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_CLUSTALW -c -o malign.o malign.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_CLUSTALW -c -o trees.o trees.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_CLUSTALW -c -o util.o util.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_CLUSTALW -c -o random.o random.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_CLUSTALW -c -o clustalw.o clustalw.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_CLUSTALW -c -o sequence.o sequence.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_CLUSTALW -c -o readmat.o readmat.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_CLUSTALW -Wl,-O1 -Wl,--as-needed -o /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/clustalw interface.o gcgcheck.o calcprf1.o prfalign.o calctree.o alnscore.o showpair.o calcgapcoeff.o pairalign.o calcprf2.o amenu.o malign.o trees.o util.o random.o clustalw.o sequence.o readmat.o -lm >interface.o: In function `open_output_file': >interface.c:(.text+0x2243): warning: the `gets' function is dangerous and should not be used. >make[5]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDE/CLUSTALW' >make[5]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDE/RAxML' >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_RAxML -fomit-frame-pointer -funroll-loops -c -o axml.o axml.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_RAxML -fomit-frame-pointer -funroll-loops -c -o raxmlParsimony.o raxmlParsimony.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_RAxML -fomit-frame-pointer -funroll-loops -c -o rev_functions.o rev_functions.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_RAxML -fomit-frame-pointer -funroll-loops -c -o optimizeModel.o optimizeModel.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_RAxML -fomit-frame-pointer -funroll-loops -c -o multiple.o multiple.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_RAxML -fomit-frame-pointer -funroll-loops -c -o searchAlgo.o searchAlgo.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_RAxML -fomit-frame-pointer -funroll-loops -c -o topologies.o topologies.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_RAxML -fomit-frame-pointer -funroll-loops -c -o parsePartitions.o parsePartitions.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_RAxML -fomit-frame-pointer -funroll-loops -c -o treeIO.o treeIO.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_RAxML -fomit-frame-pointer -funroll-loops -c -o models.o models.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_RAxML -fomit-frame-pointer -funroll-loops -c -o bipartitionList.o bipartitionList.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_RAxML -fomit-frame-pointer -funroll-loops -c -o rapidBootstrap.o rapidBootstrap.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_RAxML -fomit-frame-pointer -funroll-loops -c -o evaluatePartialGeneric.o evaluatePartialGeneric.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_RAxML -fomit-frame-pointer -funroll-loops -c -o evaluateGeneric.o evaluateGeneric.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_RAxML -fomit-frame-pointer -funroll-loops -c -o newviewGeneric.o newviewGeneric.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_RAxML -fomit-frame-pointer -funroll-loops -c -o makenewzGeneric.o makenewzGeneric.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_RAxML -fomit-frame-pointer -funroll-loops -c -o evaluateGenericVector.o evaluateGenericVector.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_RAxML -fomit-frame-pointer -funroll-loops -c -o categorizeGeneric.o categorizeGeneric.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_RAxML -fomit-frame-pointer -funroll-loops -Wl,-O1 -Wl,--as-needed -o /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/raxmlHPC axml.o raxmlParsimony.o rev_functions.o optimizeModel.o multiple.o searchAlgo.o topologies.o parsePartitions.o treeIO.o models.o bipartitionList.o rapidBootstrap.o evaluatePartialGeneric.o evaluateGeneric.o newviewGeneric.o makenewzGeneric.o evaluateGenericVector.o categorizeGeneric.o -lm >make[5]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDE/RAxML' >make[5]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDE/PHYLIP' >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -c -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_PHYLIP clique.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -c -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_PHYLIP disc.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -c -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_PHYLIP phylip.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -c -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_PHYLIP consense.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -c -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_PHYLIP cons.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -c -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_PHYLIP contml.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -c -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_PHYLIP cont.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -c -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_PHYLIP contrast.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -c -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_PHYLIP dnacomp.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -c -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_PHYLIP seq.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -c -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_PHYLIP dnadist.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -c -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_PHYLIP dnainvar.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -c -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_PHYLIP dnaml.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -c -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_PHYLIP dnamlk.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -c -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_PHYLIP dnamove.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -c -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_PHYLIP moves.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -c -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_PHYLIP dnapars.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -c -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_PHYLIP dnapenny.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -c -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_PHYLIP dolmove.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -c -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_PHYLIP dollo.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -c -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_PHYLIP dollop.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -c -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_PHYLIP dolpenny.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -c -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_PHYLIP factor.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -c -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_PHYLIP fitch.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -c -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_PHYLIP dist.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -c -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_PHYLIP gendist.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -c -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_PHYLIP kitsch.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -c -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_PHYLIP mix.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -c -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_PHYLIP wagner.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -c -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_PHYLIP move.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -c -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_PHYLIP neighbor.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -c -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_PHYLIP pars.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -c -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_PHYLIP discrete.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -c -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_PHYLIP penny.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -c -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_PHYLIP proml.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -c -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_PHYLIP promlk.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -c -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_PHYLIP protdist.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -c -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_PHYLIP protpars.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -c -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_PHYLIP restdist.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -c -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_PHYLIP restml.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -c -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_PHYLIP retree.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -c -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_PHYLIP seqboot.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -c -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_PHYLIP treedist.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -c -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_PHYLIP drawgram.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -c -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_PHYLIP draw.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -c -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_PHYLIP draw2.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -c -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_PHYLIP drawtree.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -Wl,-O1 -Wl,--as-needed -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_PHYLIP -o /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/clique clique.o disc.o phylip.o -lm -lc >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -Wl,-O1 -Wl,--as-needed -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_PHYLIP -o /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/consense consense.o phylip.o cons.o -lm -lc >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -Wl,-O1 -Wl,--as-needed -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_PHYLIP -o /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/contml contml.o cont.o phylip.o -lm -lc >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -Wl,-O1 -Wl,--as-needed -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_PHYLIP -o /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/contrast contrast.o cont.o phylip.o -lm -lc >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -Wl,-O1 -Wl,--as-needed -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_PHYLIP -o /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/dnacomp dnacomp.o seq.o phylip.o -lm -lc >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -Wl,-O1 -Wl,--as-needed -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_PHYLIP -o /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/dnadist dnadist.o seq.o phylip.o -lm -lc >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -Wl,-O1 -Wl,--as-needed -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_PHYLIP -o /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/dnainvar dnainvar.o seq.o phylip.o -lm -lc >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -Wl,-O1 -Wl,--as-needed -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_PHYLIP -o /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/dnaml dnaml.o seq.o phylip.o -lm -lc >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -Wl,-O1 -Wl,--as-needed -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_PHYLIP -o /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/dnamlk dnamlk.o seq.o phylip.o -lm -lc >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -Wl,-O1 -Wl,--as-needed -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_PHYLIP -o /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/dnamove dnamove.o seq.o moves.o phylip.o -lm -lc >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -Wl,-O1 -Wl,--as-needed -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_PHYLIP -o /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/dnapars dnapars.o seq.o phylip.o -lm -lc >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -Wl,-O1 -Wl,--as-needed -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_PHYLIP -o /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/dnapenny dnapenny.o seq.o phylip.o -lm -lc >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -Wl,-O1 -Wl,--as-needed -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_PHYLIP -o /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/dolmove dolmove.o disc.o moves.o dollo.o phylip.o -lm -lc >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -Wl,-O1 -Wl,--as-needed -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_PHYLIP -o /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/dollop dollop.o disc.o dollo.o phylip.o -lm -lc >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -Wl,-O1 -Wl,--as-needed -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_PHYLIP -o /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/dolpenny dolpenny.o disc.o dollo.o phylip.o -lm -lc >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -Wl,-O1 -Wl,--as-needed -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_PHYLIP -o /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/factor factor.o phylip.o -lm -lc >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -Wl,-O1 -Wl,--as-needed -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_PHYLIP -o /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/fitch fitch.o dist.o phylip.o -lm -lc >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -Wl,-O1 -Wl,--as-needed -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_PHYLIP -o /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/gendist gendist.o phylip.o -lm -lc >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -Wl,-O1 -Wl,--as-needed -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_PHYLIP -o /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/kitsch kitsch.o dist.o phylip.o -lm -lc >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -Wl,-O1 -Wl,--as-needed -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_PHYLIP -o /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/mix mix.o disc.o wagner.o phylip.o -lm -lc >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -Wl,-O1 -Wl,--as-needed -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_PHYLIP -o /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/move move.o disc.o moves.o wagner.o phylip.o -lm -lc >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -Wl,-O1 -Wl,--as-needed -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_PHYLIP -o /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/neighbor neighbor.o dist.o phylip.o -lm -lc >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -Wl,-O1 -Wl,--as-needed -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_PHYLIP -o /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/pars pars.o discrete.o phylip.o -lm -lc >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -Wl,-O1 -Wl,--as-needed -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_PHYLIP -o /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/penny penny.o disc.o wagner.o phylip.o -lm -lc >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -Wl,-O1 -Wl,--as-needed -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_PHYLIP -o /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/proml proml.o seq.o phylip.o -lm -lc >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -Wl,-O1 -Wl,--as-needed -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_PHYLIP -o /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/promlk promlk.o seq.o phylip.o -lm -lc >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -Wl,-O1 -Wl,--as-needed -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_PHYLIP -o /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/protdist protdist.o seq.o phylip.o -lm -lc >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -Wl,-O1 -Wl,--as-needed -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_PHYLIP -o /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/protpars protpars.o seq.o phylip.o -lm -lc >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -Wl,-O1 -Wl,--as-needed -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_PHYLIP -o /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/restdist restdist.o seq.o phylip.o -lm -lc >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -Wl,-O1 -Wl,--as-needed -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_PHYLIP -o /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/restml restml.o seq.o phylip.o -lm -lc >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -Wl,-O1 -Wl,--as-needed -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_PHYLIP -o /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/retree retree.o moves.o phylip.o -lm -lc >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -Wl,-O1 -Wl,--as-needed -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_PHYLIP -o /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/seqboot seqboot.o seq.o phylip.o -lm -lc >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -Wl,-O1 -Wl,--as-needed -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_PHYLIP -o /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/treedist treedist.o phylip.o cons.o -lm -lc >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -Wl,-O1 -Wl,--as-needed -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_PHYLIP -o /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/drawgram drawgram.o draw.o draw2.o phylip.o -lm -lc >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -Wl,-O1 -Wl,--as-needed -fmessage-length=0 -funit-at-a-time -fPIC -w -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_PHYLIP -o /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/drawtree drawtree.o draw.o draw2.o phylip.o -lm -lc >make[5]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDE/PHYLIP' >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDE' >----------------- warnings enabled again >make[3]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDE' >make[2]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3' >make binlink >make[2]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3' >make -C bin all >make[3]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin' >find . -type l -exec rm {} \; >ln -s -f `find ../SH ../PERL_SCRIPTS -perm -100 ! -type d ! -name 'config*' -print` . >make[3]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin' >make[2]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3' >make perl >make[2]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3' >-------------------------------------------------------------------------------- Make everything in ARBDBPP >make[3]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/ARBDBPP' >make[3]: 'libARBDBPP.a' is up to date. >make[3]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/ARBDBPP' >-------------------------------------------------------------------------------- Make everything in ARBDB >make[3]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/ARBDB' >make[3]: 'libARBDB.a' is up to date. >make[3]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/ARBDB' >-------------------------------------------------------------------------------- Make everything in SERVERCNTRL >make[3]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SERVERCNTRL' >make[3]: 'SERVERCNTRL.a' is up to date. >make[3]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SERVERCNTRL' >-------------------------------------------------------------------------------- Make everything in ARBDBS >make[3]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/ARBDBS' >make[3]: 'libARBDB.a' is up to date. >make[3]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/ARBDBS' >-------------------------------------------------------------------------------- Make everything in ARBDB2 >make[3]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/ARBDB2' >make[3]: 'libARBDB.a' is up to date. >make[3]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/ARBDB2' >-------------------------------------------------------------------------------- Make everything in WINDOW >make[3]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/WINDOW' >make[3]: 'libAW.a' is up to date. >make[3]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/WINDOW' >-------------------------------------------------------------------------------- Make everything in AWT >make[3]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/AWT' >make[3]: 'libAWT.a' is up to date. >make[3]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/AWT' >-------------------- Updating shared libraries >make libs >make[3]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3' >-------------------------------------------------------------------------------- Make everything in AISC_MKPTPS >make[3]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/AISC_MKPTPS' >make[3]: Nothing to be done for 'dummy.a'. >make[3]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/AISC_MKPTPS' >-------------------------------------------------------------------------------- Make everything in AISC >make[3]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/AISC' >make[3]: Nothing to be done for 'dummy.a'. >make[3]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/AISC' >-------------------------------------------------------------------------------- Make everything in PROBE_COM >make[3]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PROBE_COM' >make[3]: 'server.a' is up to date. >make[3]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PROBE_COM' >-------------------------------------------------------------------------------- Make everything in SL >make[3]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL' >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/TREE_READ' >make[4]: 'TREE_READ.a' is up to date. >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/TREE_READ' >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/HELIX' >make[4]: 'HELIX.a' is up to date. >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/HELIX' >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/AW_HELIX' >make[4]: 'AW_HELIX.a' is up to date. >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/AW_HELIX' >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/TREE_WRITE' >make[4]: 'TREE_WRITE.a' is up to date. >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/TREE_WRITE' >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/AW_NAME' >make[4]: 'AW_NAME.a' is up to date. >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/AW_NAME' >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/DB_SCANNER' >make[4]: 'DB_SCANNER.a' is up to date. >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/DB_SCANNER' >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/FILE_BUFFER' >make[4]: 'FILE_BUFFER.a' is up to date. >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/FILE_BUFFER' >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/REGEXPR' >make[4]: 'REGEXPR.a' is up to date. >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/REGEXPR' >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/FAST_ALIGNER' >make[4]: 'FAST_ALIGNER.a' is up to date. >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/FAST_ALIGNER' >make[3]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL' >make[3]: Nothing to be done for 'libs'. >make[3]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3' >-------------------------------------------------------------------------------- Make everything in TOOLS >make[3]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/TOOLS' >make[3]: Nothing to be done for 'all'. >make[3]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/TOOLS' >-------------------------------------------------------------------------------- Make everything in PERL2ARB >make[3]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PERL2ARB' >touch depends.stamp >test -f ARB.c || make -f Makefile.main "AUTODEPENDS=0" ARB.c >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PERL2ARB' >make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. >( PATH=/usr/arb/bin:/scratch/mmokrejs/gentoo_rap/usr/lib/portage/python2.7/ebuild-helpers/unprivileged:/scratch/mmokrejs/gentoo_rap/usr/lib/portage/python2.7/ebuild-helpers:/scratch/mmokrejs/gentoo_rap/usr/local/sbin:/scratch/mmokrejs/gentoo_rap/usr/local/bin:/scratch/mmokrejs/gentoo_rap/usr/sbin:/scratch/mmokrejs/gentoo_rap/usr/bin:/scratch/mmokrejs/gentoo_rap/sbin:/scratch/mmokrejs/gentoo_rap/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/scratch/mmokrejs/gentoo_rap/opt/bin:/scratch/mmokrejs/gentoo_rap/usr/x86_64-pc-linux-gnu/gcc-bin/5.4.0:/scratch/mmokrejs/gentoo_rap/opt/intel/compilers_and_libraries_2016.2.181/linux/bin/intel64:/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin; \ > export PATH; \ > echo calling perl LINUX.PL; \ > perl LINUX.PL ) >calling perl LINUX.PL >Warning: -L../ARBDB2 changed to -L/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PERL2ARB/../ARBDB2 >Generating a Unix-style Makefile >Writing Makefile for ARB >Writing MYMETA.yml and MYMETA.json >cat /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/ARBDB/ad_prot.h /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/ARBDB/ad_t_prot.h > proto.h >make[4]: [Makefile.main:82: ARB.xs] Error 1 (ignored) >LD_LIBRARY_PATH=/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/lib::/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/lib /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/arb_proto_2_xsub proto.h ARB.xs.default > ARB.xs >echo "#undef DEBUG" > debug.h >echo "#undef NDEBUG" >> debug.h >echo "#define NDEBUG" >> debug.h >cp -p LINUX.PL Makefile.PL >-------- calling MakeMaker-Makefile (to get depends) >( make "dflags=-DNDEBUG -DARB_64 -DLINUX " ARB.c || \ > (echo "------ failed.. retry once"; \ > make "dflags=-DNDEBUG -DARB_64 -DLINUX " ARB.c )) >make[5]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PERL2ARB' >"/scratch/mmokrejs/gentoo_rap/usr/bin/perl" "/scratch/mmokrejs/gentoo_rap/usr/lib64/perl5/5.24.0/ExtUtils/xsubpp" -typemap "/scratch/mmokrejs/gentoo_rap/usr/lib64/perl5/5.24.0/ExtUtils/typemap" -typemap "typemap" ARB.xs > ARB.xsc && mv ARB.xsc ARB.c >make[5]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PERL2ARB' >-------- end of MakeMaker-Makefile >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PERL2ARB' >umask 002;makedepend -f- -- -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -- -DARB_OPENGL -I. -Y/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE ARB.c 2>/dev/null | \ > perl -ne 's/ARB.o:/depends.stamp:/g; print $_;' | \ > ../SOURCE_TOOLS/fix_depends.pl > .depends >cp perlmain_source.c perlmain.c >cp ARB.pm /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/lib/ARB.pm >rm blib/arch/auto/ARB/ARB.so >rm: cannot remove 'blib/arch/auto/ARB/ARB.so': No such file or directory >make[3]: [Makefile.main:56: blib/arch/auto/ARB/ARB.so] Error 1 (ignored) >-------- calling MakeMaker-Makefile >( make "dflags=-DNDEBUG -DARB_64 -DLINUX -Wl,-O1 -Wl,--as-needed" blib/arch/auto/ARB/ARB.so || \ > (echo "------ failed.. retry once"; \ > make "dflags=-DNDEBUG -DARB_64 -DLINUX -Wl,-O1 -Wl,--as-needed" blib/arch/auto/ARB/ARB.so)) >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PERL2ARB' >"/scratch/mmokrejs/gentoo_rap/usr/bin/perl" "/scratch/mmokrejs/gentoo_rap/usr/lib64/perl5/5.24.0/ExtUtils/xsubpp" -typemap "/scratch/mmokrejs/gentoo_rap/usr/lib64/perl5/5.24.0/ExtUtils/typemap" -typemap "typemap" ARB.xs > ARB.xsc && mv ARB.xsc ARB.c >x86_64-pc-linux-gnu-gcc -c -I../INCLUDE -D_REENTRANT -D_GNU_SOURCE -fwrapv -fno-strict-aliasing -pipe -I/scratch/mmokrejs/gentoo_rap/usr/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -O2 -pipe -march=native -DVERSION=\"0.01\" -DXS_VERSION=\"0.01\" -fPIC "-I/scratch/mmokrejs/gentoo_rap/usr/lib64/perl5/5.24.0/x86_64-linux-thread-multi/CORE" ARB.c >[01m[KARB.xs:[m[K In function '[01m[KXS_ARB_get_error[m[K': >[01m[KARB.xs:244:4:[m[K [01;35m[Kwarning: [m[K'[01m[KGB_get_error[m[K' is deprecated [-Wdeprecated-declarations] > RETVAL = (char *)GB_get_error(); >[01;32m[K ^[m[K >In file included from [01m[K../INCLUDE/arbdb.h:268:0[m[K, > from [01m[KARB.xs:16[m[K: >[01m[K../INCLUDE/ad_prot.h:43:10:[m[K [01;36m[Knote: [m[Kdeclared here > GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; >[01;32m[K ^[m[K >rm -f blib/arch/auto/ARB/ARB.so >x86_64-pc-linux-gnu-gcc -shared -O2 -pipe -O2 -pipe -march=native -Wl,-O1 -Wl,--as-needed ARB.o -o blib/arch/auto/ARB/ARB.so \ > -L/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PERL2ARB/../ARBDB2 -lARBDB \ > >chmod 755 blib/arch/auto/ARB/ARB.so >"/scratch/mmokrejs/gentoo_rap/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- ARB.bs blib/arch/auto/ARB/ARB.bs 644 >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PERL2ARB' >-------- post-recreating .depends >make -f Makefile.main "DEPENDS=0" .depends >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PERL2ARB' >make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. >make[4]: '.depends' is up to date. >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PERL2ARB' >make -f Makefile.main blib/arch/auto/ARB/ARB.so # recurse >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PERL2ARB' >make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. >make[4]: 'blib/arch/auto/ARB/ARB.so' is up to date. >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PERL2ARB' >cp blib/arch/auto/ARB/ARB.so /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/lib/ARB.so >make[3]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PERL2ARB' >make[3]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3' >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PERL_SCRIPTS/test' >-------------------------------------------------------------------------------- Testing scripts in PERL_SCRIPTS >testScripts.pl syntax OK >Testing SAI.pm OK FAILED >(eval 2):18: Can't locate B/LintSubs.pm in @INC (you may need to install the B::LintSubs module) (@INC contains: /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/lib /etc/perl /scratch/mmokrejs/gentoo_rap/usr/local/lib64/perl5/5.24.0/x86_64-linux-thread-multi /scratch/mmokrejs/gentoo_rap/usr/local/lib64/perl5/5.24.0 /scratch/mmokrejs/gentoo_rap/usr/lib64/perl5/vendor_perl/5.24.0/x86_64-linux-thread-multi /scratch/mmokrejs/gentoo_rap/usr/lib64/perl5/vendor_perl/5.24.0 /scratch/mmokrejs/gentoo_rap/usr/lib64/perl5/5.24.0/x86_64-linux-thread-multi /scratch/mmokrejs/gentoo_rap/usr/lib64/perl5/5.24.0 .). >(eval 2):18: BEGIN failed--compilation aborted. >BEGIN failed--compilation aborted. >Testing GI.pm OK FAILED >(eval 2):18: Can't locate B/LintSubs.pm in @INC (you may need to install the B::LintSubs module) (@INC contains: /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/lib /etc/perl /scratch/mmokrejs/gentoo_rap/usr/local/lib64/perl5/5.24.0/x86_64-linux-thread-multi /scratch/mmokrejs/gentoo_rap/usr/local/lib64/perl5/5.24.0 /scratch/mmokrejs/gentoo_rap/usr/lib64/perl5/vendor_perl/5.24.0/x86_64-linux-thread-multi /scratch/mmokrejs/gentoo_rap/usr/lib64/perl5/vendor_perl/5.24.0 /scratch/mmokrejs/gentoo_rap/usr/lib64/perl5/5.24.0/x86_64-linux-thread-multi /scratch/mmokrejs/gentoo_rap/usr/lib64/perl5/5.24.0 .). >(eval 2):18: BEGIN failed--compilation aborted. >BEGIN failed--compilation aborted. >Testing tools.pm OK FAILED >(eval 2):18: Can't locate B/LintSubs.pm in @INC (you may need to install the B::LintSubs module) (@INC contains: /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/lib /etc/perl /scratch/mmokrejs/gentoo_rap/usr/local/lib64/perl5/5.24.0/x86_64-linux-thread-multi /scratch/mmokrejs/gentoo_rap/usr/local/lib64/perl5/5.24.0 /scratch/mmokrejs/gentoo_rap/usr/lib64/perl5/vendor_perl/5.24.0/x86_64-linux-thread-multi /scratch/mmokrejs/gentoo_rap/usr/lib64/perl5/vendor_perl/5.24.0 /scratch/mmokrejs/gentoo_rap/usr/lib64/perl5/5.24.0/x86_64-linux-thread-multi /scratch/mmokrejs/gentoo_rap/usr/lib64/perl5/5.24.0 .). >(eval 2):18: BEGIN failed--compilation aborted. >BEGIN failed--compilation aborted. >Testing beautifyNewick.pl OK FAILED >(eval 2):18: Can't locate B/LintSubs.pm in @INC (you may need to install the B::LintSubs module) (@INC contains: /etc/perl /scratch/mmokrejs/gentoo_rap/usr/local/lib64/perl5/5.24.0/x86_64-linux-thread-multi /scratch/mmokrejs/gentoo_rap/usr/local/lib64/perl5/5.24.0 /scratch/mmokrejs/gentoo_rap/usr/lib64/perl5/vendor_perl/5.24.0/x86_64-linux-thread-multi /scratch/mmokrejs/gentoo_rap/usr/lib64/perl5/vendor_perl/5.24.0 /scratch/mmokrejs/gentoo_rap/usr/lib64/perl5/5.24.0/x86_64-linux-thread-multi /scratch/mmokrejs/gentoo_rap/usr/lib64/perl5/5.24.0 .). >(eval 2):18: BEGIN failed--compilation aborted. >BEGIN failed--compilation aborted. >Testing listDiff.pl OK FAILED >(eval 2):18: Can't locate B/LintSubs.pm in @INC (you may need to install the B::LintSubs module) (@INC contains: /etc/perl /scratch/mmokrejs/gentoo_rap/usr/local/lib64/perl5/5.24.0/x86_64-linux-thread-multi /scratch/mmokrejs/gentoo_rap/usr/local/lib64/perl5/5.24.0 /scratch/mmokrejs/gentoo_rap/usr/lib64/perl5/vendor_perl/5.24.0/x86_64-linux-thread-multi /scratch/mmokrejs/gentoo_rap/usr/lib64/perl5/vendor_perl/5.24.0 /scratch/mmokrejs/gentoo_rap/usr/lib64/perl5/5.24.0/x86_64-linux-thread-multi /scratch/mmokrejs/gentoo_rap/usr/lib64/perl5/5.24.0 .). >(eval 2):18: BEGIN failed--compilation aborted. >BEGIN failed--compilation aborted. >Testing SAI_demo.pl OK FAILED >(eval 2):18: Can't locate B/LintSubs.pm in @INC (you may need to install the B::LintSubs module) (@INC contains: /etc/perl /scratch/mmokrejs/gentoo_rap/usr/local/lib64/perl5/5.24.0/x86_64-linux-thread-multi /scratch/mmokrejs/gentoo_rap/usr/local/lib64/perl5/5.24.0 /scratch/mmokrejs/gentoo_rap/usr/lib64/perl5/vendor_perl/5.24.0/x86_64-linux-thread-multi /scratch/mmokrejs/gentoo_rap/usr/lib64/perl5/vendor_perl/5.24.0 /scratch/mmokrejs/gentoo_rap/usr/lib64/perl5/5.24.0/x86_64-linux-thread-multi /scratch/mmokrejs/gentoo_rap/usr/lib64/perl5/5.24.0 .). >(eval 2):18: BEGIN failed--compilation aborted. >BEGIN failed--compilation aborted. >Testing import_proteomdata.pl OK FAILED >(eval 2):18: Can't locate B/LintSubs.pm in @INC (you may need to install the B::LintSubs module) (@INC contains: /etc/perl /scratch/mmokrejs/gentoo_rap/usr/local/lib64/perl5/5.24.0/x86_64-linux-thread-multi /scratch/mmokrejs/gentoo_rap/usr/local/lib64/perl5/5.24.0 /scratch/mmokrejs/gentoo_rap/usr/lib64/perl5/vendor_perl/5.24.0/x86_64-linux-thread-multi /scratch/mmokrejs/gentoo_rap/usr/lib64/perl5/vendor_perl/5.24.0 /scratch/mmokrejs/gentoo_rap/usr/lib64/perl5/5.24.0/x86_64-linux-thread-multi /scratch/mmokrejs/gentoo_rap/usr/lib64/perl5/5.24.0 .). >(eval 2):18: BEGIN failed--compilation aborted. >BEGIN failed--compilation aborted. >Testing testScripts.pl OK FAILED >(eval 2):18: Can't locate B/LintSubs.pm in @INC (you may need to install the B::LintSubs module) (@INC contains: /etc/perl /scratch/mmokrejs/gentoo_rap/usr/local/lib64/perl5/5.24.0/x86_64-linux-thread-multi /scratch/mmokrejs/gentoo_rap/usr/local/lib64/perl5/5.24.0 /scratch/mmokrejs/gentoo_rap/usr/lib64/perl5/vendor_perl/5.24.0/x86_64-linux-thread-multi /scratch/mmokrejs/gentoo_rap/usr/lib64/perl5/vendor_perl/5.24.0 /scratch/mmokrejs/gentoo_rap/usr/lib64/perl5/5.24.0/x86_64-linux-thread-multi /scratch/mmokrejs/gentoo_rap/usr/lib64/perl5/5.24.0 .). >(eval 2):18: BEGIN failed--compilation aborted. >BEGIN failed--compilation aborted. >Testing raxml2arb.pl OK FAILED >(eval 2):18: Can't locate B/LintSubs.pm in @INC (you may need to install the B::LintSubs module) (@INC contains: /etc/perl /scratch/mmokrejs/gentoo_rap/usr/local/lib64/perl5/5.24.0/x86_64-linux-thread-multi /scratch/mmokrejs/gentoo_rap/usr/local/lib64/perl5/5.24.0 /scratch/mmokrejs/gentoo_rap/usr/lib64/perl5/vendor_perl/5.24.0/x86_64-linux-thread-multi /scratch/mmokrejs/gentoo_rap/usr/lib64/perl5/vendor_perl/5.24.0 /scratch/mmokrejs/gentoo_rap/usr/lib64/perl5/5.24.0/x86_64-linux-thread-multi /scratch/mmokrejs/gentoo_rap/usr/lib64/perl5/5.24.0 .). >(eval 2):18: BEGIN failed--compilation aborted. >BEGIN failed--compilation aborted. >Testing format_dssp.pl OK FAILED >(eval 2):18: Can't locate B/LintSubs.pm in @INC (you may need to install the B::LintSubs module) (@INC contains: /etc/perl /scratch/mmokrejs/gentoo_rap/usr/local/lib64/perl5/5.24.0/x86_64-linux-thread-multi /scratch/mmokrejs/gentoo_rap/usr/local/lib64/perl5/5.24.0 /scratch/mmokrejs/gentoo_rap/usr/lib64/perl5/vendor_perl/5.24.0/x86_64-linux-thread-multi /scratch/mmokrejs/gentoo_rap/usr/lib64/perl5/vendor_perl/5.24.0 /scratch/mmokrejs/gentoo_rap/usr/lib64/perl5/5.24.0/x86_64-linux-thread-multi /scratch/mmokrejs/gentoo_rap/usr/lib64/perl5/5.24.0 .). >(eval 2):18: BEGIN failed--compilation aborted. >BEGIN failed--compilation aborted. >Testing genbank_gen_long_features.pl OK FAILED >(eval 2):18: Can't locate B/LintSubs.pm in @INC (you may need to install the B::LintSubs module) (@INC contains: /etc/perl /scratch/mmokrejs/gentoo_rap/usr/local/lib64/perl5/5.24.0/x86_64-linux-thread-multi /scratch/mmokrejs/gentoo_rap/usr/local/lib64/perl5/5.24.0 /scratch/mmokrejs/gentoo_rap/usr/lib64/perl5/vendor_perl/5.24.0/x86_64-linux-thread-multi /scratch/mmokrejs/gentoo_rap/usr/lib64/perl5/vendor_perl/5.24.0 /scratch/mmokrejs/gentoo_rap/usr/lib64/perl5/5.24.0/x86_64-linux-thread-multi /scratch/mmokrejs/gentoo_rap/usr/lib64/perl5/5.24.0 .). >(eval 2):18: BEGIN failed--compilation aborted. >BEGIN failed--compilation aborted. >Testing embl_gen_long_features.pl OK FAILED >(eval 2):18: Can't locate B/LintSubs.pm in @INC (you may need to install the B::LintSubs module) (@INC contains: /etc/perl /scratch/mmokrejs/gentoo_rap/usr/local/lib64/perl5/5.24.0/x86_64-linux-thread-multi /scratch/mmokrejs/gentoo_rap/usr/local/lib64/perl5/5.24.0 /scratch/mmokrejs/gentoo_rap/usr/lib64/perl5/vendor_perl/5.24.0/x86_64-linux-thread-multi /scratch/mmokrejs/gentoo_rap/usr/lib64/perl5/vendor_perl/5.24.0 /scratch/mmokrejs/gentoo_rap/usr/lib64/perl5/5.24.0/x86_64-linux-thread-multi /scratch/mmokrejs/gentoo_rap/usr/lib64/perl5/5.24.0 .). >(eval 2):18: BEGIN failed--compilation aborted. >BEGIN failed--compilation aborted. >Testing listMarkedSpecies.pl OK FAILED >(eval 2):18: Can't locate B/LintSubs.pm in @INC (you may need to install the B::LintSubs module) (@INC contains: /etc/perl /scratch/mmokrejs/gentoo_rap/usr/local/lib64/perl5/5.24.0/x86_64-linux-thread-multi /scratch/mmokrejs/gentoo_rap/usr/local/lib64/perl5/5.24.0 /scratch/mmokrejs/gentoo_rap/usr/lib64/perl5/vendor_perl/5.24.0/x86_64-linux-thread-multi /scratch/mmokrejs/gentoo_rap/usr/lib64/perl5/vendor_perl/5.24.0 /scratch/mmokrejs/gentoo_rap/usr/lib64/perl5/5.24.0/x86_64-linux-thread-multi /scratch/mmokrejs/gentoo_rap/usr/lib64/perl5/5.24.0 .). >(eval 2):18: BEGIN failed--compilation aborted. >BEGIN failed--compilation aborted. >Testing markSpecies.pl OK FAILED >(eval 2):18: Can't locate B/LintSubs.pm in @INC (you may need to install the B::LintSubs module) (@INC contains: /etc/perl /scratch/mmokrejs/gentoo_rap/usr/local/lib64/perl5/5.24.0/x86_64-linux-thread-multi /scratch/mmokrejs/gentoo_rap/usr/local/lib64/perl5/5.24.0 /scratch/mmokrejs/gentoo_rap/usr/lib64/perl5/vendor_perl/5.24.0/x86_64-linux-thread-multi /scratch/mmokrejs/gentoo_rap/usr/lib64/perl5/vendor_perl/5.24.0 /scratch/mmokrejs/gentoo_rap/usr/lib64/perl5/5.24.0/x86_64-linux-thread-multi /scratch/mmokrejs/gentoo_rap/usr/lib64/perl5/5.24.0 .). >(eval 2):18: BEGIN failed--compilation aborted. >BEGIN failed--compilation aborted. >Testing test.amc OK FAILED >(eval 2):18: Can't locate B/LintSubs.pm in @INC (you may need to install the B::LintSubs module) (@INC contains: /etc/perl /scratch/mmokrejs/gentoo_rap/usr/local/lib64/perl5/5.24.0/x86_64-linux-thread-multi /scratch/mmokrejs/gentoo_rap/usr/local/lib64/perl5/5.24.0 /scratch/mmokrejs/gentoo_rap/usr/lib64/perl5/vendor_perl/5.24.0/x86_64-linux-thread-multi /scratch/mmokrejs/gentoo_rap/usr/lib64/perl5/vendor_perl/5.24.0 /scratch/mmokrejs/gentoo_rap/usr/lib64/perl5/5.24.0/x86_64-linux-thread-multi /scratch/mmokrejs/gentoo_rap/usr/lib64/perl5/5.24.0 .). >(eval 2):18: BEGIN failed--compilation aborted. >BEGIN failed--compilation aborted. >Testing replamb.amc OK FAILED >(eval 2):18: Can't locate B/LintSubs.pm in @INC (you may need to install the B::LintSubs module) (@INC contains: /etc/perl /scratch/mmokrejs/gentoo_rap/usr/local/lib64/perl5/5.24.0/x86_64-linux-thread-multi /scratch/mmokrejs/gentoo_rap/usr/local/lib64/perl5/5.24.0 /scratch/mmokrejs/gentoo_rap/usr/lib64/perl5/vendor_perl/5.24.0/x86_64-linux-thread-multi /scratch/mmokrejs/gentoo_rap/usr/lib64/perl5/vendor_perl/5.24.0 /scratch/mmokrejs/gentoo_rap/usr/lib64/perl5/5.24.0/x86_64-linux-thread-multi /scratch/mmokrejs/gentoo_rap/usr/lib64/perl5/5.24.0 .). >(eval 2):18: BEGIN failed--compilation aborted. >BEGIN failed--compilation aborted. >Testing xopen.amc OK FAILED >(eval 2):18: Can't locate B/LintSubs.pm in @INC (you may need to install the B::LintSubs module) (@INC contains: /etc/perl /scratch/mmokrejs/gentoo_rap/usr/local/lib64/perl5/5.24.0/x86_64-linux-thread-multi /scratch/mmokrejs/gentoo_rap/usr/local/lib64/perl5/5.24.0 /scratch/mmokrejs/gentoo_rap/usr/lib64/perl5/vendor_perl/5.24.0/x86_64-linux-thread-multi /scratch/mmokrejs/gentoo_rap/usr/lib64/perl5/vendor_perl/5.24.0 /scratch/mmokrejs/gentoo_rap/usr/lib64/perl5/5.24.0/x86_64-linux-thread-multi /scratch/mmokrejs/gentoo_rap/usr/lib64/perl5/5.24.0 .). >(eval 2):18: BEGIN failed--compilation aborted. >BEGIN failed--compilation aborted. >Testing testwl.amc OK FAILED >(eval 2):18: Can't locate B/LintSubs.pm in @INC (you may need to install the B::LintSubs module) (@INC contains: /etc/perl /scratch/mmokrejs/gentoo_rap/usr/local/lib64/perl5/5.24.0/x86_64-linux-thread-multi /scratch/mmokrejs/gentoo_rap/usr/local/lib64/perl5/5.24.0 /scratch/mmokrejs/gentoo_rap/usr/lib64/perl5/vendor_perl/5.24.0/x86_64-linux-thread-multi /scratch/mmokrejs/gentoo_rap/usr/lib64/perl5/vendor_perl/5.24.0 /scratch/mmokrejs/gentoo_rap/usr/lib64/perl5/5.24.0/x86_64-linux-thread-multi /scratch/mmokrejs/gentoo_rap/usr/lib64/perl5/5.24.0 .). >(eval 2):18: BEGIN failed--compilation aborted. >BEGIN failed--compilation aborted. >Testing toggle_color.amc OK FAILED >(eval 2):18: Can't locate B/LintSubs.pm in @INC (you may need to install the B::LintSubs module) (@INC contains: /etc/perl /scratch/mmokrejs/gentoo_rap/usr/local/lib64/perl5/5.24.0/x86_64-linux-thread-multi /scratch/mmokrejs/gentoo_rap/usr/local/lib64/perl5/5.24.0 /scratch/mmokrejs/gentoo_rap/usr/lib64/perl5/vendor_perl/5.24.0/x86_64-linux-thread-multi /scratch/mmokrejs/gentoo_rap/usr/lib64/perl5/vendor_perl/5.24.0 /scratch/mmokrejs/gentoo_rap/usr/lib64/perl5/5.24.0/x86_64-linux-thread-multi /scratch/mmokrejs/gentoo_rap/usr/lib64/perl5/5.24.0 .). >(eval 2):18: BEGIN failed--compilation aborted. >BEGIN failed--compilation aborted. >Testing dashes2dots_at_sequenceends_of_marked.amc OK FAILED >(eval 2):18: Can't locate B/LintSubs.pm in @INC (you may need to install the B::LintSubs module) (@INC contains: /etc/perl /scratch/mmokrejs/gentoo_rap/usr/local/lib64/perl5/5.24.0/x86_64-linux-thread-multi /scratch/mmokrejs/gentoo_rap/usr/local/lib64/perl5/5.24.0 /scratch/mmokrejs/gentoo_rap/usr/lib64/perl5/vendor_perl/5.24.0/x86_64-linux-thread-multi /scratch/mmokrejs/gentoo_rap/usr/lib64/perl5/vendor_perl/5.24.0 /scratch/mmokrejs/gentoo_rap/usr/lib64/perl5/5.24.0/x86_64-linux-thread-multi /scratch/mmokrejs/gentoo_rap/usr/lib64/perl5/5.24.0 .). >(eval 2):18: BEGIN failed--compilation aborted. >BEGIN failed--compilation aborted. >20 perl scripts failed to compile >You either lack S::LintSubs and/or Bio::TreeIO or the perl scripts are buggy. We continue anyway.. >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PERL_SCRIPTS/test' >make[3]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3' >make[2]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3' >make tryxtras >make[2]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3' >-------------------------------------------------------------------------------- >make[3]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3' >-------------------------------------------------------------------------------- Make everything in SL/HELIX >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/HELIX' >make[4]: 'HELIX.a' is up to date. >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/HELIX' >-------------------------------------------------------------------------------- Make everything in ARBDBPP >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/ARBDBPP' >make[4]: 'libARBDBPP.a' is up to date. >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/ARBDBPP' >-------------------------------------------------------------------------------- Make everything in ARBDB >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/ARBDB' >make[4]: 'libARBDB.a' is up to date. >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/ARBDB' >-------------------------------------------------------------------------------- Make everything in ARBDBS >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/ARBDBS' >make[4]: 'libARBDB.a' is up to date. >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/ARBDBS' >-------------------------------------------------------------------------------- Make everything in ARBDB2 >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/ARBDB2' >make[4]: 'libARBDB.a' is up to date. >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/ARBDB2' >-------------------------------------------------------------------------------- Make everything in WINDOW >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/WINDOW' >make[4]: 'libAW.a' is up to date. >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/WINDOW' >-------------------------------------------------------------------------------- Make everything in AWT >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/AWT' >make[4]: 'libAWT.a' is up to date. >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/AWT' >-------------------------------------------------------------------------------- Make everything in XML_IMPORT >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/XML_IMPORT' >Makefile:19: XML_IMPORT compile broken atm >true >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/XML_IMPORT' >-------------------- Updating shared libraries >make libs >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3' >make[4]: Nothing to be done for 'libs'. >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3' >-------------------------------------------------------------------------------- Make everything in TREEGEN >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/TREEGEN' >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_TREEGEN -c base.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_TREEGEN -c defines.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_TREEGEN -c frand.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_TREEGEN -c readcfg.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_TREEGEN -c rns.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >rns.c: In function 'calcMutationMatrix': >rns.c:367:66: warning: unused parameter 'muteRate' [-Wunused-parameter] > static void calcMutationMatrix(DoubleProb mutationMatrix, double muteRate, double gcDruck, double gcRate, double atRate, double *pairProb) > ^ >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_TREEGEN -c sim.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_TREEGEN -c simcfg.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_TREEGEN -c spreadin.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >ld -r -o TREEGEN.a base.o defines.o frand.o readcfg.o rns.o sim.o simcfg.o spreadin.o >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/TREEGEN' >-------------------- Checking bin/arb_treegen >Target 'bin/arb_treegen' not found >-> rebuilding bin/arb_treegen (Thu Jan 1 00:59:59 1970) >Link bin/arb_treegen >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -Wl,-O1 -Wl,--as-needed -Wl,--export-dynamic -rdynamic -o bin/arb_treegen -L/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/LIBLINK TREEGEN/TREEGEN.a >-------------------------------------------------------------------------------- Make everything in ALIV3 >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/ALIV3' >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ALIV3 -c a3.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ALIV3 -c a3_seq.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >a3_seq.cxx: In function 'char* CompressSequence(str, UINT)': >a3_seq.cxx:85:21: warning: case label value is less than minimum value for type > case INSERT: break; // Insertionen werden uebersprungen > ^ >a3_seq.cxx:86:21: warning: case label value is less than minimum value for type > case INVALID: > ^ >a3.cxx:32:20: warning: 'DArray* ReadMatches(str)' defined but not used [-Wunused-function] > static DArray *ReadMatches ( str file ) > ^ >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ALIV3 -c a3_ptree1.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ALIV3 -c a3_ptree2.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ALIV3 -c a3_helix.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ALIV3 -c a3_darray.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ALIV3 -c a3_ali.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ALIV3 -c a3_matrix.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >a3_helix.cxx: In function 'int FindHelices(str, int, int, A3Matrix&)': >a3_helix.cxx:67:80: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] > if (last < 0) last = mark.Add((vp)pos); > ^ >a3_helix.cxx:68:81: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] > else if ((back - (long)mark[last]) > 1) last = mark.Add((vp)pos); > ^ >a3_helix.cxx:103:92: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] > if (last < 0) last = mark.Add((vp)pos); > ^ >a3_helix.cxx:104:93: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] > else if ((back - (long)mark[last]) > 1) last = mark.Add((vp)pos); > ^ >a3_helix.cxx: At global scope: >a3_helix.cxx:303:36: warning: unused parameter 'minlen' [-Wunused-parameter] > int minlen ) > ^ >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ALIV3 -c a3_arbdb.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >a3_darray.cxx: In member function 'int DArray::Del(int)': >a3_darray.cxx:155:53: warning: deleting 'vp {aka void*}' is undefined [-Wdelete-incomplete] > if (free && array[index]) delete array[index]; > ^ >a3_darray.cxx: In member function 'void DArray::Sort(cmpfunc)': >a3_darray.cxx:204:13: warning: unused variable 'count' [-Wunused-variable] > int count = 0, > ^ >a3_darray.cxx: In member function 'void DArray::Clear()': >a3_darray.cxx:254:61: warning: deleting 'vp {aka void*}' is undefined [-Wdelete-incomplete] > while (count--) if (array[count]) delete array[count]; > ^ >a3_ali.cxx:69:33: warning: unused parameter 'hel' [-Wunused-parameter] > str hel, > ^ >a3_ali.cxx:70:33: warning: unused parameter 'kon' [-Wunused-parameter] > str kon, > ^ >a3_matrix.cxx: In member function 'int A3Matrix::Set(int, int, vp)': >a3_matrix.cxx:78:47: warning: deleting 'vp {aka void*}' is undefined [-Wdelete-incomplete] > if (free && matrix[p]) delete matrix[p]; > ^ >a3_matrix.cxx: In member function 'void A3Matrix::Clear()': >a3_matrix.cxx:121:51: warning: deleting 'vp {aka void*}' is undefined [-Wdelete-incomplete] > if (free && matrix[p]) delete matrix[p]; > ^ >x86_64-pc-linux-gnu-gcc -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ALIV3 -c a3_basen.c -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >ld -r -o ALIV3.a a3.o a3_seq.o a3_ptree1.o a3_ptree2.o a3_helix.o a3_darray.o a3_ali.o a3_matrix.o a3_arbdb.o a3_basen.o >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/ALIV3' >-------------------------------------------------------------------------------- Link bin/aliv3 >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -Wl,-O1 -Wl,--as-needed -Wl,--export-dynamic -rdynamic -o bin/aliv3 -L/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/LIBLINK ALIV3/ALIV3.a SL/HELIX/HELIX.a -lARBDB -lm >-------------------------------------------------------------------------------- Make everything in PROBE_SET >make[4]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PROBE_SET' >mkdir -p bin >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PROBE_SET -c -o ps_node.o ps_node.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PROBE_SET -c -o ps_filebuffer.o ps_filebuffer.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PROBE_SET -c -o ps_database.o ps_database.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PROBE_SET -c -o ps_tools.o ps_tools.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PROBE_SET -c -o ps_show_result.o ps_show_result.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PROBE_SET -c -o ps_arb2asciipaths.o ps_arb2asciipaths.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PROBE_SET -c -o ps_my2asciipaths.o ps_my2asciipaths.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PROBE_SET -c -o ps_my2ascii.o ps_my2ascii.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PROBE_SET -c -o ps_get_probes.o ps_get_probes.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PROBE_SET -c -o ps_eval_candidates.o ps_eval_candidates.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PROBE_SET -c -o ps_find_probes.o ps_find_probes.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PROBE_SET -c -o ps_detect_weak_differences.o ps_detect_weak_differences.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PROBE_SET -c -o ps_merge_my_dbs.o ps_merge_my_dbs.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PROBE_SET -c -o ps_convert_db.o ps_convert_db.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PROBE_SET -c -o fb_test.o fb_test.cxx -I. -I/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -Wl,-O1 -Wl,--as-needed -Wl,--export-dynamic -rdynamic -o /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PROBE_SET/bin/ps_arb2asciipaths ps_node.o ps_filebuffer.o ps_database.o ps_tools.o ps_arb2asciipaths.o -L/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/LIBLINK -lARBDB -lm >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -Wl,-O1 -Wl,--as-needed -Wl,--export-dynamic -rdynamic -o /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PROBE_SET/bin/ps_my2asciipaths ps_node.o ps_filebuffer.o ps_database.o ps_tools.o ps_my2asciipaths.o -L/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/LIBLINK -lARBDB -lm >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -Wl,-O1 -Wl,--as-needed -Wl,--export-dynamic -rdynamic -o /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PROBE_SET/bin/ps_my2ascii ps_node.o ps_filebuffer.o ps_database.o ps_tools.o ps_my2ascii.o -L/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/LIBLINK -lARBDB -lm >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -Wl,-O1 -Wl,--as-needed -Wl,--export-dynamic -rdynamic -o /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PROBE_SET/bin/ps_get_probes ps_node.o ps_filebuffer.o ps_database.o ps_tools.o ps_get_probes.o -L/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/LIBLINK -lARBDB -lm >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -Wl,-O1 -Wl,--as-needed -Wl,--export-dynamic -rdynamic -o /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PROBE_SET/bin/ps_merge ps_node.o ps_filebuffer.o ps_database.o ps_tools.o ps_merge_my_dbs.o -L/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/LIBLINK -lARBDB -lm >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -Wl,-O1 -Wl,--as-needed -Wl,--export-dynamic -rdynamic -o /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PROBE_SET/bin/ps_show_result ps_node.o ps_filebuffer.o ps_database.o ps_tools.o ps_show_result.o -L/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/LIBLINK -lARBDB -lm >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -Wl,-O1 -Wl,--as-needed -Wl,--export-dynamic -rdynamic -o /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PROBE_SET/bin/fb_test ps_node.o ps_filebuffer.o ps_database.o ps_tools.o fb_test.o -L/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/LIBLINK -lARBDB -lm >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -Wl,-O1 -Wl,--as-needed -Wl,--export-dynamic -rdynamic -o /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PROBE_SET/bin/ps_convert ps_node.o ps_filebuffer.o ps_database.o ps_tools.o ps_convert_db.o -L/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/LIBLINK -lARBDB -lm >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -Wl,-O1 -Wl,--as-needed -Wl,--export-dynamic -rdynamic -o /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PROBE_SET/bin/ps_detect ps_node.o ps_filebuffer.o ps_database.o ps_tools.o ps_detect_weak_differences.o -L/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/LIBLINK -lARBDB -lm >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -Wl,-O1 -Wl,--as-needed -Wl,--export-dynamic -rdynamic -o /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PROBE_SET/bin/ps_eval ps_node.o ps_filebuffer.o ps_database.o ps_tools.o ps_eval_candidates.o -L/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/LIBLINK -lARBDB -lm >x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native -Wl,-O1 -Wl,--as-needed -Wl,--export-dynamic -rdynamic -o /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PROBE_SET/bin/ps_find ps_node.o ps_filebuffer.o ps_database.o ps_tools.o ps_find_probes.o -L/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/LIBLINK -lARBDB -lm >make[4]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PROBE_SET' >make[3]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3' >make[2]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3' >-------------------------------------------------------------------------------- >made 'all' with success. >to start arb enter 'arb' >make[1]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3' >make addlibs >make[1]: Entering directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3' >(perl /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SOURCE_TOOLS/provide_libs.pl \ > "arbhome=/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3" \ > "opengl=0" \ > "link_static=0" \ >) >Updating additional libs >make[1]: Leaving directory '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3' >util/arb_compress >find: 'Xlib': No such file or directory >demo.arb >arb_install.sh >arb_CHANGES.txt >arb_DEBUG.txt >arb_INSTALL.txt >arb_LICENSE.txt >arb_OS_X.txt >arb_OS_X_MacPorts.txt >arb_README.txt >arb_UBUNTU.txt >bin/arb_clean >bin/listDiff.pl >bin/retree >bin/format_dssp.pl >bin/arb_dnapars >bin/count >bin/Zuk_to_gen >bin/clustalv >bin/sho_helix >bin/dnaml >bin/fastdnaml >bin/arb_ntree >bin/arb_primer >bin/consense >bin/dolpenny >bin/arb_dist >bin/arb_sleep >bin/arb_2_ascii >bin/dszmconnect.pl >bin/arb_a2ps >bin/mix >bin/arb_textprint >bin/dolmove >bin/listMarkedSpecies.pl >bin/arb_message >bin/penny >bin/arb_protpars >bin/dnacomp >bin/arb_export_tree >bin/arb_convert_aln >bin/arb_wait >bin/arb_readseq >bin/genbank_gen_long_features.pl >bin/clustalw >bin/arb_pt_server >bin/arb_2_bin >bin/axml >bin/arb_proto_2_xsub >bin/findall >bin/arb_panic >bin/drawtree >bin/gendist >bin/seqboot >bin/dollop >bin/arb_ludwig >bin/arb_notify >bin/arb_echo >bin/arb_wetc >bin/raxml2arb.pl >bin/arb_trace >bin/arb_swap_rnastr >bin/treedist >bin/arb_proml >bin/SAI_demo.pl >bin/arb_probe >bin/move >bin/protdist >bin/arb_name_server >bin/beautifyNewick.pl >bin/dnapenny >bin/pars >bin/embl_gen_long_features.pl >bin/arb_bootstrap >bin/lsadt >bin/arb_db_server >bin/arb_count_chars >bin/restml >bin/arb_pars >bin/arb_read_tree >bin/clique >bin/arb_textedit >bin/varpos >bin/dnainvar >bin/contrast >bin/fitch >bin/neighbor >bin/dnadist >bin/kitsch >bin/protpars >bin/arb_naligner >bin/arb_phyml >bin/example_batch_probe_match.sh >bin/raxmlHPC >bin/import_proteomdata.pl >bin/arb_ign >bin/arb_installubuntu4arb.sh >bin/arb_fastdnaml >bin/puzzle >bin/arb_dnarates >bin/arb_raxml >bin/arb_pgt >bin/Restriction >bin/factor >bin/restdist >bin/arb_repair >bin/arb_phylo >bin/arb_who >bin/dnamlk >bin/promlk >bin/CAP2 >bin/arb_edit4 >bin/Makefile >bin/proml >bin/arb_gene_probe >bin/dnamove >bin/arb_edit >bin/drawgram >bin/arb >bin/aliv3 >bin/phyml >bin/arb_help2xml >bin/arb_replace >bin/arb_treegen >bin/markSpecies.pl >bin/dnapars >bin/arb_export_rates >bin/contml >bin/arb_remote >PERL_SCRIPTS/BIOPERL/README >PERL_SCRIPTS/BIOPERL/beautifyNewick.pl >PERL_SCRIPTS/GENERAL/listDiff.pl >PERL_SCRIPTS/SAI/SAI.pm >PERL_SCRIPTS/SAI/SAI_demo.pl >PERL_SCRIPTS/GENOME/import_proteomdata.pl >PERL_SCRIPTS/GENOME/GI.pm >PERL_SCRIPTS/test/testScripts.pl >PERL_SCRIPTS/test/Makefile >PERL_SCRIPTS/test/test.stamp >PERL_SCRIPTS/ARBTOOLS/raxml2arb.pl >PERL_SCRIPTS/ARBTOOLS/IFTHELP/format_dssp.pl >PERL_SCRIPTS/ARBTOOLS/IFTHELP/genbank_gen_long_features.pl >PERL_SCRIPTS/ARBTOOLS/IFTHELP/embl_gen_long_features.pl >PERL_SCRIPTS/SPECIES/listMarkedSpecies.pl >PERL_SCRIPTS/SPECIES/tools.pm >PERL_SCRIPTS/SPECIES/markSpecies.pl >SH/arb_clean >SH/arb_dnapars >SH/arb_sleep >SH/dszmconnect.pl >SH/arb_textprint >SH/arb_protpars >SH/arb_wait >SH/arb_panic >SH/arb_ludwig >SH/arb_echo >SH/README >SH/arb_trace >SH/arb_proml >SH/arb_bootstrap >SH/arb_textedit >SH/arb_phyml >SH/example_batch_probe_match.sh >SH/arb_ign >SH/arb_installubuntu4arb.sh >SH/arb_fastdnaml >SH/arb_raxml >SH/arb_repair >SH/arb_who >SH/arb >SH/arb_remote >GDEHELP/ARB_GDEmenus >GDEHELP/DATA_FILES/enzymes >lib/libARBDBPP.so >lib/ARB.so >lib/libARBDO.so >lib/ARB.pm >lib/macros/test.amc >lib/macros/replamb.amc >lib/macros/xopen.amc >lib/macros/ARB/SEQ_DATA/dashes2dots_at_sequenceends_of_marked.amc >lib/macros/testwl.amc >lib/macros/toggle_color.amc >lib/BUGS/known_bugs.txt >lib/pixmaps/logo.xpm >lib/pixmaps/redo.bitmap >lib/pixmaps/uncheck.xpm >lib/pixmaps/undo.bitmap >lib/pixmaps/print/landscape.bitmap >lib/pixmaps/print/clipscreen.bitmap >lib/pixmaps/print/portrait.bitmap >lib/pixmaps/print/nohandles.bitmap >lib/pixmaps/print/clipall.bitmap >lib/pixmaps/print/handles.bitmap >lib/pixmaps/lzoom.bitmap >lib/pixmaps/gen_map.xpm >lib/pixmaps/leftright.bitmap >lib/pixmaps/listdisp.bitmap >lib/pixmaps/gen_book.bitmap >lib/pixmaps/moveRight.bitmap >lib/pixmaps/edit/nokeymap.bitmap >lib/pixmaps/edit/r2l.bitmap >lib/pixmaps/edit/zoom.bitmap >lib/pixmaps/edit/kill.bitmap >lib/pixmaps/edit/nocons.bitmap >lib/pixmaps/edit/last.bitmap >lib/pixmaps/edit/3to5.bitmap >lib/pixmaps/edit/detail.bitmap >lib/pixmaps/edit/l2r.bitmap >lib/pixmaps/edit/arrow.bitmap >lib/pixmaps/edit/rna3d.xpm >lib/pixmaps/edit/keymap.bitmap >lib/pixmaps/edit/next.bitmap >lib/pixmaps/edit/secedit.xpm >lib/pixmaps/edit/mark.bitmap >lib/pixmaps/edit/editseq.xpm >lib/pixmaps/edit/cons.bitmap >lib/pixmaps/edit/align.xpm >lib/pixmaps/edit/norepeat.bitmap >lib/pixmaps/edit/5to3.bitmap >lib/pixmaps/edit/clear.bitmap >lib/pixmaps/edit/repeat.bitmap >lib/pixmaps/rectangle.bitmap >lib/pixmaps/check.xpm >lib/pixmaps/beautifyb.bitmap >lib/pixmaps/select.bitmap >lib/pixmaps/rot.bitmap >lib/pixmaps/close_text.xpm >lib/pixmaps/less.bitmap >lib/pixmaps/group.bitmap >lib/pixmaps/weighted2.bitmap >lib/pixmaps/bases.xpm >lib/pixmaps/sec_modify.bitmap >lib/pixmaps/rightleft_small.bitmap >lib/pixmaps/dendro.xpm >lib/pixmaps/mapping.xpm >lib/pixmaps/yes.bitmap >lib/pixmaps/dendroIrs.xpm >lib/pixmaps/closeText.xpm >lib/pixmaps/radial.xpm >lib/pixmaps/README >lib/pixmaps/spread.bitmap >lib/pixmaps/length.bitmap >lib/pixmaps/reset.bitmap >lib/pixmaps/list.bitmap >lib/pixmaps/moveDownAll.bitmap >lib/pixmaps/circle.bitmap >lib/pixmaps/polygon.bitmap >lib/pixmaps/moveAll.bitmap >lib/pixmaps/notEqual.xpm >lib/pixmaps/swap.bitmap >lib/pixmaps/colors.xpm >lib/pixmaps/optimize.bitmap >lib/pixmaps/basesText.xpm >lib/pixmaps/rightleft.bitmap >lib/pixmaps/mask.xpm >lib/pixmaps/conf_save.xpm >lib/pixmaps/stretch.bitmap >lib/pixmaps/colorMaps.xpm >lib/pixmaps/pgt/circle22.xpm >lib/pixmaps/pgt/exit.xpm >lib/pixmaps/pgt/markinvert22.xpm >lib/pixmaps/pgt/config.xpm >lib/pixmaps/pgt/markid22.xpm >lib/pixmaps/pgt/visualize.xpm >lib/pixmaps/pgt/textonly22.xpm >lib/pixmaps/pgt/msg.xpm >lib/pixmaps/pgt/mark2arb22.xpm >lib/pixmaps/pgt/marknone22.xpm >lib/pixmaps/pgt/help22.xpm >lib/pixmaps/pgt/info.xpm >lib/pixmaps/pgt/text22.xpm >lib/pixmaps/pgt/import.xpm 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>lib/help_html/sp_umrk_tree.html >lib/help_html/csp_2_gnuplot.html >lib/help_html/arb_gde.html >lib/help_html/mode_rotate.html >lib/help_html/sec_main.html >lib/Makefile >lib/dtd/arb_seq_export.dtd >lib/dtd/arb_tree.dtd >lib/nas/names.dat.template >lib/nas/Makefile >lib/LoVPBN.txt >lib/arb_tcp.dat >lib/GPL.txt >lib/LoVPBN.readme >-rw-r--r-- 1 mmokrejs mmokrejs 11624931 Nov 8 20:27 arb.tgz >>>> Source compiled. >>>> Test phase [not enabled]: sci-biology/arb-5.3 > >>>> Install arb-5.3 into /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/image/ category sci-biology > >******************************************* >Welcome to the ARB Package > >******************************************* > Note: - You may abort this script with ctrl-"C" > - You can rerun this script as often as you like > - Old ARB data will be kept if requested (in this case > you can simply change some options) > - Pressing <return> will select the value in brackets > >******************************************* >Please answer some questions: > >******************************************* >Enter path where to install ARB ? > ARB is not a single program but a set of programs, datafiles ... > To install ARB correctly all files are stored in a single > directory. This script creates such a directory and copies all > data into it, sets the correct permissions and optionally installs > some X11 stuff. Please enter the path of the directory where you want > to install ARB. > Notes: This script optionally creates the destination directory. > You should have write permission at the destination location. > - To install ARB in your home directory: Enter "/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/homedir/arb" > - Otherwise become root and rerun script. > - On Linux computers this script should be run under root > > Example: If there is enough space (~50 MB) at your /usr partition and > you want to install arb at /usr/arb, enter "/usr/arb" >Enter full installation path: [/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/image//opt/arb] > > >-rw-r--r-- 1 mmokrejs mmokrejs 11624931 Nov 8 20:27 arb.64.gentoo.tgz >lrwxrwxrwx 1 mmokrejs mmokrejs 17 Nov 8 20:27 arb.tgz -> arb.64.gentoo.tgz >>>> /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/image//opt/arb created >demo.arb >arb_install.sh >arb_CHANGES.txt >arb_DEBUG.txt >arb_INSTALL.txt >arb_LICENSE.txt >arb_OS_X.txt >arb_OS_X_MacPorts.txt >arb_README.txt >arb_UBUNTU.txt >bin/arb_clean >bin/listDiff.pl >bin/retree >bin/format_dssp.pl >bin/arb_dnapars >bin/count >bin/Zuk_to_gen >bin/clustalv >bin/sho_helix >bin/dnaml >bin/fastdnaml >bin/arb_ntree >bin/arb_primer >bin/consense >bin/dolpenny >bin/arb_dist >bin/arb_sleep >bin/arb_2_ascii >bin/dszmconnect.pl >bin/arb_a2ps >bin/mix >bin/arb_textprint >bin/dolmove >bin/listMarkedSpecies.pl >bin/arb_message >bin/penny >bin/arb_protpars >bin/dnacomp >bin/arb_export_tree >bin/arb_convert_aln >bin/arb_wait >bin/arb_readseq >bin/genbank_gen_long_features.pl >bin/clustalw >bin/arb_pt_server >bin/arb_2_bin >bin/axml >bin/arb_proto_2_xsub >bin/findall >bin/arb_panic >bin/drawtree >bin/gendist >bin/seqboot >bin/dollop >bin/arb_ludwig >bin/arb_notify >bin/arb_echo >bin/arb_wetc >bin/raxml2arb.pl >bin/arb_trace >bin/arb_swap_rnastr >bin/treedist >bin/arb_proml >bin/SAI_demo.pl >bin/arb_probe >bin/move >bin/protdist >bin/arb_name_server 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>lib/dtd/arb_tree.dtd >lib/nas/names.dat.template >lib/nas/Makefile >lib/LoVPBN.txt >lib/arb_tcp.dat >lib/GPL.txt >lib/LoVPBN.readme >>>> arb.tgz uncompressed and untared > >******************************************* >Specify PT_SERVER files location > ARB needs a writeable directory to store the pt_server files. > Those files are needed for fast database search > (by probe_design, probe_match and the automatic aligner) > and need a lot of disc space (up to several 100 mega bytes, > e.g. 4000 16S RNA sequences require about 40 MB). > This files are not created now. They can be build by any user via > <ARB_NTREE/Probes/PT_SERVER admin/Build server> > You may define a special directory as the pt_server files location. > This prevents any loss of data installing a new version of > ARB. >Where do you want to put your pt_server data > 1. <CR> - (new installation of ARB) > for placing pt_server data within ARB directory tree > (Default location). > - (updating ARB) > using the previous location > 2. "Path" to link pt_server data directory to > (if you choose this option you won't loose your PT-Servers when doing future software updates) >Enter path: > >installing the pt_server data in /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/image/opt/arb/lib/pts > >******************************************* >Who is responsible for the PT_SERVER index files ? > Answer y: if you trust your users (less administration) > n: if YOU want to administrate all PT_SERVER files > or simply press return to keep the settings of an old installation. >Should everybody be allowed to build/update PT_SERVER files (y/n/dont_change)[dont_change]? > >>>> flags unchanged > >******************************************* >NameServer installation > The NameServer is a program, that synchronizes all species names > of the databases of different users. > Users that import foreign data into their database and want to > export those data to other ARB users should be allowed to change > the names file in $ARBHOME/lib/nas/names.dat > Answer y: if all users may import foreign databases > n: if there are some mean untrusty users > or simply press return to keep the old settings >Do you trust your users (y/n/dont_change)[dont_change]? > >>>> flags unchanged > >******************************************* >Networking > To speed up calculation one special host can be assigned as > the PT_SERVER host. That means that all database search is done > on that host. This saves computer resources as different users > may share one server. > To get the best results this host "H" should: > 1. be fast, > 2. have a lot of real memory (>=64 meg), > 3. have a lot of swap space (>=400 meg), > 4. allow all users to run "ssh H ...", > 5. contain the discs with the PT_SERVER files. > n You want to assign a special Network host > s You have a Stand alone computer >Choose (s/n)[s]? > >>>> server installed > >******************************************* >>>> Installation Complete > >******************************************* > >Note for sysadmins: > In order to provide arb for all users, > edit the global shell init file(s) in /etc > (/etc/bash.bashrc, /etc/csh.cshrc or similar) > in the same manner as described above for the > local shell init files. > >Please read the files > /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/image/opt/arb/arb_INSTALL.txt > /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/image/opt/arb/arb_UBUNTU.txt (if you're using ubuntu) >about additional libraries and tools needed by ARB. > >When you installed everything and performed the changes to your init file, >open a new terminal window and start arb by typing > > arb > >Have much fun using ARB >ARB Team <arb@arb-home.de> > >>>> Completed installing arb-5.3 into /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/image/ > > [32;01m*[0m Final size of build directory: 97727 KiB > [32;01m*[0m Final size of installed tree: 16280 KiB > >[33;01m * [39;49;00mQA Notice: make jobserver unavailable: >[33;01m * [39;49;00m >[33;01m * [39;49;00m make[1]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. >[33;01m * [39;49;00m make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. >[33;01m * [39;49;00m make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. >[33;01m * [39;49;00m make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. >[33;01m * [39;49;00m make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. > [33;01m*[0m QA Notice: the following files are outside of the prefix: > [33;01m*[0m /opt > [33;01m*[0m /opt/arb > [33;01m*[0m /opt/arb/arb_install.sh > [33;01m*[0m /opt/arb/arb_CHANGES.txt > [33;01m*[0m /opt/arb/arb_UBUNTU.txt > [33;01m*[0m /opt/arb/PERL_SCRIPTS > [33;01m*[0m /opt/arb/PERL_SCRIPTS/BIOPERL > [33;01m*[0m /opt/arb/PERL_SCRIPTS/BIOPERL/README > [33;01m*[0m /opt/arb/PERL_SCRIPTS/BIOPERL/beautifyNewick.pl > [33;01m*[0m /opt/arb/PERL_SCRIPTS/GENERAL > [33;01m*[0m /opt/arb/PERL_SCRIPTS/GENERAL/listDiff.pl > [33;01m*[0m /opt/arb/PERL_SCRIPTS/SAI > [33;01m*[0m /opt/arb/PERL_SCRIPTS/SAI/SAI.pm > [33;01m*[0m /opt/arb/PERL_SCRIPTS/SAI/SAI_demo.pl > [33;01m*[0m /opt/arb/PERL_SCRIPTS/GENOME > [33;01m*[0m /opt/arb/PERL_SCRIPTS/GENOME/import_proteomdata.pl > [33;01m*[0m /opt/arb/PERL_SCRIPTS/GENOME/GI.pm > [33;01m*[0m /opt/arb/PERL_SCRIPTS/test > [33;01m*[0m /opt/arb/PERL_SCRIPTS/test/testScripts.pl > [33;01m*[0m /opt/arb/PERL_SCRIPTS/test/Makefile > [33;01m*[0m /opt/arb/PERL_SCRIPTS/test/test.stamp > [33;01m*[0m /opt/arb/PERL_SCRIPTS/ARBTOOLS > [33;01m*[0m /opt/arb/PERL_SCRIPTS/ARBTOOLS/raxml2arb.pl > [33;01m*[0m /opt/arb/PERL_SCRIPTS/ARBTOOLS/IFTHELP > [33;01m*[0m /opt/arb/PERL_SCRIPTS/ARBTOOLS/IFTHELP/format_dssp.pl > [33;01m*[0m /opt/arb/PERL_SCRIPTS/ARBTOOLS/IFTHELP/genbank_gen_long_features.pl > [33;01m*[0m /opt/arb/PERL_SCRIPTS/ARBTOOLS/IFTHELP/embl_gen_long_features.pl > [33;01m*[0m /opt/arb/PERL_SCRIPTS/SPECIES > [33;01m*[0m /opt/arb/PERL_SCRIPTS/SPECIES/listMarkedSpecies.pl > [33;01m*[0m /opt/arb/PERL_SCRIPTS/SPECIES/tools.pm > [33;01m*[0m /opt/arb/PERL_SCRIPTS/SPECIES/markSpecies.pl > [33;01m*[0m /opt/arb/arb_README.txt > [33;01m*[0m /opt/arb/arb_DEBUG.txt > [33;01m*[0m /opt/arb/bin > [33;01m*[0m /opt/arb/bin/arb_clean > [33;01m*[0m /opt/arb/bin/listDiff.pl > [33;01m*[0m /opt/arb/bin/retree > [33;01m*[0m /opt/arb/bin/format_dssp.pl > [33;01m*[0m /opt/arb/bin/arb_dnapars > [33;01m*[0m /opt/arb/bin/count > [33;01m*[0m 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> [33;01m*[0m /opt/arb/lib/pixmaps/icons/ARB_EDIT4.xpm > [33;01m*[0m /opt/arb/lib/pixmaps/leftright_small.bitmap > [33;01m*[0m /opt/arb/lib/pixmaps/merge > [33;01m*[0m /opt/arb/lib/pixmaps/merge/icon_vertical.bitmap > [33;01m*[0m /opt/arb/lib/pixmaps/merge/icon.bitmap > [33;01m*[0m /opt/arb/lib/pixmaps/moveUpAll.bitmap > [33;01m*[0m /opt/arb/lib/pixmaps/quit.xpm > [33;01m*[0m /opt/arb/lib/pixmaps/www_mode.bitmap > [33;01m*[0m /opt/arb/lib/pixmaps/nearestn.bitmap > [33;01m*[0m /opt/arb/lib/pixmaps/star.bitmap > [33;01m*[0m /opt/arb/lib/pixmaps/helix.xpm > [33;01m*[0m /opt/arb/lib/pixmaps/info.bitmap > [33;01m*[0m /opt/arb/lib/pixmaps/save.xpm > [33;01m*[0m /opt/arb/lib/pixmaps/saveAs.xpm > [33;01m*[0m /opt/arb/lib/pixmaps/equal.xpm > [33;01m*[0m /opt/arb/lib/pixmaps/edit.xpm > [33;01m*[0m /opt/arb/lib/pixmaps/beautifyt.bitmap > [33;01m*[0m /opt/arb/lib/pixmaps/molText.xpm > [33;01m*[0m /opt/arb/lib/pixmaps/helpText.xpm > [33;01m*[0m /opt/arb/lib/pixmaps/setroot.bitmap > [33;01m*[0m 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[33;01m*[0m /opt/arb/lib/arb_default/pars.arb > [33;01m*[0m /opt/arb/lib/arb_default/ntree.arb > [33;01m*[0m /opt/arb/lib/arb_default/status.arb > [33;01m*[0m /opt/arb/lib/arb_default/edit4.arb > [33;01m*[0m /opt/arb/lib/arb_default/dist.arb > [33;01m*[0m /opt/arb/lib/arb_default/phyl.arb > [33;01m*[0m /opt/arb/lib/arb_default/phylo.arb > [33;01m*[0m /opt/arb/lib/arb_default/edit.arb > [33;01m*[0m /opt/arb/lib/arb_default/merge.arb > [33;01m*[0m /opt/arb/lib/libAW.so > [33;01m*[0m /opt/arb/lib/export > [33;01m*[0m /opt/arb/lib/export/phylip.eft > [33;01m*[0m /opt/arb/lib/export/fasta_wide.eft > [33;01m*[0m /opt/arb/lib/export/paup.eft > [33;01m*[0m /opt/arb/lib/export/fasta.eft > [33;01m*[0m /opt/arb/lib/export/genbank_list.eft > [33;01m*[0m /opt/arb/lib/export/pir.eft > [33;01m*[0m /opt/arb/lib/export/ae2.eft > [33;01m*[0m /opt/arb/lib/export/fasta_wacc.eft > [33;01m*[0m /opt/arb/lib/export/xml.eft > [33;01m*[0m /opt/arb/lib/export/gcg_8x.eft > [33;01m*[0m 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[33;01m*[0m /opt/arb/lib/help_html/sec_mode.html > [33;01m*[0m /opt/arb/lib/help_html/arb_envar.html > [33;01m*[0m /opt/arb/lib/help_html/mode_select.html > [33;01m*[0m /opt/arb/lib/help_html/props_nds.html > [33;01m*[0m /opt/arb/lib/help_html/spaf_scandb.html > [33;01m*[0m /opt/arb/lib/help_html/mg_species.html > [33;01m*[0m /opt/arb/lib/help_html/set_protection.html > [33;01m*[0m /opt/arb/lib/help_html/sp_info.html > [33;01m*[0m /opt/arb/lib/help_html/sp_sort_fld.html > [33;01m*[0m /opt/arb/lib/help_html/copyright.html > [33;01m*[0m /opt/arb/lib/help_html/ne_align_seq.html > [33;01m*[0m /opt/arb/lib/help_html/macro.html > [33;01m*[0m /opt/arb/lib/help_html/set_meny_fields.html > [33;01m*[0m /opt/arb/lib/help_html/fasta_ift.html > [33;01m*[0m /opt/arb/lib/help_html/Protection.html > [33;01m*[0m /opt/arb/lib/help_html/exportcursor.html > [33;01m*[0m /opt/arb/lib/help_html/insdelchar.html > [33;01m*[0m /opt/arb/lib/help_html/primer.html > [33;01m*[0m 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> [33;01m*[0m /opt/arb/lib/help_html/trm_boot.html > [33;01m*[0m /opt/arb/lib/help_html/sel_box.html > [33;01m*[0m /opt/arb/lib/help_html/gene_hide.html > [33;01m*[0m /opt/arb/lib/help_html/concatenate.html > [33;01m*[0m /opt/arb/lib/help_html/help_index.html > [33;01m*[0m /opt/arb/lib/help_html/vn_search.html > [33;01m*[0m /opt/arb/lib/help_html/arb.html > [33;01m*[0m /opt/arb/lib/help_html/props_frame.html > [33;01m*[0m /opt/arb/lib/help_html/multiproberesults.html > [33;01m*[0m /opt/arb/lib/help_html/next_neighbours_common.html > [33;01m*[0m /opt/arb/lib/help_html/tkeep_mrkd.html > [33;01m*[0m /opt/arb/lib/help_html/tbl_scale.html > [33;01m*[0m /opt/arb/lib/help_html/e4_options.html > [33;01m*[0m /opt/arb/lib/help_html/ebi_ift.html > [33;01m*[0m /opt/arb/lib/help_html/probeadmin.html > [33;01m*[0m /opt/arb/lib/help_html/ne_pretty.html > [33;01m*[0m /opt/arb/lib/help_html/sel_fil.html > [33;01m*[0m /opt/arb/lib/help_html/mg_alignment.html > [33;01m*[0m 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/opt/arb/lib/GPL.txt > [33;01m*[0m /opt/arb/lib/LoVPBN.readme > [33;01m*[0m /opt/arb/SH > [33;01m*[0m /opt/arb/SH/arb_clean > [33;01m*[0m /opt/arb/SH/arb_dnapars > [33;01m*[0m /opt/arb/SH/arb_sleep > [33;01m*[0m /opt/arb/SH/dszmconnect.pl > [33;01m*[0m /opt/arb/SH/arb_textprint > [33;01m*[0m /opt/arb/SH/arb_protpars > [33;01m*[0m /opt/arb/SH/arb_wait > [33;01m*[0m /opt/arb/SH/arb_panic > [33;01m*[0m /opt/arb/SH/arb_ludwig > [33;01m*[0m /opt/arb/SH/arb_echo > [33;01m*[0m /opt/arb/SH/README > [33;01m*[0m /opt/arb/SH/arb_trace > [33;01m*[0m /opt/arb/SH/arb_proml > [33;01m*[0m /opt/arb/SH/arb_bootstrap > [33;01m*[0m /opt/arb/SH/arb_textedit > [33;01m*[0m /opt/arb/SH/arb_phyml > [33;01m*[0m /opt/arb/SH/example_batch_probe_match.sh > [33;01m*[0m /opt/arb/SH/arb_ign > [33;01m*[0m /opt/arb/SH/arb_installubuntu4arb.sh > [33;01m*[0m /opt/arb/SH/arb_fastdnaml > [33;01m*[0m /opt/arb/SH/arb_raxml > [33;01m*[0m /opt/arb/SH/arb_repair > [33;01m*[0m /opt/arb/SH/arb_who > [33;01m*[0m /opt/arb/SH/arb > [33;01m*[0m /opt/arb/SH/arb_remote > [33;01m*[0m /opt/arb/GDEHELP > [33;01m*[0m /opt/arb/GDEHELP/DATA_FILES > [33;01m*[0m /opt/arb/GDEHELP/DATA_FILES/enzymes > [33;01m*[0m /opt/arb/GDEHELP/ARB_GDEmenus > [33;01m*[0m /opt/arb/arb_OS_X_MacPorts.txt > [33;01m*[0m /opt/arb/arb_INSTALL.txt > [33;01m*[0m /opt/arb/demo.arb > [33;01m*[0m /opt/arb/arb_LICENSE.txt > [33;01m*[0m /opt/arb/arb_OS_X.txt > [31;01m*[0m ERROR: sci-biology/arb-5.3::gentoo failed: > [31;01m*[0m Aborting due to QA concerns: there are files installed outside the prefix > [31;01m*[0m > [31;01m*[0m Call stack: > [31;01m*[0m misc-functions.sh, line 603: Called install_qa_check > [31;01m*[0m misc-functions.sh, line 217: Called source 'install_symlink_html_docs' > [31;01m*[0m 05prefix, line 114: Called install_qa_check_prefix > [31;01m*[0m 05prefix, line 27: Called die > [31;01m*[0m The specific snippet of code: > [31;01m*[0m die "Aborting due to QA concerns: there are files installed outside the prefix" > [31;01m*[0m > [31;01m*[0m If you need support, post the output of `emerge --info '=sci-biology/arb-5.3::gentoo'`, > [31;01m*[0m the complete build log and the output of `emerge -pqv '=sci-biology/arb-5.3::gentoo'`. > [31;01m*[0m The complete build log is located at '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/temp/build.log'. > [31;01m*[0m The ebuild environment file is located at '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/temp/environment'. > [31;01m*[0m Working directory: '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/image/scratch/mmokrejs/gentoo_rap' > [31;01m*[0m S: '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3'
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