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Gentoo's Bugzilla – Attachment 449256 Details for
Bug 596254
sci-biology/arb-5.3 : NT_validManual.cxx:56:75: error: no match for ‘operator<<’ (operand types are ‘std::basic_ostream<char>’ and ‘std::ostream {aka std::basic_ostream<char>}’)
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sci-biology:arb-5.3:20161005-141555.log
sci-biology:arb-5.3:20161005-141555.log (text/plain), 248.24 KB, created by
Toralf Förster
on 2016-10-05 14:41:48 UTC
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hide
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Description:
sci-biology:arb-5.3:20161005-141555.log
Filename:
MIME Type:
Creator:
Toralf Förster
Created:
2016-10-05 14:41:48 UTC
Size:
248.24 KB
patch
obsolete
> * Package: sci-biology/arb-5.3 > * Repository: gentoo > * Maintainer: sci-biology@gentoo.org > * USE: abi_x86_64 amd64 elibc_glibc kernel_linux userland_GNU > * FEATURES: preserve-libs sandbox userpriv usersandbox >>>> Unpacking source... >>>> Unpacking arb-5.3.tgz to /var/tmp/portage/sci-biology/arb-5.3/work >>>> Unpacking arb-5.3-linker.patch.xz to /var/tmp/portage/sci-biology/arb-5.3/work >>>> Source unpacked in /var/tmp/portage/sci-biology/arb-5.3/work >>>> Preparing source in /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3 ... > * Applying arb-5.3-linker.patch ... > [ ok ] > * Applying 5.1-libs.patch ... > [ ok ] > * Applying 5.1-bfr-overflow.patch ... > [ ok ] > * Applying 5.2-libpng15.patch ... > [ ok ] > * Applying arb-5.2-gcc-47.patch ... > [ ok ] >make -j1 ARBHOME=/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3 links >SOURCE_TOOLS/generate_all_links.sh >make[1]: Entering directory '/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 '/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 /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3 ... >>>> Source configured. >>>> Compiling source in /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3 ... >make -j1 ARBHOME=/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3 PATH=/usr/lib/portage/python3.4/ebuild-helpers/xattr:/usr/lib/portage/python3.4/ebuild-helpers:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/opt/bin:/usr/x86_64-pc-linux-gnu/gcc-bin/6.2.0:/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin LD_LIBRARY_PATH=:/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/lib tarfile >make clean2 >make[1]: Entering directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3' >make[2]: Entering directory '/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]: Leaving directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PROBE' >make[2]: Entering directory '/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]: Leaving directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/AISC' >make[2]: Entering directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/AISC_MKPTPS' >rm -f mkptypes.o aisc_mkpt >make[2]: Leaving directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/AISC_MKPTPS' >make[2]: Entering directory '/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]: Leaving directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/ALIV3' >make[2]: Entering directory '/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]: Leaving directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/ARBDB' >make[2]: Entering directory '/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 '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/ARBDB2' >make[2]: Entering directory '/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]: Leaving directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/ARBDBPP' >make[2]: Entering directory '/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 '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/ARBDBS' >make[2]: Entering directory '/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]: Leaving directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/ARB_GDE' >make[2]: Entering directory '/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]: Leaving directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/AWT' >make[2]: Entering directory '/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]: Leaving directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/AWTC' >make[2]: Entering directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/AWTI' >rm -f AWTI_import.o AWTI_export.o *.a >make[2]: Leaving directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/AWTI' >make[2]: Entering directory '/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]: Leaving directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/CONSENSUS_TREE' >make[2]: Entering directory '/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 /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/arb_convert_aln >make[2]: Leaving directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/CONVERTALN' >make[2]: Entering directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/DBSERVER' >rm -f db_server.o *.a >make[2]: Leaving directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/DBSERVER' >make[2]: Entering directory '/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 '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/DIST' >make[2]: Entering directory '/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 '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/EDIT' >make[2]: Entering directory '/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]: Leaving directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/EDIT4' >make[2]: Entering directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/EISPACK' >rm -f eispack.o d_sign.o *.a >make[2]: Leaving directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/EISPACK' >make[2]: Entering directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDE' >make[3]: Entering directory '/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 /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/clustalv >make[3]: Leaving directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDE/CLUSTAL' >make[3]: Entering directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDE/SUPPORT' >rm -f /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/CAP2 /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/Restriction /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/Zuk_to_gen /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/count /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/findall /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/lsadt /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/sho_helix /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/varpos >make[3]: Leaving directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDE/SUPPORT' >make[3]: Entering directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDE/AxML' >rm -f axml.o /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/axml >make[3]: Leaving directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDE/AxML' >make[3]: Entering directory '/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 /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/raxmlHPC >make[3]: Leaving directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDE/RAxML' >make[3]: Entering directory '/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 /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/phyml >make[3]: Leaving directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDE/PHYML' >make[3]: Entering directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDE/CLUSTALW' >rm -f *.o /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/clustalw >make[3]: Leaving directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDE/CLUSTALW' >make[3]: Entering directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDE/PHYLIP' >rm -f /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/clique /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/consense /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/contml /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/contrast /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/dnacomp /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/dnadist /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/dnainvar /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/dnaml /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/dnamlk /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/dnamove /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/dnapars /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/dnapenny /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/dolmove /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/dollop /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/dolpenny /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/factor /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/fitch /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/gendist /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/kitsch /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/mix /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/move /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/neighbor /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/pars /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/penny /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/proml /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/promlk /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/protdist /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/protpars /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/restdist /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/restml /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/retree /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/seqboot /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/treedist /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/drawgram /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/drawtree *.o >make[3]: Leaving directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDE/PHYLIP' >make[3]: Entering directory '/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 /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/puzzle >make[3]: Leaving directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDE/TREEPUZZLE' >make[3]: Entering directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDE/FASTDNAML' >rm -f fastDNAml.o /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/fastdnaml >make[3]: Leaving directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDE/FASTDNAML' >make[2]: Leaving directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDE' >make[2]: Entering directory '/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]: Leaving directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GENOM' >make[2]: Entering directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GENOM_IMPORT' >rm *.o >rm: cannot remove '*.o': No such file or directory >make[2]: [Makefile:33: clean] Error 1 (ignored) >rm *.a >rm: cannot remove '*.a': No such file or directory >make[2]: [Makefile:34: clean] Error 1 (ignored) >rm *.bak >rm: cannot remove '*.bak': No such file or directory >make[2]: [Makefile:35: clean] Error 1 (ignored) >rm *~ >rm: cannot remove '*~': No such file or directory >make[2]: [Makefile:36: clean] Error 1 (ignored) >rm *# >rm: cannot remove '*#': No such file or directory >make[2]: [Makefile:37: clean] Error 1 (ignored) >rm *\% >rm: cannot remove '*%': No such file or directory >make[2]: [Makefile:38: clean] Error 1 (ignored) >make[2]: Leaving directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GENOM_IMPORT' >make[2]: Entering directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GL' >make[3]: Entering directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GL/glpng' >rm -f glpng.o *.a >make[3]: Leaving directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GL/glpng' >make[3]: Entering directory '/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]: Leaving directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GL/glAW' >make[2]: Leaving directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GL' >make[2]: Entering directory '/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 '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/ISLAND_HOPPING' >make[2]: Entering directory '/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]: Leaving directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/MERGE' >make[2]: Entering directory '/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 >make[2]: Leaving directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/MULTI_PROBE' >make[2]: Entering directory '/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[2]: Leaving directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/NALIGNER' >make[2]: Entering directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/NAMES' >rm -f names.o *.a >make[2]: Leaving directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/NAMES' >make[2]: Entering directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/NAMES_COM' >make[3]: Entering directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/NAMES_COM' >rm -f *.[ao] >rm -f */*.[ao] >rm -f GENH/* >rm -f GENC/* >rm -f .depends >make[3]: Leaving directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/NAMES_COM' >make[2]: Leaving directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/NAMES_COM' >make[2]: Entering directory '/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 '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/NTREE' >make[2]: Entering directory '/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[2]: Leaving directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PARSIMONY' >make[2]: Entering directory '/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 >make[2]: Leaving directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PGT' >make[2]: Entering directory '/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 '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PHYLO' >make[2]: Entering directory '/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 '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PRIMER_DESIGN' >make[2]: Entering directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PROBE_COM' >make[3]: Entering directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PROBE_COM' >rm -f *.[ao] >rm -f */*.[ao] >rm -f GENH/* >rm -f GENC/* >rm -f .depends >make[3]: Leaving directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PROBE_COM' >make[2]: Leaving directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PROBE_COM' >make[2]: Entering directory '/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]: Leaving directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PROBE_DESIGN' >make[2]: Entering directory '/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 >rm -f /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PROBE_SET/bin/ps_show_result /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PROBE_SET/bin/ps_arb2asciipaths /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PROBE_SET/bin/ps_my2asciipaths /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PROBE_SET/bin/ps_my2ascii /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PROBE_SET/bin/ps_get_probes /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PROBE_SET/bin/ps_eval /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PROBE_SET/bin/ps_find /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PROBE_SET/bin/ps_detect /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PROBE_SET/bin/ps_merge /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PROBE_SET/bin/ps_convert /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PROBE_SET/bin/fb_test >make[2]: Leaving directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PROBE_SET' >make[2]: Entering directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/READSEQ' >rm -f readseq.o ureadseq.o /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/arb_readseq >make[2]: Leaving directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/READSEQ' >make[2]: Entering directory '/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 '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/RNA3D' >make[2]: Entering directory '/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[2]: Leaving directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SECEDIT' >make[2]: Entering directory '/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 '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SEQ_QUALITY' >make[2]: Entering directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SERVERCNTRL' >rm -f servercntrl.o *.a >make[2]: Leaving directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SERVERCNTRL' >make[2]: Entering directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL' >make[3]: Entering directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/TREE_READ' >rm -f TreeRead.o TreeTools.o *.a >make[3]: Leaving directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/TREE_READ' >make[3]: Entering directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/TREE_WRITE' >rm -f TreeWrite.o *.a >make[3]: Leaving directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/TREE_WRITE' >make[3]: Entering directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/HELIX' >rm -f BI_helix.o *.a >make[3]: Leaving directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/HELIX' >make[3]: Entering directory '/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 '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/AW_HELIX' >make[3]: Entering directory '/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 >make[3]: Leaving directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/AW_NAME' >make[3]: Entering directory '/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 '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/DB_SCANNER' >make[3]: Entering directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/FILE_BUFFER' >rm -f FileBuffer.o *.a >make[3]: Leaving directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/FILE_BUFFER' >make[3]: Entering directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/REGEXPR' >rm -f RegExpr.o *.a >make[3]: Leaving directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/REGEXPR' >make[3]: Entering directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/FAST_ALIGNER' >rm -f fast_aligner.o ClustalV.o *.a >make[3]: Leaving directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/FAST_ALIGNER' >make[2]: Leaving directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL' >make[2]: Entering directory '/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]: Leaving directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/STAT' >make[2]: Entering directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/TOOLS' >rm -f /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/arb_2_ascii /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/arb_2_bin /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/arb_a2ps /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/arb_count_chars /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/arb_dnarates /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/arb_export_rates /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/arb_export_tree /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/arb_gene_probe /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/arb_message /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/arb_notify /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/arb_primer /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/arb_probe /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/arb_proto_2_xsub /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/arb_read_tree /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/arb_replace /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin/arb_swap_rnastr >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 >make[2]: Leaving directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/TOOLS' >make[2]: Entering directory '/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 '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/TREEGEN' >make[2]: Entering directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/WETC' >rm -f WETC_main.o *.a >make[2]: Leaving directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/WETC' >make[2]: Entering directory '/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 '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/WINDOW' >make[2]: Entering directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/XML' >rm -f xml.o *.a >make[2]: Leaving directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/XML' >make[2]: Entering directory '/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[3]: Entering directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDEHELP' >cat: helpfiles.lst: No such file or directory >rm -f ./HELP_GEN/*.help >rm -f ./HELP_DOC_GEN/*.doc >make[3]: Leaving directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDEHELP' >make[2]: Leaving directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDEHELP' >make[2]: Entering directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/HELP_SOURCE' >rm -f arb_help2xml.o /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: â../lib/help_htmlâ: No such file or directory >rm -f xml.stamp dummy _index.html >rm -f `find Xml -name "*.xml"` >find: âXmlâ: No such file or directory >make -C genhelp clean >make[3]: Entering directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/HELP_SOURCE/genhelp' >rm -f *.hlp >make[3]: Leaving directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/HELP_SOURCE/genhelp' >make[2]: Leaving directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/HELP_SOURCE' >make[2]: Entering directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SOURCE_TOOLS' >rm -f generate_all_links.stamp >make[2]: Leaving directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SOURCE_TOOLS' >make[2]: Entering directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin' >find . -type l -exec rm {} \; >find . -type f -perm -100 -exec rm {} \; >make[2]: Leaving directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin' >make[2]: Entering directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PERL2ARB' >test -f Makefile && make clean >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 /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/lib/ARB.pm /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/lib/ARB.so >make[2]: Leaving directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PERL2ARB' >rm -f *.last_gcc >make[1]: Leaving directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3' >make all >make[1]: Entering directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3' >make links >make[2]: Entering directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3' >SOURCE_TOOLS/generate_all_links.sh >make[3]: Entering directory '/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 '/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 '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3' >make com >make[2]: Entering directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3' >-------------------------------------------------------------------------------- Make everything in AISC_MKPTPS >make[3]: Entering directory '/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++ -march=native -O2 -pipe -Wl,-O1 -Wl,--as-needed -Wl,--export-dynamic -rdynamic -o aisc_mkpt mkptypes.o >make[3]: Leaving directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/AISC_MKPTPS' >-------------------------------------------------------------------------------- Make everything in AISC >make[3]: Entering directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/AISC' >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >aisc_commands.c: In function âint do_com_next(const char*)â: >aisc_commands.c:906:21: warning: variable âpâ set but not used [-Wunused-but-set-variable] > char *p; > ^ >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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 '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/AISC' >-------------------------------------------------------------------------------- Make everything in NAMES_COM >make[3]: Entering directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/NAMES_COM' >make[4]: Entering directory '/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 >makedepend: warning: C/aisc_extern.c (reading /usr/include/stdio.h, line 33): cannot find include file "stddef.h" > not in GENH/stddef.h > not in C/stddef.h > not in /usr/include/stddef.h >makedepend: warning: C/aisc_extern.c (reading /usr/include/_G_config.h, line 15): cannot find include file "stddef.h" > not in GENH/stddef.h > not in C/stddef.h > not in /usr/include/stddef.h >makedepend: warning: C/aisc_extern.c (reading /usr/include/wchar.h, line 51): cannot find include file "stddef.h" > not in GENH/stddef.h > not in C/stddef.h > not in /usr/include/stddef.h >makedepend: warning: C/aisc_extern.c (reading /usr/include/libio.h, line 49): cannot find include file "stdarg.h" > not in GENH/stdarg.h > not in C/stdarg.h > not in /usr/include/stdarg.h >makedepend: warning: C/aisc_extern.c (reading /usr/include/string.h, line 32): cannot find include file "stddef.h" > not in GENH/stddef.h > not in C/stddef.h > not in /usr/include/stddef.h >makedepend: warning: C/aisc_extern.c, line 3: cannot find include file "aisc.h" > not in GENH/aisc.h > not in C/aisc.h > not in /usr/include/aisc.h >makedepend: warning: C/aisc_extern.c (reading C/aisc_extern_privat.h, line 19): cannot find include file "attributes.h" > not in GENH/attributes.h > not in C/attributes.h > not in /usr/include/attributes.h >makedepend: warning: C/client.c (reading /usr/include/stdlib.h, line 32): cannot find include file "stddef.h" > not in GENH/stddef.h > not in C/stddef.h > not in /usr/include/stddef.h >makedepend: warning: C/client.c (reading /usr/include/sys/types.h, line 146): cannot find include file "stddef.h" > not in GENH/stddef.h > not in C/stddef.h > not in /usr/include/stddef.h >makedepend: warning: C/client.c (reading /usr/include/alloca.h, line 24): cannot find include file "stddef.h" > not in GENH/stddef.h > not in C/stddef.h > not in /usr/include/stddef.h >makedepend: warning: C/client.c (reading /usr/include/unistd.h, line 229): cannot find include file "stddef.h" > not in GENH/stddef.h > not in C/stddef.h > not in /usr/include/stddef.h >makedepend: warning: C/client.c (reading C/ad_varargs.h, line 1): cannot find include file "stdarg.h" > not in GENH/stdarg.h > not in C/stdarg.h > not in /usr/include/stdarg.h >makedepend: warning: C/client.c (reading /usr/include/sys/socket.h, line 28): cannot find include file "stddef.h" > not in GENH/stddef.h > not in C/stddef.h > not in /usr/include/stddef.h >makedepend: warning: C/client.c (reading /usr/include/bits/socket.h, line 27): cannot find include file "stddef.h" > not in GENH/stddef.h > not in C/stddef.h > not in /usr/include/stddef.h >makedepend: warning: C/client.c (reading /usr/include/rpc/netdb.h, line 42): cannot find include file "stddef.h" > not in GENH/stddef.h > not in C/stddef.h > not in /usr/include/stddef.h >makedepend: warning: C/client.c (reading /usr/include/signal.h, line 316): cannot find include file "stddef.h" > not in GENH/stddef.h > not in C/stddef.h > not in /usr/include/stddef.h >makedepend: warning: C/client.c (reading C/client.h, line 22): cannot find include file "attributes.h" > not in GENH/attributes.h > not in C/attributes.h > not in /usr/include/attributes.h >makedepend: warning: C/debug.c, line 6: cannot find include file "aisc_com.h" > not in GENH/aisc_com.h > not in C/aisc_com.h > not in /usr/include/aisc_com.h >makedepend: warning: C/server.c (reading /usr/include/limits.h, line 123): cannot find include file "limits.h" >makedepend: warning: C/server.c, line 33: cannot find include file "aisc_com.h" > not in aisc_com.h > not in C/aisc_com.h > not in GENH/aisc_com.h > not in C/aisc_com.h > not in /usr/include/aisc_com.h >makedepend: warning: C/server.c (reading C/server.h, line 22): cannot find include file "attributes.h" > not in GENH/attributes.h > not in C/attributes.h > not in /usr/include/attributes.h >makedepend: warning: C/server.c (reading ../INCLUDE/arb_assert.h), line 33: # error Neither DEBUG nor NDEBUG is defined! >makedepend: warning: C/server.c (reading ../INCLUDE/arb_assert.h, line 183): cannot find include file "arbdb_base.h" > not in GENH/arbdb_base.h > not in C/arbdb_base.h > not in /usr/include/arbdb_base.h >makedepend: warning: C/struct_man.c, line 5: cannot find include file "aisc.h" > not in aisc.h > not in C/aisc.h > not in GENH/aisc.h > not in C/aisc.h > not in /usr/include/aisc.h >makedepend: warning: C/struct_man.c (reading C/struct_man.h, line 19): cannot find include file "attributes.h" > not in GENH/attributes.h > not in C/attributes.h > not in /usr/include/attributes.h >makedepend: warning: cannot open "GENC/*.c" >/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 >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NAMES_COM -I/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++ -march=native -O2 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NAMES_COM -I/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 >rm -f GENH/aisc_server_extern.aisc >../MAKEBIN/aisc_mkpt -a C/aisc_extern.c names_extern.c >GENH/aisc_server_extern.aisc >../MAKEBIN/aisc AISC/aisc_debug_globals.pa names.aisc GENC/aisc_debug_globals.c GENH/aisc_server_extern.aisc GENH/import_proto.h >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NAMES_COM -I/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 >ld -r -o client.a O/client.o O/debug.o GENC/aisc_debug_globals.o >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NAMES_COM -I/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++ -march=native -O2 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NAMES_COM -I/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++ -march=native -O2 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NAMES_COM -I/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 >rm -f GENH/aisc_server_proto.h >../MAKEBIN/aisc_mkpt -C GENC/aisc_server.c >GENH/aisc_server_proto.h >rm -f GENH/aisc_server_extern.h >../MAKEBIN/aisc_mkpt -C C/aisc_extern.c names_extern.c >GENH/aisc_server_extern.h >../MAKEBIN/aisc AISC/aisc_global.pa names.aisc GENC/aisc_global.c GENH/aisc_server_extern.aisc GENH/import_proto.h >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NAMES_COM -I/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++ -march=native -O2 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NAMES_COM -I/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++ -march=native -O2 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NAMES_COM -I/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 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 '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/NAMES_COM' >make[3]: Leaving directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/NAMES_COM' >-------------------------------------------------------------------------------- Make everything in PROBE_COM >make[3]: Entering directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PROBE_COM' >make[4]: Entering directory '/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 >makedepend: warning: C/aisc_extern.c (reading /usr/include/stdio.h, line 33): cannot find include file "stddef.h" > not in GENH/stddef.h > not in C/stddef.h > not in /usr/include/stddef.h >makedepend: warning: C/aisc_extern.c (reading /usr/include/_G_config.h, line 15): cannot find include file "stddef.h" > not in GENH/stddef.h > not in C/stddef.h > not in /usr/include/stddef.h >makedepend: warning: C/aisc_extern.c (reading /usr/include/wchar.h, line 51): cannot find include file "stddef.h" > not in GENH/stddef.h > not in C/stddef.h > not in /usr/include/stddef.h >makedepend: warning: C/aisc_extern.c (reading /usr/include/libio.h, line 49): cannot find include file "stdarg.h" > not in GENH/stdarg.h > not in C/stdarg.h > not in /usr/include/stdarg.h >makedepend: warning: C/aisc_extern.c (reading /usr/include/string.h, line 32): cannot find include file "stddef.h" > not in GENH/stddef.h > not in C/stddef.h > not in /usr/include/stddef.h >makedepend: warning: C/aisc_extern.c, line 3: cannot find include file "aisc.h" > not in GENH/aisc.h > not in C/aisc.h > not in /usr/include/aisc.h >makedepend: warning: C/aisc_extern.c (reading C/aisc_extern_privat.h, line 19): cannot find include file "attributes.h" > not in GENH/attributes.h > not in C/attributes.h > not in /usr/include/attributes.h >makedepend: warning: C/client.c (reading /usr/include/stdlib.h, line 32): cannot find include file "stddef.h" > not in GENH/stddef.h > not in C/stddef.h > not in /usr/include/stddef.h >makedepend: warning: C/client.c (reading /usr/include/sys/types.h, line 146): cannot find include file "stddef.h" > not in GENH/stddef.h > not in C/stddef.h > not in /usr/include/stddef.h >makedepend: warning: C/client.c (reading /usr/include/alloca.h, line 24): cannot find include file "stddef.h" > not in GENH/stddef.h > not in C/stddef.h > not in /usr/include/stddef.h >makedepend: warning: C/client.c (reading /usr/include/unistd.h, line 229): cannot find include file "stddef.h" > not in GENH/stddef.h > not in C/stddef.h > not in /usr/include/stddef.h >makedepend: warning: C/client.c (reading C/ad_varargs.h, line 1): cannot find include file "stdarg.h" > not in GENH/stdarg.h > not in C/stdarg.h > not in /usr/include/stdarg.h >makedepend: warning: C/client.c (reading /usr/include/sys/socket.h, line 28): cannot find include file "stddef.h" > not in GENH/stddef.h > not in C/stddef.h > not in /usr/include/stddef.h >makedepend: warning: C/client.c (reading /usr/include/bits/socket.h, line 27): cannot find include file "stddef.h" > not in GENH/stddef.h > not in C/stddef.h > not in /usr/include/stddef.h >makedepend: warning: C/client.c (reading /usr/include/rpc/netdb.h, line 42): cannot find include file "stddef.h" > not in GENH/stddef.h > not in C/stddef.h > not in /usr/include/stddef.h >makedepend: warning: C/client.c (reading /usr/include/signal.h, line 316): cannot find include file "stddef.h" > not in GENH/stddef.h > not in C/stddef.h > not in /usr/include/stddef.h >makedepend: warning: C/client.c (reading C/client.h, line 22): cannot find include file "attributes.h" > not in GENH/attributes.h > not in C/attributes.h > not in /usr/include/attributes.h >makedepend: warning: C/debug.c, line 6: cannot find include file "aisc_com.h" > not in GENH/aisc_com.h > not in C/aisc_com.h > not in /usr/include/aisc_com.h >makedepend: warning: C/server.c (reading /usr/include/limits.h, line 123): cannot find include file "limits.h" >makedepend: warning: C/server.c, line 33: cannot find include file "aisc_com.h" > not in aisc_com.h > not in C/aisc_com.h > not in GENH/aisc_com.h > not in C/aisc_com.h > not in /usr/include/aisc_com.h >makedepend: warning: C/server.c (reading C/server.h, line 22): cannot find include file "attributes.h" > not in GENH/attributes.h > not in C/attributes.h > not in /usr/include/attributes.h >makedepend: warning: C/server.c (reading ../INCLUDE/arb_assert.h), line 33: # error Neither DEBUG nor NDEBUG is defined! >makedepend: warning: C/server.c (reading ../INCLUDE/arb_assert.h, line 183): cannot find include file "arbdb_base.h" > not in GENH/arbdb_base.h > not in C/arbdb_base.h > not in /usr/include/arbdb_base.h >makedepend: warning: C/struct_man.c, line 5: cannot find include file "aisc.h" > not in aisc.h > not in C/aisc.h > not in GENH/aisc.h > not in C/aisc.h > not in /usr/include/aisc.h >makedepend: warning: C/struct_man.c (reading C/struct_man.h, line 19): cannot find include file "attributes.h" > not in GENH/attributes.h > not in C/attributes.h > not in /usr/include/attributes.h >makedepend: warning: cannot open "GENC/*.c" >/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 >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PROBE_COM -I/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++ -march=native -O2 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PROBE_COM -I/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 >rm -f GENH/aisc_server_extern.aisc >../MAKEBIN/aisc_mkpt -a C/aisc_extern.c PT_extern.c >GENH/aisc_server_extern.aisc >../MAKEBIN/aisc AISC/aisc_debug_globals.pa PT.aisc GENC/aisc_debug_globals.c GENH/aisc_server_extern.aisc GENH/import_proto.h >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PROBE_COM -I/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 >ld -r -o client.a O/client.o O/debug.o GENC/aisc_debug_globals.o >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PROBE_COM -I/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++ -march=native -O2 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PROBE_COM -I/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++ -march=native -O2 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PROBE_COM -I/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 >rm -f GENH/aisc_server_proto.h >../MAKEBIN/aisc_mkpt -C GENC/aisc_server.c >GENH/aisc_server_proto.h >rm -f GENH/aisc_server_extern.h >../MAKEBIN/aisc_mkpt -C C/aisc_extern.c PT_extern.c >GENH/aisc_server_extern.h >../MAKEBIN/aisc AISC/aisc_global.pa PT.aisc GENC/aisc_global.c GENH/aisc_server_extern.aisc GENH/import_proto.h >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PROBE_COM -I/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++ -march=native -O2 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PROBE_COM -I/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++ -march=native -O2 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PROBE_COM -I/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 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 '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PROBE_COM' >make[3]: Leaving directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PROBE_COM' >make[2]: Leaving directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3' >make arb >make[2]: Entering directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3' >(cd lib;make all) >make[3]: Entering directory '/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 '/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 '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/lib/nas' >make[3]: Leaving directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/lib' >make arbbasic2 >make[3]: Entering directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3' >-------------------------------------------------------------------------------- Make everything in TEMPLATES >make[4]: Entering directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/TEMPLATES' >../SOURCE_TOOLS/build_info.pl >make[4]: Leaving directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/TEMPLATES' >-------------------------------------------------------------------------------- Make everything in AISC_MKPTPS >make[4]: Entering directory '/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 '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/AISC_MKPTPS' >-------------------------------------------------------------------------------- Make everything in AISC >make[4]: Entering directory '/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 '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/AISC' >-------------------------------------------------------------------------------- Make everything in NAMES_COM >make[4]: Entering directory '/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 '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/NAMES_COM' >-------------------------------------------------------------------------------- Make everything in PROBE_COM >make[4]: Entering directory '/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 '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PROBE_COM' >-------------------------------------------------------------------------------- Make everything in NAMES_COM >make[4]: Entering directory '/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 '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/NAMES_COM' >make SL/SL.dummy >make[4]: Entering directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3' >-------------------------------------------------------------------------------- Make everything in SL >make[5]: Entering directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL' >make[6]: Entering directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/TREE_READ' >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/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 '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/TREE_READ' >make[6]: Entering directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/TREE_WRITE' >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/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 '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/TREE_WRITE' >make[6]: Entering directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/HELIX' >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/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 '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/HELIX' >make[6]: Entering directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/AW_HELIX' >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/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 '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/AW_HELIX' >make[6]: Entering directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/AW_NAME' >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/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 '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/AW_NAME' >make[6]: Entering directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/DB_SCANNER' >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/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 '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/DB_SCANNER' >make[6]: Entering directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/FILE_BUFFER' >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/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 '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/FILE_BUFFER' >make[6]: Entering directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/REGEXPR' >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/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 '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/REGEXPR' >make[6]: Entering directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/FAST_ALIGNER' >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >fast_aligner.cxx: In function âconst char* alignCompactedTo(AWTC_CompactedSubSequence*, const AWTC_FastSearchSequence*, int, GB_CSTR, long int, GBDATA*, GBDATA*, const AlignParams&)â: >fast_aligner.cxx:1254:31: warning: âGBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)â is deprecated [-Wdeprecated-declarations] > GBDATA *gbd = GBT_add_data(gb_toAlign, alignment, "data", GB_STRING); > ^~~~~~~~~~~~ >In file included from /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from fast_aligner.cxx:19: >/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: âGBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)â is deprecated [-Wdeprecated-declarations] > GBDATA *gbd = GBT_add_data(gb_toAlign, alignment, "data", GB_STRING); > ^ >In file included from /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from fast_aligner.cxx:19: >/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 âvoid AWTC_start_faligning(AW_window*, AW_CL)â: >fast_aligner.cxx:2368:57: warning: narrowing conversion of âroot->AW_root::awar(((const char*)"faligner/next_relatives"))->AW_awar::read_int()â from âlong intâ to âintâ inside { } [-Wnarrowing] > root->awar(FA_AWAR_NEXT_RELATIVES)->read_int(), > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ >fast_aligner.cxx:2369:52: warning: narrowing conversion of âroot->AW_root::awar(((const char*)"next_neighbours/oligo_len"))->AW_awar::read_int()â from âlong intâ to âintâ inside { } [-Wnarrowing] > root->awar(AWAR_NN_OLIGO_LEN)->read_int(), > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ >fast_aligner.cxx:2370:53: warning: narrowing conversion of âroot->AW_root::awar(((const char*)"next_neighbours/mismatches"))->AW_awar::read_int()â from âlong intâ to âintâ inside { } [-Wnarrowing] > root->awar(AWAR_NN_MISMATCHES)->read_int(), > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >ld -r -o FAST_ALIGNER.a fast_aligner.o ClustalV.o >make[6]: Leaving directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL/FAST_ALIGNER' >make[5]: Leaving directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/SL' >make[4]: Leaving directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3' >make[3]: Leaving directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3' >make arbshared arbapplications help >make[3]: Entering directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3' >-------------------------------------------------------------------------------- Make everything in ARBDB >make[4]: Entering directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/ARBDB' >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >admatch.c: In function âGBS_string_evalâ: >admatch.c:763:13: warning: ignoring return value of âgbs_build_replace_stringâ, 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 -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >In file included from adlocal.h:577:0, > from arbdb.c:12: >arbdb.c: In function âGB_copy_with_protectionâ: >adlmacros.h:483:18: warning: null argument where non-null required (argument 2) [-Wnonnull] > if (dat) memcpy(&((gbd)->info.istr.data[0]), (char *)(dat), (size_t)(memsiz)); \ > ^ >arbdb.c:1469:13: note: in expansion of macro âGB_SETSMDMALLOCâ > GB_SETSMDMALLOC(dest, GB_GETSIZE(source), > ^~~~~~~~~~~~~~~ >adlmacros.h:491:18: warning: null argument where non-null required (argument 2) [-Wnonnull] > if (dat) memcpy(exData, (char *)(dat), (size_t)(memsiz)); \ > ^ >arbdb.c:1469:13: note: in expansion of macro âGB_SETSMDMALLOCâ > GB_SETSMDMALLOC(dest, GB_GETSIZE(source), > ^~~~~~~~~~~~~~~ >arbdb.c: In function âgb_remove_callbackâ: >arbdb.c:2239:13: warning: variable âremovedâ set but not used [-Wunused-but-set-variable] > GB_BOOL removed = GB_FALSE; > ^~~~~~~ >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >ad_core.c: In function âad_useâ: >ad_core.c:11:17: warning: parameter âdummyâ set but not used [-Wunused-but-set-parameter] > void ad_use(int dummy, ...) { > ^~~~~ >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >adsystem.c: In function âgb_load_single_key_dataâ: >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 -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >adsocket.c: In function âGB_get_full_pathâ: >adsocket.c:1256:13: warning: ignoring return value of ârealpathâ, declared with attribute warn_unused_result [-Wunused-result] > realpath(newpath, path_buf[path_toggle]); > ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >adsocket.c:1260:13: warning: ignoring return value of ârealpathâ, declared with attribute warn_unused_result [-Wunused-result] > realpath(anypath, path_buf[path_toggle]); > ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >adcomm.c: In function âgbcms_write_updatedâ: >adcomm.c:303:23: warning: variable âhsâ set but not used [-Wunused-but-set-variable] > struct Hs_struct *hs; > ^~ >adcomm.c: In function âgbcms_talking_init_transactionâ: >adcomm.c:533:14: warning: variable âbufferâ set but not used [-Wunused-but-set-variable] > long *buffer; > ^~~~~~ >adcomm.c: In function âgbcm_read_binâ: >adcomm.c:1231:27: warning: variable âflags3â set but not used [-Wunused-but-set-variable] > struct gb_flag_types3 flags3; > ^~~~~~ >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >adquery.c: In function âgb_searchâ: >adquery.c:449:28: warning: comparison between âGB_TYPES {aka enum gb_key_types}â and âenum gb_search_enumâ [-Wenum-compare] > if (create == GB_CREATE_CONTAINER) { > ^~ >adquery.c:455:28: warning: comparison between âGB_TYPES {aka enum gb_key_types}â and âenum gb_search_enumâ [-Wenum-compare] > if (create == GB_CREATE_CONTAINER) { > ^~ >adquery.c:526:31: warning: comparison between âGB_TYPES {aka enum gb_key_types}â and âenum gb_search_enumâ [-Wenum-compare] > if (s2 || (create == GB_CREATE_CONTAINER)) { > ^~ >adquery.c: In function âGB_command_interpreterâ: >adquery.c:861:19: warning: variable âlenâ set but not used [-Wunused-but-set-variable] > int len; > ^~~ >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >ad_save_load.c: In function âgb_write_bin_rekâ: >ad_save_load.c:799:17: 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 âGB_save_asâ: >ad_save_load.c:1079:5: warning: âGB_get_errorâ 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 âGB_save_quick_asâ: >ad_save_load.c:1126:5: warning: âGB_get_errorâ 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: âGB_get_errorâ 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: âGB_get_errorâ 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: âGB_get_errorâ 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 âGB_save_quickâ: >ad_save_load.c:1213:5: warning: âGB_get_errorâ 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: âGB_get_errorâ 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: âGB_get_errorâ 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 âgb_check_saveableâ: >ad_save_load.c:1307:9: warning: âGB_get_errorâ 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: âGB_get_errorâ 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 -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >ad_load.c: In function âGB_loginâ: >ad_load.c:1380:17: warning: ignoring return value of âgb_scan_directoryâ, declared with attribute warn_unused_result [-Wunused-result] > gb_scan_directory(base,&dir); > ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >admap.c: In function âgb_save_mapfileâ: >admap.c:636:9: warning: variable âwriteOffsetâ set but not used [-Wunused-but-set-variable] > writeOffset; > ^~~~~~~~~~~ >admap.c:635:10: warning: variable âcalcOffsetâ set but not used [-Wunused-but-set-variable] > long calcOffset, > ^~~~~~~~~~ >admap.c: In function âgb_is_valid_mapfileâ: >admap.c:722:9: warning: ignoring return value of âfreadâ, declared with attribute warn_unused_result [-Wunused-result] > fread((char *)mheader, sizeof(*mheader),1,in); > ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >adTest.c: In function âtestDataâ: >adTest.c:36:9: warning: variable âerrâ set but not used [-Wunused-but-set-variable] > int err = 0; > ^~~ >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >adtools.c: In function âGBT_check_arb_fileâ: >adtools.c:74:5: warning: ignoring return value of âfgetsâ, declared with attribute warn_unused_result [-Wunused-result] > fgets(buffer,50,in); > ^~~~~~~~~~~~~~~~~~~ >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >adali.c: In function âGBT_create_sequence_dataâ: >adali.c:597:5: warning: âGBT_add_dataâ 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 -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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 '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/ARBDB' >-------------------------------------------------------------------------------- Make everything in ARBDBS >make[4]: Entering directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/ARBDBS' >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >admatch.c: In function âGBS_string_evalâ: >admatch.c:763:13: warning: ignoring return value of âgbs_build_replace_stringâ, 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 -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >In file included from adlocal.h:577:0, > from arbdb.c:12: >arbdb.c: In function âGB_copy_with_protectionâ: >adlmacros.h:483:18: warning: null argument where non-null required (argument 2) [-Wnonnull] > if (dat) memcpy(&((gbd)->info.istr.data[0]), (char *)(dat), (size_t)(memsiz)); \ > ^ >arbdb.c:1469:13: note: in expansion of macro âGB_SETSMDMALLOCâ > GB_SETSMDMALLOC(dest, GB_GETSIZE(source), > ^~~~~~~~~~~~~~~ >adlmacros.h:491:18: warning: null argument where non-null required (argument 2) [-Wnonnull] > if (dat) memcpy(exData, (char *)(dat), (size_t)(memsiz)); \ > ^ >arbdb.c:1469:13: note: in expansion of macro âGB_SETSMDMALLOCâ > GB_SETSMDMALLOC(dest, GB_GETSIZE(source), > ^~~~~~~~~~~~~~~ >arbdb.c: In function âgb_remove_callbackâ: >arbdb.c:2239:13: warning: variable âremovedâ set but not used [-Wunused-but-set-variable] > GB_BOOL removed = GB_FALSE; > ^~~~~~~ >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >ad_core.c: In function âad_useâ: >ad_core.c:11:17: warning: parameter âdummyâ set but not used [-Wunused-but-set-parameter] > void ad_use(int dummy, ...) { > ^~~~~ >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >adsystem.c: In function âgb_load_single_key_dataâ: >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 -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >adsocket.c: In function âGB_get_full_pathâ: >adsocket.c:1256:13: warning: ignoring return value of ârealpathâ, declared with attribute warn_unused_result [-Wunused-result] > realpath(newpath, path_buf[path_toggle]); > ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >adsocket.c:1260:13: warning: ignoring return value of ârealpathâ, declared with attribute warn_unused_result [-Wunused-result] > realpath(anypath, path_buf[path_toggle]); > ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >adcomm.c: In function âgbcms_write_updatedâ: >adcomm.c:303:23: warning: variable âhsâ set but not used [-Wunused-but-set-variable] > struct Hs_struct *hs; > ^~ >adcomm.c: In function âgbcms_talking_init_transactionâ: >adcomm.c:533:14: warning: variable âbufferâ set but not used [-Wunused-but-set-variable] > long *buffer; > ^~~~~~ >adcomm.c: In function âgbcm_read_binâ: >adcomm.c:1231:27: warning: variable âflags3â set but not used [-Wunused-but-set-variable] > struct gb_flag_types3 flags3; > ^~~~~~ >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >adquery.c: In function âgb_searchâ: >adquery.c:449:28: warning: comparison between âGB_TYPES {aka enum gb_key_types}â and âenum gb_search_enumâ [-Wenum-compare] > if (create == GB_CREATE_CONTAINER) { > ^~ >adquery.c:455:28: warning: comparison between âGB_TYPES {aka enum gb_key_types}â and âenum gb_search_enumâ [-Wenum-compare] > if (create == GB_CREATE_CONTAINER) { > ^~ >adquery.c:526:31: warning: comparison between âGB_TYPES {aka enum gb_key_types}â and âenum gb_search_enumâ [-Wenum-compare] > if (s2 || (create == GB_CREATE_CONTAINER)) { > ^~ >adquery.c: In function âGB_command_interpreterâ: >adquery.c:861:19: warning: variable âlenâ set but not used [-Wunused-but-set-variable] > int len; > ^~~ >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >ad_save_load.c: In function âgb_write_bin_rekâ: >ad_save_load.c:799:17: 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 âGB_save_asâ: >ad_save_load.c:1079:5: warning: âGB_get_errorâ 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 âGB_save_quick_asâ: >ad_save_load.c:1126:5: warning: âGB_get_errorâ 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: âGB_get_errorâ 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: âGB_get_errorâ 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: âGB_get_errorâ 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 âGB_save_quickâ: >ad_save_load.c:1213:5: warning: âGB_get_errorâ 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: âGB_get_errorâ 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: âGB_get_errorâ 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 âgb_check_saveableâ: >ad_save_load.c:1307:9: warning: âGB_get_errorâ 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: âGB_get_errorâ 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 -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >ad_load.c: In function âGB_loginâ: >ad_load.c:1380:17: warning: ignoring return value of âgb_scan_directoryâ, declared with attribute warn_unused_result [-Wunused-result] > gb_scan_directory(base,&dir); > ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >admap.c: In function âgb_save_mapfileâ: >admap.c:636:9: warning: variable âwriteOffsetâ set but not used [-Wunused-but-set-variable] > writeOffset; > ^~~~~~~~~~~ >admap.c:635:10: warning: variable âcalcOffsetâ set but not used [-Wunused-but-set-variable] > long calcOffset, > ^~~~~~~~~~ >admap.c: In function âgb_is_valid_mapfileâ: >admap.c:722:9: warning: ignoring return value of âfreadâ, declared with attribute warn_unused_result [-Wunused-result] > fread((char *)mheader, sizeof(*mheader),1,in); > ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >adTest.c: In function âtestDataâ: >adTest.c:36:9: warning: variable âerrâ set but not used [-Wunused-but-set-variable] > int err = 0; > ^~~ >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >adtools.c: In function âGBT_check_arb_fileâ: >adtools.c:74:5: warning: ignoring return value of âfgetsâ, declared with attribute warn_unused_result [-Wunused-result] > fgets(buffer,50,in); > ^~~~~~~~~~~~~~~~~~~ >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >adali.c: In function âGBT_create_sequence_dataâ: >adali.c:597:5: warning: âGBT_add_dataâ 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 -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/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 '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/ARBDBS' >-------------------------------------------------------------------------------- Make everything in ARBDB2 >make[4]: Entering directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/ARBDB2' >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >admatch.c: In function âGBS_string_evalâ: >admatch.c:763:13: warning: ignoring return value of âgbs_build_replace_stringâ, 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 -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >In file included from adlocal.h:577:0, > from arbdb.c:12: >arbdb.c: In function âGB_copy_with_protectionâ: >adlmacros.h:483:18: warning: null argument where non-null required (argument 2) [-Wnonnull] > if (dat) memcpy(&((gbd)->info.istr.data[0]), (char *)(dat), (size_t)(memsiz)); \ > ^ >arbdb.c:1469:13: note: in expansion of macro âGB_SETSMDMALLOCâ > GB_SETSMDMALLOC(dest, GB_GETSIZE(source), > ^~~~~~~~~~~~~~~ >adlmacros.h:491:18: warning: null argument where non-null required (argument 2) [-Wnonnull] > if (dat) memcpy(exData, (char *)(dat), (size_t)(memsiz)); \ > ^ >arbdb.c:1469:13: note: in expansion of macro âGB_SETSMDMALLOCâ > GB_SETSMDMALLOC(dest, GB_GETSIZE(source), > ^~~~~~~~~~~~~~~ >arbdb.c: In function âgb_remove_callbackâ: >arbdb.c:2239:13: warning: variable âremovedâ set but not used [-Wunused-but-set-variable] > GB_BOOL removed = GB_FALSE; > ^~~~~~~ >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >ad_core.c: In function âad_useâ: >ad_core.c:11:17: warning: parameter âdummyâ set but not used [-Wunused-but-set-parameter] > void ad_use(int dummy, ...) { > ^~~~~ >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >adsystem.c: In function âgb_load_single_key_dataâ: >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 -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >adsocket.c: In function âGB_get_full_pathâ: >adsocket.c:1256:13: warning: ignoring return value of ârealpathâ, declared with attribute warn_unused_result [-Wunused-result] > realpath(newpath, path_buf[path_toggle]); > ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >adsocket.c:1260:13: warning: ignoring return value of ârealpathâ, declared with attribute warn_unused_result [-Wunused-result] > realpath(anypath, path_buf[path_toggle]); > ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >adcomm.c: In function âgbcms_write_updatedâ: >adcomm.c:303:23: warning: variable âhsâ set but not used [-Wunused-but-set-variable] > struct Hs_struct *hs; > ^~ >adcomm.c: In function âgbcms_talking_init_transactionâ: >adcomm.c:533:14: warning: variable âbufferâ set but not used [-Wunused-but-set-variable] > long *buffer; > ^~~~~~ >adcomm.c: In function âgbcm_read_binâ: >adcomm.c:1231:27: warning: variable âflags3â set but not used [-Wunused-but-set-variable] > struct gb_flag_types3 flags3; > ^~~~~~ >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >adquery.c: In function âgb_searchâ: >adquery.c:449:28: warning: comparison between âGB_TYPES {aka enum gb_key_types}â and âenum gb_search_enumâ [-Wenum-compare] > if (create == GB_CREATE_CONTAINER) { > ^~ >adquery.c:455:28: warning: comparison between âGB_TYPES {aka enum gb_key_types}â and âenum gb_search_enumâ [-Wenum-compare] > if (create == GB_CREATE_CONTAINER) { > ^~ >adquery.c:526:31: warning: comparison between âGB_TYPES {aka enum gb_key_types}â and âenum gb_search_enumâ [-Wenum-compare] > if (s2 || (create == GB_CREATE_CONTAINER)) { > ^~ >adquery.c: In function âGB_command_interpreterâ: >adquery.c:861:19: warning: variable âlenâ set but not used [-Wunused-but-set-variable] > int len; > ^~~ >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >ad_save_load.c: In function âgb_write_bin_rekâ: >ad_save_load.c:799:17: 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 âGB_save_asâ: >ad_save_load.c:1079:5: warning: âGB_get_errorâ 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 âGB_save_quick_asâ: >ad_save_load.c:1126:5: warning: âGB_get_errorâ 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: âGB_get_errorâ 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: âGB_get_errorâ 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: âGB_get_errorâ 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 âGB_save_quickâ: >ad_save_load.c:1213:5: warning: âGB_get_errorâ 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: âGB_get_errorâ 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: âGB_get_errorâ 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 âgb_check_saveableâ: >ad_save_load.c:1307:9: warning: âGB_get_errorâ 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: âGB_get_errorâ 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 -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >ad_load.c: In function âGB_loginâ: >ad_load.c:1380:17: warning: ignoring return value of âgb_scan_directoryâ, declared with attribute warn_unused_result [-Wunused-result] > gb_scan_directory(base,&dir); > ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >admap.c: In function âgb_save_mapfileâ: >admap.c:636:9: warning: variable âwriteOffsetâ set but not used [-Wunused-but-set-variable] > writeOffset; > ^~~~~~~~~~~ >admap.c:635:10: warning: variable âcalcOffsetâ set but not used [-Wunused-but-set-variable] > long calcOffset, > ^~~~~~~~~~ >admap.c: In function âgb_is_valid_mapfileâ: >admap.c:722:9: warning: ignoring return value of âfreadâ, declared with attribute warn_unused_result [-Wunused-result] > fread((char *)mheader, sizeof(*mheader),1,in); > ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >adTest.c: In function âtestDataâ: >adTest.c:36:9: warning: variable âerrâ set but not used [-Wunused-but-set-variable] > int err = 0; > ^~~ >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >adtools.c: In function âGBT_check_arb_fileâ: >adtools.c:74:5: warning: ignoring return value of âfgetsâ, declared with attribute warn_unused_result [-Wunused-result] > fgets(buffer,50,in); > ^~~~~~~~~~~~~~~~~~~ >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >adali.c: In function âGBT_create_sequence_dataâ: >adali.c:597:5: warning: âGBT_add_dataâ 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 -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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 '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/ARBDB2' >-------------------------------------------------------------------------------- Make everything in ARBDBPP >make[4]: Entering directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/ARBDBPP' >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >adt_edit.cxx: In member function âAD_ERR* ADT_SEQUENCE::show_edit_search(ADT_SEARCH*, ADT_EDIT*)â: >adt_edit.cxx:581:13: warning: variable âseq_empty_varâ set but not used [-Wunused-but-set-variable] > long seq_empty_var; > ^~~~~~~~~~~~~ >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >adseq.cxx: In member function âAD_ERR* AD_CONT::create(AD_SPECIES*, AD_ALI*)â: >adseq.cxx:1012:20: warning: âGBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)â is deprecated [-Wdeprecated-declarations] > GBDATA *erg = GBT_add_data(adptr1->gb_species,adptr2->name(),"data", GB_STRING); > ^~~~~~~~~~~~ >In file included from /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from adseq.cxx:16: >/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: âGBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)â is deprecated [-Wdeprecated-declarations] > GBDATA *erg = GBT_add_data(adptr1->gb_species,adptr2->name(),"data", GB_STRING); > ^ >In file included from /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from adseq.cxx:16: >/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++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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 '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/ARBDBPP' >-------------------------------------------------------------------------------- Make everything in WINDOW >make[4]: Entering directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/WINDOW' >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >AW_button.cxx: In function âvoid AW_variable_update_callback(Widget, XtPointer, XtPointer)â: >AW_button.cxx:199:37: warning: variable âfoundâ set but not used [-Wunused-but-set-variable] > bool found; > ^~~~~ >AW_button.cxx: In member function âint AW_window::get_index_of_element(AW_selection_list*, const char*)â: >AW_button.cxx:1617:17: warning: variable âfound_indexâ set but not used [-Wunused-but-set-variable] > int found_index = -1; > ^~~~~~~~~~~ >AW_button.cxx: In function âconst char* detect_bitmap_size(const char*, int*, int*)â: >AW_button.cxx:398:47: warning: ignoring return value of âchar* fgets(char*, int, FILE*)â, declared with attribute warn_unused_result [-Wunused-result] > fgets(buffer, MAX_LINE_LENGTH, in); > ^ >AW_button.cxx:417:51: warning: ignoring return value of âchar* fgets(char*, int, FILE*)â, declared with attribute warn_unused_result [-Wunused-result] > fgets(buffer, MAX_LINE_LENGTH, in); > ^ >AW_button.cxx:418:51: warning: ignoring return value of âchar* fgets(char*, int, FILE*)â, declared with attribute warn_unused_result [-Wunused-result] > fgets(buffer, MAX_LINE_LENGTH, in); > ^ >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >AW_device.cxx: In member function âint 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))â: >AW_device.cxx:721:22: warning: variable âyiâ set but not used [-Wunused-but-set-variable] > int xi, yi; > ^~ >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >AW_nawar.cxx: In member function âAW_awar* AW_root::awar_pointer(const char*, void*, AW_default)â: >AW_nawar.cxx:193:111: warning: passing NULL to non-pointer argument 4 of âAW_awar::AW_awar(AW_VARIABLE_TYPE, const char*, const char*, double, AW_default, AW_root*)â [-Wconversion-null] > vs = new AW_awar(AW_POINTER, var_name, (const char *)default_value, NULL, default_file, this); > ^ >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >AW_preset.cxx: In function âvoid* 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*, ...)â: >AW_preset.cxx:613:18: warning: variable âflag_no_color_selectorâ set but not used [-Wunused-but-set-variable] > bool flag_no_color_selector = false; > ^~~~~~~~~~~~~~~~~~~~~~ >AW_preset.cxx:614:18: warning: variable âflag_append_in_same_lineâ set but not used [-Wunused-but-set-variable] > bool flag_append_in_same_line = false; > ^~~~~~~~~~~~~~~~~~~~~~~~ >AW_preset.cxx: In function âbool aw_insert_gcs(AW_root*, AW_window_simple*, aw_gc_manager*, bool)â: >AW_preset.cxx:786:17: warning: variable âfirstâ set but not used [-Wunused-but-set-variable] > bool first = true; > ^~~~~ >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >AW_status.cxx: In function âint aw_status_read_int(int, int)â: >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 âvoid aw_status_timer_event(AW_root*, AW_CL, AW_CL)â: >AW_status.cxx:419:28: warning: ignoring return value of âint system(const char*)â, declared with attribute warn_unused_result [-Wunused-result] > system(buf); > ^ >AW_status.cxx: In function âvoid aw_help_edit_help(AW_window*)â: >AW_status.cxx:1746:25: warning: ignoring return value of âint system(const char*)â, declared with attribute warn_unused_result [-Wunused-result] > system(copy_cmd); > ^ >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >AW_window.cxx: In member function âvoid AW_window::insert_separator()â: >AW_window.cxx:3002:12: warning: variable âseparatorâ set but not used [-Wunused-but-set-variable] > Widget separator; > ^~~~~~~~~ >AW_window.cxx: In member function âvoid AW_window::insert_separator_help()â: >AW_window.cxx:3011:12: warning: variable âseparatorâ set but not used [-Wunused-but-set-variable] > Widget separator; > ^~~~~~~~~ >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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 '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/WINDOW' >-------------------------------------------------------------------------------- Make everything in AWT >make[4]: Entering directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/AWT' >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >AWT_input_mask.cxx: In function âvoid create_new_mask_cb(AW_window*)â: >AWT_input_mask.cxx:2242:18: warning: variable âcloseWindowâ set but not used [-Wunused-but-set-variable] > bool closeWindow = false; > ^~~~~~~~~~~ >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/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 âvoid awt_create_aww_vars(AW_root*, AW_default)â: >/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/static_assert.h:25:19: warning: typedef â_arb_compile_assertion_typedef___LINE__â locally defined but not used [-Wunused-local-typedefs] > CA_UNIQUETYPE(_arb_compile_assertion_typedef_) > ^ >/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/static_assert.h:20:26: note: in definition of macro âCA_JOINTYPEâ > #define CA_JOINTYPE(X,Y) X##Y > ^ >/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/static_assert.h:25:5: note: in expansion of macro âCA_UNIQUETYPEâ > CA_UNIQUETYPE(_arb_compile_assertion_typedef_) > ^~~~~~~~~~~~~ >AWT_www.cxx:61:5: note: in expansion of macro âCOMPILE_ASSERTâ > COMPILE_ASSERT(EXAMPLE_COUNT <= WWW_COUNT); > ^~~~~~~~~~~~~~ >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >AWT_tables.cxx: In function âvoid ad_table_field_reorder_cb(AW_window*, awt_table*)â: >AWT_tables.cxx:25:14: warning: variable âwarningâ set but not used [-Wunused-but-set-variable] > GB_ERROR warning = 0; > ^~~~~~~ >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >AWT_canio.cxx: In function âvoid AWT_print_tree_to_file_xfig(AW_window*, AW_CL)â: >AWT_canio.cxx:268:53: warning: ignoring return value of âint system(const char*)â, declared with attribute warn_unused_result [-Wunused-result] > system(GBS_global_string("xfig %s &", dest)); > ^ >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >AWT_codon_table.cxx: In function âbool AWT_is_codon(char, const char*, const AWT_allowedCode&, AWT_allowedCode&, const char**)â: >AWT_codon_table.cxx:518:18: warning: variable âcorrect_disallowed_translationâ set but not used [-Wunused-but-set-variable] > bool correct_disallowed_translation = false; > ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >AWT_config_manager.cxx: In function âvoid AWT_start_config_manager(AW_window*, AW_CL)â: >AWT_config_manager.cxx:119:24: warning: variable âreopenâ set but not used [-Wunused-but-set-variable] > bool reopen = false; > ^~~~~~ >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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 '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/AWT' >make -C bin all >make[4]: Entering directory '/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[4]: Leaving directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/bin' >-------------------------------------------------------------------------------- Make everything in GDEHELP >make[4]: Entering directory '/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 '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDEHELP' >---------------------------------------------------------------- >Collecting documentation for external programs used in GDE menus >lynx -dump -nolist -display_charset=iso-8859-1 ../GDE/PHYLIP/doc/proml.html | sed -e 's/©/(C)/' > HELP_DOC_GEN/proml.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) >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/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 >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/CAP2.help "CAP2" arb_help.head HELP_PLAIN/CAP2.help >./genhelptree.sh HELP_GEN/clustalw.help "clustalw" arb_help.head /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDE/CLUSTALW/clustalw_help /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 /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDE/AxML/AxML.doc /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/DNAml_rates.help "DNAml_rates" arb_help.head HELP_PLAIN/DNAml_rates.help >./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 >test -s HELP_DOC_GEN/fitch.doc || (echo HELP_DOC_GEN/fitch.doc not generated or empty && rm HELP_DOC_GEN/fitch.doc && false) >lynx -dump -nolist -display_charset=iso-8859-1 ../GDE/PHYLIP/doc/kitsch.html | sed -e 's/©/(C)/' > HELP_DOC_GEN/kitsch.doc >test -s HELP_DOC_GEN/kitsch.doc || (echo HELP_DOC_GEN/kitsch.doc not generated or empty && rm HELP_DOC_GEN/kitsch.doc && false) >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/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 >test -s HELP_DOC_GEN/protdist.doc || (echo HELP_DOC_GEN/protdist.doc not generated or empty && rm HELP_DOC_GEN/protdist.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/phyml.help "phyml" arb_help.head HELP_DOC_GEN/phyml.doc >./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 /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/READSEQ/Readme /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/READSEQ/Formats /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) >./genhelp.sh HELP_GEN/treepuzzle.help "treepuzzle" arb_help.head HELP_DOC_GEN/treepuzzle.doc >make[5]: Leaving directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDEHELP' >make[4]: Leaving directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GDEHELP' >-------------------------------------------------------------------------------- Make everything in AISC_MKPTPS >make[4]: Entering directory '/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 '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/AISC_MKPTPS' >-------------------------------------------------------------------------------- Make everything in AISC >make[4]: Entering directory '/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 '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/AISC' >-------------------------------------------------------------------------------- Make everything in PROBE_COM >make[4]: Entering directory '/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 '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PROBE_COM' >-------------------------------------------------------------------------------- Building prototyper >make AISC_MKPTPS/AISC_MKPTPS.dummy >make[4]: Entering directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3' >-------------------------------------------------------------------------------- Make everything in AISC_MKPTPS >make[5]: Entering directory '/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 '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/AISC_MKPTPS' >make[4]: Leaving directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3' >-------------------------------------------------------------------------------- Make everything in ARB_GDE >make[4]: Entering directory '/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++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >GDE_event.cxx: In function âvoid GDE_export(NA_Alignment*, char*, long int)â: >GDE_event.cxx:305:39: warning: âGBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)â is deprecated [-Wdeprecated-declarations] > GBDATA *gb_data = GBT_add_data(gb_extended, align, "data", GB_STRING); > ^~~~~~~~~~~~ >In file included from /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from GDE_event.cxx:12: >/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: âGBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)â is deprecated [-Wdeprecated-declarations] > GBDATA *gb_data = GBT_add_data(gb_extended, align, "data", GB_STRING); > ^ >In file included from /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from GDE_event.cxx:12: >/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: âGBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)â 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 /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from GDE_event.cxx:12: >/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: âGBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)â 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 /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from GDE_event.cxx:12: >/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: âGBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)â is deprecated [-Wdeprecated-declarations] > GBDATA *gb_color = GBT_add_data(gb_extended, align, "colmask", GB_BYTES); > ^~~~~~~~~~~~ >In file included from /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from GDE_event.cxx:12: >/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: âGBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)â is deprecated [-Wdeprecated-declarations] > GBDATA *gb_color = GBT_add_data(gb_extended, align, "colmask", GB_BYTES); > ^ >In file included from /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from GDE_event.cxx:12: >/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 âvoid GDE_startaction_cb(AW_window*, GmenuItem*, AW_CL)â: >GDE_event.cxx:557:23: warning: ignoring return value of âint system(const char*)â, declared with attribute warn_unused_result [-Wunused-result] > system(Action); > ^ >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >GDE_HGLfile.cxx: In function âvoid StripSpecial(char*)â: >GDE_HGLfile.cxx:69:9: warning: variable âiâ set but not used [-Wunused-but-set-variable] > int i,j,len; > ^ >GDE_HGLfile.cxx: In function âvoid ReadGDE(char*, NA_Alignment*, int)â: >GDE_HGLfile.cxx:199:26: warning: variable âcountâ set but not used [-Wunused-but-set-variable] > int success,count,temp = 0; > ^~~~~ >GDE_HGLfile.cxx:200:35: warning: variable âcâ set but not used [-Wunused-but-set-variable] > char in_line[GBUFSIZ],c; > ^ >GDE_HGLfile.cxx:203:18: warning: variable âgenclenâ set but not used [-Wunused-but-set-variable] > int genclen = 0,curelem = 0; > ^~~~~~~ >GDE_HGLfile.cxx:195:55: warning: parameter âtypeâ set but not used [-Wunused-but-set-parameter] > void ReadGDE(char *filename,NA_Alignment *dataset,int type) > ^~~~ >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >GDE_Genbank.cxx: In function âvoid ReadGen(char*, NA_Alignment*, int)â: >GDE_Genbank.cxx:94:13: warning: variable âcountâ set but not used [-Wunused-but-set-variable] > int count,IS_REALLY_AA = FALSE; > ^~~~~ >GDE_Genbank.cxx:89:55: warning: parameter âtypeâ set but not used [-Wunused-but-set-parameter] > void ReadGen(char *filename,NA_Alignment *dataset,int type) > ^~~~ >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >GDE_FileIO.cxx: In function âvoid ReadNA_Flat(char*, char*, int)â: >GDE_FileIO.cxx:125:9: warning: variable âiâ set but not used [-Wunused-but-set-variable] > int i, jj, c, curelem=0,offset; > ^ >GDE_FileIO.cxx:125:16: warning: variable âcâ set but not used [-Wunused-but-set-variable] > int i, jj, c, curelem=0,offset; > ^ >GDE_FileIO.cxx:128:10: warning: variable âcurnameâ set but not used [-Wunused-but-set-variable] > char curname[GBUFSIZ]; > ^~~~~~~ >GDE_FileIO.cxx:122:58: warning: parameter âtypeâ set but not used [-Wunused-but-set-parameter] > static void ReadNA_Flat(char *filename,char *dataset,int type) > ^~~~ >GDE_FileIO.cxx: In function âvoid AppendNA(NA_Base*, int, NA_Sequence*)â: >GDE_FileIO.cxx:422:14: warning: variable âtempâ set but not used [-Wunused-but-set-variable] > NA_Base *temp; > ^~~~ >GDE_FileIO.cxx: In function âvoid ReadCMask(const char*)â: >GDE_FileIO.cxx:710:24: warning: variable âorig_ctypeâ set but not used [-Wunused-but-set-variable] > int *colors = 0,orig_ctype,jj,indx = 0; > ^~~~~~~~~~ >GDE_FileIO.cxx: In function âint WriteStatus(NA_Alignment*, char*, int)â: >GDE_FileIO.cxx:860:54: warning: parameter âmethodâ set but not used [-Wunused-but-set-parameter] > int WriteStatus(NA_Alignment *aln,char *filename,int method) > ^~~~~~ >GDE_FileIO.cxx: In function âvoid ReadStatus(char*)â: >GDE_FileIO.cxx:927:23: warning: parameter âfilenameâ set but not used [-Wunused-but-set-parameter] > void ReadStatus(char *filename) > ^~~~~~~~ >GDE_FileIO.cxx: In function âvoid NormalizeOffset(NA_Alignment*)â: >GDE_FileIO.cxx:962:9: warning: variable âiâ set but not used [-Wunused-but-set-variable] > int i; > ^ >GDE_FileIO.cxx: In function âvoid ReadCMask(const char*)â: >GDE_FileIO.cxx:837:48: warning: ignoring return value of âchar* fgets(char*, int, FILE*)â, 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 '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/ARB_GDE' >-------------------------------------------------------------------------------- Make everything in NAMES_COM >make[4]: Entering directory '/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 '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/NAMES_COM' >-------------------------------------------------------------------------------- Make everything in PROBE_COM >make[4]: Entering directory '/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 '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/PROBE_COM' >-------------------------------------------------------------------------------- Make everything in AWTC >make[4]: Entering directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/AWTC' >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >AWTC_constructSequence.cxx: In function âchar* AWTC_constructSequence(int, const char**, int, char**)â: >AWTC_constructSequence.cxx:507:11: warning: unused variable âresultSeqâ [-Wunused-variable] > char *resultSeq = new char[sequenceLength+1]; > ^~~~~~~~~ >AWTC_constructSequence.cxx:509:9: warning: unused variable âoffâ [-Wunused-variable] > int off = 0; > ^~~ >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/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 '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/AWTC' >-------------------------------------------------------------------------------- Make everything in AWTI >make[4]: Entering directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/AWTI' >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >AWTI_import.cxx: In function âchar* awtc_read_line(int, char*, char*)â: >AWTI_import.cxx:559:13: warning: this âifâ clause does not guard... [-Wmisleading-indentation] > if (awtcig.in) fclose(awtcig.in);awtcig.in= 0; > ^~ >AWTI_import.cxx:559:46: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the âifâ > if (awtcig.in) fclose(awtcig.in);awtcig.in= 0; > ^~~~~~ >AWTI_import.cxx:583:13: warning: this âifâ clause does not guard... [-Wmisleading-indentation] > if (awtcig.in) fclose(awtcig.in);awtcig.in= 0; > ^~ >AWTI_import.cxx:583:46: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the âifâ > if (awtcig.in) fclose(awtcig.in);awtcig.in= 0; > ^~~~~~ >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/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 '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/AWTI' >-------------------------------------------------------------------------------- Make everything in GENOM >make[4]: Entering directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GENOM' >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >GEN_map.cxx: In function âvoid gen_extract_gene_2_pseudoSpecies(GBDATA*, GBDATA*, EG2PS_data*)â: >GEN_map.cxx:882:39: warning: âGBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)â is deprecated [-Wdeprecated-declarations] > GBDATA *gb_data = GBT_add_data(gb_exist_geneSpec, ali, "data", GB_STRING); > ^~~~~~~~~~~~ >In file included from /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from GEN_map.cxx:14: >/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: âGBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)â is deprecated [-Wdeprecated-declarations] > GBDATA *gb_data = GBT_add_data(gb_exist_geneSpec, ali, "data", GB_STRING); > ^ >In file included from /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from GEN_map.cxx:14: >/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++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >GEN_graphic.cxx: In function âint smart_text(AW_world&, AW_device*, int, const char*, AW_pos, AW_pos, AW_pos, AW_bitset, AW_CL, AW_CL, long int)â: >GEN_graphic.cxx:158:33: warning: unused parameter âselected_rangeâ [-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++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/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++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/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 '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GENOM' >-------------------------------------------------------------------------------- Make everything in GENOM_IMPORT >make[4]: Entering directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GENOM_IMPORT' >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >DBwriter.cxx: In member function âvoid DBwriter::writeSequence(const SequenceBuffer&)â: >DBwriter.cxx:226:23: warning: âGBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)â is deprecated [-Wdeprecated-declarations] > GBDATA *gb_data = GBT_add_data(gb_organism, ali_name, "data", GB_STRING); > ^~~~~~~~~~~~ >In file included from /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from DBwriter.cxx:16: >/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: âGBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)â is deprecated [-Wdeprecated-declarations] > GBDATA *gb_data = GBT_add_data(gb_organism, ali_name, "data", GB_STRING); > ^ >In file included from /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from DBwriter.cxx:16: >/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++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >SequenceBuffer.cxx: In member function âvoid BaseCounter::checkOverallCounter() constâ: >SequenceBuffer.cxx:55:67: warning: format â%uâ expects argument of type âunsigned intâ, but argument 2 has type âsize_t {aka long unsigned int}â [-Wformat=] > count[BC_ALL], all, source.c_str()); > ^ >SequenceBuffer.cxx:55:67: warning: format â%uâ expects argument of type âunsigned intâ, but argument 3 has type âsize_t {aka long unsigned int}â [-Wformat=] >SequenceBuffer.cxx: In member function âvoid BaseCounter::expectEqual(const BaseCounter&) constâ: >SequenceBuffer.cxx:116:114: warning: format â%uâ expects argument of type âunsigned intâ, but argument 2 has type âsize_t {aka long unsigned int}â [-Wformat=] > error = error+"\n "+whichCounter+": "+GBS_global_string("%u <> %u", count[i], other.count[i]); > ^ >SequenceBuffer.cxx:116:114: warning: format â%uâ expects argument of type âunsigned intâ, but argument 3 has type âsize_t {aka long unsigned int}â [-Wformat=] >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/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 '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/GENOM_IMPORT' >-------------------------------------------------------------------------------- Make everything in MERGE >make[4]: Entering directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/MERGE' >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/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 '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/MERGE' >-------------------------------------------------------------------------------- Make everything in MULTI_PROBE >make[4]: Entering directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/MULTI_PROBE' >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >MP_sondentopf.cxx: In member function âSonde* ST_Container::cache_Sonde(char*, int, double)â: >MP_sondentopf.cxx:67:13: warning: variable âhashreturnvalâ set but not used [-Wunused-but-set-variable] > long hashreturnval; > ^~~~~~~~~~~~~ >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >MP_mo_liste.cxx: In member function âlong int MO_Liste::put_entry(const char*)â: >MP_mo_liste.cxx:184:13: warning: variable âhashreturnvalâ set but not used [-Wunused-but-set-variable] > long hashreturnval; > ^~~~~~~~~~~~~ >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >MP_probe.cxx: In member function âvoid ProbeValuation::init_valuation()â: >MP_probe.cxx:178:22: warning: variable âstcâ set but not used [-Wunused-but-set-variable] > ST_Container *stc; > ^~~ >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/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 '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/MULTI_PROBE' >-------------------------------------------------------------------------------- Make everything in NTREE >make[4]: Entering directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/NTREE' >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >AP_consensus.cxx: In function âconst char* CON_export(char*, char*, int**, char*, int*, char*, int, long int, long int, int, int, int, double, double, int, int)â: >AP_consensus.cxx:409:23: warning: âGBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)â is deprecated [-Wdeprecated-declarations] > GBDATA *gb_data = GBT_add_data(gb_extended, align,"data", GB_STRING); > ^~~~~~~~~~~~ >In file included from /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from AP_consensus.cxx:52: >/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: âGBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)â is deprecated [-Wdeprecated-declarations] > GBDATA *gb_data = GBT_add_data(gb_extended, align,"data", GB_STRING); > ^ >In file included from /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from AP_consensus.cxx:52: >/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: âGBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)â is deprecated [-Wdeprecated-declarations] > GBDATA *gb_options= GBT_add_data(gb_extended, align,"_TYPE", GB_STRING); > ^~~~~~~~~~~~ >In file included from /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from AP_consensus.cxx:52: >/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: âGBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)â is deprecated [-Wdeprecated-declarations] > GBDATA *gb_options= GBT_add_data(gb_extended, align,"_TYPE", GB_STRING); > ^ >In file included from /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from AP_consensus.cxx:52: >/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: âGBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)â is deprecated [-Wdeprecated-declarations] > GBDATA *gb_graph = GBT_add_data(gb_extended, align,"FREQUENCIES", GB_DB); > ^~~~~~~~~~~~ >In file included from /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from AP_consensus.cxx:52: >/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: âGBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)â is deprecated [-Wdeprecated-declarations] > GBDATA *gb_graph = GBT_add_data(gb_extended, align,"FREQUENCIES", GB_DB); > ^ >In file included from /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from AP_consensus.cxx:52: >/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: In function âvoid CON_calc_max_freq_cb(AW_window*)â: >AP_consensus.cxx:962:27: warning: âGBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)â is deprecated [-Wdeprecated-declarations] > GBDATA *gb_data = GBT_add_data(gb_extended, align,"data", GB_STRING); > ^~~~~~~~~~~~ >In file included from /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from AP_consensus.cxx:52: >/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: âGBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)â is deprecated [-Wdeprecated-declarations] > GBDATA *gb_data = GBT_add_data(gb_extended, align,"data", GB_STRING); > ^ >In file included from /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from AP_consensus.cxx:52: >/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: âGBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)â is deprecated [-Wdeprecated-declarations] > GBDATA *gb_data2 = GBT_add_data(gb_extended, align,"dat2", GB_STRING); > ^~~~~~~~~~~~ >In file included from /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from AP_consensus.cxx:52: >/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: âGBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)â is deprecated [-Wdeprecated-declarations] > GBDATA *gb_data2 = GBT_add_data(gb_extended, align,"dat2", GB_STRING); > ^ >In file included from /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from AP_consensus.cxx:52: >/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: âGBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)â is deprecated [-Wdeprecated-declarations] > GBDATA *gb_options = GBT_add_data(gb_extended, align,"_TYPE", GB_STRING); > ^~~~~~~~~~~~ >In file included from /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from AP_consensus.cxx:52: >/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: âGBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)â is deprecated [-Wdeprecated-declarations] > GBDATA *gb_options = GBT_add_data(gb_extended, align,"_TYPE", GB_STRING); > ^ >In file included from /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from AP_consensus.cxx:52: >/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++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >AP_conservProfile2Gnuplot.cxx: In function âvoid AP_conservProfile2Gnuplot_callback(AW_window*)â: >AP_conservProfile2Gnuplot.cxx:58:42: warning: ignoring return value of âconst char* GB_xcmd(const char*, GB_BOOL, GB_BOOL)â, 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++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >AP_cprofile.cxx: In function âvoid CPRO_workupstatistic(unsigned char)â: >AP_cprofile.cxx:234:17: warning: variable âcolmaxâ set but not used [-Wunused-but-set-variable] > long column,colmax,memneeded=0; > ^~~~~~ >AP_cprofile.cxx: In function âvoid CPRO_memrequirement_cb(AW_root*)â: >AP_cprofile.cxx:663:10: warning: variable âversusâ set but not used [-Wunused-but-set-variable] > char versus=0; /* all vs all */ > ^~~~~~ >AP_cprofile.cxx: In function âvoid CPRO_condense_cb(AW_window*, AW_CL)â: >AP_cprofile.cxx:1420:14: warning: âGBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)â is deprecated [-Wdeprecated-declarations] > gb_param=GBT_add_data(gb_extended,align,"_TYPE",GB_STRING); > ^~~~~~~~~~~~ >In file included from /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from AP_cprofile.cxx:51: >/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: âGBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)â is deprecated [-Wdeprecated-declarations] > gb_param=GBT_add_data(gb_extended,align,"_TYPE",GB_STRING); > ^ >In file included from /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from AP_cprofile.cxx:51: >/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: âGBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)â is deprecated [-Wdeprecated-declarations] > GBDATA *gb_data = GBT_add_data(gb_extended, align,"data", GB_STRING); > ^~~~~~~~~~~~ >In file included from /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from AP_cprofile.cxx:51: >/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: âGBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)â is deprecated [-Wdeprecated-declarations] > GBDATA *gb_data = GBT_add_data(gb_extended, align,"data", GB_STRING); > ^ >In file included from /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from AP_cprofile.cxx:51: >/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++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >AP_csp_2_gnuplot.cxx: In function âchar* get_overlay_files(AW_root*, const char*, const char*&)â: >AP_csp_2_gnuplot.cxx:92:50: warning: âconst char* GB_get_error()â is deprecated [-Wdeprecated-declarations] > if (!found_prefix_files) error = GB_get_error(); > ^~~~~~~~~~~~ >In file included from /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdb.h:268:0, > from AP_csp_2_gnuplot.cxx:8: >/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: âconst char* GB_get_error()â is deprecated [-Wdeprecated-declarations] > if (!found_prefix_files) error = GB_get_error(); > ^ >In file included from /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdb.h:268:0, > from AP_csp_2_gnuplot.cxx:8: >/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: âconst char* GB_get_error()â is deprecated [-Wdeprecated-declarations] > if (!found_postfix_files) error = GB_get_error(); > ^~~~~~~~~~~~ >In file included from /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdb.h:268:0, > from AP_csp_2_gnuplot.cxx:8: >/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: âconst char* GB_get_error()â is deprecated [-Wdeprecated-declarations] > if (!found_postfix_files) error = GB_get_error(); > ^ >In file included from /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdb.h:268:0, > from AP_csp_2_gnuplot.cxx:8: >/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 âvoid AP_csp_2_gnuplot_cb(AW_window*, AW_CL, AW_CL)â: >AP_csp_2_gnuplot.cxx:388:62: warning: ignoring return value of âconst char* GB_xcmd(const char*, GB_BOOL, GB_BOOL)â, declared with attribute warn_unused_result [-Wunused-result] > GB_xcmd(script, GB_TRUE, GB_TRUE); > ^ >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >NT_cb.cxx: In function âvoid NT_system_cb2(AW_window*, AW_CL, AW_CL)â: >NT_cb.cxx:128:35: warning: ignoring return value of âconst char* GB_xcmd(const char*, GB_BOOL, GB_BOOL)â, declared with attribute warn_unused_result [-Wunused-result] > GB_xcmd(sys,GB_TRUE, GB_FALSE); > ^ >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >NT_concatenate.cxx: In function âconst char* displayAlignmentInfo(GBDATA*, GB_ERROR, char*, char*)â: >NT_concatenate.cxx:310:37: warning: âGBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)â is deprecated [-Wdeprecated-declarations] > GBDATA *gb_data = GBT_add_data(gb_extended, new_ali_name,"data", GB_STRING); > ^~~~~~~~~~~~ >In file included from /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from NT_concatenate.cxx:22: >/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: âGBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)â is deprecated [-Wdeprecated-declarations] > GBDATA *gb_data = GBT_add_data(gb_extended, new_ali_name,"data", GB_STRING); > ^ >In file included from /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from NT_concatenate.cxx:22: >/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 âvoid concatenateAlignments(AW_window*)â: >NT_concatenate.cxx:415:39: warning: âGBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)â is deprecated [-Wdeprecated-declarations] > GBDATA *gb_data = GBT_add_data(gb_species, new_ali_name, "data", GB_STRING); > ^~~~~~~~~~~~ >In file included from /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from NT_concatenate.cxx:22: >/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: âGBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)â is deprecated [-Wdeprecated-declarations] > GBDATA *gb_data = GBT_add_data(gb_species, new_ali_name, "data", GB_STRING); > ^ >In file included from /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from NT_concatenate.cxx:22: >/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 âGBDATA* concatenateFieldsCreateNewSpecies(AW_window*, GBDATA*, speciesConcatenateList)â: >NT_concatenate.cxx:664:39: warning: âGBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)â 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 /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from NT_concatenate.cxx:22: >/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: âGBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)â 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 /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/arbdbt.h:82:0, > from NT_concatenate.cxx:22: >/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++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >NT_edconf.cxx:384:38: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] > GBCMC_system(GLOBAL_gb_main, "arb_edit4 -c "CONFNAME" &"); > ^ >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >NT_import.cxx: In function âvoid NT_import_sequences(AW_window*, AW_CL, AW_CL)â: >NT_import.cxx:52:30: warning: variable âgb_merge_is_genom_dbâ 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++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >NT_main.cxx: In function âint main(int, char**)â: >NT_main.cxx:399:50: warning: ignoring return value of âint system(const char*)â, declared with attribute warn_unused_result [-Wunused-result] > system("touch ${HOME}/.arb_prop/msgtime"); > ^ >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -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/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE -I/usr/X11R6/include >NT_validManual.cxx: In function âvoid fillSelNamList(selectValidNameStruct*)â: >NT_validManual.cxx:56:75: error: no match for âoperator<<â (operand types are âstd::basic_ostream<char>â and âstd::ostream {aka std::basic_ostream<char>}â) > if (!GB_validNamesCont){std::cout << "validNames Container not found" << std:: cout; } > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ >In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/istream:39:0, > from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/fstream:38, > from NT_validManual.cxx:18: >/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:628:5: note: candidate: std::basic_ostream<_CharT, _Traits>& std::operator<<(std::basic_ostream<_CharT, _Traits>&&, const _Tp&) [with _CharT = char; _Traits = std::char_traits<char>; _Tp = std::basic_ostream<char>] <near match> > operator<<(basic_ostream<_CharT, _Traits>&& __os, const _Tp& __x) > ^~~~~~~~ >/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:628:5: note: conversion of argument 1 would be ill-formed: >NT_validManual.cxx:56:39: error: cannot bind âstd::basic_ostream<char>â lvalue to âstd::basic_ostream<char>&&â > if (!GB_validNamesCont){std::cout << "validNames Container not found" << std:: cout; } > ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >NT_validManual.cxx:56:75: note: candidate: operator<<(int, int) <built-in> > if (!GB_validNamesCont){std::cout << "validNames Container not found" << std:: cout; } > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ >NT_validManual.cxx:56:75: note: no known conversion for argument 2 from âstd::ostream {aka std::basic_ostream<char>}â to âintâ >In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/istream:39:0, > from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/fstream:38, > from NT_validManual.cxx:18: >/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:108:7: note: candidate: std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(std::basic_ostream<_CharT, _Traits>::__ostream_type& (*)(std::basic_ostream<_CharT, _Traits>::__ostream_type&)) [with _CharT = char; _Traits = std::char_traits<char>; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream<char>] > operator<<(__ostream_type& (*__pf)(__ostream_type&)) > ^~~~~~~~ >/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:108:7: note: no known conversion for argument 1 from âstd::ostream {aka std::basic_ostream<char>}â to âstd::basic_ostream<char>::__ostream_type& (*)(std::basic_ostream<char>::__ostream_type&) {aka std::basic_ostream<char>& (*)(std::basic_ostream<char>&)}â >/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:117:7: note: candidate: std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(std::basic_ostream<_CharT, _Traits>::__ios_type& (*)(std::basic_ostream<_CharT, _Traits>::__ios_type&)) [with _CharT = char; _Traits = std::char_traits<char>; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream<char>; std::basic_ostream<_CharT, _Traits>::__ios_type = std::basic_ios<char>] > operator<<(__ios_type& (*__pf)(__ios_type&)) > ^~~~~~~~ >/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:117:7: note: no known conversion for argument 1 from âstd::ostream {aka std::basic_ostream<char>}â to âstd::basic_ostream<char>::__ios_type& (*)(std::basic_ostream<char>::__ios_type&) {aka std::basic_ios<char>& (*)(std::basic_ios<char>&)}â >/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:127:7: note: candidate: std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(std::ios_base& (*)(std::ios_base&)) [with _CharT = char; _Traits = std::char_traits<char>; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream<char>] > operator<<(ios_base& (*__pf) (ios_base&)) > ^~~~~~~~ >/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:127:7: note: no known conversion for argument 1 from âstd::ostream {aka std::basic_ostream<char>}â to âstd::ios_base& (*)(std::ios_base&)â >/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:166:7: note: candidate: std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(long int) [with _CharT = char; _Traits = std::char_traits<char>; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream<char>] > operator<<(long __n) > ^~~~~~~~ >/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:166:7: note: no known conversion for argument 1 from âstd::ostream {aka std::basic_ostream<char>}â to âlong intâ >/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:170:7: note: candidate: std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(long unsigned int) [with _CharT = char; _Traits = std::char_traits<char>; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream<char>] > operator<<(unsigned long __n) > ^~~~~~~~ >/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:170:7: note: no known conversion for argument 1 from âstd::ostream {aka std::basic_ostream<char>}â to âlong unsigned intâ >/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:174:7: note: candidate: std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(bool) [with _CharT = char; _Traits = std::char_traits<char>; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream<char>] > operator<<(bool __n) > ^~~~~~~~ >/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:174:7: note: no known conversion for argument 1 from âstd::ostream {aka std::basic_ostream<char>}â to âboolâ >In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:638:0, > from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/istream:39, > from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/fstream:38, > from NT_validManual.cxx:18: >/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/ostream.tcc:91:5: note: candidate: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(short int) [with _CharT = char; _Traits = std::char_traits<char>] > basic_ostream<_CharT, _Traits>:: > ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/ostream.tcc:91:5: note: no known conversion for argument 1 from âstd::ostream {aka std::basic_ostream<char>}â to âshort intâ >In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/istream:39:0, > from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/fstream:38, > from NT_validManual.cxx:18: >/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:181:7: note: candidate: std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(short unsigned int) [with _CharT = char; _Traits = std::char_traits<char>; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream<char>] > operator<<(unsigned short __n) > ^~~~~~~~ >/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:181:7: note: no known conversion for argument 1 from âstd::ostream {aka std::basic_ostream<char>}â to âshort unsigned intâ >In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:638:0, > from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/istream:39, > from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/fstream:38, > from NT_validManual.cxx:18: >/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/ostream.tcc:105:5: note: candidate: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(int) [with _CharT = char; _Traits = std::char_traits<char>] > basic_ostream<_CharT, _Traits>:: > ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/ostream.tcc:105:5: note: no known conversion for argument 1 from âstd::ostream {aka std::basic_ostream<char>}â to âintâ >In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/istream:39:0, > from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/fstream:38, > from NT_validManual.cxx:18: >/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:192:7: note: candidate: std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(unsigned int) [with _CharT = char; _Traits = std::char_traits<char>; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream<char>] > operator<<(unsigned int __n) > ^~~~~~~~ >/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:192:7: note: no known conversion for argument 1 from âstd::ostream {aka std::basic_ostream<char>}â to âunsigned intâ >/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:201:7: note: candidate: std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(long long int) [with _CharT = char; _Traits = std::char_traits<char>; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream<char>] > operator<<(long long __n) > ^~~~~~~~ >/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:201:7: note: no known conversion for argument 1 from âstd::ostream {aka std::basic_ostream<char>}â to âlong long intâ >/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:205:7: note: candidate: std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(long long unsigned int) [with _CharT = char; _Traits = std::char_traits<char>; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream<char>] > operator<<(unsigned long long __n) > ^~~~~~~~ >/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:205:7: note: no known conversion for argument 1 from âstd::ostream {aka std::basic_ostream<char>}â to âlong long unsigned intâ >/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:220:7: note: candidate: std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits<char>; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream<char>] > operator<<(double __f) > ^~~~~~~~ >/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:220:7: note: no known conversion for argument 1 from âstd::ostream {aka std::basic_ostream<char>}â to âdoubleâ >/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:224:7: note: candidate: std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(float) [with _CharT = char; _Traits = std::char_traits<char>; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream<char>] > operator<<(float __f) > ^~~~~~~~ >/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:224:7: note: no known conversion for argument 1 from âstd::ostream {aka std::basic_ostream<char>}â to âfloatâ >/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:232:7: note: candidate: std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(long double) [with _CharT = char; _Traits = std::char_traits<char>; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream<char>] > operator<<(long double __f) > ^~~~~~~~ >/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:232:7: note: no known conversion for argument 1 from âstd::ostream {aka std::basic_ostream<char>}â to âlong doubleâ >/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:245:7: note: candidate: std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(const void*) [with _CharT = char; _Traits = std::char_traits<char>; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream<char>] > operator<<(const void* __p) > ^~~~~~~~ >/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:245:7: note: no known conversion for argument 1 from âstd::ostream {aka std::basic_ostream<char>}â to âconst void*â >In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:638:0, > from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/istream:39, > from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/fstream:38, > from NT_validManual.cxx:18: >/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/ostream.tcc:119:5: note: candidate: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(std::basic_ostream<_CharT, _Traits>::__streambuf_type*) [with _CharT = char; _Traits = std::char_traits<char>; std::basic_ostream<_CharT, _Traits>::__streambuf_type = std::basic_streambuf<char>] > basic_ostream<_CharT, _Traits>:: > ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/ostream.tcc:119:5: note: no known conversion for argument 1 from âstd::ostream {aka std::basic_ostream<char>}â to âstd::basic_ostream<char>::__streambuf_type* {aka std::basic_streambuf<char>*}â >In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/istream:39:0, > from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/fstream:38, > from NT_validManual.cxx:18: >/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:574:5: note: candidate: template<class _Traits> std::basic_ostream<char, _Traits>& std::operator<<(std::basic_ostream<char, _Traits>&, const unsigned char*) > operator<<(basic_ostream<char, _Traits>& __out, const unsigned char* __s) > ^~~~~~~~ >/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:574:5: note: template argument deduction/substitution failed: >NT_validManual.cxx:56:84: note: cannot convert âstd::coutâ (type âstd::ostream {aka std::basic_ostream<char>}â) to type âconst unsigned char*â > if (!GB_validNamesCont){std::cout << "validNames Container not found" << std:: cout; } > ^~~~ >In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/istream:39:0, > from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/fstream:38, > from NT_validManual.cxx:18: >/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:569:5: note: candidate: template<class _Traits> std::basic_ostream<char, _Traits>& std::operator<<(std::basic_ostream<char, _Traits>&, const signed char*) > operator<<(basic_ostream<char, _Traits>& __out, const signed char* __s) > ^~~~~~~~ >/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:569:5: note: template argument deduction/substitution failed: >NT_validManual.cxx:56:84: note: cannot convert âstd::coutâ (type âstd::ostream {aka std::basic_ostream<char>}â) to type âconst signed char*â > if (!GB_validNamesCont){std::cout << "validNames Container not found" << std:: cout; } > ^~~~ >In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/istream:39:0, > from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/fstream:38, > from NT_validManual.cxx:18: >/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:556:5: note: candidate: template<class _Traits> std::basic_ostream<char, _Traits>& std::operator<<(std::basic_ostream<char, _Traits>&, const char*) > operator<<(basic_ostream<char, _Traits>& __out, const char* __s) > ^~~~~~~~ >/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:556:5: note: template argument deduction/substitution failed: >NT_validManual.cxx:56:84: note: cannot convert âstd::coutâ (type âstd::ostream {aka std::basic_ostream<char>}â) to type âconst char*â > if (!GB_validNamesCont){std::cout << "validNames Container not found" << std:: cout; } > ^~~~ >In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:638:0, > from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/istream:39, > from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/fstream:38, > from NT_validManual.cxx:18: >/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/ostream.tcc:321:5: note: candidate: template<class _CharT, class _Traits> std::basic_ostream<_CharT, _Traits>& std::operator<<(std::basic_ostream<_CharT, _Traits>&, const char*) > operator<<(basic_ostream<_CharT, _Traits>& __out, const char* __s) > ^~~~~~~~ >/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/ostream.tcc:321:5: note: template argument deduction/substitution failed: >NT_validManual.cxx:56:84: note: cannot convert âstd::coutâ (type âstd::ostream {aka std::basic_ostream<char>}â) to type âconst char*â > if (!GB_validNamesCont){std::cout << "validNames Container not found" << std:: cout; } > ^~~~ >In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/istream:39:0, > from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/fstream:38, > from NT_validManual.cxx:18: >/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:539:5: note: candidate: template<class _CharT, class _Traits> std::basic_ostream<_CharT, _Traits>& std::operator<<(std::basic_ostream<_CharT, _Traits>&, const _CharT*) > operator<<(basic_ostream<_CharT, _Traits>& __out, const _CharT* __s) > ^~~~~~~~ >/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:539:5: note: template argument deduction/substitution failed: >NT_validManual.cxx:56:84: note: mismatched types âconst _CharT*â and âstd::basic_ostream<char>â > if (!GB_validNamesCont){std::cout << "validNames Container not found" << std:: cout; } > ^~~~ >In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/istream:39:0, > from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/fstream:38, > from NT_validManual.cxx:18: >/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:519:5: note: candidate: template<class _Traits> std::basic_ostream<char, _Traits>& std::operator<<(std::basic_ostream<char, _Traits>&, unsigned char) > operator<<(basic_ostream<char, _Traits>& __out, unsigned char __c) > ^~~~~~~~ >/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:519:5: note: template argument deduction/substitution failed: >NT_validManual.cxx:56:84: note: cannot convert âstd::coutâ (type âstd::ostream {aka std::basic_ostream<char>}â) to type âunsigned charâ > if (!GB_validNamesCont){std::cout << "validNames Container not found" << std:: cout; } > ^~~~ >In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/istream:39:0, > from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/fstream:38, > from NT_validManual.cxx:18: >/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:514:5: note: candidate: template<class _Traits> std::basic_ostream<char, _Traits>& std::operator<<(std::basic_ostream<char, _Traits>&, signed char) > operator<<(basic_ostream<char, _Traits>& __out, signed char __c) > ^~~~~~~~ >/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:514:5: note: template argument deduction/substitution failed: >NT_validManual.cxx:56:84: note: cannot convert âstd::coutâ (type âstd::ostream {aka std::basic_ostream<char>}â) to type âsigned charâ > if (!GB_validNamesCont){std::cout << "validNames Container not found" << std:: cout; } > ^~~~ >In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/istream:39:0, > from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/fstream:38, > from NT_validManual.cxx:18: >/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:508:5: note: candidate: template<class _Traits> std::basic_ostream<char, _Traits>& std::operator<<(std::basic_ostream<char, _Traits>&, char) > operator<<(basic_ostream<char, _Traits>& __out, char __c) > ^~~~~~~~ >/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:508:5: note: template argument deduction/substitution failed: >NT_validManual.cxx:56:84: note: cannot convert âstd::coutâ (type âstd::ostream {aka std::basic_ostream<char>}â) to type âcharâ > if (!GB_validNamesCont){std::cout << "validNames Container not found" << std:: cout; } > ^~~~ >In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/istream:39:0, > from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/fstream:38, > from NT_validManual.cxx:18: >/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:502:5: note: candidate: template<class _CharT, class _Traits> std::basic_ostream<_CharT, _Traits>& std::operator<<(std::basic_ostream<_CharT, _Traits>&, char) > operator<<(basic_ostream<_CharT, _Traits>& __out, char __c) > ^~~~~~~~ >/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:502:5: note: template argument deduction/substitution failed: >NT_validManual.cxx:56:84: note: cannot convert âstd::coutâ (type âstd::ostream {aka std::basic_ostream<char>}â) to type âcharâ > if (!GB_validNamesCont){std::cout << "validNames Container not found" << std:: cout; } > ^~~~ >In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/istream:39:0, > from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/fstream:38, > from NT_validManual.cxx:18: >/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:497:5: note: candidate: template<class _CharT, class _Traits> std::basic_ostream<_CharT, _Traits>& std::operator<<(std::basic_ostream<_CharT, _Traits>&, _CharT) > operator<<(basic_ostream<_CharT, _Traits>& __out, _CharT __c) > ^~~~~~~~ >/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:497:5: note: template argument deduction/substitution failed: >NT_validManual.cxx:56:84: note: deduced conflicting types for parameter â_CharTâ (âcharâ and âstd::basic_ostream<char>â) > if (!GB_validNamesCont){std::cout << "validNames Container not found" << std:: cout; } > ^~~~ >In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/ios_base.h:46:0, > from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ios:42, > from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/istream:38, > from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/fstream:38, > from NT_validManual.cxx:18: >/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/system_error:209:5: note: candidate: template<class _CharT, class _Traits> std::basic_ostream<_CharT, _Traits>& std::operator<<(std::basic_ostream<_CharT, _Traits>&, const std::error_code&) > operator<<(basic_ostream<_CharT, _Traits>& __os, const error_code& __e) > ^~~~~~~~ >/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/system_error:209:5: note: template argument deduction/substitution failed: >NT_validManual.cxx:56:84: note: cannot convert âstd::coutâ (type âstd::ostream {aka std::basic_ostream<char>}â) to type âconst std::error_code&â > if (!GB_validNamesCont){std::cout << "validNames Container not found" << std:: cout; } > ^~~~ >In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/string:52:0, > from NT_validManual.cxx:4: >/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/basic_string.h:5325:5: note: candidate: template<class _CharT, class _Traits, class _Alloc> std::basic_ostream<_CharT, _Traits>& std::operator<<(std::basic_ostream<_CharT, _Traits>&, const std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&) > operator<<(basic_ostream<_CharT, _Traits>& __os, > ^~~~~~~~ >/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/basic_string.h:5325:5: note: template argument deduction/substitution failed: >NT_validManual.cxx:56:84: note: âstd::ostream {aka std::basic_ostream<char>}â is not derived from âconst std::__cxx11::basic_string<_CharT, _Traits, _Alloc>â > if (!GB_validNamesCont){std::cout << "validNames Container not found" << std:: cout; } > ^~~~ >make[4]: *** [Makefile:48: NT_validManual.o] Error 1 >make[4]: Leaving directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/NTREE' >make[3]: *** [Makefile:983: NTREE/NTREE.dummy] Error 1 >make[3]: Leaving directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3' >make[2]: *** [Makefile:1410: arb] Error 2 >make[2]: Leaving directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3' >make[1]: *** [Makefile:1415: all] Error 2 >make[1]: Leaving directory '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3' >make: *** [Makefile:1335: rebuild] Error 2 > * ERROR: sci-biology/arb-5.3::gentoo failed (compile phase): > * emake failed > * > * If you need support, post the output of `emerge --info '=sci-biology/arb-5.3::gentoo'`, > * the complete build log and the output of `emerge -pqv '=sci-biology/arb-5.3::gentoo'`. > * The complete build log is located at '/var/log/portage/sci-biology:arb-5.3:20161005-141555.log'. > * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/arb-5.3/temp/build.log'. > * The ebuild environment file is located at '/var/tmp/portage/sci-biology/arb-5.3/temp/environment'. > * Working directory: '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3' > * S: '/var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3'
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