* 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: ‘../lib/help_html’: No such file or directory rm -f xml.stamp dummy _index.html rm -f `find Xml -name "*.xml"` find: ‘Xml’: No such file or directory make -C genhelp clean make[3]: Entering directory '/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 ‘int do_com_next(const char*)’: aisc_commands.c:906:21: warning: variable ‘p’ set but not used [-Wunused-but-set-variable] char *p; ^ x86_64-pc-linux-gnu-g++ -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 ‘const char* alignCompactedTo(AWTC_CompactedSubSequence*, const AWTC_FastSearchSequence*, int, GB_CSTR, long int, GBDATA*, GBDATA*, const AlignParams&)’: fast_aligner.cxx:1254:31: warning: ‘GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)’ is deprecated [-Wdeprecated-declarations] GBDATA *gbd = GBT_add_data(gb_toAlign, alignment, "data", GB_STRING); ^~~~~~~~~~~~ In file included from /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: ‘GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)’ is deprecated [-Wdeprecated-declarations] GBDATA *gbd = GBT_add_data(gb_toAlign, alignment, "data", GB_STRING); ^ In file included from /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 ‘void AWTC_start_faligning(AW_window*, AW_CL)’: fast_aligner.cxx:2368:57: warning: narrowing conversion of ‘root->AW_root::awar(((const char*)"faligner/next_relatives"))->AW_awar::read_int()’ from ‘long int’ to ‘int’ inside { } [-Wnarrowing] root->awar(FA_AWAR_NEXT_RELATIVES)->read_int(), ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ fast_aligner.cxx:2369:52: warning: narrowing conversion of ‘root->AW_root::awar(((const char*)"next_neighbours/oligo_len"))->AW_awar::read_int()’ from ‘long int’ to ‘int’ inside { } [-Wnarrowing] root->awar(AWAR_NN_OLIGO_LEN)->read_int(), ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ fast_aligner.cxx:2370:53: warning: narrowing conversion of ‘root->AW_root::awar(((const char*)"next_neighbours/mismatches"))->AW_awar::read_int()’ from ‘long int’ to ‘int’ inside { } [-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 ‘GBS_string_eval’: admatch.c:763:13: warning: ignoring return value of ‘gbs_build_replace_string’, declared with attribute warn_unused_result [-Wunused-result] gbs_build_replace_string(strstruct,bar,wildcard, max_wildcard, mwildcard, max_mwildcard,gb_container); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -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 ‘GB_copy_with_protection’: 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 ‘GB_SETSMDMALLOC’ 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 ‘GB_SETSMDMALLOC’ GB_SETSMDMALLOC(dest, GB_GETSIZE(source), ^~~~~~~~~~~~~~~ arbdb.c: In function ‘gb_remove_callback’: arbdb.c:2239:13: warning: variable ‘removed’ set but not used [-Wunused-but-set-variable] GB_BOOL removed = GB_FALSE; ^~~~~~~ x86_64-pc-linux-gnu-gcc -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 ‘ad_use’: ad_core.c:11:17: warning: parameter ‘dummy’ set but not used [-Wunused-but-set-parameter] void ad_use(int dummy, ...) { ^~~~~ x86_64-pc-linux-gnu-gcc -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 ‘gb_load_single_key_data’: adsystem.c:141:101: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] GB_ensure_callback(gb_key,(GB_CB_TYPE)(GB_CB_CHANGED|GB_CB_DELETE),gb_system_key_changed_cb,(int *)q); ^ adsystem.c:159:123: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] GB_remove_callback(ks->gb_master_ali,(GB_CB_TYPE)(GB_CB_CHANGED|GB_CB_DELETE),gb_system_master_changed_cb,(int *)q); ^ adsystem.c:160:123: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] GB_add_callback (ks->gb_master_ali,(GB_CB_TYPE)(GB_CB_CHANGED|GB_CB_DELETE),gb_system_master_changed_cb,(int *)q); ^ x86_64-pc-linux-gnu-gcc -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 ‘GB_get_full_path’: adsocket.c:1256:13: warning: ignoring return value of ‘realpath’, declared with attribute warn_unused_result [-Wunused-result] realpath(newpath, path_buf[path_toggle]); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ adsocket.c:1260:13: warning: ignoring return value of ‘realpath’, declared with attribute warn_unused_result [-Wunused-result] realpath(anypath, path_buf[path_toggle]); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -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 ‘gbcms_write_updated’: adcomm.c:303:23: warning: variable ‘hs’ set but not used [-Wunused-but-set-variable] struct Hs_struct *hs; ^~ adcomm.c: In function ‘gbcms_talking_init_transaction’: adcomm.c:533:14: warning: variable ‘buffer’ set but not used [-Wunused-but-set-variable] long *buffer; ^~~~~~ adcomm.c: In function ‘gbcm_read_bin’: adcomm.c:1231:27: warning: variable ‘flags3’ set but not used [-Wunused-but-set-variable] struct gb_flag_types3 flags3; ^~~~~~ x86_64-pc-linux-gnu-gcc -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 ‘gb_search’: adquery.c:449:28: warning: comparison between ‘GB_TYPES {aka enum gb_key_types}’ and ‘enum gb_search_enum’ [-Wenum-compare] if (create == GB_CREATE_CONTAINER) { ^~ adquery.c:455:28: warning: comparison between ‘GB_TYPES {aka enum gb_key_types}’ and ‘enum gb_search_enum’ [-Wenum-compare] if (create == GB_CREATE_CONTAINER) { ^~ adquery.c:526:31: warning: comparison between ‘GB_TYPES {aka enum gb_key_types}’ and ‘enum gb_search_enum’ [-Wenum-compare] if (s2 || (create == GB_CREATE_CONTAINER)) { ^~ adquery.c: In function ‘GB_command_interpreter’: adquery.c:861:19: warning: variable ‘len’ set but not used [-Wunused-but-set-variable] int len; ^~~ x86_64-pc-linux-gnu-gcc -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 ‘gb_write_bin_rek’: 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 ‘GB_save_as’: ad_save_load.c:1079:5: warning: ‘GB_get_error’ is deprecated [-Wdeprecated-declarations] return GB_get_error(); ^~~~~~ In file included from arbdb.h:268:0, from adlocal.h:573, from ad_save_load.c:13: ./ad_prot.h:43:10: note: declared here GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; ^~~~~~~~~~~~ ad_save_load.c: In function ‘GB_save_quick_as’: ad_save_load.c:1126:5: warning: ‘GB_get_error’ is deprecated [-Wdeprecated-declarations] if (gb_check_saveable(gb_main,path,"bn")) return GB_get_error(); ^~ In file included from arbdb.h:268:0, from adlocal.h:573, from ad_save_load.c:13: ./ad_prot.h:43:10: note: declared here GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; ^~~~~~~~~~~~ ad_save_load.c:1148:9: warning: ‘GB_get_error’ is deprecated [-Wdeprecated-declarations] return GB_get_error(); ^~~~~~ In file included from arbdb.h:268:0, from adlocal.h:573, from ad_save_load.c:13: ./ad_prot.h:43:10: note: declared here GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; ^~~~~~~~~~~~ ad_save_load.c:1173:9: warning: ‘GB_get_error’ is deprecated [-Wdeprecated-declarations] return GB_get_error(); ^~~~~~ In file included from arbdb.h:268:0, from adlocal.h:573, from ad_save_load.c:13: ./ad_prot.h:43:10: note: declared here GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; ^~~~~~~~~~~~ ad_save_load.c:1184:9: warning: ‘GB_get_error’ is deprecated [-Wdeprecated-declarations] GB_warning(GB_get_error()); ^~~~~~~~~~ In file included from arbdb.h:268:0, from adlocal.h:573, from ad_save_load.c:13: ./ad_prot.h:43:10: note: declared here GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; ^~~~~~~~~~~~ ad_save_load.c: In function ‘GB_save_quick’: ad_save_load.c:1213:5: warning: ‘GB_get_error’ is deprecated [-Wdeprecated-declarations] if (gb_check_saveable(gb,refpath,"q")) return GB_get_error(); ^~ In file included from arbdb.h:268:0, from adlocal.h:573, from ad_save_load.c:13: ./ad_prot.h:43:10: note: declared here GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; ^~~~~~~~~~~~ ad_save_load.c:1234:9: warning: ‘GB_get_error’ is deprecated [-Wdeprecated-declarations] return GB_get_error(); ^~~~~~ In file included from arbdb.h:268:0, from adlocal.h:573, from ad_save_load.c:13: ./ad_prot.h:43:10: note: declared here GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; ^~~~~~~~~~~~ ad_save_load.c:1267:5: warning: ‘GB_get_error’ is deprecated [-Wdeprecated-declarations] if (GB_rename_file(sec_path,path)) return GB_get_error(); ^~ In file included from arbdb.h:268:0, from adlocal.h:573, from ad_save_load.c:13: ./ad_prot.h:43:10: note: declared here GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; ^~~~~~~~~~~~ ad_save_load.c: In function ‘gb_check_saveable’: ad_save_load.c:1307:9: warning: ‘GB_get_error’ is deprecated [-Wdeprecated-declarations] return GB_get_error(); ^~~~~~ In file included from arbdb.h:268:0, from adlocal.h:573, from ad_save_load.c:13: ./ad_prot.h:43:10: note: declared here GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; ^~~~~~~~~~~~ ad_save_load.c:1312:9: warning: ‘GB_get_error’ is deprecated [-Wdeprecated-declarations] return GB_get_error(); ^~~~~~ In file included from arbdb.h:268:0, from adlocal.h:573, from ad_save_load.c:13: ./ad_prot.h:43:10: note: declared here GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; ^~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -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 ‘GB_login’: ad_load.c:1380:17: warning: ignoring return value of ‘gb_scan_directory’, declared with attribute warn_unused_result [-Wunused-result] gb_scan_directory(base,&dir); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -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 ‘gb_save_mapfile’: admap.c:636:9: warning: variable ‘writeOffset’ set but not used [-Wunused-but-set-variable] writeOffset; ^~~~~~~~~~~ admap.c:635:10: warning: variable ‘calcOffset’ set but not used [-Wunused-but-set-variable] long calcOffset, ^~~~~~~~~~ admap.c: In function ‘gb_is_valid_mapfile’: admap.c:722:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread((char *)mheader, sizeof(*mheader),1,in); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -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 ‘testData’: adTest.c:36:9: warning: variable ‘err’ set but not used [-Wunused-but-set-variable] int err = 0; ^~~ x86_64-pc-linux-gnu-gcc -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 ‘GBT_check_arb_file’: adtools.c:74:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(buffer,50,in); ^~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -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 ‘GBT_create_sequence_data’: adali.c:597:5: warning: ‘GBT_add_data’ is deprecated [-Wdeprecated-declarations] GBDATA *gb_data = GBT_add_data(species, ali_name, key, type); ^~~~~~ adali.c:568:9: note: declared here GBDATA *GBT_add_data(GBDATA *species,const char *ali_name, const char *key, GB_TYPES type) { ^~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -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 ‘GBS_string_eval’: admatch.c:763:13: warning: ignoring return value of ‘gbs_build_replace_string’, declared with attribute warn_unused_result [-Wunused-result] gbs_build_replace_string(strstruct,bar,wildcard, max_wildcard, mwildcard, max_mwildcard,gb_container); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -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 ‘GB_copy_with_protection’: 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 ‘GB_SETSMDMALLOC’ 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 ‘GB_SETSMDMALLOC’ GB_SETSMDMALLOC(dest, GB_GETSIZE(source), ^~~~~~~~~~~~~~~ arbdb.c: In function ‘gb_remove_callback’: arbdb.c:2239:13: warning: variable ‘removed’ set but not used [-Wunused-but-set-variable] GB_BOOL removed = GB_FALSE; ^~~~~~~ x86_64-pc-linux-gnu-gcc -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 ‘ad_use’: ad_core.c:11:17: warning: parameter ‘dummy’ set but not used [-Wunused-but-set-parameter] void ad_use(int dummy, ...) { ^~~~~ x86_64-pc-linux-gnu-gcc -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 ‘gb_load_single_key_data’: adsystem.c:141:101: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] GB_ensure_callback(gb_key,(GB_CB_TYPE)(GB_CB_CHANGED|GB_CB_DELETE),gb_system_key_changed_cb,(int *)q); ^ adsystem.c:159:123: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] GB_remove_callback(ks->gb_master_ali,(GB_CB_TYPE)(GB_CB_CHANGED|GB_CB_DELETE),gb_system_master_changed_cb,(int *)q); ^ adsystem.c:160:123: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] GB_add_callback (ks->gb_master_ali,(GB_CB_TYPE)(GB_CB_CHANGED|GB_CB_DELETE),gb_system_master_changed_cb,(int *)q); ^ x86_64-pc-linux-gnu-gcc -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 ‘GB_get_full_path’: adsocket.c:1256:13: warning: ignoring return value of ‘realpath’, declared with attribute warn_unused_result [-Wunused-result] realpath(newpath, path_buf[path_toggle]); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ adsocket.c:1260:13: warning: ignoring return value of ‘realpath’, declared with attribute warn_unused_result [-Wunused-result] realpath(anypath, path_buf[path_toggle]); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -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 ‘gbcms_write_updated’: adcomm.c:303:23: warning: variable ‘hs’ set but not used [-Wunused-but-set-variable] struct Hs_struct *hs; ^~ adcomm.c: In function ‘gbcms_talking_init_transaction’: adcomm.c:533:14: warning: variable ‘buffer’ set but not used [-Wunused-but-set-variable] long *buffer; ^~~~~~ adcomm.c: In function ‘gbcm_read_bin’: adcomm.c:1231:27: warning: variable ‘flags3’ set but not used [-Wunused-but-set-variable] struct gb_flag_types3 flags3; ^~~~~~ x86_64-pc-linux-gnu-gcc -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 ‘gb_search’: adquery.c:449:28: warning: comparison between ‘GB_TYPES {aka enum gb_key_types}’ and ‘enum gb_search_enum’ [-Wenum-compare] if (create == GB_CREATE_CONTAINER) { ^~ adquery.c:455:28: warning: comparison between ‘GB_TYPES {aka enum gb_key_types}’ and ‘enum gb_search_enum’ [-Wenum-compare] if (create == GB_CREATE_CONTAINER) { ^~ adquery.c:526:31: warning: comparison between ‘GB_TYPES {aka enum gb_key_types}’ and ‘enum gb_search_enum’ [-Wenum-compare] if (s2 || (create == GB_CREATE_CONTAINER)) { ^~ adquery.c: In function ‘GB_command_interpreter’: adquery.c:861:19: warning: variable ‘len’ set but not used [-Wunused-but-set-variable] int len; ^~~ x86_64-pc-linux-gnu-gcc -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 ‘gb_write_bin_rek’: 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 ‘GB_save_as’: ad_save_load.c:1079:5: warning: ‘GB_get_error’ is deprecated [-Wdeprecated-declarations] return GB_get_error(); ^~~~~~ In file included from arbdb.h:268:0, from adlocal.h:573, from ad_save_load.c:13: ./ad_prot.h:43:10: note: declared here GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; ^~~~~~~~~~~~ ad_save_load.c: In function ‘GB_save_quick_as’: ad_save_load.c:1126:5: warning: ‘GB_get_error’ is deprecated [-Wdeprecated-declarations] if (gb_check_saveable(gb_main,path,"bn")) return GB_get_error(); ^~ In file included from arbdb.h:268:0, from adlocal.h:573, from ad_save_load.c:13: ./ad_prot.h:43:10: note: declared here GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; ^~~~~~~~~~~~ ad_save_load.c:1148:9: warning: ‘GB_get_error’ is deprecated [-Wdeprecated-declarations] return GB_get_error(); ^~~~~~ In file included from arbdb.h:268:0, from adlocal.h:573, from ad_save_load.c:13: ./ad_prot.h:43:10: note: declared here GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; ^~~~~~~~~~~~ ad_save_load.c:1173:9: warning: ‘GB_get_error’ is deprecated [-Wdeprecated-declarations] return GB_get_error(); ^~~~~~ In file included from arbdb.h:268:0, from adlocal.h:573, from ad_save_load.c:13: ./ad_prot.h:43:10: note: declared here GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; ^~~~~~~~~~~~ ad_save_load.c:1184:9: warning: ‘GB_get_error’ is deprecated [-Wdeprecated-declarations] GB_warning(GB_get_error()); ^~~~~~~~~~ In file included from arbdb.h:268:0, from adlocal.h:573, from ad_save_load.c:13: ./ad_prot.h:43:10: note: declared here GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; ^~~~~~~~~~~~ ad_save_load.c: In function ‘GB_save_quick’: ad_save_load.c:1213:5: warning: ‘GB_get_error’ is deprecated [-Wdeprecated-declarations] if (gb_check_saveable(gb,refpath,"q")) return GB_get_error(); ^~ In file included from arbdb.h:268:0, from adlocal.h:573, from ad_save_load.c:13: ./ad_prot.h:43:10: note: declared here GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; ^~~~~~~~~~~~ ad_save_load.c:1234:9: warning: ‘GB_get_error’ is deprecated [-Wdeprecated-declarations] return GB_get_error(); ^~~~~~ In file included from arbdb.h:268:0, from adlocal.h:573, from ad_save_load.c:13: ./ad_prot.h:43:10: note: declared here GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; ^~~~~~~~~~~~ ad_save_load.c:1267:5: warning: ‘GB_get_error’ is deprecated [-Wdeprecated-declarations] if (GB_rename_file(sec_path,path)) return GB_get_error(); ^~ In file included from arbdb.h:268:0, from adlocal.h:573, from ad_save_load.c:13: ./ad_prot.h:43:10: note: declared here GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; ^~~~~~~~~~~~ ad_save_load.c: In function ‘gb_check_saveable’: ad_save_load.c:1307:9: warning: ‘GB_get_error’ is deprecated [-Wdeprecated-declarations] return GB_get_error(); ^~~~~~ In file included from arbdb.h:268:0, from adlocal.h:573, from ad_save_load.c:13: ./ad_prot.h:43:10: note: declared here GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; ^~~~~~~~~~~~ ad_save_load.c:1312:9: warning: ‘GB_get_error’ is deprecated [-Wdeprecated-declarations] return GB_get_error(); ^~~~~~ In file included from arbdb.h:268:0, from adlocal.h:573, from ad_save_load.c:13: ./ad_prot.h:43:10: note: declared here GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; ^~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -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 ‘GB_login’: ad_load.c:1380:17: warning: ignoring return value of ‘gb_scan_directory’, declared with attribute warn_unused_result [-Wunused-result] gb_scan_directory(base,&dir); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -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 ‘gb_save_mapfile’: admap.c:636:9: warning: variable ‘writeOffset’ set but not used [-Wunused-but-set-variable] writeOffset; ^~~~~~~~~~~ admap.c:635:10: warning: variable ‘calcOffset’ set but not used [-Wunused-but-set-variable] long calcOffset, ^~~~~~~~~~ admap.c: In function ‘gb_is_valid_mapfile’: admap.c:722:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread((char *)mheader, sizeof(*mheader),1,in); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -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 ‘testData’: adTest.c:36:9: warning: variable ‘err’ set but not used [-Wunused-but-set-variable] int err = 0; ^~~ x86_64-pc-linux-gnu-gcc -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 ‘GBT_check_arb_file’: adtools.c:74:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(buffer,50,in); ^~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -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 ‘GBT_create_sequence_data’: adali.c:597:5: warning: ‘GBT_add_data’ is deprecated [-Wdeprecated-declarations] GBDATA *gb_data = GBT_add_data(species, ali_name, key, type); ^~~~~~ adali.c:568:9: note: declared here GBDATA *GBT_add_data(GBDATA *species,const char *ali_name, const char *key, GB_TYPES type) { ^~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -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 ‘GBS_string_eval’: admatch.c:763:13: warning: ignoring return value of ‘gbs_build_replace_string’, declared with attribute warn_unused_result [-Wunused-result] gbs_build_replace_string(strstruct,bar,wildcard, max_wildcard, mwildcard, max_mwildcard,gb_container); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -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 ‘GB_copy_with_protection’: 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 ‘GB_SETSMDMALLOC’ 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 ‘GB_SETSMDMALLOC’ GB_SETSMDMALLOC(dest, GB_GETSIZE(source), ^~~~~~~~~~~~~~~ arbdb.c: In function ‘gb_remove_callback’: arbdb.c:2239:13: warning: variable ‘removed’ set but not used [-Wunused-but-set-variable] GB_BOOL removed = GB_FALSE; ^~~~~~~ x86_64-pc-linux-gnu-gcc -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 ‘ad_use’: ad_core.c:11:17: warning: parameter ‘dummy’ set but not used [-Wunused-but-set-parameter] void ad_use(int dummy, ...) { ^~~~~ x86_64-pc-linux-gnu-gcc -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 ‘gb_load_single_key_data’: adsystem.c:141:101: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] GB_ensure_callback(gb_key,(GB_CB_TYPE)(GB_CB_CHANGED|GB_CB_DELETE),gb_system_key_changed_cb,(int *)q); ^ adsystem.c:159:123: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] GB_remove_callback(ks->gb_master_ali,(GB_CB_TYPE)(GB_CB_CHANGED|GB_CB_DELETE),gb_system_master_changed_cb,(int *)q); ^ adsystem.c:160:123: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] GB_add_callback (ks->gb_master_ali,(GB_CB_TYPE)(GB_CB_CHANGED|GB_CB_DELETE),gb_system_master_changed_cb,(int *)q); ^ x86_64-pc-linux-gnu-gcc -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 ‘GB_get_full_path’: adsocket.c:1256:13: warning: ignoring return value of ‘realpath’, declared with attribute warn_unused_result [-Wunused-result] realpath(newpath, path_buf[path_toggle]); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ adsocket.c:1260:13: warning: ignoring return value of ‘realpath’, declared with attribute warn_unused_result [-Wunused-result] realpath(anypath, path_buf[path_toggle]); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -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 ‘gbcms_write_updated’: adcomm.c:303:23: warning: variable ‘hs’ set but not used [-Wunused-but-set-variable] struct Hs_struct *hs; ^~ adcomm.c: In function ‘gbcms_talking_init_transaction’: adcomm.c:533:14: warning: variable ‘buffer’ set but not used [-Wunused-but-set-variable] long *buffer; ^~~~~~ adcomm.c: In function ‘gbcm_read_bin’: adcomm.c:1231:27: warning: variable ‘flags3’ set but not used [-Wunused-but-set-variable] struct gb_flag_types3 flags3; ^~~~~~ x86_64-pc-linux-gnu-gcc -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 ‘gb_search’: adquery.c:449:28: warning: comparison between ‘GB_TYPES {aka enum gb_key_types}’ and ‘enum gb_search_enum’ [-Wenum-compare] if (create == GB_CREATE_CONTAINER) { ^~ adquery.c:455:28: warning: comparison between ‘GB_TYPES {aka enum gb_key_types}’ and ‘enum gb_search_enum’ [-Wenum-compare] if (create == GB_CREATE_CONTAINER) { ^~ adquery.c:526:31: warning: comparison between ‘GB_TYPES {aka enum gb_key_types}’ and ‘enum gb_search_enum’ [-Wenum-compare] if (s2 || (create == GB_CREATE_CONTAINER)) { ^~ adquery.c: In function ‘GB_command_interpreter’: adquery.c:861:19: warning: variable ‘len’ set but not used [-Wunused-but-set-variable] int len; ^~~ x86_64-pc-linux-gnu-gcc -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 ‘gb_write_bin_rek’: 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 ‘GB_save_as’: ad_save_load.c:1079:5: warning: ‘GB_get_error’ is deprecated [-Wdeprecated-declarations] return GB_get_error(); ^~~~~~ In file included from arbdb.h:268:0, from adlocal.h:573, from ad_save_load.c:13: ./ad_prot.h:43:10: note: declared here GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; ^~~~~~~~~~~~ ad_save_load.c: In function ‘GB_save_quick_as’: ad_save_load.c:1126:5: warning: ‘GB_get_error’ is deprecated [-Wdeprecated-declarations] if (gb_check_saveable(gb_main,path,"bn")) return GB_get_error(); ^~ In file included from arbdb.h:268:0, from adlocal.h:573, from ad_save_load.c:13: ./ad_prot.h:43:10: note: declared here GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; ^~~~~~~~~~~~ ad_save_load.c:1148:9: warning: ‘GB_get_error’ is deprecated [-Wdeprecated-declarations] return GB_get_error(); ^~~~~~ In file included from arbdb.h:268:0, from adlocal.h:573, from ad_save_load.c:13: ./ad_prot.h:43:10: note: declared here GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; ^~~~~~~~~~~~ ad_save_load.c:1173:9: warning: ‘GB_get_error’ is deprecated [-Wdeprecated-declarations] return GB_get_error(); ^~~~~~ In file included from arbdb.h:268:0, from adlocal.h:573, from ad_save_load.c:13: ./ad_prot.h:43:10: note: declared here GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; ^~~~~~~~~~~~ ad_save_load.c:1184:9: warning: ‘GB_get_error’ is deprecated [-Wdeprecated-declarations] GB_warning(GB_get_error()); ^~~~~~~~~~ In file included from arbdb.h:268:0, from adlocal.h:573, from ad_save_load.c:13: ./ad_prot.h:43:10: note: declared here GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; ^~~~~~~~~~~~ ad_save_load.c: In function ‘GB_save_quick’: ad_save_load.c:1213:5: warning: ‘GB_get_error’ is deprecated [-Wdeprecated-declarations] if (gb_check_saveable(gb,refpath,"q")) return GB_get_error(); ^~ In file included from arbdb.h:268:0, from adlocal.h:573, from ad_save_load.c:13: ./ad_prot.h:43:10: note: declared here GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; ^~~~~~~~~~~~ ad_save_load.c:1234:9: warning: ‘GB_get_error’ is deprecated [-Wdeprecated-declarations] return GB_get_error(); ^~~~~~ In file included from arbdb.h:268:0, from adlocal.h:573, from ad_save_load.c:13: ./ad_prot.h:43:10: note: declared here GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; ^~~~~~~~~~~~ ad_save_load.c:1267:5: warning: ‘GB_get_error’ is deprecated [-Wdeprecated-declarations] if (GB_rename_file(sec_path,path)) return GB_get_error(); ^~ In file included from arbdb.h:268:0, from adlocal.h:573, from ad_save_load.c:13: ./ad_prot.h:43:10: note: declared here GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; ^~~~~~~~~~~~ ad_save_load.c: In function ‘gb_check_saveable’: ad_save_load.c:1307:9: warning: ‘GB_get_error’ is deprecated [-Wdeprecated-declarations] return GB_get_error(); ^~~~~~ In file included from arbdb.h:268:0, from adlocal.h:573, from ad_save_load.c:13: ./ad_prot.h:43:10: note: declared here GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; ^~~~~~~~~~~~ ad_save_load.c:1312:9: warning: ‘GB_get_error’ is deprecated [-Wdeprecated-declarations] return GB_get_error(); ^~~~~~ In file included from arbdb.h:268:0, from adlocal.h:573, from ad_save_load.c:13: ./ad_prot.h:43:10: note: declared here GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED; ^~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -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 ‘GB_login’: ad_load.c:1380:17: warning: ignoring return value of ‘gb_scan_directory’, declared with attribute warn_unused_result [-Wunused-result] gb_scan_directory(base,&dir); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -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 ‘gb_save_mapfile’: admap.c:636:9: warning: variable ‘writeOffset’ set but not used [-Wunused-but-set-variable] writeOffset; ^~~~~~~~~~~ admap.c:635:10: warning: variable ‘calcOffset’ set but not used [-Wunused-but-set-variable] long calcOffset, ^~~~~~~~~~ admap.c: In function ‘gb_is_valid_mapfile’: admap.c:722:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread((char *)mheader, sizeof(*mheader),1,in); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -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 ‘testData’: adTest.c:36:9: warning: variable ‘err’ set but not used [-Wunused-but-set-variable] int err = 0; ^~~ x86_64-pc-linux-gnu-gcc -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 ‘GBT_check_arb_file’: adtools.c:74:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(buffer,50,in); ^~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -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 ‘GBT_create_sequence_data’: adali.c:597:5: warning: ‘GBT_add_data’ is deprecated [-Wdeprecated-declarations] GBDATA *gb_data = GBT_add_data(species, ali_name, key, type); ^~~~~~ adali.c:568:9: note: declared here GBDATA *GBT_add_data(GBDATA *species,const char *ali_name, const char *key, GB_TYPES type) { ^~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -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 ‘AD_ERR* ADT_SEQUENCE::show_edit_search(ADT_SEARCH*, ADT_EDIT*)’: adt_edit.cxx:581:13: warning: variable ‘seq_empty_var’ set but not used [-Wunused-but-set-variable] long seq_empty_var; ^~~~~~~~~~~~~ x86_64-pc-linux-gnu-g++ -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 ‘AD_ERR* AD_CONT::create(AD_SPECIES*, AD_ALI*)’: adseq.cxx:1012:20: warning: ‘GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)’ is deprecated [-Wdeprecated-declarations] GBDATA *erg = GBT_add_data(adptr1->gb_species,adptr2->name(),"data", GB_STRING); ^~~~~~~~~~~~ In file included from /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: ‘GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)’ is deprecated [-Wdeprecated-declarations] GBDATA *erg = GBT_add_data(adptr1->gb_species,adptr2->name(),"data", GB_STRING); ^ In file included from /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 ‘void AW_variable_update_callback(Widget, XtPointer, XtPointer)’: AW_button.cxx:199:37: warning: variable ‘found’ set but not used [-Wunused-but-set-variable] bool found; ^~~~~ AW_button.cxx: In member function ‘int AW_window::get_index_of_element(AW_selection_list*, const char*)’: AW_button.cxx:1617:17: warning: variable ‘found_index’ set but not used [-Wunused-but-set-variable] int found_index = -1; ^~~~~~~~~~~ AW_button.cxx: In function ‘const char* detect_bitmap_size(const char*, int*, int*)’: AW_button.cxx:398:47: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(buffer, MAX_LINE_LENGTH, in); ^ AW_button.cxx:417:51: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(buffer, MAX_LINE_LENGTH, in); ^ AW_button.cxx:418:51: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(buffer, MAX_LINE_LENGTH, in); ^ x86_64-pc-linux-gnu-g++ -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 ‘int AW_device::text_overlay(int, const char*, long int, AW_pos, AW_pos, AW_pos, AW_bitset, AW_CL, AW_CL, AW_CL, AW_pos, AW_pos, int (*)(AW_device*, int, const char*, size_t, size_t, size_t, AW_pos, AW_pos, AW_pos, AW_pos, AW_CL, AW_CL, AW_CL))’: AW_device.cxx:721:22: warning: variable ‘yi’ set but not used [-Wunused-but-set-variable] int xi, yi; ^~ x86_64-pc-linux-gnu-g++ -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 ‘AW_awar* AW_root::awar_pointer(const char*, void*, AW_default)’: AW_nawar.cxx:193:111: warning: passing NULL to non-pointer argument 4 of ‘AW_awar::AW_awar(AW_VARIABLE_TYPE, const char*, const char*, double, AW_default, AW_root*)’ [-Wconversion-null] vs = new AW_awar(AW_POINTER, var_name, (const char *)default_value, NULL, default_file, this); ^ 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 ‘void* AW_manage_GC(AW_window*, AW_device*, int, int, AW_GCM_AREA, void (*)(AW_window*, AW_CL, AW_CL), AW_CL, AW_CL, bool, const char*, ...)’: AW_preset.cxx:613:18: warning: variable ‘flag_no_color_selector’ set but not used [-Wunused-but-set-variable] bool flag_no_color_selector = false; ^~~~~~~~~~~~~~~~~~~~~~ AW_preset.cxx:614:18: warning: variable ‘flag_append_in_same_line’ set but not used [-Wunused-but-set-variable] bool flag_append_in_same_line = false; ^~~~~~~~~~~~~~~~~~~~~~~~ AW_preset.cxx: In function ‘bool aw_insert_gcs(AW_root*, AW_window_simple*, aw_gc_manager*, bool)’: AW_preset.cxx:786:17: warning: variable ‘first’ set but not used [-Wunused-but-set-variable] bool first = true; ^~~~~ x86_64-pc-linux-gnu-g++ -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 ‘int aw_status_read_int(int, int)’: AW_status.cxx:281:19: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] return *(int*)buffer; ^~~~~~ AW_status.cxx: In function ‘void aw_status_timer_event(AW_root*, AW_CL, AW_CL)’: AW_status.cxx:419:28: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result] system(buf); ^ AW_status.cxx: In function ‘void aw_help_edit_help(AW_window*)’: AW_status.cxx:1746:25: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result] system(copy_cmd); ^ x86_64-pc-linux-gnu-g++ -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 ‘void AW_window::insert_separator()’: AW_window.cxx:3002:12: warning: variable ‘separator’ set but not used [-Wunused-but-set-variable] Widget separator; ^~~~~~~~~ AW_window.cxx: In member function ‘void AW_window::insert_separator_help()’: AW_window.cxx:3011:12: warning: variable ‘separator’ set but not used [-Wunused-but-set-variable] Widget separator; ^~~~~~~~~ x86_64-pc-linux-gnu-g++ -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 ‘void create_new_mask_cb(AW_window*)’: AWT_input_mask.cxx:2242:18: warning: variable ‘closeWindow’ set but not used [-Wunused-but-set-variable] bool closeWindow = false; ^~~~~~~~~~~ x86_64-pc-linux-gnu-g++ -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 ‘void awt_create_aww_vars(AW_root*, AW_default)’: /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/static_assert.h:25:19: warning: typedef ‘_arb_compile_assertion_typedef___LINE__’ locally defined but not used [-Wunused-local-typedefs] CA_UNIQUETYPE(_arb_compile_assertion_typedef_) ^ /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/static_assert.h:20:26: note: in definition of macro ‘CA_JOINTYPE’ #define CA_JOINTYPE(X,Y) X##Y ^ /var/tmp/portage/sci-biology/arb-5.3/work/arb-5.3/INCLUDE/static_assert.h:25:5: note: in expansion of macro ‘CA_UNIQUETYPE’ CA_UNIQUETYPE(_arb_compile_assertion_typedef_) ^~~~~~~~~~~~~ AWT_www.cxx:61:5: note: in expansion of macro ‘COMPILE_ASSERT’ COMPILE_ASSERT(EXAMPLE_COUNT <= WWW_COUNT); ^~~~~~~~~~~~~~ x86_64-pc-linux-gnu-g++ -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 ‘void ad_table_field_reorder_cb(AW_window*, awt_table*)’: AWT_tables.cxx:25:14: warning: variable ‘warning’ set but not used [-Wunused-but-set-variable] GB_ERROR warning = 0; ^~~~~~~ x86_64-pc-linux-gnu-g++ -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 ‘void AWT_print_tree_to_file_xfig(AW_window*, AW_CL)’: AWT_canio.cxx:268:53: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result] system(GBS_global_string("xfig %s &", dest)); ^ x86_64-pc-linux-gnu-g++ -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 ‘bool AWT_is_codon(char, const char*, const AWT_allowedCode&, AWT_allowedCode&, const char**)’: AWT_codon_table.cxx:518:18: warning: variable ‘correct_disallowed_translation’ set but not used [-Wunused-but-set-variable] bool correct_disallowed_translation = false; ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-g++ -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 ‘void AWT_start_config_manager(AW_window*, AW_CL)’: AWT_config_manager.cxx:119:24: warning: variable ‘reopen’ set but not used [-Wunused-but-set-variable] bool reopen = false; ^~~~~~ x86_64-pc-linux-gnu-g++ -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 ‘void GDE_export(NA_Alignment*, char*, long int)’: GDE_event.cxx:305:39: warning: ‘GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)’ is deprecated [-Wdeprecated-declarations] GBDATA *gb_data = GBT_add_data(gb_extended, align, "data", GB_STRING); ^~~~~~~~~~~~ In file included from /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: ‘GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)’ is deprecated [-Wdeprecated-declarations] GBDATA *gb_data = GBT_add_data(gb_extended, align, "data", GB_STRING); ^ In file included from /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: ‘GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)’ is deprecated [-Wdeprecated-declarations] GBDATA *gb_data = GBT_add_data(gb_species, align, "data", GB_STRING); // does only add if not already existing ^~~~~~~~~~~~ In file included from /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: ‘GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)’ is deprecated [-Wdeprecated-declarations] GBDATA *gb_data = GBT_add_data(gb_species, align, "data", GB_STRING); // does only add if not already existing ^ In file included from /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: ‘GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)’ is deprecated [-Wdeprecated-declarations] GBDATA *gb_color = GBT_add_data(gb_extended, align, "colmask", GB_BYTES); ^~~~~~~~~~~~ In file included from /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: ‘GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)’ is deprecated [-Wdeprecated-declarations] GBDATA *gb_color = GBT_add_data(gb_extended, align, "colmask", GB_BYTES); ^ In file included from /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 ‘void GDE_startaction_cb(AW_window*, GmenuItem*, AW_CL)’: GDE_event.cxx:557:23: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result] system(Action); ^ 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 ‘void StripSpecial(char*)’: GDE_HGLfile.cxx:69:9: warning: variable ‘i’ set but not used [-Wunused-but-set-variable] int i,j,len; ^ GDE_HGLfile.cxx: In function ‘void ReadGDE(char*, NA_Alignment*, int)’: GDE_HGLfile.cxx:199:26: warning: variable ‘count’ set but not used [-Wunused-but-set-variable] int success,count,temp = 0; ^~~~~ GDE_HGLfile.cxx:200:35: warning: variable ‘c’ set but not used [-Wunused-but-set-variable] char in_line[GBUFSIZ],c; ^ GDE_HGLfile.cxx:203:18: warning: variable ‘genclen’ set but not used [-Wunused-but-set-variable] int genclen = 0,curelem = 0; ^~~~~~~ GDE_HGLfile.cxx:195:55: warning: parameter ‘type’ set but not used [-Wunused-but-set-parameter] void ReadGDE(char *filename,NA_Alignment *dataset,int type) ^~~~ 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 ‘void ReadGen(char*, NA_Alignment*, int)’: GDE_Genbank.cxx:94:13: warning: variable ‘count’ set but not used [-Wunused-but-set-variable] int count,IS_REALLY_AA = FALSE; ^~~~~ GDE_Genbank.cxx:89:55: warning: parameter ‘type’ set but not used [-Wunused-but-set-parameter] void ReadGen(char *filename,NA_Alignment *dataset,int type) ^~~~ x86_64-pc-linux-gnu-g++ -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 ‘void ReadNA_Flat(char*, char*, int)’: GDE_FileIO.cxx:125:9: warning: variable ‘i’ set but not used [-Wunused-but-set-variable] int i, jj, c, curelem=0,offset; ^ GDE_FileIO.cxx:125:16: warning: variable ‘c’ set but not used [-Wunused-but-set-variable] int i, jj, c, curelem=0,offset; ^ GDE_FileIO.cxx:128:10: warning: variable ‘curname’ set but not used [-Wunused-but-set-variable] char curname[GBUFSIZ]; ^~~~~~~ GDE_FileIO.cxx:122:58: warning: parameter ‘type’ set but not used [-Wunused-but-set-parameter] static void ReadNA_Flat(char *filename,char *dataset,int type) ^~~~ GDE_FileIO.cxx: In function ‘void AppendNA(NA_Base*, int, NA_Sequence*)’: GDE_FileIO.cxx:422:14: warning: variable ‘temp’ set but not used [-Wunused-but-set-variable] NA_Base *temp; ^~~~ GDE_FileIO.cxx: In function ‘void ReadCMask(const char*)’: GDE_FileIO.cxx:710:24: warning: variable ‘orig_ctype’ set but not used [-Wunused-but-set-variable] int *colors = 0,orig_ctype,jj,indx = 0; ^~~~~~~~~~ GDE_FileIO.cxx: In function ‘int WriteStatus(NA_Alignment*, char*, int)’: GDE_FileIO.cxx:860:54: warning: parameter ‘method’ set but not used [-Wunused-but-set-parameter] int WriteStatus(NA_Alignment *aln,char *filename,int method) ^~~~~~ GDE_FileIO.cxx: In function ‘void ReadStatus(char*)’: GDE_FileIO.cxx:927:23: warning: parameter ‘filename’ set but not used [-Wunused-but-set-parameter] void ReadStatus(char *filename) ^~~~~~~~ GDE_FileIO.cxx: In function ‘void NormalizeOffset(NA_Alignment*)’: GDE_FileIO.cxx:962:9: warning: variable ‘i’ set but not used [-Wunused-but-set-variable] int i; ^ GDE_FileIO.cxx: In function ‘void ReadCMask(const char*)’: GDE_FileIO.cxx:837:48: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(in_line,GBUFSIZ,file); ^ ld -r -o ARB_GDE.a GDE_ParseMenu.o GDE.o GDE_event.o GDE_arbdb_io.o GDE_HGLfile.o GDE_Genbank.o GDE_FileIO.o make[4]: Leaving directory '/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 ‘char* AWTC_constructSequence(int, const char**, int, char**)’: AWTC_constructSequence.cxx:507:11: warning: unused variable ‘resultSeq’ [-Wunused-variable] char *resultSeq = new char[sequenceLength+1]; ^~~~~~~~~ AWTC_constructSequence.cxx:509:9: warning: unused variable ‘off’ [-Wunused-variable] int off = 0; ^~~ x86_64-pc-linux-gnu-g++ -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 ‘char* awtc_read_line(int, char*, char*)’: AWTI_import.cxx:559:13: warning: this ‘if’ 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 ‘if’ if (awtcig.in) fclose(awtcig.in);awtcig.in= 0; ^~~~~~ AWTI_import.cxx:583:13: warning: this ‘if’ 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 ‘if’ 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 ‘void gen_extract_gene_2_pseudoSpecies(GBDATA*, GBDATA*, EG2PS_data*)’: GEN_map.cxx:882:39: warning: ‘GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)’ is deprecated [-Wdeprecated-declarations] GBDATA *gb_data = GBT_add_data(gb_exist_geneSpec, ali, "data", GB_STRING); ^~~~~~~~~~~~ In file included from /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: ‘GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)’ is deprecated [-Wdeprecated-declarations] GBDATA *gb_data = GBT_add_data(gb_exist_geneSpec, ali, "data", GB_STRING); ^ In file included from /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 ‘int smart_text(AW_world&, AW_device*, int, const char*, AW_pos, AW_pos, AW_pos, AW_bitset, AW_CL, AW_CL, long int)’: GEN_graphic.cxx:158:33: warning: unused parameter ‘selected_range’ [-Wunused-parameter] inline int smart_text(AW_world& selected_range, AW_device *device, int gc, const char *str,AW_pos x,AW_pos y, AW_pos alignment, AW_bitset filteri, AW_CL cd1, AW_CL cd2,long opt_strlen) { ^~~~~~~~~~~~~~ x86_64-pc-linux-gnu-g++ -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 ‘void DBwriter::writeSequence(const SequenceBuffer&)’: DBwriter.cxx:226:23: warning: ‘GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)’ is deprecated [-Wdeprecated-declarations] GBDATA *gb_data = GBT_add_data(gb_organism, ali_name, "data", GB_STRING); ^~~~~~~~~~~~ In file included from /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: ‘GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)’ is deprecated [-Wdeprecated-declarations] GBDATA *gb_data = GBT_add_data(gb_organism, ali_name, "data", GB_STRING); ^ In file included from /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 ‘void BaseCounter::checkOverallCounter() const’: SequenceBuffer.cxx:55:67: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘size_t {aka long unsigned int}’ [-Wformat=] count[BC_ALL], all, source.c_str()); ^ SequenceBuffer.cxx:55:67: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘size_t {aka long unsigned int}’ [-Wformat=] SequenceBuffer.cxx: In member function ‘void BaseCounter::expectEqual(const BaseCounter&) const’: SequenceBuffer.cxx:116:114: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘size_t {aka long unsigned int}’ [-Wformat=] error = error+"\n "+whichCounter+": "+GBS_global_string("%u <> %u", count[i], other.count[i]); ^ SequenceBuffer.cxx:116:114: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘size_t {aka long unsigned int}’ [-Wformat=] 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 ‘Sonde* ST_Container::cache_Sonde(char*, int, double)’: MP_sondentopf.cxx:67:13: warning: variable ‘hashreturnval’ set but not used [-Wunused-but-set-variable] long hashreturnval; ^~~~~~~~~~~~~ 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 ‘long int MO_Liste::put_entry(const char*)’: MP_mo_liste.cxx:184:13: warning: variable ‘hashreturnval’ set but not used [-Wunused-but-set-variable] long hashreturnval; ^~~~~~~~~~~~~ x86_64-pc-linux-gnu-g++ -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 ‘void ProbeValuation::init_valuation()’: MP_probe.cxx:178:22: warning: variable ‘stc’ set but not used [-Wunused-but-set-variable] ST_Container *stc; ^~~ x86_64-pc-linux-gnu-g++ -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 ‘const char* CON_export(char*, char*, int**, char*, int*, char*, int, long int, long int, int, int, int, double, double, int, int)’: AP_consensus.cxx:409:23: warning: ‘GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)’ is deprecated [-Wdeprecated-declarations] GBDATA *gb_data = GBT_add_data(gb_extended, align,"data", GB_STRING); ^~~~~~~~~~~~ In file included from /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: ‘GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)’ is deprecated [-Wdeprecated-declarations] GBDATA *gb_data = GBT_add_data(gb_extended, align,"data", GB_STRING); ^ In file included from /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: ‘GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)’ is deprecated [-Wdeprecated-declarations] GBDATA *gb_options= GBT_add_data(gb_extended, align,"_TYPE", GB_STRING); ^~~~~~~~~~~~ In file included from /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: ‘GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)’ is deprecated [-Wdeprecated-declarations] GBDATA *gb_options= GBT_add_data(gb_extended, align,"_TYPE", GB_STRING); ^ In file included from /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: ‘GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)’ is deprecated [-Wdeprecated-declarations] GBDATA *gb_graph = GBT_add_data(gb_extended, align,"FREQUENCIES", GB_DB); ^~~~~~~~~~~~ In file included from /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: ‘GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)’ is deprecated [-Wdeprecated-declarations] GBDATA *gb_graph = GBT_add_data(gb_extended, align,"FREQUENCIES", GB_DB); ^ In file included from /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 ‘void CON_calc_max_freq_cb(AW_window*)’: AP_consensus.cxx:962:27: warning: ‘GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)’ is deprecated [-Wdeprecated-declarations] GBDATA *gb_data = GBT_add_data(gb_extended, align,"data", GB_STRING); ^~~~~~~~~~~~ In file included from /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: ‘GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)’ is deprecated [-Wdeprecated-declarations] GBDATA *gb_data = GBT_add_data(gb_extended, align,"data", GB_STRING); ^ In file included from /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: ‘GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)’ is deprecated [-Wdeprecated-declarations] GBDATA *gb_data2 = GBT_add_data(gb_extended, align,"dat2", GB_STRING); ^~~~~~~~~~~~ In file included from /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: ‘GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)’ is deprecated [-Wdeprecated-declarations] GBDATA *gb_data2 = GBT_add_data(gb_extended, align,"dat2", GB_STRING); ^ In file included from /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: ‘GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)’ is deprecated [-Wdeprecated-declarations] GBDATA *gb_options = GBT_add_data(gb_extended, align,"_TYPE", GB_STRING); ^~~~~~~~~~~~ In file included from /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: ‘GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)’ is deprecated [-Wdeprecated-declarations] GBDATA *gb_options = GBT_add_data(gb_extended, align,"_TYPE", GB_STRING); ^ In file included from /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 ‘void AP_conservProfile2Gnuplot_callback(AW_window*)’: AP_conservProfile2Gnuplot.cxx:58:42: warning: ignoring return value of ‘const char* GB_xcmd(const char*, GB_BOOL, GB_BOOL)’, declared with attribute warn_unused_result [-Wunused-result] GB_xcmd(script, GB_TRUE, GB_TRUE); // execute GNUPLOT using command_file ^ x86_64-pc-linux-gnu-g++ -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 ‘void CPRO_workupstatistic(unsigned char)’: AP_cprofile.cxx:234:17: warning: variable ‘colmax’ set but not used [-Wunused-but-set-variable] long column,colmax,memneeded=0; ^~~~~~ AP_cprofile.cxx: In function ‘void CPRO_memrequirement_cb(AW_root*)’: AP_cprofile.cxx:663:10: warning: variable ‘versus’ set but not used [-Wunused-but-set-variable] char versus=0; /* all vs all */ ^~~~~~ AP_cprofile.cxx: In function ‘void CPRO_condense_cb(AW_window*, AW_CL)’: AP_cprofile.cxx:1420:14: warning: ‘GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)’ is deprecated [-Wdeprecated-declarations] gb_param=GBT_add_data(gb_extended,align,"_TYPE",GB_STRING); ^~~~~~~~~~~~ In file included from /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: ‘GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)’ is deprecated [-Wdeprecated-declarations] gb_param=GBT_add_data(gb_extended,align,"_TYPE",GB_STRING); ^ In file included from /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: ‘GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)’ is deprecated [-Wdeprecated-declarations] GBDATA *gb_data = GBT_add_data(gb_extended, align,"data", GB_STRING); ^~~~~~~~~~~~ In file included from /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: ‘GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)’ is deprecated [-Wdeprecated-declarations] GBDATA *gb_data = GBT_add_data(gb_extended, align,"data", GB_STRING); ^ In file included from /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 ‘char* get_overlay_files(AW_root*, const char*, const char*&)’: AP_csp_2_gnuplot.cxx:92:50: warning: ‘const char* GB_get_error()’ is deprecated [-Wdeprecated-declarations] if (!found_prefix_files) error = GB_get_error(); ^~~~~~~~~~~~ In file included from /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: ‘const char* GB_get_error()’ 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: ‘const char* GB_get_error()’ 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: ‘const char* GB_get_error()’ 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 ‘void AP_csp_2_gnuplot_cb(AW_window*, AW_CL, AW_CL)’: AP_csp_2_gnuplot.cxx:388:62: warning: ignoring return value of ‘const char* GB_xcmd(const char*, GB_BOOL, GB_BOOL)’, declared with attribute warn_unused_result [-Wunused-result] GB_xcmd(script, GB_TRUE, GB_TRUE); ^ x86_64-pc-linux-gnu-g++ -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 ‘void NT_system_cb2(AW_window*, AW_CL, AW_CL)’: NT_cb.cxx:128:35: warning: ignoring return value of ‘const char* GB_xcmd(const char*, GB_BOOL, GB_BOOL)’, declared with attribute warn_unused_result [-Wunused-result] GB_xcmd(sys,GB_TRUE, GB_FALSE); ^ 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 ‘const char* displayAlignmentInfo(GBDATA*, GB_ERROR, char*, char*)’: NT_concatenate.cxx:310:37: warning: ‘GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)’ is deprecated [-Wdeprecated-declarations] GBDATA *gb_data = GBT_add_data(gb_extended, new_ali_name,"data", GB_STRING); ^~~~~~~~~~~~ In file included from /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: ‘GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)’ is deprecated [-Wdeprecated-declarations] GBDATA *gb_data = GBT_add_data(gb_extended, new_ali_name,"data", GB_STRING); ^ In file included from /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 ‘void concatenateAlignments(AW_window*)’: NT_concatenate.cxx:415:39: warning: ‘GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)’ is deprecated [-Wdeprecated-declarations] GBDATA *gb_data = GBT_add_data(gb_species, new_ali_name, "data", GB_STRING); ^~~~~~~~~~~~ In file included from /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: ‘GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)’ is deprecated [-Wdeprecated-declarations] GBDATA *gb_data = GBT_add_data(gb_species, new_ali_name, "data", GB_STRING); ^ In file included from /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 ‘GBDATA* concatenateFieldsCreateNewSpecies(AW_window*, GBDATA*, speciesConcatenateList)’: NT_concatenate.cxx:664:39: warning: ‘GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)’ is deprecated [-Wdeprecated-declarations] GBDATA *gb_data = GBT_add_data(gb_new_species, ali_names[no_of_alignments], "data", GB_STRING); ^~~~~~~~~~~~ In file included from /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: ‘GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)’ is deprecated [-Wdeprecated-declarations] GBDATA *gb_data = GBT_add_data(gb_new_species, ali_names[no_of_alignments], "data", GB_STRING); ^ In file included from /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 ‘void NT_import_sequences(AW_window*, AW_CL, AW_CL)’: NT_import.cxx:52:30: warning: variable ‘gb_merge_is_genom_db’ set but not used [-Wunused-but-set-variable] int gb_main_is_genom_db, gb_merge_is_genom_db; ^~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-g++ -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 ‘int main(int, char**)’: NT_main.cxx:399:50: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result] system("touch ${HOME}/.arb_prop/msgtime"); ^ x86_64-pc-linux-gnu-g++ -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 ‘void fillSelNamList(selectValidNameStruct*)’: NT_validManual.cxx:56:75: error: no match for ‘operator<<’ (operand types are ‘std::basic_ostream’ and ‘std::ostream {aka std::basic_ostream}’) 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; _Tp = std::basic_ostream] 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 ‘std::basic_ostream’ lvalue to ‘std::basic_ostream&&’ if (!GB_validNamesCont){std::cout << "validNames Container not found" << std:: cout; } ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ NT_validManual.cxx:56:75: note: candidate: operator<<(int, int) if (!GB_validNamesCont){std::cout << "validNames Container not found" << std:: cout; } ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ NT_validManual.cxx:56:75: note: no known conversion for argument 2 from ‘std::ostream {aka std::basic_ostream}’ to ‘int’ 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; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream] 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 ‘std::ostream {aka std::basic_ostream}’ to ‘std::basic_ostream::__ostream_type& (*)(std::basic_ostream::__ostream_type&) {aka std::basic_ostream& (*)(std::basic_ostream&)}’ /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; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream; std::basic_ostream<_CharT, _Traits>::__ios_type = std::basic_ios] 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 ‘std::ostream {aka std::basic_ostream}’ to ‘std::basic_ostream::__ios_type& (*)(std::basic_ostream::__ios_type&) {aka std::basic_ios& (*)(std::basic_ios&)}’ /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; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream] 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 ‘std::ostream {aka std::basic_ostream}’ to ‘std::ios_base& (*)(std::ios_base&)’ /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; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream] 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 ‘std::ostream {aka std::basic_ostream}’ to ‘long int’ /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; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream] 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 ‘std::ostream {aka std::basic_ostream}’ to ‘long unsigned int’ /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; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream] 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 ‘std::ostream {aka std::basic_ostream}’ to ‘bool’ 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] 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 ‘std::ostream {aka std::basic_ostream}’ to ‘short int’ 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; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream] 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 ‘std::ostream {aka std::basic_ostream}’ to ‘short unsigned int’ 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] 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 ‘std::ostream {aka std::basic_ostream}’ to ‘int’ 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; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream] 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 ‘std::ostream {aka std::basic_ostream}’ to ‘unsigned int’ /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; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream] 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 ‘std::ostream {aka std::basic_ostream}’ to ‘long long int’ /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; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream] 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 ‘std::ostream {aka std::basic_ostream}’ to ‘long long unsigned int’ /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; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream] 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 ‘std::ostream {aka std::basic_ostream}’ to ‘double’ /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; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream] 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 ‘std::ostream {aka std::basic_ostream}’ to ‘float’ /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; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream] 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 ‘std::ostream {aka std::basic_ostream}’ to ‘long double’ /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; std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream] 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 ‘std::ostream {aka std::basic_ostream}’ to ‘const void*’ 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; std::basic_ostream<_CharT, _Traits>::__streambuf_type = std::basic_streambuf] 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 ‘std::ostream {aka std::basic_ostream}’ to ‘std::basic_ostream::__streambuf_type* {aka std::basic_streambuf*}’ 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 std::basic_ostream& std::operator<<(std::basic_ostream&, const unsigned char*) operator<<(basic_ostream& __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 ‘std::cout’ (type ‘std::ostream {aka std::basic_ostream}’) to type ‘const unsigned char*’ 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 std::basic_ostream& std::operator<<(std::basic_ostream&, const signed char*) operator<<(basic_ostream& __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 ‘std::cout’ (type ‘std::ostream {aka std::basic_ostream}’) to type ‘const signed char*’ 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 std::basic_ostream& std::operator<<(std::basic_ostream&, const char*) operator<<(basic_ostream& __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 ‘std::cout’ (type ‘std::ostream {aka std::basic_ostream}’) to type ‘const char*’ 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 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 ‘std::cout’ (type ‘std::ostream {aka std::basic_ostream}’) to type ‘const char*’ 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 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 ‘const _CharT*’ and ‘std::basic_ostream’ 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 std::basic_ostream& std::operator<<(std::basic_ostream&, unsigned char) operator<<(basic_ostream& __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 ‘std::cout’ (type ‘std::ostream {aka std::basic_ostream}’) to type ‘unsigned char’ 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 std::basic_ostream& std::operator<<(std::basic_ostream&, signed char) operator<<(basic_ostream& __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 ‘std::cout’ (type ‘std::ostream {aka std::basic_ostream}’) to type ‘signed char’ 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 std::basic_ostream& std::operator<<(std::basic_ostream&, char) operator<<(basic_ostream& __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 ‘std::cout’ (type ‘std::ostream {aka std::basic_ostream}’) to type ‘char’ 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 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 ‘std::cout’ (type ‘std::ostream {aka std::basic_ostream}’) to type ‘char’ 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 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 ‘_CharT’ (‘char’ and ‘std::basic_ostream’) 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 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 ‘std::cout’ (type ‘std::ostream {aka std::basic_ostream}’) to type ‘const std::error_code&’ 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 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: ‘std::ostream {aka std::basic_ostream}’ is not derived from ‘const std::__cxx11::basic_string<_CharT, _Traits, _Alloc>’ 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'