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Gentoo's Bugzilla – Attachment 250261 Details for
Bug 340579
sci-biology/arb _FORTIFY_SOURCE indicates presence of overflow
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Build log
arb-5.1-r1:20101011-125451.log (text/plain), 424.23 KB, created by
Diego Elio Pettenò (RETIRED)
on 2010-10-11 18:40:42 UTC
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hide
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Description:
Build log
Filename:
MIME Type:
Creator:
Diego Elio Pettenò (RETIRED)
Created:
2010-10-11 18:40:42 UTC
Size:
424.23 KB
patch
obsolete
> * Package: sci-biology/arb-5.1-r1 > * Repository: gentoo > * Maintainer: weaver@gentoo.org sci-biology@gentoo.org > * USE: elibc_glibc kernel_linux opengl test userland_GNU x86 >>>> Unpacking source... >>>> Unpacking arb-5.1.tgz to /var/tmp/portage/sci-biology/arb-5.1-r1/work >>>> Unpacking arb-5.1-glibc2.10.patch.bz2 to /var/tmp/portage/sci-biology/arb-5.1-r1/work >>>> Unpacking arb-5.1-linker.patch.bz2 to /var/tmp/portage/sci-biology/arb-5.1-r1/work >>>> Source unpacked in /var/tmp/portage/sci-biology/arb-5.1-r1/work >>>> Preparing source in /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213 ... > * Applying arb-5.1-glibc2.10.patch ... > [ ok ] > * Applying arb-5.1-linker.patch ... > [ ok ] > * Applying 5.1-libs.patch ... > [ ok ] >make -j14 ARBHOME=/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213 links >SOURCE_TOOLS/generate_all_links.sh >make[1]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/bin' >make[1]: warning: jobserver unavailable: using -j1. Add `+' to parent make rule. >find . -type l -exec rm {} \; >ln -s -f `find ../SH ../PERL_SCRIPTS -perm -100 ! -type d ! -name 'config*' -print` . >make[1]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/bin' >generate_all_links.sh done. >touch SOURCE_TOOLS/generate_all_links.stamp >>>> Source prepared. >>>> Configuring source in /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213 ... >>>> Source configured. >>>> Compiling source in /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213 ... >make -j14 ARBHOME=/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213 PATH=/usr/lib/portage/bin/ebuild-helpers:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/opt/bin:/usr/i486-pc-linux-gnu/gcc-bin/4.1.2:/usr/i686-pc-linux-gnu/gcc-bin/4.5.1:/opt/intel/Compiler/11.1/072/bin/ia32:/opt/stuffit/bin:/opt/gwydion-dylan/:/opt/gwydion-dylan/bin:/opt/blackdown-jdk-1.4.2.03/bin:/opt/blackdown-jdk-1.4.2.03/jre/bin:/opt/dmd/bin:/usr/lib/plan9/bin:/opt/c3-4:/opt/hp/hpacucli:/usr/i686-pc-linux-gnu/gnat-gpl-bin/4.1:/usr/libexec/gnat-gpl/i686-pc-linux-gnu/4.1:/usr/libexec/gpc/i686-pc-linux-gnu/3.4:/opt/tivoli/tsm/client/admin/bin:/opt/tivoli/tsm/client/ba/bin:/opt/eagle-5.10.0/bin:/opt/flexlm/bin:/opt/vmware/server/console/bin:/opt/vmware/vix/bin:/opt/cuda/bin:/usr/GNUstep/System/Tools:/usr/GNUstep/Local/Tools:/usr/ti-linux-gnu/tigcc-bin/4.1.2:/usr/ti-linux-gnu/bin:/var/vpopmail/bin:/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/bin LD_LIBRARY_PATH=:/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/lib tarfile >make clean2 >make[1]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213' >make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/PROBE' >rm -f PT_new_design.o PT_family.o PT_prefixtree.o PT_main.o PT_io.o PT_etc.o PT_secundaer.o PT_buildtree.o PT_match.o PT_findEx.o *.a >make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/AISC_MKPTPS' >rm -f mkptypes.o aisc_mkpt >make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/AISC' >rm -f aisc.o aisc_commands.o aisc_var_ref.o aisc_mix.o aisc >make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/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-5.1-r1/work/arbsrc_6213/AISC_MKPTPS' >make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/AISC' >make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/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-5.1-r1/work/arbsrc_6213/PROBE' >make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/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-5.1-r1/work/arbsrc_6213/ALIV3' >make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/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]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/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]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/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-5.1-r1/work/arbsrc_6213/ARBDB' >make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/ARBDBPP' >make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/ARB_GDE' >make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/AWTI' >rm -f AWTI_import.o AWTI_export.o *.a >make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/ARBDB2' >make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/AWT' >rm -f AWT_input_mask.o AWT_hotkeys.o AWT_www.o AWT_tables.o AWT_irstree.o AWT_asciiprint.o AWT_map_key.o AWT_tree_cmp.o AWT_seq_colors.o AWT_pro_a_nucs.o AWT_csp.o AWT_canvas.o AWT_dtree.o AWT_tree.o AWT_tree_cb.o AWT_nei.o AWT_filter.o AWT_sel_boxes.o AWT_canio.o AWT_nds.o AWT_query_and_functions.o AWT_file_selection.o AWT_preset.o AWT_seq_dna.o AWT_seq_protein.o AWT_seq_simple_pro.o AWT_codon_table.o AWT_iupac.o AWT_config_manager.o AWT_advice.o AWT_db_browser.o AWT_attributes.o AWT_changekey.o AWT_item_sel_list.o AWT_macro.o AWT_translate.o *.a *.so >make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/CONSENSUS_TREE' >rm -f CT_part.o CT_hash.o CT_ntree.o CT_rbtree.o CT_dtree.o CT_ctree.o CT_mem.o *.a >make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/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-5.1-r1/work/arbsrc_6213/bin/arb_convert_aln >make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/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-5.1-r1/work/arbsrc_6213/ARBDBS' >make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/DBSERVER' >rm -f db_server.o *.a >make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/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-5.1-r1/work/arbsrc_6213/CONSENSUS_TREE' >make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/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-5.1-r1/work/arbsrc_6213/CONVERTALN' >make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/AWTI' >make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/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-5.1-r1/work/arbsrc_6213/DBSERVER' >make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/EDIT' >make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/EISPACK' >rm -f eispack.o d_sign.o *.a >make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/AWTC' >make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/DIST' >make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/GDE' >make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/AWT' >make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/EDIT4' >make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/GENOM' >rm -f GEN_interface.o GEN_map.o GEN_graphic.o GEN_gene.o GEN_nds.o GEN_color_groups.o GEN_translations.o EXP_interface.o EXP_main.o *.a >make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/GENOM_IMPORT' >rm *.o >make[3]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/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-5.1-r1/work/arbsrc_6213/bin/clustalv >make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/EISPACK' >make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/ISLAND_HOPPING' >rm -f island_hopping.o i-hopper.o align.o memory.o trnsprob.o *.a >make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/GL' >make[3]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/GDE/CLUSTAL' >make[3]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/GDE/MOLPHY' >rm -f Dpstree.o Ndistan.o Njdist.o Nmlklhd.o Nseqstat.o Ntranprb.o Nucml.o Nucst.o Nuctpm.o Prottpm.o abratio.o altree.o distan.o distproc.o dyhfjtt.o getseq.o matrixut.o mlklhd.o mltree.o mtrev22.o mtrev24.o mygetopt.o njmtree.o njproc.o njtree.o nucproc.o optimtpm.o protml.o protproc.o protst.o prtree.o pstree.o qltree.o seqproc.o seqstat.o sltree.o totalml.o tranprb.o tridist.o triproc.o protml >make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/GENOM' >make[3]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/GDE/SUPPORT' >rm -f /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/bin/CAP2 /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/bin/Restriction /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/bin/Zuk_to_gen /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/bin/count /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/bin/findall /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/bin/lsadt /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/bin/sho_helix /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/bin/varpos >rm: cannot remove `*.o': No such file or directory >make[2]: [clean] Error 1 (ignored) >rm *.a >make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/MERGE' >rm -f MG_checkfield.o MG_main.o MG_trees.o MG_alignment.o MG_species.o MG_extendeds.o MG_names.o MG_gene_species.o MG_configs.o MG_preserves.o *.a >make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/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]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/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 >rm: cannot remove `*.a': No such file or directory >make[2]: [clean] Error 1 (ignored) >rm *.bak >make[3]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/GDE/SUPPORT' >make[3]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/GL/glpng' >rm -f glpng.o *.a >make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/ISLAND_HOPPING' >make[3]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/GDE/MOLPHY' >make[3]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/GDE/AxML' >rm -f axml.o /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/bin/axml >make[3]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/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-5.1-r1/work/arbsrc_6213/bin/phyml >make[3]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/GDE/AxML' >make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/NAMES' >rm -f names.o *.a >make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/NAMES_COM' >make[3]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/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-5.1-r1/work/arbsrc_6213/bin/raxmlHPC >make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/MULTI_PROBE' >make[3]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/NAMES_COM' >rm -f *.[ao] >make[3]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/GL/glAW' >rm -f GLwMDrawA.o AW_window_ogl.o *.a >make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/NALIGNER' >make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/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[3]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/GL/glpng' >make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/MERGE' >rm: cannot remove `*.bak': No such file or directory >make[2]: [clean] Error 1 (ignored) >rm *~ >make[3]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/GDE/PHYML' >make[3]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/GDE/CLUSTALW' >rm -f *.o /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/bin/clustalw >make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/NAMES' >make[3]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/GDE/RAxML' >make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/PARSIMONY' >rm -f PARS_main.o PARS_dtree.o PARS_debug.o PARS_klprops.o AP_buffer.o AP_main.o AP_tree_nlen.o AP_tree_edge.o *.a >make[3]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/GDE/PHYLIP' >rm -f /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/bin/clique /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/bin/consense /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/bin/contml /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/bin/contrast /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/bin/dnacomp /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/bin/dnadist /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/bin/dnainvar /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/bin/dnaml /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/bin/dnamlk /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/bin/dnamove /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/bin/dnapars /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/bin/dnapenny /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/bin/dolmove /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/bin/dollop /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/bin/dolpenny /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/bin/factor /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/bin/fitch /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/bin/gendist /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/bin/kitsch /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/bin/mix /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/bin/move /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/bin/neighbor /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/bin/pars /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/bin/penny /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/bin/proml /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/bin/promlk /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/bin/protdist /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/bin/protpars /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/bin/restdist /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/bin/restml /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/bin/retree /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/bin/seqboot /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/bin/treedist /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/bin/drawgram /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/bin/drawtree *.o >rm -f */*.[ao] >make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/NTREE' >rm: cannot remove `*~': No such file or directory >make[2]: [clean] Error 1 (ignored) >rm *# >make[3]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/GL/glAW' >make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/GL' >make[3]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/GDE/CLUSTALW' >make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/PARSIMONY' >make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/PHYLO' >rm -f PH_data.o PH_root.o PH_main.o PH_filt.o PH_display.o PH_matr.o *.a >make[3]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/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-5.1-r1/work/arbsrc_6213/bin/puzzle >make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/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]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/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 >rm -f GENH/* >make[3]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/GDE/FASTDNAML' >rm -f fastDNAml.o /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/bin/fastdnaml >make[3]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/GDE/TREEPUZZLE' >rm: cannot remove `*#': No such file or directory >make[2]: [clean] Error 1 (ignored) >rm *\% >make[3]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/GDE/FASTDNAML' >make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/PHYLO' >make[3]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/GDE/PHYLIP' >make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/GDE' >make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/PGT' >make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/PROBE_COM' >rm -f GENC/* >make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/PROBE_SET' >rm -f ps_node.o ps_filebuffer.o ps_database.o ps_tools.o fb_test.o ps_convert_db.o ps_merge_my_dbs.o ps_detect_weak_differences.o ps_find_probes.o ps_eval_candidates.o ps_get_probes.o ps_my2ascii.o ps_my2asciipaths.o ps_arb2asciipaths.o ps_show_result.o >make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/READSEQ' >rm -f readseq.o ureadseq.o /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/bin/arb_readseq >make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/PRIMER_DESIGN' >make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/PROBE_DESIGN' >rm -f probe_design.o SaiProbeVisualization.o probe_match_parser.o *.a >rm: cannot remove `*%': No such file or directory >make[2]: [clean] Error 1 (ignored) >make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/GENOM_IMPORT' >rm -f /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/PROBE_SET/bin/ps_show_result /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/PROBE_SET/bin/ps_arb2asciipaths /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/PROBE_SET/bin/ps_my2asciipaths /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/PROBE_SET/bin/ps_my2ascii /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/PROBE_SET/bin/ps_get_probes /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/PROBE_SET/bin/ps_eval /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/PROBE_SET/bin/ps_find /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/PROBE_SET/bin/ps_detect /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/PROBE_SET/bin/ps_merge /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/PROBE_SET/bin/ps_convert /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/PROBE_SET/bin/fb_test >make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/SEQ_QUALITY' >rm -f SQ_main.o SQ_functions.o SQ_GroupData.o *.a >make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/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-5.1-r1/work/arbsrc_6213/READSEQ' >make[3]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/PROBE_COM' >rm -f *.[ao] >make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/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-5.1-r1/work/arbsrc_6213/PROBE_SET' >make[3]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/NAMES_COM' >make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/NAMES_COM' >make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/PROBE_DESIGN' >make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/SEQ_QUALITY' >make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/SERVERCNTRL' >rm -f servercntrl.o *.a >make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/SL' >make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/RNA3D' >make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/STAT' >rm -f ST_quality.o ST_ml.o ST_window.o *.a >rm -f */*.[ao] >make[3]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/SL/TREE_READ' >rm -f TreeRead.o TreeTools.o *.a >make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/TOOLS' >rm -f /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/bin/arb_2_ascii /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/bin/arb_2_bin /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/bin/arb_a2ps /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/bin/arb_count_chars /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/bin/arb_dnarates /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/bin/arb_export_rates /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/bin/arb_export_tree /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/bin/arb_gene_probe /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/bin/arb_message /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/bin/arb_notify /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/bin/arb_primer /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/bin/arb_probe /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/bin/arb_proto_2_xsub /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/bin/arb_read_tree /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/bin/arb_replace /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/bin/arb_swap_rnastr >make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/SECEDIT' >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-5.1-r1/work/arbsrc_6213/STAT' >make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/TREEGEN' >rm -f base.o defines.o frand.o readcfg.o rns.o sim.o simcfg.o spreadin.o *.a >make[3]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/SL/TREE_WRITE' >rm -f TreeWrite.o *.a >make[3]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/SL/TREE_READ' >make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/SERVERCNTRL' >make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/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 >rm -f GENH/* >make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/XML' >rm -f xml.o *.a >make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/WETC' >rm -f WETC_main.o *.a >make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/TOOLS' >make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/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/molphy.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 >rm -f GENC/* >make[3]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/SL/HELIX' >rm -f BI_helix.o *.a >make[3]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/SL/AW_HELIX' >rm -f AW_helix.o *.a >make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/WINDOW' >make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/TREEGEN' >make[3]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/SL/AW_NAME' >rm -f AW_rename.o AW_names_admin.o *.a >make[3]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/SL/TREE_WRITE' >make[3]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/SL/DB_SCANNER' >rm -f db_scanner.o *.a >make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/SOURCE_TOOLS' >rm -f generate_all_links.stamp >make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/WETC' >make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/XML' >make[3]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/SL/FILE_BUFFER' >rm -f FileBuffer.o *.a >make[3]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/SL/AW_HELIX' >make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/SOURCE_TOOLS' >make[3]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/PROBE_COM' >make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/PROBE_COM' >make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/HELP_SOURCE' >rm -f arb_help2xml.o /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/bin/arb_help2xml >make[3]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/SL/REGEXPR' >rm -f RegExpr.o *.a >make[3]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/SL/HELIX' >make[3]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/SL/AW_NAME' >rm -f _index.html `find ../lib/help -name "*.hlp"` >make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/bin' >find . -type l -exec rm {} \; >make[3]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/SL/DB_SCANNER' >cat: helpfiles.lst: No such file or directory >make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/PERL2ARB' >test -f Makefile && make clean >make[3]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/SL/FILE_BUFFER' >make[3]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/SL/FAST_ALIGNER' >rm -f fast_aligner.o ClustalV.o *.a >make[3]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/GDEHELP' >rm -f ./HELP_GEN/*.help >make[3]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/SL/REGEXPR' >make[2]: [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-5.1-r1/work/arbsrc_6213/lib/ARB.pm /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/lib/ARB.so >rm -f ./HELP_DOC_GEN/*.doc >rm -f html.list `find ../lib/help_html -name "*.html"` >make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/PERL2ARB' >make[3]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/SL/FAST_ALIGNER' >make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/SL' >make[3]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/GDEHELP' >make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/GDEHELP' >find: `../lib/help_html': No such file or directory >rm -f xml.stamp dummy `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-5.1-r1/work/arbsrc_6213/HELP_SOURCE/genhelp' >rm -f *.hlp >make[3]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/HELP_SOURCE/genhelp' >make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/HELP_SOURCE' >find . -type f -perm -100 -exec rm {} \; >make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/bin' >rm -f *.last_gcc >make[1]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213' >make all >make[1]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213' >make links >make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213' >SOURCE_TOOLS/generate_all_links.sh >make[3]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/bin' >make[3]: warning: jobserver unavailable: using -j1. Add `+' to parent make rule. >find . -type l -exec rm {} \; >ln -s -f `find ../SH ../PERL_SCRIPTS -perm -100 ! -type d ! -name 'config*' -print` . >make[3]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/bin' >generate_all_links.sh done. >touch SOURCE_TOOLS/generate_all_links.stamp >make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213' >make com >make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213' >-------------------------------------------------------------------------------- Make everything in AISC_MKPTPS >make[3]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/AISC_MKPTPS' >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AISC_MKPTPS -c mkptypes.cxx >i686-pc-linux-gnu-g++ -O2 -pipe -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu --export-dynamic -rdynamic -o aisc_mkpt mkptypes.o >make[3]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/AISC_MKPTPS' >-------------------------------------------------------------------------------- Make everything in AISC >make[3]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/AISC' >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AISC -c aisc.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AISC -c aisc_commands.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AISC -c aisc_var_ref.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AISC -c aisc_mix.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -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-5.1-r1/work/arbsrc_6213/AISC' >-------------------------------------------------------------------------------- Make everything in NAMES_COM >make[3]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/NAMES_COM' >make[4]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/NAMES_COM' >AISC/Makefile:94: .depends: No such file or directory >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 34): 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 52): 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 53): 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 34): 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 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/client.c (reading /usr/include/sys/types.h, line 147): 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 25): 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 227): 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 30): 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 29): 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/linux/stddef.h, line 14): 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 349): 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 125): 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-5.1-r1/work/arbsrc_6213/SOURCE_TOOLS/mv_if_diff .depends_new .depends >.depends created. >make[4]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/NAMES_COM' >make[4]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/NAMES_COM' >../MAKEBIN/aisc AISC/aisc.pa names.aisc GENH/aisc.h >../MAKEBIN/aisc AISC/aisc_com.pa names.aisc GENH/aisc_com.h >rm -f GENH/aisc_server_extern.aisc >rm -f GENH/aisc_server_extern.h >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NAMES_COM -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -fno-strict-aliasing -Wno-unused -c -o O/client.o C/client.c -IGENH -I. -IC >../MAKEBIN/aisc_mkpt -a C/aisc_extern.c names_extern.c >GENH/aisc_server_extern.aisc >../MAKEBIN/aisc_mkpt -C C/aisc_extern.c names_extern.c >GENH/aisc_server_extern.h >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NAMES_COM -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -fno-strict-aliasing -Wno-unused -c -o O/debug.o C/debug.c -IGENH -I. -IC >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NAMES_COM -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -fno-strict-aliasing -Wno-unused -c -o O/server.o C/server.c -IGENH -I. -IC >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NAMES_COM -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -fno-strict-aliasing -Wno-unused -c -o O/struct_man.o C/struct_man.c -IGENH -I. -IC >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NAMES_COM -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -fno-strict-aliasing -Wno-unused -c -o O/aisc_extern.o C/aisc_extern.c -IGENH -I. -IC >../MAKEBIN/aisc AISC/aisc_server.pa names.aisc GENC/aisc_server.c GENH/aisc_server_extern.aisc GENH/import_proto.h >../MAKEBIN/aisc AISC/aisc_global.pa names.aisc GENC/aisc_global.c GENH/aisc_server_extern.aisc GENH/import_proto.h >../MAKEBIN/aisc AISC/aisc_debug_globals.pa names.aisc GENC/aisc_debug_globals.c GENH/aisc_server_extern.aisc GENH/import_proto.h >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NAMES_COM -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -fno-strict-aliasing -Wno-unused -c -o GENC/aisc_debug_globals.o GENC/aisc_debug_globals.c -IGENH -I. -IC >rm -f GENH/aisc_server_proto.h >../MAKEBIN/aisc_mkpt -C GENC/aisc_server.c >GENH/aisc_server_proto.h >C/debug.c: In function âconst char* aisc_debug_local(aisc_com*, int, long int, char*, ...)â: >C/debug.c:115:37: warning: ignoring return value of âsize_t fwrite(const void*, size_t, size_t, FILE*)â, declared with attribute warn_unused_result >echo GENH/import_proto.h >GENH/import_proto.h >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NAMES_COM -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -fno-strict-aliasing -Wno-unused -c -o GENC/aisc_global.o GENC/aisc_global.c -IGENH -I. -IC -DAISC_SAVE_YES >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NAMES_COM -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -fno-strict-aliasing -Wno-unused -c -o GENC/aisc_server.o GENC/aisc_server.c -IGENH -I. -IC -DAISC_SAVE_YES >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NAMES_COM -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -fno-strict-aliasing -Wno-unused -c -o names_extern.o names_extern.c -IGENH -I. -IC -DAISC_SAVE_YES >ld --export-dynamic -r -o client.a O/client.o O/debug.o GENC/aisc_debug_globals.o >ld --export-dynamic -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-5.1-r1/work/arbsrc_6213/NAMES_COM' >make[3]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/NAMES_COM' >-------------------------------------------------------------------------------- Make everything in PROBE_COM >make[3]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/PROBE_COM' >make[4]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/PROBE_COM' >AISC/Makefile:94: .depends: No such file or directory >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 34): 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 52): 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 53): 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 34): 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 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/client.c (reading /usr/include/sys/types.h, line 147): 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 25): 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 227): 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 30): 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 29): 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/linux/stddef.h, line 14): 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 349): 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 125): 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-5.1-r1/work/arbsrc_6213/SOURCE_TOOLS/mv_if_diff .depends_new .depends >.depends created. >make[4]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/PROBE_COM' >make[4]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/PROBE_COM' >../MAKEBIN/aisc AISC/aisc.pa PT.aisc GENH/aisc.h >../MAKEBIN/aisc AISC/aisc_com.pa PT.aisc GENH/aisc_com.h >rm -f GENH/aisc_server_extern.aisc >rm -f GENH/aisc_server_extern.h >../MAKEBIN/aisc_mkpt -a C/aisc_extern.c PT_extern.c >GENH/aisc_server_extern.aisc >../MAKEBIN/aisc_mkpt -C C/aisc_extern.c PT_extern.c >GENH/aisc_server_extern.h >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PROBE_COM -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -fno-strict-aliasing -Wno-unused -c -o O/client.o C/client.c -IGENH -I. -IC >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PROBE_COM -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -fno-strict-aliasing -Wno-unused -c -o O/debug.o C/debug.c -IGENH -I. -IC >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PROBE_COM -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -fno-strict-aliasing -Wno-unused -c -o O/server.o C/server.c -IGENH -I. -IC >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PROBE_COM -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -fno-strict-aliasing -Wno-unused -c -o O/struct_man.o C/struct_man.c -IGENH -I. -IC >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PROBE_COM -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -fno-strict-aliasing -Wno-unused -c -o O/aisc_extern.o C/aisc_extern.c -IGENH -I. -IC >../MAKEBIN/aisc AISC/aisc_server.pa PT.aisc GENC/aisc_server.c GENH/aisc_server_extern.aisc GENH/import_proto.h >../MAKEBIN/aisc AISC/aisc_global.pa PT.aisc GENC/aisc_global.c GENH/aisc_server_extern.aisc GENH/import_proto.h >../MAKEBIN/aisc AISC/aisc_debug_globals.pa PT.aisc GENC/aisc_debug_globals.c GENH/aisc_server_extern.aisc GENH/import_proto.h >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PROBE_COM -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -fno-strict-aliasing -Wno-unused -c -o GENC/aisc_debug_globals.o GENC/aisc_debug_globals.c -IGENH -I. -IC >C/debug.c: In function âconst char* aisc_debug_local(aisc_com*, int, long int, char*, ...)â: >C/debug.c:115:37: warning: ignoring return value of âsize_t fwrite(const void*, size_t, size_t, FILE*)â, declared with attribute warn_unused_result >rm -f GENH/aisc_server_proto.h >../MAKEBIN/aisc_mkpt -C GENC/aisc_server.c >GENH/aisc_server_proto.h >echo GENH/import_proto.h >GENH/import_proto.h >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PROBE_COM -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -fno-strict-aliasing -Wno-unused -c -o GENC/aisc_global.o GENC/aisc_global.c -IGENH -I. -IC -DAISC_SAVE_NO >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PROBE_COM -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -fno-strict-aliasing -Wno-unused -c -o GENC/aisc_server.o GENC/aisc_server.c -IGENH -I. -IC -DAISC_SAVE_NO >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PROBE_COM -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -fno-strict-aliasing -Wno-unused -c -o PT_extern.o PT_extern.c -IGENH -I. -IC -DAISC_SAVE_NO >ld --export-dynamic -r -o client.a O/client.o O/debug.o GENC/aisc_debug_globals.o >ld --export-dynamic -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-5.1-r1/work/arbsrc_6213/PROBE_COM' >make[3]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/PROBE_COM' >make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213' >make arb >make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213' >(cd lib;make all) >make[3]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/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-5.1-r1/work/arbsrc_6213/lib/nas' >rm -f names.dat >cp names.dat.template names.dat >rm -f *% >make[4]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/lib/nas' >make[3]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/lib' >make arbbasic2 >make[3]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213' >-------------------------------------------------------------------------------- Make everything in AISC_MKPTPS >make[4]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/AISC_MKPTPS' >make[4]: Nothing to be done for `dummy.a'. >make[4]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/AISC_MKPTPS' >-------------------------------------------------------------------------------- Make everything in AISC >make[4]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/AISC' >make[4]: Nothing to be done for `dummy.a'. >make[4]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/AISC' >-------------------------------------------------------------------------------- Make everything in TEMPLATES >make[4]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/TEMPLATES' >../SOURCE_TOOLS/build_info.pl >make[4]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/TEMPLATES' >-------------------------------------------------------------------------------- Make everything in NAMES_COM >make[4]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/NAMES_COM' >make[4]: `server.a' is up to date. >make[4]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/NAMES_COM' >-------------------------------------------------------------------------------- Make everything in NAMES_COM >make[4]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/NAMES_COM' >make[4]: `server.a' is up to date. >make[4]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/NAMES_COM' >-------------------------------------------------------------------------------- Make everything in PROBE_COM >make[4]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/PROBE_COM' >make[4]: `server.a' is up to date. >make[4]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/PROBE_COM' >make SL/SL.dummy >make[4]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213' >-------------------------------------------------------------------------------- Make everything in GL >make[4]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/GL' >make[5]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/GL/glpng' >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GL -DIN_ARB_glpng -c glpng.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >make[5]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/GL/glAW' >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GL -DIN_ARB_glAW -c GLwMDrawA.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GL -DIN_ARB_glAW -c AW_window_ogl.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/WINDOW >glpng.c: In function âpngLoadRawFâ: >glpng.c:288:5: warning: âjmpbufâ is deprecated (declared at /usr/include/png.h:1098) >glpng.c: In function âpngLoadFâ: >glpng.c:393:5: warning: âjmpbufâ is deprecated (declared at /usr/include/png.h:1098) >glpng.c:385:10: warning: ignoring return value of âfreadâ, declared with attribute warn_unused_result >glpng.c: In function âpngLoadRawFâ: >glpng.c:280:10: warning: ignoring return value of âfreadâ, declared with attribute warn_unused_result >ld --export-dynamic -r -o libglpng_arb.a glpng.o >make[5]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/GL/glpng' >ld --export-dynamic -r -o libglAW.a GLwMDrawA.o AW_window_ogl.o >make[5]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/GL/glAW' >make[4]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/GL' >-------------------------------------------------------------------------------- Make everything in SL >make[5]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/SL' >make[6]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/SL/TREE_READ' >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_SL -DIN_ARB_TREE_READ -c TreeRead.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_SL -DIN_ARB_TREE_READ -c TreeTools.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >ld --export-dynamic -r -o TREE_READ.a TreeRead.o TreeTools.o >make[6]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/SL/TREE_READ' >make[6]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/SL/DB_SCANNER' >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_SL -DIN_ARB_DB_SCANNER -c db_scanner.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >ld --export-dynamic -r -o DB_SCANNER.a db_scanner.o >make[6]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/SL/DB_SCANNER' >make[6]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/SL/REGEXPR' >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_SL -DIN_ARB_REGEXPR -c RegExpr.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >ld --export-dynamic -r -o REGEXPR.a RegExpr.o >make[6]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/SL/REGEXPR' >make[6]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/SL/FILE_BUFFER' >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_SL -DIN_ARB_FILE_BUFFER -c FileBuffer.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >ld --export-dynamic -r -o FILE_BUFFER.a FileBuffer.o >make[6]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/SL/FILE_BUFFER' >make[6]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/SL/HELIX' >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_SL -DIN_ARB_HELIX -c BI_helix.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >ld --export-dynamic -r -o HELIX.a BI_helix.o >make[6]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/SL/HELIX' >make[6]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/SL/AW_HELIX' >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_SL -DIN_ARB_AW_HELIX -c AW_helix.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >ld --export-dynamic -r -o AW_HELIX.a AW_helix.o >make[6]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/SL/AW_HELIX' >make[6]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/SL/AW_NAME' >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_SL -DIN_ARB_AW_NAME -c AW_rename.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -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-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >ld --export-dynamic -r -o AW_NAME.a AW_rename.o AW_names_admin.o >make[6]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/SL/AW_NAME' >make[6]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/SL/TREE_WRITE' >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_SL -DIN_ARB_TREE_WRITE -c TreeWrite.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >ld --export-dynamic -r -o TREE_WRITE.a TreeWrite.o >make[6]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/SL/TREE_WRITE' >make[6]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/SL/FAST_ALIGNER' >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_SL -DIN_ARB_FAST_ALIGNER -c fast_aligner.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_SL -DIN_ARB_FAST_ALIGNER -c ClustalV.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >fast_aligner.cxx: In function âconst char* alignCompactedTo(AWTC_CompactedSubSequence*, const AWTC_FastSearchSequence*, int, const char*, long int, GBDATA*, GBDATA*, const AlignParams&)â: >fast_aligner.cxx:1254:31: warning: âGBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_t_prot.h:108) >fast_aligner.cxx:1254:84: warning: âGBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_t_prot.h:108) >ld --export-dynamic -r -o FAST_ALIGNER.a fast_aligner.o ClustalV.o >make[6]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/SL/FAST_ALIGNER' >make[5]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/SL' >make[4]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213' >make[3]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213' >make arbshared arbapplications help >make[3]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213' >make -C bin all >make[4]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/bin' >find . -type l -exec rm {} \; >-------------------------------------------------------------------------------- Building prototyper >make AISC_MKPTPS/AISC_MKPTPS.dummy >-------------------------------------------------------------------------------- Make everything in AISC_MKPTPS >make[4]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/AISC_MKPTPS' >make[4]: Nothing to be done for `dummy.a'. >make[4]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/AISC_MKPTPS' >-------------------------------------------------------------------------------- Make everything in AISC >make[4]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/AISC' >make[4]: Nothing to be done for `dummy.a'. >make[4]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/AISC' >make[4]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213' >ln -s -f `find ../SH ../PERL_SCRIPTS -perm -100 ! -type d ! -name 'config*' -print` . >-------------------------------------------------------------------------------- Make everything in AISC_MKPTPS >make[5]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/AISC_MKPTPS' >make[5]: Nothing to be done for `AISC_MKPTPS.a'. >make[5]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/AISC_MKPTPS' >make[4]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/bin' >make[4]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213' >-------------------------------------------------------------------------------- Make everything in ARBDBPP >make[4]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/ARBDBPP' >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBPP -c adtsequence.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBPP -c adt_edit.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBPP -c adtali.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBPP -c adextended.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBPP -c adseq.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBPP -c adspecies.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBPP -c admain.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >adseq.cxx: In member function âAD_ERR* AD_CONT::create(AD_SPECIES*, AD_ALI*)â: >adseq.cxx:1012:20: warning: âGBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_t_prot.h:108) >adseq.cxx:1012:84: warning: âGBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_t_prot.h:108) >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBPP -c adali.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBPP -c liste.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe --export-dynamic -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -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-5.1-r1/work/arbsrc_6213/ARBDBPP' >-------------------------------------------------------------------------------- Make everything in AWTI >make[4]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/AWTI' >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWTI -c AWTI_import.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWTI -c AWTI_export.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >AWTI_export.cxx: In function âconst char* export_species_using_form(FILE*, GBDATA*, const char*)â: >AWTI_export.cxx:511:32: warning: ignoring return value of âsize_t fwrite(const void*, size_t, size_t, FILE*)â, declared with attribute warn_unused_result >ld --export-dynamic -r -o AWTI.a AWTI_import.o AWTI_export.o >make[4]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/AWTI' >-------------------------------------------------------------------------------- Make everything in GENOM >make[4]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/GENOM' >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GENOM -c GEN_interface.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GENOM -c GEN_map.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >GEN_map.cxx: In function âvoid gen_extract_gene_2_pseudoSpecies(GBDATA*, GBDATA*, EG2PS_data*)â: >GEN_map.cxx:882:39: warning: âGBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_t_prot.h:108) >GEN_map.cxx:882:93: warning: âGBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_t_prot.h:108) >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GENOM -c GEN_graphic.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GENOM -c GEN_gene.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GENOM -c GEN_nds.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GENOM -c GEN_color_groups.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GENOM -c GEN_translations.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >GEN_nds.cxx:307:2: warning: #warning make this function more general like AWT_popup_select_species_field_window >GEN_graphic.cxx:158:12: warning: unused parameter âselected_rangeâ >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GENOM -c EXP_interface.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GENOM -c EXP_main.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >ld --export-dynamic -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-5.1-r1/work/arbsrc_6213/GENOM' >-------------------------------------------------------------------------------- Make everything in MERGE >make[4]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/MERGE' >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_MERGE -c MG_checkfield.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_MERGE -c MG_main.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_MERGE -c MG_trees.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_MERGE -c MG_alignment.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_MERGE -c MG_species.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_MERGE -c MG_extendeds.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_MERGE -c MG_names.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_MERGE -c MG_gene_species.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_MERGE -c MG_configs.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_MERGE -c MG_preserves.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >ld --export-dynamic -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-5.1-r1/work/arbsrc_6213/MERGE' >-------------------------------------------------------------------------------- Make everything in SL/DB_SCANNER >make[4]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/SL/DB_SCANNER' >make[4]: `DB_SCANNER.a' is up to date. >make[4]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/SL/DB_SCANNER' >-------------------------------------------------------------------------------- Make everything in SERVERCNTRL >make[4]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/SERVERCNTRL' >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_SERVERCNTRL -c servercntrl.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >servercntrl.c: In function âarb_look_and_start_serverâ: >servercntrl.c:202:35: warning: ignoring return value of âsystemâ, declared with attribute warn_unused_result >servercntrl.c: In function âarb_start_serverâ: >servercntrl.c:145:68: warning: ignoring return value of âsystemâ, declared with attribute warn_unused_result >ld --export-dynamic -r -o SERVERCNTRL.a servercntrl.o >make[4]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/SERVERCNTRL' >-------------------------------------------------------------------------------- Make everything in SL/FILE_BUFFER >make[4]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/SL/FILE_BUFFER' >make[4]: `FILE_BUFFER.a' is up to date. >make[4]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/SL/FILE_BUFFER' >-------------------------------------------------------------------------------- Make everything in SEQ_QUALITY >make[4]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/SEQ_QUALITY' >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_SEQ_QUALITY -c SQ_main.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_SEQ_QUALITY -c SQ_functions.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_SEQ_QUALITY -c SQ_GroupData.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >SQ_functions.cxx: In function âconst char* SQ_reset_quality_calcstate(GBDATA*)â: >SQ_functions.cxx:82:21: warning: âconst char* GB_get_error()â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_prot.h:43) >SQ_functions.cxx:82:34: warning: âconst char* GB_get_error()â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_prot.h:43) >SQ_functions.cxx:92:29: warning: âconst char* GB_get_error()â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_prot.h:43) >SQ_functions.cxx:92:42: warning: âconst char* GB_get_error()â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_prot.h:43) >SQ_functions.cxx: In function âconst char* SQ_evaluate(GBDATA*, const SQ_weights&, bool)â: >SQ_functions.cxx:239:21: warning: âconst char* GB_get_error()â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_prot.h:43) >SQ_functions.cxx:239:34: warning: âconst char* GB_get_error()â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_prot.h:43) >SQ_functions.cxx: In function âconst char* SQ_pass1(SQ_GroupData*, GBDATA*, GBT_TREE*, AP_filter*)â: >SQ_functions.cxx:450:17: warning: âconst char* GB_get_error()â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_prot.h:43) >SQ_functions.cxx:450:30: warning: âconst char* GB_get_error()â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_prot.h:43) >SQ_functions.cxx:461:25: warning: âconst char* GB_get_error()â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_prot.h:43) >SQ_functions.cxx:461:38: warning: âconst char* GB_get_error()â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_prot.h:43) >SQ_functions.cxx:469:25: warning: âconst char* GB_get_error()â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_prot.h:43) >SQ_functions.cxx:469:38: warning: âconst char* GB_get_error()â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_prot.h:43) >SQ_functions.cxx: In function âconst char* SQ_pass1_no_tree(SQ_GroupData*, GBDATA*, AP_filter*)â: >SQ_functions.cxx:554:21: warning: âconst char* GB_get_error()â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_prot.h:43) >SQ_functions.cxx:554:34: warning: âconst char* GB_get_error()â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_prot.h:43) >SQ_functions.cxx:564:29: warning: âconst char* GB_get_error()â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_prot.h:43) >SQ_functions.cxx:564:42: warning: âconst char* GB_get_error()â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_prot.h:43) >SQ_functions.cxx:572:29: warning: âconst char* GB_get_error()â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_prot.h:43) >SQ_functions.cxx:572:42: warning: âconst char* GB_get_error()â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_prot.h:43) >SQ_functions.cxx: In function âconst char* SQ_pass2(const SQ_GroupData*, GBDATA*, GBT_TREE*, AP_filter*)â: >SQ_functions.cxx:649:17: warning: âconst char* GB_get_error()â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_prot.h:43) >SQ_functions.cxx:649:30: warning: âconst char* GB_get_error()â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_prot.h:43) >SQ_functions.cxx:659:25: warning: âconst char* GB_get_error()â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_prot.h:43) >SQ_functions.cxx:659:38: warning: âconst char* GB_get_error()â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_prot.h:43) >SQ_functions.cxx:664:25: warning: âconst char* GB_get_error()â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_prot.h:43) >SQ_functions.cxx:664:38: warning: âconst char* GB_get_error()â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_prot.h:43) >SQ_functions.cxx:733:29: warning: âconst char* GB_get_error()â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_prot.h:43) >SQ_functions.cxx:733:42: warning: âconst char* GB_get_error()â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_prot.h:43) >SQ_functions.cxx:737:29: warning: âconst char* GB_get_error()â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_prot.h:43) >SQ_functions.cxx:737:42: warning: âconst char* GB_get_error()â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_prot.h:43) >SQ_functions.cxx: In function âconst char* SQ_pass2_no_tree(const SQ_GroupData*, GBDATA*, AP_filter*)â: >SQ_functions.cxx:889:21: warning: âconst char* GB_get_error()â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_prot.h:43) >SQ_functions.cxx:889:34: warning: âconst char* GB_get_error()â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_prot.h:43) >SQ_functions.cxx:898:29: warning: âconst char* GB_get_error()â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_prot.h:43) >SQ_functions.cxx:898:42: warning: âconst char* GB_get_error()â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_prot.h:43) >SQ_functions.cxx:903:29: warning: âconst char* GB_get_error()â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_prot.h:43) >SQ_functions.cxx:903:42: warning: âconst char* GB_get_error()â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_prot.h:43) >SQ_functions.cxx:972:33: warning: âconst char* GB_get_error()â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_prot.h:43) >SQ_functions.cxx:972:46: warning: âconst char* GB_get_error()â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_prot.h:43) >SQ_functions.cxx:976:33: warning: âconst char* GB_get_error()â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_prot.h:43) >SQ_functions.cxx:976:46: warning: âconst char* GB_get_error()â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_prot.h:43) >SQ_functions.cxx: In function âconst char* SQ_count_nr_of_species(GBDATA*)â: >SQ_functions.cxx:1120:21: warning: âconst char* GB_get_error()â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_prot.h:43) >SQ_functions.cxx:1120:34: warning: âconst char* GB_get_error()â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_prot.h:43) >SQ_functions.cxx:1130:29: warning: âconst char* GB_get_error()â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_prot.h:43) >SQ_functions.cxx:1130:42: warning: âconst char* GB_get_error()â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_prot.h:43) >ld --export-dynamic -r -o SEQ_QUALITY.a SQ_main.o SQ_functions.o SQ_GroupData.o >make[4]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/SEQ_QUALITY' >-------------------------------------------------------------------------------- Make everything in PRIMER_DESIGN >make[4]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/PRIMER_DESIGN' >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PRIMER_DESIGN -c PRD_Pair.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PRIMER_DESIGN -c PRD_Item.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PRIMER_DESIGN -c PRD_Node.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >PRD_Node.cxx: In member function âvoid Node::print()â: >PRD_Node.cxx:64:28: warning: array subscript is above array bounds >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PRIMER_DESIGN -c PRD_Range.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PRIMER_DESIGN -c PRD_SequenceIterator.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PRIMER_DESIGN -c PRD_SearchFIFO.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PRIMER_DESIGN -c PRD_Design.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PRIMER_DESIGN -c primer_design.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >ld --export-dynamic -r -o PRIMER_DESIGN.a PRD_Pair.o PRD_Item.o PRD_Node.o PRD_Range.o PRD_SequenceIterator.o PRD_SearchFIFO.o PRD_Design.o primer_design.o >make[4]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/PRIMER_DESIGN' >-------------------------------------------------------------------------------- Make everything in SL/HELIX >make[4]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/SL/HELIX' >make[4]: `HELIX.a' is up to date. >make[4]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/SL/HELIX' >-------------------------------------------------------------------------------- Make everything in SL/REGEXPR >make[4]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/SL/REGEXPR' >make[4]: `REGEXPR.a' is up to date. >make[4]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/SL/REGEXPR' >-------------------------------------------------------------------------------- Make everything in SL/TREE_READ >make[4]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/SL/TREE_READ' >make[4]: `TREE_READ.a' is up to date. >make[4]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/SL/TREE_READ' >-------------------------------------------------------------------------------- Make everything in SL/TREE_WRITE >make[4]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/SL/TREE_WRITE' >make[4]: `TREE_WRITE.a' is up to date. >make[4]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/SL/TREE_WRITE' >-------------------------------------------------------------------------------- Make everything in STAT >make[4]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/STAT' >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_STAT -c ST_quality.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >ST_quality.cxx: In function âvoid st_ml_add_quality_string_to_species(GBDATA*, const char*, const char*, int, int, GB_HASH*, st_report_enum, const char*)â: >ST_quality.cxx:168:33: warning: âGBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_t_prot.h:108) >ST_quality.cxx:168:94: warning: âGBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_t_prot.h:108) >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_STAT -c ST_ml.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_STAT -c ST_window.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >ld --export-dynamic -r -o STAT.a ST_quality.o ST_ml.o ST_window.o >make[4]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/STAT' >-------------------------------------------------------------------------------- Make everything in GENOM_IMPORT >make[4]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/GENOM_IMPORT' >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GENOM_IMPORT -c GenomeImport.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GENOM_IMPORT -c Importer.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GENOM_IMPORT -c DBwriter.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >DBwriter.cxx: In member function âvoid DBwriter::writeSequence(const SequenceBuffer&)â: >DBwriter.cxx:226:23: warning: âGBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_t_prot.h:108) >DBwriter.cxx:226:76: warning: âGBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_t_prot.h:108) >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GENOM_IMPORT -c SequenceBuffer.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GENOM_IMPORT -c MetaInfo.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GENOM_IMPORT -c Feature.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GENOM_IMPORT -c Location.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GENOM_IMPORT -c tools.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/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 --export-dynamic -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-5.1-r1/work/arbsrc_6213/GENOM_IMPORT' >-------------------------------------------------------------------------------- Make everything in XML >make[4]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/XML' >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_XML -c xml.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >xml.cxx:40:15: warning: unused parameter âquotedTextâ >ld --export-dynamic -r -o XML.a xml.o >make[4]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/XML' >-------------------------------------------------------------------------------- Make everything in WINDOW >make[4]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/WINDOW' >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_WINDOW -c AW_position.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_WINDOW -c AW_Xm.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_WINDOW -c AW_at.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_WINDOW -c AW_button.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_WINDOW -c AW_click.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >AW_button.cxx: In function âconst char* detect_bitmap_size(const char*, int*, int*)â: >AW_button.cxx:398:47: warning: ignoring return value of âchar* fgets(char*, int, FILE*)â, declared with attribute warn_unused_result >AW_button.cxx:417:51: warning: ignoring return value of âchar* fgets(char*, int, FILE*)â, declared with attribute warn_unused_result >AW_button.cxx:418:51: warning: ignoring return value of âchar* fgets(char*, int, FILE*)â, declared with attribute warn_unused_result >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_WINDOW -c AW_debug.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_WINDOW -c AW_device.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_WINDOW -c AW_font_group.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_WINDOW -c AW_global_awars.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_WINDOW -c AW_nawar.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >AW_nawar.cxx: In member function âAW_awar* AW_root::awar_pointer(const char*, void*, GBDATA*)â: >AW_nawar.cxx:193:111: warning: passing NULL to non-pointer argument 4 of âAW_awar::AW_awar(AW_VARIABLE_TYPE, const char*, const char*, double, GBDATA*, AW_root*)â >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_WINDOW -c AW_preset.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_WINDOW -c AW_print.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_WINDOW -c AW_question.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_WINDOW -c AW_size.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_WINDOW -c AW_status.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_WINDOW -c AW_window.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_WINDOW -c AW_xfig.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >AW_status.cxx: In function âint aw_status_read_int(int, int)â: >AW_status.cxx:281:19: warning: dereferencing type-punned pointer will break strict-aliasing rules >AW_status.cxx: In function âvoid aw_help_edit_help(AW_window*)â: >AW_status.cxx:1746:25: warning: ignoring return value of âint system(const char*)â, declared with attribute warn_unused_result >AW_status.cxx: In function âvoid aw_status_timer_event(AW_root*, AW_CL, AW_CL)â: >AW_status.cxx:419:28: warning: ignoring return value of âint system(const char*)â, declared with attribute warn_unused_result >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_WINDOW -c AW_xfigfont.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_WINDOW -c AW_xfont.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_WINDOW -c AW_xkey.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_WINDOW -c AW_window_Xm_interface.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe --export-dynamic -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -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-5.1-r1/work/arbsrc_6213/WINDOW' >-------------------------------------------------------------------------------- Make everything in SL/AW_HELIX >make[4]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/SL/AW_HELIX' >make[4]: `AW_HELIX.a' is up to date. >make[4]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/SL/AW_HELIX' >-------------------------------------------------------------------------------- Make everything in ARBDB2 >make[4]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/ARBDB2' >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c adsort.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c adlang1.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c adstring.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c admatch.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c arbdb.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c ad_core.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >admatch.c: In function âGBS_string_evalâ: >admatch.c:763:37: warning: ignoring return value of âgbs_build_replace_stringâ, declared with attribute warn_unused_result >arbdb.c: In function âGB_copy_with_protectionâ: >arbdb.c:1469:13: warning: null argument where non-null required (argument 2) >arbdb.c:1469:13: warning: null argument where non-null required (argument 2) >arbdb.c:1469:13: warning: null argument where non-null required (argument 2) >arbdb.c:1469:13: warning: null argument where non-null required (argument 2) >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c admath.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c adoptimize.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c adsystem.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c adindex.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c adperl.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c adlink.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c adsocket.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >adsocket.c: In function âGB_get_full_pathâ: >adsocket.c:1256:21: warning: ignoring return value of ârealpathâ, declared with attribute warn_unused_result >adsocket.c:1260:21: warning: ignoring return value of ârealpathâ, declared with attribute warn_unused_result >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c adcomm.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c adhash.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c adquery.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >adquery.c: In function âgb_searchâ: >adquery.c:449:28: warning: comparison between âGB_TYPESâ and âenum gb_search_enumâ >adquery.c:455:28: warning: comparison between âGB_TYPESâ and âenum gb_search_enumâ >adquery.c:526:31: warning: comparison between âGB_TYPESâ and âenum gb_search_enumâ >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c ad_save_load.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >ad_save_load.c: In function âgb_write_bin_rekâ: >ad_save_load.c:799:13: warning: null argument where non-null required (argument 1) >ad_save_load.c: In function âGB_save_asâ: >ad_save_load.c:1079:5: warning: âGB_get_errorâ is deprecated (declared at ./ad_prot.h:43) >ad_save_load.c: In function âGB_save_quick_asâ: >ad_save_load.c:1122:5: warning: âGB_get_errorâ is deprecated (declared at ./ad_prot.h:43) >ad_save_load.c:1123:5: warning: âGB_get_errorâ is deprecated (declared at ./ad_prot.h:43) >ad_save_load.c:1145:9: warning: âGB_get_errorâ is deprecated (declared at ./ad_prot.h:43) >ad_save_load.c:1170:9: warning: âGB_get_errorâ is deprecated (declared at ./ad_prot.h:43) >ad_save_load.c:1181:9: warning: âGB_get_errorâ is deprecated (declared at ./ad_prot.h:43) >ad_save_load.c: In function âGB_save_quickâ: >ad_save_load.c:1206:5: warning: âGB_get_errorâ is deprecated (declared at ./ad_prot.h:43) >ad_save_load.c:1207:5: warning: âGB_get_errorâ is deprecated (declared at ./ad_prot.h:43) >ad_save_load.c:1228:9: warning: âGB_get_errorâ is deprecated (declared at ./ad_prot.h:43) >ad_save_load.c:1261:5: warning: âGB_get_errorâ is deprecated (declared at ./ad_prot.h:43) >ad_save_load.c: In function âgb_check_saveableâ: >ad_save_load.c:1301:9: warning: âGB_get_errorâ is deprecated (declared at ./ad_prot.h:43) >ad_save_load.c:1306:9: warning: âGB_get_errorâ is deprecated (declared at ./ad_prot.h:43) >ad_save_load.c: In function âgb_write_binâ: >ad_save_load.c:824:11: warning: ignoring return value of âfwriteâ, declared with attribute warn_unused_result >ad_save_load.c:827:11: warning: ignoring return value of âfwriteâ, declared with attribute warn_unused_result >ad_save_load.c:842:11: warning: ignoring return value of âfwriteâ, declared with attribute warn_unused_result >ad_save_load.c:850:11: warning: ignoring return value of âfwriteâ, declared with attribute warn_unused_result >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c adcompr.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c admalloc.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c ad_load.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c admap.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >ad_load.c: In function âGB_loginâ: >ad_load.c:1380:34: warning: ignoring return value of âgb_scan_directoryâ, declared with attribute warn_unused_result >admap.c: In function âgb_is_valid_mapfileâ: >admap.c:722:14: warning: ignoring return value of âfreadâ, declared with attribute warn_unused_result >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c adTest.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c adtune.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c adGene.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c adtcp.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c adhashtools.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c adExperiment.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c adtools.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c adseqcompr.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c adtables.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c adRevCompl.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >adtools.c: In function âGBT_check_arb_fileâ: >adtools.c:74:10: warning: ignoring return value of âfgetsâ, declared with attribute warn_unused_result >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c adChangeKey.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c adali.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c adcolumns.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >adali.c: In function âGBT_create_sequence_dataâ: >adali.c:597:5: warning: âGBT_add_dataâ is deprecated (declared at adali.c:568) >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c adtree.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c adname.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c aditem.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c ad_config.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe --export-dynamic -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -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-5.1-r1/work/arbsrc_6213/ARBDB2' >-------------------------------------------------------------------------------- Make everything in WETC >make[4]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/WETC' >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_WETC -c -o WETC_main.o WETC_main.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >ld --export-dynamic -r -o WETC.a WETC_main.o >make[4]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/WETC' >-------------------------------------------------------------------------------- Make everything in EDIT >make[4]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/EDIT' >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_EDIT -c edit.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_EDIT -c edit_naligner.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >edit_naligner.cxx: In function âvoid aed_start_naligning(AW_window*)â: >edit_naligner.cxx:102:19: warning: ignoring return value of âint system(const char*)â, declared with attribute warn_unused_result >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_EDIT -c edit_tools.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_EDIT -c ed_conf.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >ld --export-dynamic -r -o EDIT.a edit.o edit_naligner.o edit_tools.o ed_conf.o >make[4]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/EDIT' >-------------------------------------------------------------------------------- Make everything in SL/FAST_ALIGNER >make[4]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/SL/FAST_ALIGNER' >make[4]: `FAST_ALIGNER.a' is up to date. >make[4]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/SL/FAST_ALIGNER' >-------------------------------------------------------------------------------- Make everything in ARBDBS >make[4]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/ARBDBS' >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c adsort.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c adlang1.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c adstring.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c admatch.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >admatch.c: In function âGBS_string_evalâ: >admatch.c:763:37: warning: ignoring return value of âgbs_build_replace_stringâ, declared with attribute warn_unused_result >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c arbdb.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c ad_core.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >arbdb.c: In function âGB_copy_with_protectionâ: >arbdb.c:1469:13: warning: null argument where non-null required (argument 2) >arbdb.c:1469:13: warning: null argument where non-null required (argument 2) >arbdb.c:1469:13: warning: null argument where non-null required (argument 2) >arbdb.c:1469:13: warning: null argument where non-null required (argument 2) >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c admath.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c adoptimize.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c adsystem.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c adindex.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c adperl.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c adlink.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c adsocket.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >adsocket.c: In function âGB_get_full_pathâ: >adsocket.c:1256:21: warning: ignoring return value of ârealpathâ, declared with attribute warn_unused_result >adsocket.c:1260:21: warning: ignoring return value of ârealpathâ, declared with attribute warn_unused_result >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c adcomm.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c adhash.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c adquery.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >adquery.c: In function âgb_searchâ: >adquery.c:449:28: warning: comparison between âGB_TYPESâ and âenum gb_search_enumâ >adquery.c:455:28: warning: comparison between âGB_TYPESâ and âenum gb_search_enumâ >adquery.c:526:31: warning: comparison between âGB_TYPESâ and âenum gb_search_enumâ >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c ad_save_load.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c adcompr.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c admalloc.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >ad_save_load.c: In function âgb_write_bin_rekâ: >ad_save_load.c:799:13: warning: null argument where non-null required (argument 1) >ad_save_load.c: In function âGB_save_asâ: >ad_save_load.c:1079:5: warning: âGB_get_errorâ is deprecated (declared at ./ad_prot.h:43) >ad_save_load.c: In function âGB_save_quick_asâ: >ad_save_load.c:1122:5: warning: âGB_get_errorâ is deprecated (declared at ./ad_prot.h:43) >ad_save_load.c:1123:5: warning: âGB_get_errorâ is deprecated (declared at ./ad_prot.h:43) >ad_save_load.c:1145:9: warning: âGB_get_errorâ is deprecated (declared at ./ad_prot.h:43) >ad_save_load.c:1170:9: warning: âGB_get_errorâ is deprecated (declared at ./ad_prot.h:43) >ad_save_load.c:1181:9: warning: âGB_get_errorâ is deprecated (declared at ./ad_prot.h:43) >ad_save_load.c: In function âGB_save_quickâ: >ad_save_load.c:1206:5: warning: âGB_get_errorâ is deprecated (declared at ./ad_prot.h:43) >ad_save_load.c:1207:5: warning: âGB_get_errorâ is deprecated (declared at ./ad_prot.h:43) >ad_save_load.c:1228:9: warning: âGB_get_errorâ is deprecated (declared at ./ad_prot.h:43) >ad_save_load.c:1261:5: warning: âGB_get_errorâ is deprecated (declared at ./ad_prot.h:43) >ad_save_load.c: In function âgb_check_saveableâ: >ad_save_load.c:1301:9: warning: âGB_get_errorâ is deprecated (declared at ./ad_prot.h:43) >ad_save_load.c:1306:9: warning: âGB_get_errorâ is deprecated (declared at ./ad_prot.h:43) >ad_save_load.c: In function âgb_write_binâ: >ad_save_load.c:824:11: warning: ignoring return value of âfwriteâ, declared with attribute warn_unused_result >ad_save_load.c:827:11: warning: ignoring return value of âfwriteâ, declared with attribute warn_unused_result >ad_save_load.c:842:11: warning: ignoring return value of âfwriteâ, declared with attribute warn_unused_result >ad_save_load.c:850:11: warning: ignoring return value of âfwriteâ, declared with attribute warn_unused_result >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c ad_load.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >ad_load.c: In function âGB_loginâ: >ad_load.c:1380:34: warning: ignoring return value of âgb_scan_directoryâ, declared with attribute warn_unused_result >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c admap.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >admap.c: In function âgb_is_valid_mapfileâ: >admap.c:722:14: warning: ignoring return value of âfreadâ, declared with attribute warn_unused_result >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c adTest.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c adtune.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c adGene.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c adtcp.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c adhashtools.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c adExperiment.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c adtools.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c adseqcompr.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >adtools.c: In function âGBT_check_arb_fileâ: >adtools.c:74:10: warning: ignoring return value of âfgetsâ, declared with attribute warn_unused_result >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c adtables.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c adRevCompl.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c adChangeKey.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c adali.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c adcolumns.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >adali.c: In function âGBT_create_sequence_dataâ: >adali.c:597:5: warning: âGBT_add_dataâ is deprecated (declared at adali.c:568) >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c adtree.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c adname.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c aditem.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c arbdbpp.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c ad_config.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >ld --export-dynamic -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-5.1-r1/work/arbsrc_6213/ARBDBS' >-------------------------------------------------------------------------------- Make everything in ARBDB >make[4]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/ARBDB' >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c adsort.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c adlang1.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c adstring.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c admatch.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >admatch.c: In function âGBS_string_evalâ: >admatch.c:763:37: warning: ignoring return value of âgbs_build_replace_stringâ, declared with attribute warn_unused_result >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c arbdb.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >arbdb.c: In function âGB_copy_with_protectionâ: >arbdb.c:1469:13: warning: null argument where non-null required (argument 2) >arbdb.c:1469:13: warning: null argument where non-null required (argument 2) >arbdb.c:1469:13: warning: null argument where non-null required (argument 2) >arbdb.c:1469:13: warning: null argument where non-null required (argument 2) >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c ad_core.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c admath.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c adoptimize.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c adsystem.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c adindex.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c adperl.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c adlink.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c adsocket.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >adsocket.c: In function âGB_get_full_pathâ: >adsocket.c:1256:21: warning: ignoring return value of ârealpathâ, declared with attribute warn_unused_result >adsocket.c:1260:21: warning: ignoring return value of ârealpathâ, declared with attribute warn_unused_result >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c adcomm.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c adhash.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c adquery.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >adquery.c: In function âgb_searchâ: >adquery.c:449:28: warning: comparison between âGB_TYPESâ and âenum gb_search_enumâ >adquery.c:455:28: warning: comparison between âGB_TYPESâ and âenum gb_search_enumâ >adquery.c:526:31: warning: comparison between âGB_TYPESâ and âenum gb_search_enumâ >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c ad_save_load.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >ad_save_load.c: In function âgb_write_bin_rekâ: >ad_save_load.c:799:13: warning: null argument where non-null required (argument 1) >ad_save_load.c: In function âGB_save_asâ: >ad_save_load.c:1079:5: warning: âGB_get_errorâ is deprecated (declared at ./ad_prot.h:43) >ad_save_load.c: In function âGB_save_quick_asâ: >ad_save_load.c:1122:5: warning: âGB_get_errorâ is deprecated (declared at ./ad_prot.h:43) >ad_save_load.c:1123:5: warning: âGB_get_errorâ is deprecated (declared at ./ad_prot.h:43) >ad_save_load.c:1145:9: warning: âGB_get_errorâ is deprecated (declared at ./ad_prot.h:43) >ad_save_load.c:1170:9: warning: âGB_get_errorâ is deprecated (declared at ./ad_prot.h:43) >ad_save_load.c:1181:9: warning: âGB_get_errorâ is deprecated (declared at ./ad_prot.h:43) >ad_save_load.c: In function âGB_save_quickâ: >ad_save_load.c:1206:5: warning: âGB_get_errorâ is deprecated (declared at ./ad_prot.h:43) >ad_save_load.c:1207:5: warning: âGB_get_errorâ is deprecated (declared at ./ad_prot.h:43) >ad_save_load.c:1228:9: warning: âGB_get_errorâ is deprecated (declared at ./ad_prot.h:43) >ad_save_load.c:1261:5: warning: âGB_get_errorâ is deprecated (declared at ./ad_prot.h:43) >ad_save_load.c: In function âgb_check_saveableâ: >ad_save_load.c:1301:9: warning: âGB_get_errorâ is deprecated (declared at ./ad_prot.h:43) >ad_save_load.c:1306:9: warning: âGB_get_errorâ is deprecated (declared at ./ad_prot.h:43) >ad_save_load.c: In function âgb_write_binâ: >ad_save_load.c:824:11: warning: ignoring return value of âfwriteâ, declared with attribute warn_unused_result >ad_save_load.c:827:11: warning: ignoring return value of âfwriteâ, declared with attribute warn_unused_result >ad_save_load.c:842:11: warning: ignoring return value of âfwriteâ, declared with attribute warn_unused_result >ad_save_load.c:850:11: warning: ignoring return value of âfwriteâ, declared with attribute warn_unused_result >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c adcompr.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c admalloc.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c ad_load.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >ad_load.c: In function âGB_loginâ: >ad_load.c:1380:34: warning: ignoring return value of âgb_scan_directoryâ, declared with attribute warn_unused_result >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c admap.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c adTest.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >admap.c: In function âgb_is_valid_mapfileâ: >admap.c:722:14: warning: ignoring return value of âfreadâ, declared with attribute warn_unused_result >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c adtune.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c adGene.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c adtcp.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c adhashtools.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c adExperiment.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c adtools.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >adtools.c: In function âGBT_check_arb_fileâ: >adtools.c:74:10: warning: ignoring return value of âfgetsâ, declared with attribute warn_unused_result >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c adseqcompr.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c adtables.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c adRevCompl.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c adChangeKey.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c adali.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c adcolumns.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c adtree.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c adname.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >adali.c: In function âGBT_create_sequence_dataâ: >adali.c:597:5: warning: âGBT_add_dataâ is deprecated (declared at adali.c:568) >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c aditem.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c arbdbpp.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c ad_config.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe --export-dynamic -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -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-5.1-r1/work/arbsrc_6213/ARBDB' >-------------------------------------------------------------------------------- Make everything in GL >make[4]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/GL' >make[5]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/GL/glpng' >make[5]: `libglpng_arb.a' is up to date. >make[5]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/GL/glpng' >make[5]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/GL/glAW' >make[5]: `libglAW.a' is up to date. >make[5]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/GL/glAW' >make[4]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/GL' >-------------------------------------------------------------------------------- Make everything in READSEQ >make[4]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/READSEQ' >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -w -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_READSEQ -c readseq.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -w -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_READSEQ -c ureadseq.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-gcc -O2 -pipe -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -w -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_READSEQ -o /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/bin/arb_readseq readseq.o ureadseq.o >readseq.o: In function `.L206': >readseq.c:(.text+0x208c): warning: the use of `tmpnam' is dangerous, better use `mkstemp' >readseq.o: In function `chooseFormat': >readseq.c:(.text+0xb47): warning: the `gets' function is dangerous and should not be used. >make[4]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/READSEQ' >-------------------------------------------------------------------------------- Make everything in PARSIMONY >make[4]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/PARSIMONY' >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PARSIMONY -c PARS_main.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PARSIMONY -c PARS_dtree.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PARSIMONY -c PARS_debug.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PARSIMONY -c PARS_klprops.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PARSIMONY -c AP_buffer.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PARSIMONY -c AP_main.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PARSIMONY -c AP_tree_nlen.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PARSIMONY -c AP_tree_edge.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >ld --export-dynamic -r -o PARSIMONY.a PARS_main.o PARS_dtree.o PARS_debug.o PARS_klprops.o AP_buffer.o AP_main.o AP_tree_nlen.o AP_tree_edge.o >make[4]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/PARSIMONY' >-------------------------------------------------------------------------------- Make everything in CONSENSUS_TREE >make[4]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/CONSENSUS_TREE' >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_CONSENSUS_TREE -c CT_part.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_CONSENSUS_TREE -c CT_hash.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_CONSENSUS_TREE -c CT_ntree.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_CONSENSUS_TREE -c CT_rbtree.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_CONSENSUS_TREE -c CT_dtree.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_CONSENSUS_TREE -c CT_ctree.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_CONSENSUS_TREE -c CT_mem.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >ld --export-dynamic -r -o CONSENSUS_TREE.a CT_part.o CT_hash.o CT_ntree.o CT_rbtree.o CT_dtree.o CT_ctree.o CT_mem.o >make[4]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/CONSENSUS_TREE' >-------------------------------------------------------------------------------- Make everything in ISLAND_HOPPING >make[4]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/ISLAND_HOPPING' >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ISLAND_HOPPING -c island_hopping.cpp -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ISLAND_HOPPING -DARB -c i-hopper.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ISLAND_HOPPING -DARB -c align.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >align.c: In function ânewIslandâ: >align.c:312:49: warning: âiiiâ may be used uninitialized in this function >align.c:312:53: warning: âjjjâ may be used uninitialized in this function >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ISLAND_HOPPING -DARB -c memory.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-gcc -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ISLAND_HOPPING -DARB -c trnsprob.c -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >trnsprob.c: In function âupdateTrnsprobâ: >trnsprob.c:217:14: warning: âaâ may be used uninitialized in this function >trnsprob.c:217:16: warning: âbâ may be used uninitialized in this function >trnsprob.c:217:18: warning: âcâ may be used uninitialized in this function >trnsprob.c:217:20: warning: âdâ may be used uninitialized in this function >trnsprob.c:217:22: warning: âeâ may be used uninitialized in this function >trnsprob.c:217:24: warning: âfâ may be used uninitialized in this function >ld --export-dynamic -r -o ISLAND_HOPPING.a island_hopping.o i-hopper.o align.o memory.o trnsprob.o >make[4]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/ISLAND_HOPPING' >-------------------------------------------------------------------------------- Make everything in DBSERVER >make[4]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/DBSERVER' >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_DBSERVER -c db_server.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >ld --export-dynamic -r -o DBSERVER.a db_server.o >make[4]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/DBSERVER' >-------------------------------------------------------------------------------- Make everything in AWT >make[4]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/AWT' >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_input_mask.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_hotkeys.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_www.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_tables.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_irstree.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_asciiprint.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >AWT_asciiprint.cxx: In function âvoid awt_aps_go(AW_window*)â: >AWT_asciiprint.cxx:228:86: warning: ignoring return value of âsize_t fwrite(const void*, size_t, size_t, FILE*)â, declared with attribute warn_unused_result >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_map_key.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_tree_cmp.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_seq_colors.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_pro_a_nucs.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_csp.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_canvas.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_dtree.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_tree.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_tree_cb.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_nei.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_filter.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_sel_boxes.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_canio.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >AWT_canio.cxx: In function âvoid AWT_print_tree_to_file_xfig(AW_window*, AW_CL)â: >AWT_canio.cxx:268:53: warning: ignoring return value of âint system(const char*)â, declared with attribute warn_unused_result >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_nds.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_query_and_functions.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_file_selection.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_preset.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_seq_dna.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_seq_protein.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_seq_simple_pro.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_codon_table.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_iupac.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_config_manager.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_advice.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_db_browser.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_attributes.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_changekey.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_item_sel_list.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_macro.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_translate.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe --export-dynamic -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -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-5.1-r1/work/arbsrc_6213/AWT' >-------------------------------------------------------------------------------- Make everything in DIST >make[4]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/DIST' >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_DIST -c DI_mldist.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_DIST -c DI_protdist.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_DIST -c DI_compress_matrix.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_DIST -c DI_view_matrix.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_DIST -c DI_save_matr.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_DIST -c DI_main.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_DIST -c DI_matr.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_DIST -c distanalyse.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >DI_main.cxx: In function âint main(int, char**)â: >DI_main.cxx:71:63: warning: ignoring return value of âconst char* ARB_init_global_awars(AW_root*, GBDATA*, GBDATA*)â, declared with attribute warn_unused_result >DI_matr.cxx: In member function âchar* DI_MATRIX::load(char*, AP_filter*, AP_weights*, LoadWhat, const char*, bool, GBDATA**)â: >DI_matr.cxx:278:9: warning: âno_of_speciesâ may be used uninitialized in this function >DI_matr.cxx:270:13: warning: âgb_speciesâ may be used uninitialized in this function >ld --export-dynamic -r -o DIST.a DI_mldist.o DI_protdist.o DI_compress_matrix.o DI_view_matrix.o DI_save_matr.o DI_main.o DI_matr.o distanalyse.o >make[4]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/DIST' >-------------------------------------------------------------------------------- Make everything in NTREE >make[4]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/NTREE' >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NTREE -c AP_consensus.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NTREE -c AP_conservProfile2Gnuplot.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >AP_consensus.cxx: In function âconst char* CON_export(char*, char*, int**, char*, int*, char*, int, long int, long int, int, int, int, double, double, int, int)â: >AP_consensus.cxx:409:23: warning: âGBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_t_prot.h:108) >AP_consensus.cxx:409:72: warning: âGBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_t_prot.h:108) >AP_consensus.cxx:411:25: warning: âGBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_t_prot.h:108) >AP_consensus.cxx:411:75: warning: âGBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_t_prot.h:108) >AP_consensus.cxx:465:28: warning: âGBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_t_prot.h:108) >AP_consensus.cxx:465:80: warning: âGBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_t_prot.h:108) >AP_consensus.cxx: In function âvoid CON_calc_max_freq_cb(AW_window*)â: >AP_consensus.cxx:962:27: warning: âGBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_t_prot.h:108) >AP_consensus.cxx:962:76: warning: âGBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_t_prot.h:108) >AP_consensus.cxx:963:27: warning: âGBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_t_prot.h:108) >AP_consensus.cxx:963:76: warning: âGBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_t_prot.h:108) >AP_consensus.cxx:966:27: warning: âGBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_t_prot.h:108) >AP_consensus.cxx:966:77: warning: âGBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_t_prot.h:108) >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NTREE -c AP_cprofile.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >AP_conservProfile2Gnuplot.cxx: In function âvoid AP_conservProfile2Gnuplot_callback(AW_window*)â: >AP_conservProfile2Gnuplot.cxx:58:42: warning: ignoring return value of âconst char* GB_xcmd(const char*, GB_BOOL, GB_BOOL)â, declared with attribute warn_unused_result >AP_cprofile.cxx: In function âvoid CPRO_condense_cb(AW_window*, AW_CL)â: >AP_cprofile.cxx:1420:14: warning: âGBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_t_prot.h:108) >AP_cprofile.cxx:1420:62: warning: âGBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_t_prot.h:108) >AP_cprofile.cxx:1423:23: warning: âGBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_t_prot.h:108) >AP_cprofile.cxx:1423:72: warning: âGBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_t_prot.h:108) >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NTREE -c AP_csp_2_gnuplot.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >AP_csp_2_gnuplot.cxx: In function âchar* get_overlay_files(AW_root*, const char*, const char*&)â: >AP_csp_2_gnuplot.cxx:92:50: warning: âconst char* GB_get_error()â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_prot.h:43) >AP_csp_2_gnuplot.cxx:92:63: warning: âconst char* GB_get_error()â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_prot.h:43) >AP_csp_2_gnuplot.cxx:100:55: warning: âconst char* GB_get_error()â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_prot.h:43) >AP_csp_2_gnuplot.cxx:100:68: warning: âconst char* GB_get_error()â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_prot.h:43) >AP_csp_2_gnuplot.cxx: In function âvoid AP_csp_2_gnuplot_cb(AW_window*, AW_CL, AW_CL)â: >AP_csp_2_gnuplot.cxx:388:62: warning: ignoring return value of âconst char* GB_xcmd(const char*, GB_BOOL, GB_BOOL)â, declared with attribute warn_unused_result >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NTREE -c AP_pos_var_pars.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NTREE -c NT_cb.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NTREE -c NT_concatenate.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >NT_cb.cxx: In function âvoid NT_system_cb2(AW_window*, AW_CL, AW_CL)â: >NT_cb.cxx:128:35: warning: ignoring return value of âconst char* GB_xcmd(const char*, GB_BOOL, GB_BOOL)â, declared with attribute warn_unused_result >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NTREE -c NT_dbrepair.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >NT_concatenate.cxx: In function âconst char* displayAlignmentInfo(GBDATA*, const char*, char*, char*)â: >NT_concatenate.cxx:310:37: warning: âGBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_t_prot.h:108) >NT_concatenate.cxx:310:93: warning: âGBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_t_prot.h:108) >NT_concatenate.cxx: In function âvoid concatenateAlignments(AW_window*)â: >NT_concatenate.cxx:415:39: warning: âGBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_t_prot.h:108) >NT_concatenate.cxx:415:95: warning: âGBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_t_prot.h:108) >NT_concatenate.cxx: In function âGBDATA* concatenateFieldsCreateNewSpecies(AW_window*, GBDATA*, SPECIES_ConcatenateList*)â: >NT_concatenate.cxx:664:39: warning: âGBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_t_prot.h:108) >NT_concatenate.cxx:664:114: warning: âGBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_t_prot.h:108) >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NTREE -c NT_edconf.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NTREE -c NT_extern.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NTREE -c NT_import.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NTREE -c NT_ins_col.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NTREE -c NT_join.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NTREE -c NT_main.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >NT_main.cxx: In function âint main(int, char**)â: >NT_main.cxx:399:50: warning: ignoring return value of âint system(const char*)â, declared with attribute warn_unused_result >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NTREE -c NT_sort.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NTREE -c NT_trackAliChanges.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NTREE -c NT_validManual.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NTREE -c NT_validNameParser.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NTREE -c NT_validNames.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NTREE -c ad_ali.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NTREE -c ad_ext.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NTREE -c ad_spec.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NTREE -c ad_transpro.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >ad_spec.cxx: In function âvoid ad_field_convert_commit_cb(AW_window*, AW_CL)â: >ad_spec.cxx:729:29: warning: unused variable âselectorâ >ad_transpro.cxx: In function âconst char* arb_r2a(GBDATA*, bool, bool, int, bool, const char*, const char*)â: >ad_transpro.cxx:159:48: warning: âGBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_t_prot.h:108) >ad_transpro.cxx:159:100: warning: âGBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_t_prot.h:108) >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NTREE -c ad_trees.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >ad_trees.cxx: In function âchar* readXmlTree(char*)â: >ad_trees.cxx:418:44: warning: ignoring return value of âconst char* GB_xcmd(const char*, GB_BOOL, GB_BOOL)â, declared with attribute warn_unused_result >ad_trees.cxx:422:44: warning: ignoring return value of âconst char* GB_xcmd(const char*, GB_BOOL, GB_BOOL)â, declared with attribute warn_unused_result >-------------------- Checking NTREE.a >Target 'NTREE.a' not found >-> rebuilding NTREE.a (Thu Jan 1 00:59:59 1970) >ld --export-dynamic -r -o NTREE.a AP_consensus.o AP_conservProfile2Gnuplot.o AP_cprofile.o AP_csp_2_gnuplot.o AP_pos_var_pars.o NT_cb.o NT_concatenate.o NT_dbrepair.o NT_edconf.o NT_extern.o NT_import.o NT_ins_col.o NT_join.o NT_main.o NT_sort.o NT_trackAliChanges.o NT_validManual.o NT_validNameParser.o NT_validNames.o ad_ali.o ad_ext.o ad_spec.o ad_transpro.o ad_trees.o >make[4]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/NTREE' >-------------------------------------------------------------------------------- Make everything in PHYLO >make[4]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/PHYLO' >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PHYLO -c PH_data.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PHYLO -c PH_root.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >PH_data.cxx: In member function âconst char* PHDATA::calculate_matrix(const char*, double, PH_TRANSFORMATION)â: >PH_data.cxx:201:5: warning: âoptions_vector[0]â may be used uninitialized in this function >PH_data.cxx:210:5: warning: âoptions_vector[1]â may be used uninitialized in this function >PH_data.cxx:219:5: warning: âoptions_vector[2]â may be used uninitialized in this function >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PHYLO -c PH_main.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PHYLO -c PH_filt.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PHYLO -c PH_display.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >PH_main.cxx: In function âconst char* PH_create_ml_multiline_SAI(const char*, int, GBDATA**)â: >PH_main.cxx:157:31: warning: âGBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_t_prot.h:108) >PH_main.cxx:157:85: warning: âGBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_t_prot.h:108) >PH_main.cxx:162:31: warning: âGBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_t_prot.h:108) >PH_main.cxx:162:86: warning: âGBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_t_prot.h:108) >PH_main.cxx: In function âvoid PH_save_ml_cb(AW_window*)â: >PH_main.cxx:330:31: warning: âGBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_t_prot.h:108) >PH_main.cxx:330:83: warning: âGBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_t_prot.h:108) >PH_main.cxx:335:31: warning: âGBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_t_prot.h:108) >PH_main.cxx:335:86: warning: âGBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_t_prot.h:108) >PH_main.cxx: In function âint main(int, char**)â: >PH_main.cxx:576:63: warning: ignoring return value of âconst char* ARB_init_global_awars(AW_root*, GBDATA*, GBDATA*)â, declared with attribute warn_unused_result >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PHYLO -c PH_matr.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >PH_matr.cxx:9:2: warning: #warning module completely unused >ld --export-dynamic -r -o PHYLO.a PH_data.o PH_root.o PH_main.o PH_filt.o PH_display.o PH_matr.o >make[4]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/PHYLO' >-------------------------------------------------------------------------------- Make everything in RNA3D >make[4]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/RNA3D' >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_RNA3D -c -o RNA3D_Main.o RNA3D_Main.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_RNA3D -c -o RNA3D_Interface.o RNA3D_Interface.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_RNA3D -c -o RNA3D_Graphics.o RNA3D_Graphics.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_RNA3D -c -o RNA3D_OpenGLEngine.o RNA3D_OpenGLEngine.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_RNA3D -c -o RNA3D_OpenGLGraphics.o RNA3D_OpenGLGraphics.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >RNA3D_Main.cxx: In function âvoid RNA3D_StartApplication(AW_root*)â: >RNA3D_Main.cxx:73:32: warning: âconst char* GB_get_error()â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_prot.h:43) >RNA3D_Main.cxx:73:45: warning: âconst char* GB_get_error()â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_prot.h:43) >RNA3D_OpenGLEngine.cxx: In function âvoid initExtensions()â: >RNA3D_OpenGLEngine.cxx:125:44: warning: ignoring return value of âint scanf(const char*, ...)â, declared with attribute warn_unused_result >RNA3D_Interface.cxx: In function âAW_window* CreateDisplayHelices_window(AW_root*)â: >RNA3D_Interface.cxx:469:25: warning: âhelixRangeâ may be used uninitialized in this function >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_RNA3D -c -o RNA3D_Textures.o RNA3D_Textures.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_RNA3D -c -o RNA3D_StructureData.o RNA3D_StructureData.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_RNA3D -c -o RNA3D_Renderer.o RNA3D_Renderer.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >RNA3D_StructureData.cxx: In member function âvoid Structure3D::ReadCoOrdinateFile()â: >RNA3D_StructureData.cxx:222:18: warning: âposâ may be used uninitialized in this function >RNA3D_StructureData.cxx: In member function âvoid Structure3D::GetSecondaryStructureInfo()â: >RNA3D_StructureData.cxx:327:25: warning: array subscript is above array bounds >RNA3D_StructureData.cxx:326:9: warning: âposâ may be used uninitialized in this function >RNA3D_StructureData.cxx:326:14: warning: âhelixNrâ may be used uninitialized in this function >RNA3D_StructureData.cxx: In member function âvoid Structure3D::MapSearchStringsToEcoliTemplate(AW_root*)â: >RNA3D_StructureData.cxx:1542:61: warning: âvLastPt.Vector3::yâ may be used uninitialized in this function >RNA3D_StructureData.cxx:1542:61: warning: âvLastPt.Vector3::zâ may be used uninitialized in this function >RNA3D_StructureData.cxx:1542:61: warning: âvLastPt.Vector3::xâ may be used uninitialized in this function >ld --export-dynamic -r -o RNA3D.a RNA3D_Main.o RNA3D_Interface.o RNA3D_Graphics.o RNA3D_OpenGLEngine.o RNA3D_OpenGLGraphics.o RNA3D_Textures.o RNA3D_StructureData.o RNA3D_Renderer.o >make[4]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/RNA3D' >-------------------------------------------------------------------------------- Make everything in PROBE_COM >make[4]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/PROBE_COM' >make[4]: `server.a' is up to date. >make[4]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/PROBE_COM' >-------------------------------------------------------------------------------- Make everything in SECEDIT >make[4]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/SECEDIT' >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_SECEDIT -c SEC_toggle.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_SECEDIT -c SEC_bonddef.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_SECEDIT -c SEC_db.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_SECEDIT -c SEC_helix.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >SEC_db.cxx:328:2: warning: #warning @@@reread alilen >SEC_db.cxx:329:2: warning: #warning test changing ali length! >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_SECEDIT -c SEC_graphic.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_SECEDIT -c SEC_structure.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_SECEDIT -c SEC_read.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >SEC_read.cxx: In member function âconst char* SEC_region::read(std::istream&, SEC_root*, int)â: >SEC_read.cxx:133:17: warning: âseq_startâ may be used uninitialized in this function >SEC_read.cxx:133:28: warning: âseq_endâ may be used uninitialized in this function >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_SECEDIT -c SEC_io.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_SECEDIT -c SEC_paint.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >SEC_paint.cxx:368:2: warning: #warning move to SEC_db_interface >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_SECEDIT -c SEC_layout.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_SECEDIT -c SEC_split.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_SECEDIT -c SEC_abspos.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_SECEDIT -c SEC_main.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >SEC_main.cxx:88:2: warning: #warning make the refresh invisible >SEC_main.cxx:702:13: warning: unused parameter âgb_mainâ >ld --export-dynamic -r -o SECEDIT.a SEC_toggle.o SEC_bonddef.o SEC_db.o SEC_helix.o SEC_graphic.o SEC_structure.o SEC_read.o SEC_io.o SEC_paint.o SEC_layout.o SEC_split.o SEC_abspos.o SEC_main.o >make[4]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/SECEDIT' >-------------------------------------------------------------------------------- Make everything in NAMES_COM >make[4]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/NAMES_COM' >make[4]: `server.a' is up to date. >make[4]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/NAMES_COM' >-------------------------------------------------------------------------------- Make everything in PROBE_COM >make[4]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/PROBE_COM' >make[4]: `server.a' is up to date. >make[4]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/PROBE_COM' >-------------------------------------------------------------------------------- Make everything in NAMES_COM >make[4]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/NAMES_COM' >make[4]: `server.a' is up to date. >make[4]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/NAMES_COM' >-------------------------------------------------------------------------------- Make everything in NAMES_COM >make[4]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/NAMES_COM' >make[4]: `server.a' is up to date. >make[4]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/NAMES_COM' >-------------------------------------------------------------------------------- Make everything in PROBE_COM >make[4]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/PROBE_COM' >make[4]: `server.a' is up to date. >make[4]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/PROBE_COM' >-------------------- Updating shared libraries >make libs >-------------------------------------------------------------------------------- Make everything in SL/AW_NAME >make[4]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/SL/AW_NAME' >make[4]: `AW_NAME.a' is up to date. >make[4]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/SL/AW_NAME' >-------------------------------------------------------------------------------- Make everything in PGT >make[4]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/PGT' >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PGT -c -o main.o main.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PGT -c -o dialog.o dialog.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PGT -c -o arb_interface.o arb_interface.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PGT -c -o main_dialog.o main_dialog.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >arb_interface.cxx: In function âvoid set_AWAR(const char*, char*)â: >arb_interface.cxx:722:18: warning: unused variable âerrorâ >arb_interface.cxx: In function âvoid set_CONFIG(const char*, const char*)â: >arb_interface.cxx:764:18: warning: unused variable âerrorâ >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PGT -c -o import_dialog.o import_dialog.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PGT -c -o selection_dialog.o selection_dialog.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PGT -c -o file_import.o file_import.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PGT -c -o tiff_image.o tiff_image.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PGT -c -o image_dialog.o image_dialog.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PGT -c -o plot.o plot.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >image_dialog.cxx: In member function âvoid imageDialog::set_ARB_image_path(const char*)â: >image_dialog.cxx:1189:18: warning: unused variable âerrorâ >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PGT -c -o analyze_window.o analyze_window.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PGT -c -o entry_sel_dialog.o entry_sel_dialog.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PGT -c -o config_dialog.o config_dialog.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PGT -c -o help_dialog.o help_dialog.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PGT -c -o msgbox.o msgbox.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >ld --export-dynamic -r -o PGT.a main.o dialog.o arb_interface.o main_dialog.o import_dialog.o selection_dialog.o file_import.o tiff_image.o image_dialog.o plot.o analyze_window.o entry_sel_dialog.o config_dialog.o help_dialog.o msgbox.o >make[4]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/PGT' >-------------------------------------------------------------------------------- Make everything in ARB_GDE >make[4]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/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 updated. >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARB_GDE -c GDE_ParseMenu.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARB_GDE -c GDE.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARB_GDE -c GDE_event.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARB_GDE -c GDE_arbdb_io.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >GDE_event.cxx: In function âvoid GDE_export(NA_Alignment*, char*, long int)â: >GDE_event.cxx:305:39: warning: âGBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_t_prot.h:108) >GDE_event.cxx:305:89: warning: âGBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_t_prot.h:108) >GDE_event.cxx:369:43: warning: âGBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_t_prot.h:108) >GDE_event.cxx:369:92: warning: âGBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_t_prot.h:108) >GDE_event.cxx:428:36: warning: âGBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_t_prot.h:108) >GDE_event.cxx:428:88: warning: âGBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_t_prot.h:108) >GDE_event.cxx: In function âvoid GDE_startaction_cb(AW_window*, GmenuItem*, AW_CL)â: >GDE_event.cxx:557:23: warning: ignoring return value of âint system(const char*)â, declared with attribute warn_unused_result >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARB_GDE -c GDE_HGLfile.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARB_GDE -c GDE_Genbank.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARB_GDE -c GDE_FileIO.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >In file included from /usr/include/string.h:642:0, > from GDE_HGLfile.cxx:5: >In function âchar* strncpy(char*, const char*, size_t)â, > inlined from âvoid ReadGDE(char*, NA_Alignment*, int)â at GDE_HGLfile.cxx:497:64: >/usr/include/bits/string3.h:123:71: warning: call to char* __builtin___strncpy_chk(char*, const char*, unsigned int, unsigned int) will always overflow destination buffer >GDE_FileIO.cxx: In function âvoid ReadCMask(const char*)â: >GDE_FileIO.cxx:837:48: warning: ignoring return value of âchar* fgets(char*, int, FILE*)â, declared with attribute warn_unused_result >ld --export-dynamic -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-5.1-r1/work/arbsrc_6213/ARB_GDE' >make[4]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213' >cp LIBLINK/libARBDB.so lib/libARBDB.so >cp LIBLINK/libARBDBPP.so lib/libARBDBPP.so >cp LIBLINK/libARBDO.so lib/libARBDO.so >cp LIBLINK/libAW.so lib/libAW.so >-------------------------------------------------------------------------------- Make everything in EDIT4 >make[4]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/EDIT4' >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_EDIT4 -c -o ED4_protein_2nd_structure.o ED4_protein_2nd_structure.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_EDIT4 -c -o ED4_ProteinViewer.o ED4_ProteinViewer.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >ED4_ProteinViewer.cxx: In function âvoid PV_WriteTranslatedSequenceToDB(ED4_AA_sequence_terminal*, char*)â: >ED4_ProteinViewer.cxx:498:44: warning: âGBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_t_prot.h:108) >ED4_ProteinViewer.cxx:498:102: warning: âGBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_t_prot.h:108) >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_EDIT4 -c -o ED4_search.o ED4_search.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_EDIT4 -c -o ED4_cursor.o ED4_cursor.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_EDIT4 -c -o ED4_dump.o ED4_dump.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_EDIT4 -c -o ED4_nds.o ED4_nds.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >ED4_search.cxx: In function âvoid load_search_paras_from_file(AW_window*, AW_CL)â: >ED4_search.cxx:1616:38: warning: ignoring return value of âchar* fgets(char*, int, FILE*)â, declared with attribute warn_unused_result >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_EDIT4 -c -o ED4_secedit.o ED4_secedit.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_EDIT4 -c -o ED4_RNA3D.o ED4_RNA3D.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_EDIT4 -c -o ED4_main.o ED4_main.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_EDIT4 -c -o ED4_mini_classes.o ED4_mini_classes.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_EDIT4 -c -o ED4_edit_string.o ED4_edit_string.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_EDIT4 -c -o ED4_base.o ED4_base.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_EDIT4 -c -o ED4_manager.o ED4_manager.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_EDIT4 -c -o ED4_terminal.o ED4_terminal.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >ED4_terminal.cxx:164:2: warning: #warning temporary workaround - gb_type GB_INT and GB_FLOAT in the switch directive must not be displayed but ignored >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_EDIT4 -c -o ED4_root.o ED4_root.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >ED4_terminal.cxx:1422:2: warning: #warning test drawing of ED4_columnStat_terminal >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_EDIT4 -c -o EDB_root_bact.o EDB_root_bact.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_EDIT4 -c -o ED4_window.o ED4_window.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_EDIT4 -c -o ED4_members.o ED4_members.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_EDIT4 -c -o ED4_no_class.o ED4_no_class.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_EDIT4 -c -o ED4_list.o ED4_list.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_EDIT4 -c -o ED4_text_terminals.o ED4_text_terminals.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_EDIT4 -c -o ED4_tools.o ED4_tools.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_EDIT4 -c -o ED4_block.o ED4_block.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_EDIT4 -c -o ED4_visualizeSAI.o ED4_visualizeSAI.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_EDIT4 -c -o edit_naligner.o edit_naligner.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_EDIT4 -c -o graph_aligner_gui.o graph_aligner_gui.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_EDIT4 -c -o ED4_dots.o ED4_dots.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >graph_aligner_gui.cxx: In function âvoid sina_start(AW_window*, AW_CL)â: >graph_aligner_gui.cxx:171:63: warning: ignoring return value of âsize_t fwrite(const void*, size_t, size_t, FILE*)â, declared with attribute warn_unused_result >graph_aligner_gui.cxx:172:42: warning: ignoring return value of âsize_t fwrite(const void*, size_t, size_t, FILE*)â, declared with attribute warn_unused_result >graph_aligner_gui.cxx:189:55: warning: ignoring return value of âsize_t fwrite(const void*, size_t, size_t, FILE*)â, declared with attribute warn_unused_result >graph_aligner_gui.cxx:190:46: warning: ignoring return value of âsize_t fwrite(const void*, size_t, size_t, FILE*)â, declared with attribute warn_unused_result >graph_aligner_gui.cxx:204:55: warning: ignoring return value of âsize_t fwrite(const void*, size_t, size_t, FILE*)â, declared with attribute warn_unused_result >graph_aligner_gui.cxx:205:46: warning: ignoring return value of âsize_t fwrite(const void*, size_t, size_t, FILE*)â, declared with attribute warn_unused_result >edit_naligner.cxx: In function âvoid aed_start_naligning(AW_window*)â: >edit_naligner.cxx:102:19: warning: ignoring return value of âint system(const char*)â, declared with attribute warn_unused_result >ED4_dots.cxx: In function âvoid dot_missing_bases(AW_window*)â: >ED4_dots.cxx:151:21: warning: âsai_lenâ may be used uninitialized in this function >ld --export-dynamic -r -o EDIT4.a ED4_protein_2nd_structure.o ED4_ProteinViewer.o ED4_search.o ED4_cursor.o ED4_dump.o ED4_nds.o ED4_secedit.o ED4_RNA3D.o ED4_main.o ED4_mini_classes.o ED4_edit_string.o ED4_base.o ED4_manager.o ED4_terminal.o ED4_root.o EDB_root_bact.o ED4_window.o ED4_members.o ED4_no_class.o ED4_list.o ED4_text_terminals.o ED4_tools.o ED4_block.o ED4_visualizeSAI.o edit_naligner.o graph_aligner_gui.o ED4_dots.o >make[4]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/EDIT4' >cp LIBLINK/libAWT.so lib/libAWT.so >make[4]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213' >-------------------------------------------------------------------------------- Make everything in AWTC >make[4]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/AWTC' >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWTC -c AWTC_next_neighbours.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWTC -c AWTC_constructSequence.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWTC -c AWTC_seq_search.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWTC -c AWTC_submission.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >AWTC_constructSequence.cxx: In function âchar* AWTC_constructSequence(int, const char**, int, char**)â: >AWTC_constructSequence.cxx:507:11: warning: unused variable âresultSeqâ >AWTC_constructSequence.cxx:509:9: warning: unused variable âoffâ >ld --export-dynamic -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-5.1-r1/work/arbsrc_6213/AWTC' >-------------------- Checking bin/arb_pars >Target 'bin/arb_pars' not found >-> rebuilding bin/arb_pars (Thu Jan 1 00:59:59 1970) >-------------------------------------------------------------------------------- Make everything in NAMES >make[4]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/NAMES' >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NAMES -I/opt/gcc.3.4.3/include/c++/3.4.3/include -c names.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >ld --export-dynamic -r -o NAMES.a names.o >make[4]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/NAMES' >Link bin/arb_pars >i686-pc-linux-gnu-g++ -O2 -pipe -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu --export-dynamic -rdynamic -o bin/arb_pars -L/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/LIBLINK NAMES_COM/client.a SERVERCNTRL/SERVERCNTRL.a PARSIMONY/PARSIMONY.a SL/HELIX/HELIX.a SL/AW_NAME/AW_NAME.a XML/XML.a -L/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/GL/glAW -lglAW -lGL -L/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/GL/glpng -lglpng_arb -lpng -lGLEW -lGLw -lglut -lGLU -lARBDB -lm -lAW -lAWT -L/usr/X11R6//lib -lXm -lXpm -lXp -lXt -lXext -lX11 >-------------------- Checking bin/arb_edit >Target 'bin/arb_edit' not found >-> rebuilding bin/arb_edit (Thu Jan 1 00:59:59 1970) >Link bin/arb_edit >i686-pc-linux-gnu-g++ -O2 -pipe -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu --export-dynamic -rdynamic -o bin/arb_edit -L/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/LIBLINK NAMES_COM/client.a SERVERCNTRL/SERVERCNTRL.a EDIT/EDIT.a ARB_GDE/ARB_GDE.a STAT/STAT.a XML/XML.a SL/HELIX/HELIX.a SL/AW_HELIX/AW_HELIX.a SL/AW_NAME/AW_NAME.a -lARBDBPP -L/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/GL/glAW -lglAW -lGL -L/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/GL/glpng -lglpng_arb -lpng -lGLEW -lGLw -lglut -lGLU -lARBDB -lm -lAW -lAWT -L/usr/X11R6//lib -lXm -lXpm -lXp -lXt -lXext -lX11 >-------------------- Checking bin/arb_wetc >Target 'bin/arb_wetc' not found >-> rebuilding bin/arb_wetc (Thu Jan 1 00:59:59 1970) >Link bin/arb_wetc >i686-pc-linux-gnu-g++ -O2 -pipe -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu --export-dynamic -rdynamic -o bin/arb_wetc -L/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/LIBLINK WETC/WETC.a SL/HELIX/HELIX.a XML/XML.a -L/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/GL/glAW -lglAW -lGL -L/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/GL/glpng -lglpng_arb -lpng -lGLEW -lGLw -lglut -lGLU -lARBDB -lm -lAW -lAWT -L/usr/X11R6//lib -lXm -lXpm -lXp -lXt -lXext -lX11 >-------------------- Checking bin/arb_edit4 >Target 'bin/arb_edit4' not found >-> rebuilding bin/arb_edit4 (Thu Jan 1 00:59:59 1970) >Link bin/arb_edit4 >i686-pc-linux-gnu-g++ -O2 -pipe -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu --export-dynamic -rdynamic -o bin/arb_edit4 -L/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/LIBLINK NAMES_COM/client.a AWTC/AWTC.a EDIT4/EDIT4.a SECEDIT/SECEDIT.a SERVERCNTRL/SERVERCNTRL.a STAT/STAT.a ARB_GDE/ARB_GDE.a ISLAND_HOPPING/ISLAND_HOPPING.a SL/FAST_ALIGNER/FAST_ALIGNER.a SL/HELIX/HELIX.a SL/AW_HELIX/AW_HELIX.a SL/AW_NAME/AW_NAME.a SL/FILE_BUFFER/FILE_BUFFER.a XML/XML.a RNA3D/RNA3D.a -lARBDB -lm -lAW -lAWT -L/usr/X11R6//lib -lXm -lXpm -lXp -lXt -lXext -lX11 -L/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/GL/glAW -lglAW -lGL -L/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/GL/glpng -lglpng_arb -lpng -lGLEW -lGLw -lglut -lGLU >-------------------------------------------------------------------------------- Make everything in GDEHELP >make[4]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/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/molphy.menu > MENUS/molphy.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]: [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-5.1-r1/work/arbsrc_6213/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 >lynx -dump -nolist -display_charset=iso-8859-1 ../GDE/PHYLIP/doc/dnapars.html | sed -e 's/©/(C)/' > HELP_DOC_GEN/dnapars.doc >test -s HELP_DOC_GEN/proml.doc || (echo HELP_DOC_GEN/proml.doc not generated or empty && rm HELP_DOC_GEN/proml.doc && false) >test -s HELP_DOC_GEN/dnapars.doc || (echo HELP_DOC_GEN/dnapars.doc not generated or empty && rm HELP_DOC_GEN/dnapars.doc && false) >lynx -dump -nolist -display_charset=iso-8859-1 ../GDE/PHYLIP/doc/protpars.html | sed -e 's/©/(C)/' > HELP_DOC_GEN/protpars.doc >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/protpars.doc || (echo HELP_DOC_GEN/protpars.doc not generated or empty && rm HELP_DOC_GEN/protpars.doc && false) >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-5.1-r1/work/arbsrc_6213/GDE/CLUSTALW/clustalw_help /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/GDE/CLUSTALW/clustalw.doc >./genhelptree.sh HELP_GEN/dnaml.help "dnaml" arb_help.head /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/GDE/AxML/AxML.doc /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/GDE/FASTDNAML/fastDNAml.doc >BASE='clustalw' PREFIX='HELP_GEN' >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 >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 >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/fitch.doc || (echo HELP_DOC_GEN/fitch.doc not generated or empty && rm HELP_DOC_GEN/fitch.doc && false) >test -s HELP_DOC_GEN/neighbor.doc || (echo HELP_DOC_GEN/neighbor.doc not generated or empty && rm HELP_DOC_GEN/neighbor.doc && false) >test -s HELP_DOC_GEN/dnadist.doc || (echo HELP_DOC_GEN/dnadist.doc not generated or empty && rm HELP_DOC_GEN/dnadist.doc && false) >lynx -dump -nolist -display_charset=iso-8859-1 ../GDE/PHYLIP/doc/protdist.html | sed -e 's/©/(C)/' > HELP_DOC_GEN/protdist.doc >./genhelp.sh HELP_GEN/phyml.help "phyml" arb_help.head HELP_DOC_GEN/phyml.doc >test -s HELP_DOC_GEN/protdist.doc || (echo HELP_DOC_GEN/protdist.doc not generated or empty && rm HELP_DOC_GEN/protdist.doc && false) >./genhelp.sh HELP_GEN/proml.help "proml" arb_help.head HELP_DOC_GEN/proml.doc >./genhelptree.sh HELP_GEN/protml.help "protml" arb_help.head /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/GDE/MOLPHY/doc/protml.doc /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/GDE/MOLPHY/doc/protml_cli.doc >BASE='protml' PREFIX='HELP_GEN' >./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-5.1-r1/work/arbsrc_6213/READSEQ/Readme /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/READSEQ/Formats /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/READSEQ/Readseq.help >BASE='readseq' PREFIX='HELP_GEN' >lynx -dump -nolist -display_charset=iso-8859-1 ../GDE/TREEPUZZLE/doc/manual.html | sed -e 's/©/(C)/' > HELP_DOC_GEN/treepuzzle.doc >test -s HELP_DOC_GEN/treepuzzle.doc || (echo HELP_DOC_GEN/treepuzzle.doc not generated or empty && rm HELP_DOC_GEN/treepuzzle.doc && false) >./genhelptree.sh HELP_GEN/phylip_distance.help "phylip_distance" arb_help.head HELP_DOC_GEN/fitch.doc HELP_DOC_GEN/kitsch.doc HELP_DOC_GEN/neighbor.doc HELP_DOC_GEN/dnadist.doc HELP_DOC_GEN/protdist.doc >./genhelp.sh HELP_GEN/treepuzzle.help "treepuzzle" arb_help.head HELP_DOC_GEN/treepuzzle.doc >BASE='phylip_distance' PREFIX='HELP_GEN' >make[5]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/GDEHELP' >make[4]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/GDEHELP' >-------------------- Checking bin/arb_name_server >Target 'bin/arb_name_server' not found >-> rebuilding bin/arb_name_server (Thu Jan 1 00:59:59 1970) >Link bin/arb_name_server >i686-pc-linux-gnu-g++ -O2 -pipe -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu --export-dynamic -rdynamic -o bin/arb_name_server -L/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/LIBLINK NAMES_COM/server.a NAMES/NAMES.a SERVERCNTRL/SERVERCNTRL.a -lARBDB NAMES_COM/client.a -lm >-------------------- Checking bin/arb_phylo >Target 'bin/arb_phylo' not found >-> rebuilding bin/arb_phylo (Thu Jan 1 00:59:59 1970) >Link bin/arb_phylo >i686-pc-linux-gnu-g++ -O2 -pipe -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu --export-dynamic -rdynamic -o bin/arb_phylo -L/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/LIBLINK PHYLO/PHYLO.a SL/HELIX/HELIX.a XML/XML.a -L/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/GL/glAW -lglAW -lGL -L/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/GL/glpng -lglpng_arb -lpng -lGLEW -lGLw -lglut -lGLU -lARBDB -lm -lAW -lAWT -L/usr/X11R6//lib -lXm -lXpm -lXp -lXt -lXext -lX11 >-------------------- Checking bin/arb_db_server >Target 'bin/arb_db_server' not found >-> rebuilding bin/arb_db_server (Thu Jan 1 00:59:59 1970) >Link bin/arb_db_server >i686-pc-linux-gnu-g++ -O2 -pipe -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu --export-dynamic -rdynamic -o bin/arb_db_server -L/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/LIBLINK DBSERVER/DBSERVER.a SERVERCNTRL/SERVERCNTRL.a -lARBDB -lm >-------------------- Checking bin/arb_pgt >Target 'bin/arb_pgt' not found >-> rebuilding bin/arb_pgt (Thu Jan 1 00:59:59 1970) >Link bin/arb_pgt >i686-pc-linux-gnu-g++ -O2 -pipe -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu --export-dynamic -rdynamic -o bin/arb_pgt -L/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/LIBLINK PGT/PGT.a -L/usr/X11R6//lib -lXm -lXpm -lXp -lXt -lXext -lX11 -ltiff -lARBDB -lm >-------------------------------------------------------------------------------- Make everything in PROBE >make[4]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/PROBE' >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PROBE -c PT_new_design.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include -I./../probe_bank/COM >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PROBE -c PT_family.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include -I./../probe_bank/COM >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PROBE -c PT_prefixtree.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include -I./../probe_bank/COM >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PROBE -c PT_main.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include -I./../probe_bank/COM >PT_prefixtree.cxx: In function âint PTD(POS_TREE*)â: >PT_prefixtree.cxx:174:5: warning: dereferencing type-punned pointer will break strict-aliasing rules >PT_prefixtree.cxx: In function âPOS_TREE* PT_change_leaf_to_node(PTM2*, POS_TREE*)â: >PT_prefixtree.cxx:252:5: warning: dereferencing type-punned pointer will break strict-aliasing rules >PT_prefixtree.cxx:258:5: warning: dereferencing type-punned pointer will break strict-aliasing rules >PT_prefixtree.cxx: In function âPOS_TREE* PT_leaf_to_chain(PTM2*, POS_TREE*)â: >PT_prefixtree.cxx:270:5: warning: dereferencing type-punned pointer will break strict-aliasing rules >PT_prefixtree.cxx:282:5: warning: dereferencing type-punned pointer will break strict-aliasing rules >PT_prefixtree.cxx: In function âPOS_TREE* PT_create_leaf(PTM2*, POS_TREE**, PT_BASES, int, int, int)â: >PT_prefixtree.cxx:317:9: warning: dereferencing type-punned pointer will break strict-aliasing rules >PT_prefixtree.cxx:321:13: warning: dereferencing type-punned pointer will break strict-aliasing rules >PT_prefixtree.cxx:331:21: warning: dereferencing type-punned pointer will break strict-aliasing rules >PT_prefixtree.cxx:340:17: warning: dereferencing type-punned pointer will break strict-aliasing rules >PT_prefixtree.cxx: In function âvoid PTD_clear_fathers(PTM2*, POS_TREE*)â: >PT_prefixtree.cxx:389:5: warning: dereferencing type-punned pointer will break strict-aliasing rules >PT_prefixtree.cxx: In function âvoid PTD_put_int(FILE*, ULONG)â: >PT_prefixtree.cxx:424:5: warning: dereferencing type-punned pointer will break strict-aliasing rules >PT_prefixtree.cxx: In function âvoid PTD_put_short(FILE*, ULONG)â: >PT_prefixtree.cxx:436:5: warning: dereferencing type-punned pointer will break strict-aliasing rules >PT_prefixtree.cxx: In function âvoid PTD_set_object_to_saved_status(POS_TREE*, long int, int)â: >PT_prefixtree.cxx:443:5: warning: dereferencing type-punned pointer will break strict-aliasing rules >PT_prefixtree.cxx: In function âlong int PTD_write_leafs_to_disk(FILE*, PTM2*, POS_TREE*, long int, long int*, int*)â: >PT_prefixtree.cxx:759:9: warning: dereferencing type-punned pointer will break strict-aliasing rules >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PROBE -c PT_io.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include -I./../probe_bank/COM >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PROBE -c PT_etc.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include -I./../probe_bank/COM >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PROBE -c PT_secundaer.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include -I./../probe_bank/COM >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PROBE -c PT_buildtree.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include -I./../probe_bank/COM >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PROBE -c PT_match.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include -I./../probe_bank/COM >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PROBE -c PT_findEx.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include -I./../probe_bank/COM >ld --export-dynamic -r -o PROBE.a PT_new_design.o PT_family.o PT_prefixtree.o PT_main.o PT_io.o PT_etc.o PT_secundaer.o PT_buildtree.o PT_match.o PT_findEx.o >make[4]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/PROBE' >-------------------- Checking bin/arb_pt_server >Target 'bin/arb_pt_server' not found >-> rebuilding bin/arb_pt_server (Thu Jan 1 00:59:59 1970) >Link bin/arb_pt_server >i686-pc-linux-gnu-g++ -O2 -pipe -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu --export-dynamic -rdynamic -o bin/arb_pt_server -L/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/LIBLINK PROBE_COM/server.a SERVERCNTRL/SERVERCNTRL.a SL/HELIX/HELIX.a PROBE/PROBE.a -lARBDB PROBE_COM/client.a -lm >RNA3D/RNA3D.a: In function `InitializeOpenGLWindow(_WidgetRec*)': >(.text+0x5276): undefined reference to `GLwDrawingAreaMakeCurrent' >collect2: ld returned 1 exit status >make[3]: *** [bin/arb_edit4] Error 1 >make[3]: *** Waiting for unfinished jobs.... >-------------------------------------------------------------------------------- Make everything in PROBE_DESIGN >make[4]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/PROBE_DESIGN' >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PROBE_DESIGN -c -o probe_design.o probe_design.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PROBE_DESIGN -c -o SaiProbeVisualization.o SaiProbeVisualization.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >probe_design.cxx: In function âvoid pd_query_pt_server(AW_window*)â: >probe_design.cxx:1769:35: warning: ignoring return value of âconst char* GB_xcmd(const char*, GB_BOOL, GB_BOOL)â, declared with attribute warn_unused_result >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PROBE_DESIGN -c -o probe_match_parser.o probe_match_parser.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >ld --export-dynamic -r -o PROBE_DESIGN.a probe_design.o SaiProbeVisualization.o probe_match_parser.o >make[4]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/PROBE_DESIGN' >-------------------------------------------------------------------------------- Make everything in MULTI_PROBE >make[4]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/MULTI_PROBE' >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_MULTI_PROBE -c MP_main.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_MULTI_PROBE -c MP_Window.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_MULTI_PROBE -c MP_noclass.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_MULTI_PROBE -c MP_sonde.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_MULTI_PROBE -c MP_sondentopf.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_MULTI_PROBE -c MP_mo_liste.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_MULTI_PROBE -c MP_probe.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_MULTI_PROBE -c MP_GenerationDuplicates.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_MULTI_PROBE -c MP_Generation.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_MULTI_PROBE -c MP_probe_combi_statistic.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_MULTI_PROBE -c MP_probe_tabs.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_MULTI_PROBE -c MP_permute.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >ld --export-dynamic -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-5.1-r1/work/arbsrc_6213/MULTI_PROBE' >-------------------------------------------------------------------------------- Make everything in NALIGNER >make[4]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/NALIGNER' >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NALIGNER -c -o ali_aligner.o ali_aligner.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NALIGNER -c -o ali_arbdb.o ali_arbdb.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >ali_arbdb.cxx: In member function âint ALI_ARBDB::put_SAI(const char*, char*)â: >ali_arbdb.cxx:157:27: warning: âGBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_t_prot.h:108) >ali_arbdb.cxx:157:78: warning: âGBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)â is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE/ad_t_prot.h:108) >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NALIGNER -c -o ali_global.o ali_global.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NALIGNER -c -o ali_main.o ali_main.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NALIGNER -c -o ali_pathmap.o ali_pathmap.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NALIGNER -c -o ali_prealigner.o ali_prealigner.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NALIGNER -c -o ali_profile.o ali_profile.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NALIGNER -c -o ali_pt.o ali_pt.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NALIGNER -c -o ali_sequence.o ali_sequence.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NALIGNER -c -o ali_solution.o ali_solution.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >ld --export-dynamic -r -o NALIGNER.a ali_aligner.o ali_arbdb.o ali_global.o ali_main.o ali_pathmap.o ali_prealigner.o ali_profile.o ali_pt.o ali_sequence.o ali_solution.o >make[4]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/NALIGNER' >-------------------------------------------------------------------------------- Make everything in EISPACK >make[4]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/EISPACK' >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_EISPACK -c eispack.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_EISPACK -c d_sign.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >ld --export-dynamic -r -o EISPACK.a eispack.o d_sign.o >make[4]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/EISPACK' >-------------------------------------------------------------------------------- Make everything in HELP_SOURCE >make[4]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/HELP_SOURCE' >make date.xsl.tmp >make[5]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/HELP_SOURCE' >cat date.xsl.header >date.xsl.tmp >bash -c "(export LC_ALL=C;date '+%d. %b %Y')" >>date.xsl.tmp >mkdir -p Xml >--------------------------------------------------- >mkdir -p Xml/prompt >------------ Generating some help files: >(cd genhelp;make all) >mkdir -p ../lib/help_html >mkdir -p ../lib/help_html/prompt >cat date.xsl.footer >>date.xsl.tmp >mkdir -p ../lib/help >make[5]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/HELP_SOURCE/genhelp' >i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_HELP_SOURCE -c arb_help2xml.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include >make[5]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/HELP_SOURCE' >Updating copyright.hlp from /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/arb_LICENSE.txt >../SOURCE_TOOLS/mv_if_diff date.xsl.tmp date.xsl >mkdir -p ../lib/help/prompt >date.xsl created. >Updating changes.hlp from /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/arb_CHANGES.txt >cp -p oldhelp/pos_variability.ps.gz ../lib/help/pos_variability.ps.gz >Updating agde_dnaml_sub_fastDNAml_doc.hlp from /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/GDEHELP/HELP_GEN/dnaml_sub_fastDNAml_doc.help >cp -p oldhelp/consensus.ps.gz ../lib/help/consensus.ps.gz >cp -p oldhelp/arb.pdf.gz ../lib/help/arb.pdf.gz >cp -p oldhelp/rna3d_manual.pdf.gz ../lib/help/rna3d_manual.pdf.gz >find ../lib/help_html -name "*.html" -size -1 -exec rm {} \; >Updating agde_protpars.hlp from /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/GDEHELP/HELP_GEN/protpars.help >Updating agde_readseq_sub_Formats.hlp from /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/GDEHELP/HELP_GEN/readseq_sub_Formats.help >Updating agde_treepuzzle.hlp from /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/GDEHELP/HELP_GEN/treepuzzle.help >Updating agde_clustalw_sub_clustalw_help.hlp from /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/GDEHELP/HELP_GEN/clustalw_sub_clustalw_help.help >Updating agde_phylip_distance_sub_fitch_doc.hlp from /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/GDEHELP/HELP_GEN/phylip_distance_sub_fitch_doc.help >Updating agde_clustalw_sub_clustalw_doc.hlp from /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/GDEHELP/HELP_GEN/clustalw_sub_clustalw_doc.help >Updating agde_phylip_distance.hlp from /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/GDEHELP/HELP_GEN/phylip_distance.help >Updating agde_lsadt.hlp from /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/GDEHELP/HELP_GEN/lsadt.help >Updating agde_dnaml.hlp from /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/GDEHELP/HELP_GEN/dnaml.help >Updating agde_phyml.hlp from /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/GDEHELP/HELP_GEN/phyml.help >Updating agde_phylip_distance_sub_dnadist_doc.hlp from /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/GDEHELP/HELP_GEN/phylip_distance_sub_dnadist_doc.help >Updating agde_CAP2.hlp from /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/GDEHELP/HELP_GEN/CAP2.help >Updating agde_phylip_distance_sub_kitsch_doc.hlp from /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/GDEHELP/HELP_GEN/phylip_distance_sub_kitsch_doc.help >Updating agde_phylip_distance_sub_protdist_doc.hlp from /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/GDEHELP/HELP_GEN/phylip_distance_sub_protdist_doc.help >Updating agde_readseq.hlp from /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/GDEHELP/HELP_GEN/readseq.help >Updating agde_readseq_sub_Readseq_help.hlp from /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/GDEHELP/HELP_GEN/readseq_sub_Readseq_help.help >Updating agde_clustalw.hlp from /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/GDEHELP/HELP_GEN/clustalw.help >Updating agde_protml_sub_protml_doc.hlp from /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/GDEHELP/HELP_GEN/protml_sub_protml_doc.help >Updating agde_protml_sub_protml_cli_doc.hlp from /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/GDEHELP/HELP_GEN/protml_sub_protml_cli_doc.help >Updating agde_readseq_sub_Readme.hlp from /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/GDEHELP/HELP_GEN/readseq_sub_Readme.help >Updating agde_proml.hlp from /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/GDEHELP/HELP_GEN/proml.help >Updating agde_phylip_distance_sub_neighbor_doc.hlp from /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/GDEHELP/HELP_GEN/phylip_distance_sub_neighbor_doc.help >Updating agde_DNAml_rates.hlp from /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/GDEHELP/HELP_GEN/DNAml_rates.help >Updating agde_protml.hlp from /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/GDEHELP/HELP_GEN/protml.help >Updating agde_dnapars.hlp from /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/GDEHELP/HELP_GEN/dnapars.help >Updating agde_dnaml_sub_AxML_doc.hlp from /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/GDEHELP/HELP_GEN/dnaml_sub_AxML_doc.help >Updating agde_raxml.hlp from /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/GDEHELP/HELP_WRITTEN/raxml.help >Updating GDE overview agde.hlp >make[5]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/HELP_SOURCE/genhelp' >i686-pc-linux-gnu-g++ -O2 -pipe -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu --export-dynamic -rdynamic -o /var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/bin/arb_help2xml arb_help2xml.o ../XML/XML.a -L/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/LIBLINK -lARBDB >--------------------------------------------------- >------------ Converting old hlp 2 xml: >make xml >make[5]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/HELP_SOURCE' >touch xml.stamp >arb_help2xml oldhelp/arb.hlp Xml/arb.xml >arb_help2xml genhelp/agde_protml_sub_protml_doc.hlp Xml/agde_protml_sub_protml_doc.xml >arb_help2xml genhelp/changes.hlp Xml/changes.xml >arb_help2xml genhelp/agde_protml_sub_protml_cli_doc.hlp Xml/agde_protml_sub_protml_cli_doc.xml >arb_help2xml genhelp/agde_DNAml_rates.hlp Xml/agde_DNAml_rates.xml >arb_help2xml genhelp/agde_dnapars.hlp Xml/agde_dnapars.xml >arb_help2xml genhelp/agde_proml.hlp Xml/agde_proml.xml >arb_help2xml genhelp/agde_dnaml_sub_AxML_doc.hlp Xml/agde_dnaml_sub_AxML_doc.xml >arb_help2xml genhelp/agde_dnaml_sub_fastDNAml_doc.hlp Xml/agde_dnaml_sub_fastDNAml_doc.xml >arb_help2xml genhelp/agde_phylip_distance_sub_neighbor_doc.hlp Xml/agde_phylip_distance_sub_neighbor_doc.xml >arb_help2xml genhelp/agde_lsadt.hlp Xml/agde_lsadt.xml >arb_help2xml genhelp/agde_readseq_sub_Formats.hlp Xml/agde_readseq_sub_Formats.xml >arb_help2xml genhelp/agde_protml.hlp Xml/agde_protml.xml >arb_help2xml genhelp/agde_clustalw_sub_clustalw_help.hlp Xml/agde_clustalw_sub_clustalw_help.xml >arb_help2xml genhelp/agde_treepuzzle.hlp Xml/agde_treepuzzle.xml >arb_help2xml genhelp/agde_clustalw_sub_clustalw_doc.hlp Xml/agde_clustalw_sub_clustalw_doc.xml >arb_help2xml genhelp/agde.hlp Xml/agde.xml >arb_help2xml genhelp/agde_CAP2.hlp Xml/agde_CAP2.xml >arb_help2xml genhelp/agde_readseq.hlp Xml/agde_readseq.xml >arb_help2xml genhelp/agde_protpars.hlp Xml/agde_protpars.xml >arb_help2xml genhelp/agde_phylip_distance_sub_fitch_doc.hlp Xml/agde_phylip_distance_sub_fitch_doc.xml >arb_help2xml genhelp/agde_phylip_distance.hlp Xml/agde_phylip_distance.xml >arb_help2xml genhelp/copyright.hlp Xml/copyright.xml >arb_help2xml genhelp/agde_raxml.hlp Xml/agde_raxml.xml >arb_help2xml genhelp/agde_phyml.hlp Xml/agde_phyml.xml >arb_help2xml genhelp/agde_readseq_sub_Readseq_help.hlp Xml/agde_readseq_sub_Readseq_help.xml >arb_help2xml genhelp/agde_phylip_distance_sub_dnadist_doc.hlp Xml/agde_phylip_distance_sub_dnadist_doc.xml >arb_help2xml genhelp/agde_dnaml.hlp Xml/agde_dnaml.xml >arb_help2xml genhelp/agde_phylip_distance_sub_kitsch_doc.hlp Xml/agde_phylip_distance_sub_kitsch_doc.xml >arb_help2xml genhelp/agde_phylip_distance_sub_protdist_doc.hlp Xml/agde_phylip_distance_sub_protdist_doc.xml >arb_help2xml genhelp/agde_readseq_sub_Readme.hlp Xml/agde_readseq_sub_Readme.xml >arb_help2xml genhelp/agde_clustalw.hlp Xml/agde_clustalw.xml >arb_help2xml oldhelp/checkfield.hlp Xml/checkfield.xml >arb_help2xml oldhelp/set_protection.hlp Xml/set_protection.xml >arb_help2xml oldhelp/FAQS.hlp Xml/FAQS.xml >arb_help2xml oldhelp/pa_partial.hlp Xml/pa_partial.xml >arb_help2xml oldhelp/mode_reset.hlp Xml/mode_reset.xml >arb_help2xml oldhelp/gde_ift.hlp Xml/gde_ift.xml >arb_help2xml oldhelp/tbl_boot2len.hlp Xml/tbl_boot2len.xml >arb_help2xml oldhelp/props_frame.hlp Xml/props_frame.xml >arb_help2xml oldhelp/treeadm.hlp Xml/treeadm.xml >oldhelp/treeadm.hlp:6: Warning: Dead link to 'tr_export.hlp' >arb_help2xml oldhelp/rna3d_mapSeqData.hlp Xml/rna3d_mapSeqData.xml >arb_help2xml oldhelp/mode_set_root.hlp Xml/mode_set_root.xml >arb_help2xml oldhelp/seq_quality.hlp Xml/seq_quality.xml >arb_help2xml oldhelp/arb_export_nds.hlp Xml/arb_export_nds.xml >arb_help2xml oldhelp/gene_options.hlp Xml/gene_options.xml >arb_help2xml oldhelp/tr_jump.hlp Xml/tr_jump.xml >arb_help2xml oldhelp/mp_params.hlp Xml/mp_params.xml >arb_help2xml oldhelp/gene_species.hlp Xml/gene_species.xml >arb_help2xml oldhelp/glossary.hlp Xml/glossary.xml >arb_help2xml oldhelp/vn_delete.hlp Xml/vn_delete.xml >arb_help2xml oldhelp/exportcursor.hlp Xml/exportcursor.xml >arb_help2xml oldhelp/tbl_reset.hlp Xml/tbl_reset.xml >arb_help2xml oldhelp/markcolor.hlp Xml/markcolor.xml >arb_help2xml oldhelp/ne_pretty.hlp Xml/ne_pretty.xml >arb_help2xml oldhelp/mode.hlp Xml/mode.xml >arb_help2xml oldhelp/neprops.hlp Xml/neprops.xml >arb_help2xml oldhelp/macro.hlp Xml/macro.xml >arb_help2xml oldhelp/tr_type_irs.hlp Xml/tr_type_irs.xml >arb_help2xml oldhelp/help.hlp Xml/help.xml >arb_help2xml oldhelp/tbl_justify.hlp Xml/tbl_justify.xml >arb_help2xml oldhelp/merge_species.hlp Xml/merge_species.xml >arb_help2xml oldhelp/next_neighbours.hlp Xml/next_neighbours.xml >arb_help2xml oldhelp/probe_param.hlp Xml/probe_param.xml >arb_help2xml oldhelp/rna3d_dispMolecule.hlp Xml/rna3d_dispMolecule.xml >arb_help2xml oldhelp/next_neighbours_common.hlp Xml/next_neighbours_common.xml >arb_help2xml oldhelp/mg_species.hlp Xml/mg_species.xml >arb_help2xml oldhelp/importift.hlp Xml/importift.xml >arb_help2xml oldhelp/spaf_scandb.hlp Xml/spaf_scandb.xml >arb_help2xml oldhelp/user_matrix.hlp Xml/user_matrix.xml >arb_help2xml oldhelp/mode_rotate.hlp Xml/mode_rotate.xml >arb_help2xml oldhelp/neprops_data.hlp Xml/neprops_data.xml >arb_help2xml oldhelp/ad_align.hlp Xml/ad_align.xml >arb_help2xml oldhelp/arb_edit4.hlp Xml/arb_edit4.xml >arb_help2xml oldhelp/vn_import.hlp Xml/vn_import.xml >arb_help2xml oldhelp/consensus.hlp Xml/consensus.xml >arb_help2xml oldhelp/sp_del_mrkd.hlp Xml/sp_del_mrkd.xml >arb_help2xml oldhelp/probematch.hlp Xml/probematch.xml >arb_help2xml oldhelp/e4_block.hlp Xml/e4_block.xml >arb_help2xml oldhelp/input_mask.hlp Xml/input_mask.xml >arb_help2xml oldhelp/arb_pars_init.hlp Xml/arb_pars_init.xml >arb_help2xml oldhelp/commands.hlp Xml/commands.xml >arb_help2xml oldhelp/mg_preserve.hlp Xml/mg_preserve.xml >arb_help2xml oldhelp/pd_spec_param.hlp Xml/pd_spec_param.xml >arb_help2xml oldhelp/tree2prt.hlp Xml/tree2prt.xml >arb_help2xml oldhelp/primer_new.hlp Xml/primer_new.xml >arb_help2xml oldhelp/pa_bootstrap.hlp Xml/pa_bootstrap.xml >arb_help2xml oldhelp/st_ml.hlp Xml/st_ml.xml >arb_help2xml oldhelp/e4_options.hlp Xml/e4_options.xml >arb_help2xml oldhelp/sp_info.hlp Xml/sp_info.xml >arb_help2xml oldhelp/tgroupcolor.hlp Xml/tgroupcolor.xml >arb_help2xml oldhelp/tkeep_mrkd.hlp Xml/tkeep_mrkd.xml >arb_help2xml oldhelp/dewachter_ift.hlp Xml/dewachter_ift.xml >arb_help2xml oldhelp/ne_compl.hlp Xml/ne_compl.xml >arb_help2xml oldhelp/iupac-codes.hlp Xml/iupac-codes.xml >arb_help2xml oldhelp/awt_csp.hlp Xml/awt_csp.xml >arb_help2xml oldhelp/gene_info.hlp Xml/gene_info.xml >arb_help2xml oldhelp/sv_def.hlp Xml/sv_def.xml >arb_help2xml oldhelp/ad_extended.hlp Xml/ad_extended.xml >arb_help2xml oldhelp/extended.hlp Xml/extended.xml >arb_help2xml oldhelp/set_color_of_listed.hlp Xml/set_color_of_listed.xml >arb_help2xml oldhelp/mode_www.hlp Xml/mode_www.xml >arb_help2xml oldhelp/mode_kernlin.hlp Xml/mode_kernlin.xml >arb_help2xml oldhelp/sec_main.hlp Xml/sec_main.xml >arb_help2xml oldhelp/arb_merge.hlp Xml/arb_merge.xml >arb_help2xml oldhelp/ne_copy_sequence.hlp Xml/ne_copy_sequence.xml >arb_help2xml oldhelp/pa_quick_sel.hlp Xml/pa_quick_sel.xml >arb_help2xml oldhelp/nekey_map.hlp Xml/nekey_map.xml >arb_help2xml oldhelp/spaf_convert.hlp Xml/spaf_convert.xml >arb_help2xml oldhelp/rename.hlp Xml/rename.xml >arb_help2xml oldhelp/realign_dna.hlp Xml/realign_dna.xml >arb_help2xml oldhelp/tgroupnmrkd.hlp Xml/tgroupnmrkd.xml >arb_help2xml oldhelp/ae2_ift.hlp Xml/ae2_ift.xml >arb_help2xml oldhelp/spaf_delete.hlp Xml/spaf_delete.xml >arb_help2xml oldhelp/tungroupall.hlp Xml/tungroupall.xml >arb_help2xml oldhelp/e4.hlp Xml/e4.xml >arb_help2xml oldhelp/nt_align_select.hlp Xml/nt_align_select.xml >arb_help2xml oldhelp/ecoliref.hlp Xml/ecoliref.xml >arb_help2xml oldhelp/track_ali_changes.hlp Xml/track_ali_changes.xml >arb_help2xml oldhelp/mg_trees.hlp Xml/mg_trees.xml >arb_help2xml oldhelp/tbl_scale.hlp Xml/tbl_scale.xml >arb_help2xml oldhelp/mg_configs.hlp Xml/mg_configs.xml >arb_help2xml oldhelp/tree2file.hlp Xml/tree2file.xml >arb_help2xml oldhelp/gene_species_field_transfer.hlp Xml/gene_species_field_transfer.xml >arb_help2xml oldhelp/manual.hlp Xml/manual.xml >arb_help2xml oldhelp/multiproberesults.hlp Xml/multiproberesults.xml >arb_help2xml oldhelp/rst_log_zoom.hlp Xml/rst_log_zoom.xml >arb_help2xml oldhelp/spaf_reorder.hlp Xml/spaf_reorder.xml >arb_help2xml oldhelp/searching.hlp Xml/searching.xml >arb_help2xml oldhelp/trm_boot.hlp Xml/trm_boot.xml >arb_help2xml oldhelp/organisms.hlp Xml/organisms.xml >arb_help2xml oldhelp/tr_type_nds.hlp Xml/tr_type_nds.xml >arb_help2xml oldhelp/gde_flat_ift.hlp Xml/gde_flat_ift.xml >arb_help2xml oldhelp/helix.hlp Xml/helix.xml >arb_help2xml oldhelp/resorttree.hlp Xml/resorttree.xml >arb_help2xml oldhelp/concatenate.hlp Xml/concatenate.xml >arb_help2xml oldhelp/partial_sequences.hlp Xml/partial_sequences.xml >arb_help2xml oldhelp/primer_parameters.hlp Xml/primer_parameters.xml >arb_help2xml oldhelp/spa_create.hlp Xml/spa_create.xml >arb_help2xml oldhelp/vn_suggest.hlp Xml/vn_suggest.xml >arb_help2xml oldhelp/mode_info.hlp Xml/mode_info.xml >arb_help2xml oldhelp/selected_gene.hlp Xml/selected_gene.xml >arb_help2xml oldhelp/rdp_ift.hlp Xml/rdp_ift.xml >arb_help2xml oldhelp/ne_replace.hlp Xml/ne_replace.xml >arb_help2xml oldhelp/mg_alignment.hlp Xml/mg_alignment.xml >arb_help2xml oldhelp/mode_optimize.hlp Xml/mode_optimize.xml >arb_help2xml oldhelp/trm_del.hlp Xml/trm_del.xml >arb_help2xml oldhelp/props_www.hlp Xml/props_www.xml >arb_help2xml oldhelp/organism_mark.hlp Xml/organism_mark.xml >arb_help2xml oldhelp/tree_cmp.hlp Xml/tree_cmp.xml >arb_help2xml oldhelp/spa_delete.hlp Xml/spa_delete.xml >arb_help2xml oldhelp/security.hlp Xml/security.xml >arb_help2xml oldhelp/arb_ntree.hlp Xml/arb_ntree.xml >arb_help2xml oldhelp/gene_mode.hlp Xml/gene_mode.xml >arb_help2xml oldhelp/mark_list.hlp Xml/mark_list.xml >arb_help2xml oldhelp/arb_edit.hlp Xml/arb_edit.xml >arb_help2xml oldhelp/mg_spec_sel_field.hlp Xml/mg_spec_sel_field.xml >arb_help2xml oldhelp/nt_keys.hlp Xml/nt_keys.xml >arb_help2xml oldhelp/input_mask_format.hlp Xml/input_mask_format.xml >arb_help2xml oldhelp/tr_type_radial.hlp Xml/tr_type_radial.xml >arb_help2xml oldhelp/input_mask_new.hlp Xml/input_mask_new.xml >arb_help2xml oldhelp/helixsym.hlp Xml/helixsym.xml >arb_help2xml oldhelp/phyl.hlp Xml/phyl.xml >arb_help2xml oldhelp/sequence_colors.hlp Xml/sequence_colors.xml >arb_help2xml oldhelp/registration.hlp Xml/registration.xml >arb_help2xml oldhelp/pos_var_pars.hlp Xml/pos_var_pars.xml >arb_help2xml oldhelp/save.hlp Xml/save.xml >arb_help2xml oldhelp/sp_sort_fld.hlp Xml/sp_sort_fld.xml >arb_help2xml oldhelp/sec_props.hlp Xml/sec_props.xml >arb_help2xml oldhelp/savedef.hlp Xml/savedef.xml >arb_help2xml oldhelp/pars.hlp Xml/pars.xml >arb_help2xml oldhelp/spa_rename.hlp Xml/spa_rename.xml >arb_help2xml oldhelp/translate_dna_2_pro.hlp Xml/translate_dna_2_pro.xml >arb_help2xml oldhelp/mode_move.hlp Xml/mode_move.xml >arb_help2xml oldhelp/arb_export.hlp Xml/arb_export.xml >arb_help2xml oldhelp/pa_add.hlp Xml/pa_add.xml >arb_help2xml oldhelp/e4_consensus.hlp Xml/e4_consensus.xml >arb_help2xml oldhelp/sec_display.hlp Xml/sec_display.xml >arb_help2xml oldhelp/search_duplicates.hlp Xml/search_duplicates.xml >arb_help2xml oldhelp/parser.hlp Xml/parser.xml >arb_help2xml oldhelp/pa_add_sel.hlp Xml/pa_add_sel.xml >arb_help2xml oldhelp/mode_lzoom.hlp Xml/mode_lzoom.xml >arb_help2xml oldhelp/galign_main.hlp Xml/galign_main.xml >arb_help2xml oldhelp/version.hlp Xml/version.xml >arb_help2xml oldhelp/species_join.hlp Xml/species_join.xml >arb_help2xml oldhelp/pa_ranchlengths.hlp Xml/pa_ranchlengths.xml >arb_help2xml oldhelp/sp_count_mrk.hlp Xml/sp_count_mrk.xml >arb_help2xml oldhelp/mark_long_branches.hlp Xml/mark_long_branches.xml >arb_help2xml oldhelp/gene_map.hlp Xml/gene_map.xml >arb_help2xml oldhelp/gene_species_mark.hlp Xml/gene_species_mark.xml >arb_help2xml oldhelp/trees.hlp Xml/trees.xml >arb_help2xml oldhelp/insdelchar.hlp Xml/insdelchar.xml >arb_help2xml oldhelp/mode_pzoom.hlp Xml/mode_pzoom.xml >arb_help2xml oldhelp/mode_mark.hlp Xml/mode_mark.xml >arb_help2xml oldhelp/dssp_ift.hlp Xml/dssp_ift.xml >arb_help2xml oldhelp/color_props.hlp Xml/color_props.xml >arb_help2xml oldhelp/acisrt.hlp Xml/acisrt.xml >arb_help2xml oldhelp/genes.hlp Xml/genes.xml >arb_help2xml oldhelp/mode_nni.hlp Xml/mode_nni.xml >arb_help2xml oldhelp/mg_names.hlp Xml/mg_names.xml >arb_help2xml oldhelp/mode_width.hlp Xml/mode_width.xml >arb_help2xml oldhelp/trans_anal.hlp Xml/trans_anal.xml >arb_help2xml oldhelp/probeadmin.hlp Xml/probeadmin.xml >arb_help2xml oldhelp/color.hlp Xml/color.xml >arb_help2xml oldhelp/sp_sp_2_ext.hlp Xml/sp_sp_2_ext.xml >arb_help2xml oldhelp/pfold_sai.hlp Xml/pfold_sai.xml >arb_help2xml oldhelp/saveas.hlp Xml/saveas.xml >arb_help2xml oldhelp/bootstrap.hlp Xml/bootstrap.xml >arb_help2xml oldhelp/rna3d_general.hlp Xml/rna3d_general.xml >arb_help2xml oldhelp/search_equal_fields.hlp Xml/search_equal_fields.xml >arb_help2xml oldhelp/spaf_create.hlp Xml/spaf_create.xml >arb_help2xml oldhelp/nt_tree_select.hlp Xml/nt_tree_select.xml >arb_help2xml oldhelp/props_nds.hlp Xml/props_nds.xml >arb_help2xml oldhelp/checkgcg.hlp Xml/checkgcg.xml >arb_help2xml oldhelp/csp_2_gnuplot.hlp Xml/csp_2_gnuplot.xml >arb_help2xml oldhelp/ne_search.hlp Xml/ne_search.xml >arb_help2xml oldhelp/check_quality.hlp Xml/check_quality.xml >arb_help2xml oldhelp/asciiprint.hlp Xml/asciiprint.xml >arb_help2xml oldhelp/configuration.hlp Xml/configuration.xml >arb_help2xml oldhelp/mark_genes.hlp Xml/mark_genes.xml >arb_help2xml oldhelp/max_freq.hlp Xml/max_freq.xml >arb_help2xml oldhelp/save_matrix.hlp Xml/save_matrix.xml >arb_help2xml oldhelp/arb_pars.hlp Xml/arb_pars.xml >arb_help2xml oldhelp/trm_mrkd.hlp Xml/trm_mrkd.xml >arb_help2xml oldhelp/pt_server.hlp Xml/pt_server.xml >arb_help2xml oldhelp/ne_align_seq.hlp Xml/ne_align_seq.xml >arb_help2xml oldhelp/regexpr.hlp Xml/regexpr.xml >arb_help2xml oldhelp/arb_commands.hlp Xml/arb_commands.xml >arb_help2xml oldhelp/tr_type_list.hlp Xml/tr_type_list.xml >arb_help2xml oldhelp/sp_invert_mrk.hlp Xml/sp_invert_mrk.xml >arb_help2xml oldhelp/tr_import.hlp Xml/tr_import.xml >arb_help2xml oldhelp/configurations.hlp Xml/configurations.xml >arb_help2xml oldhelp/submission.hlp Xml/submission.xml >arb_help2xml oldhelp/set_meny_fields.hlp Xml/set_meny_fields.xml >arb_help2xml oldhelp/unmark_list.hlp Xml/unmark_list.xml >arb_help2xml oldhelp/arb_secedit.hlp Xml/arb_secedit.xml >arb_help2xml oldhelp/mod_field_list.hlp Xml/mod_field_list.xml >arb_help2xml oldhelp/pa_quick.hlp Xml/pa_quick.xml >arb_help2xml oldhelp/visualizeSAI.hlp Xml/visualizeSAI.xml >arb_help2xml oldhelp/write_field_list.hlp Xml/write_field_list.xml >arb_help2xml oldhelp/alignment.hlp Xml/alignment.xml >arb_help2xml oldhelp/gene_mark.hlp Xml/gene_mark.xml >arb_help2xml oldhelp/colorize.hlp Xml/colorize.xml >arb_help2xml oldhelp/consensus_def.hlp Xml/consensus_def.xml >arb_help2xml oldhelp/primer.hlp Xml/primer.xml >arb_help2xml oldhelp/del_list.hlp Xml/del_list.xml >arb_help2xml oldhelp/saiProbeHelp.hlp Xml/saiProbeHelp.xml >arb_help2xml oldhelp/ebi_ift.hlp Xml/ebi_ift.xml >arb_help2xml oldhelp/change_security.hlp Xml/change_security.xml >arb_help2xml oldhelp/sel_spec.hlp Xml/sel_spec.xml >arb_help2xml oldhelp/gde.hlp Xml/gde.xml >arb_help2xml oldhelp/mode_length.hlp Xml/mode_length.xml >arb_help2xml oldhelp/sec_keys.hlp Xml/sec_keys.xml >oldhelp/gde.hlp:6: Warning: Dead link to 'ale.hlp' >arb_help2xml oldhelp/gene_extract.hlp Xml/gene_extract.xml >arb_help2xml oldhelp/selected.hlp Xml/selected.xml >arb_help2xml oldhelp/spa_copy.hlp Xml/spa_copy.xml >arb_help2xml oldhelp/rst_phys_zoom.hlp Xml/rst_phys_zoom.xml >arb_help2xml oldhelp/sp_mrk_all.hlp Xml/sp_mrk_all.xml >arb_help2xml oldhelp/man_arb_edit4.hlp Xml/man_arb_edit4.xml >arb_help2xml oldhelp/probedesign.hlp Xml/probedesign.xml >arb_help2xml oldhelp/mode_group.hlp Xml/mode_group.xml >arb_help2xml oldhelp/undo.hlp Xml/undo.xml >arb_help2xml oldhelp/islandhopping.hlp Xml/islandhopping.xml >arb_help2xml oldhelp/sel_box.hlp Xml/sel_box.xml >arb_help2xml oldhelp/missbase.hlp Xml/missbase.xml >arb_help2xml oldhelp/pfold_props.hlp Xml/pfold_props.xml >arb_help2xml oldhelp/gene_search.hlp Xml/gene_search.xml >arb_help2xml oldhelp/quit.hlp Xml/quit.xml >arb_help2xml oldhelp/ph_export_markerline.hlp Xml/ph_export_markerline.xml >arb_help2xml oldhelp/tgroupall.hlp Xml/tgroupall.xml >arb_help2xml oldhelp/mg_extendeds.hlp Xml/mg_extendeds.xml >arb_help2xml oldhelp/scandb.hlp Xml/scandb.xml >arb_help2xml oldhelp/arb_db.hlp Xml/arb_db.xml >arb_help2xml oldhelp/arb_intro.hlp Xml/arb_intro.xml >arb_help2xml oldhelp/arb_gde.hlp Xml/arb_gde.xml >arb_help2xml oldhelp/universal_ift.hlp Xml/universal_ift.xml >arb_help2xml oldhelp/sp_mrk_tree.hlp Xml/sp_mrk_tree.xml >arb_help2xml oldhelp/sp_umrk_all.hlp Xml/sp_umrk_all.xml >arb_help2xml oldhelp/proteinViewer.hlp Xml/proteinViewer.xml >arb_help2xml oldhelp/vn_search.hlp Xml/vn_search.xml >arb_help2xml oldhelp/pfold.hlp Xml/pfold.xml >arb_help2xml oldhelp/secedit_imexport.hlp Xml/secedit_imexport.xml >arb_help2xml oldhelp/color_props_groups.hlp Xml/color_props_groups.xml >arb_help2xml oldhelp/export_format.hlp Xml/export_format.xml >arb_help2xml oldhelp/mode_swap.hlp Xml/mode_swap.xml >arb_help2xml oldhelp/rna3d_dispBases.hlp Xml/rna3d_dispBases.xml >arb_help2xml oldhelp/save_def.hlp Xml/save_def.xml >arb_help2xml oldhelp/ne_new_sequence.hlp Xml/ne_new_sequence.xml >arb_help2xml oldhelp/e4_replace.hlp Xml/e4_replace.xml >arb_help2xml oldhelp/gene_hide.hlp Xml/gene_hide.xml >arb_help2xml oldhelp/optimize.hlp Xml/optimize.xml >arb_help2xml oldhelp/mode_angle.hlp Xml/mode_angle.xml >arb_help2xml oldhelp/sp_rename.hlp Xml/sp_rename.xml >arb_help2xml oldhelp/sp_search.hlp Xml/sp_search.xml >arb_help2xml oldhelp/sp_umrk_tree.hlp Xml/sp_umrk_tree.xml >arb_help2xml oldhelp/sp_sort_phyl.hlp Xml/sp_sort_phyl.xml >arb_help2xml oldhelp/species.hlp Xml/species.xml >arb_help2xml oldhelp/nt_tree_settings.hlp Xml/nt_tree_settings.xml >arb_help2xml oldhelp/nt_props_data.hlp Xml/nt_props_data.xml >arb_help2xml oldhelp/namesadmin.hlp Xml/namesadmin.xml >arb_help2xml oldhelp/sec_mode.hlp Xml/sec_mode.xml >arb_help2xml oldhelp/faligner.hlp Xml/faligner.xml >arb_help2xml oldhelp/mode_select.hlp Xml/mode_select.xml >arb_help2xml oldhelp/mark.hlp Xml/mark.xml >arb_help2xml oldhelp/arb_import.hlp Xml/arb_import.xml >arb_help2xml oldhelp/ed4_nds.hlp Xml/ed4_nds.xml >arb_help2xml oldhelp/rna3d_dispHelices.hlp Xml/rna3d_dispHelices.xml >arb_help2xml oldhelp/fasta_ift.hlp Xml/fasta_ift.xml >arb_help2xml oldhelp/no_tree.hlp Xml/no_tree.xml >arb_help2xml oldhelp/exec_bug.hlp Xml/exec_bug.xml >arb_help2xml oldhelp/pa_optimizer.hlp Xml/pa_optimizer.xml >arb_help2xml oldhelp/result.hlp Xml/result.xml >arb_help2xml oldhelp/phylo.hlp Xml/phylo.xml >arb_help2xml oldhelp/e4_search.hlp Xml/e4_search.xml >arb_help2xml oldhelp/multiprobe.hlp Xml/multiprobe.xml >arb_help2xml oldhelp/arb_envar.hlp Xml/arb_envar.xml >arb_help2xml oldhelp/next_neighbours_listed.hlp Xml/next_neighbours_listed.xml >arb_help2xml oldhelp/align.hlp Xml/align.xml >arb_help2xml oldhelp/cons_params.hlp Xml/cons_params.xml >arb_help2xml oldhelp/Protection.hlp Xml/Protection.xml >arb_help2xml oldhelp/ap_stack.hlp Xml/ap_stack.xml >arb_help2xml oldhelp/dist.hlp Xml/dist.xml >arb_help2xml oldhelp/sel_fil.hlp Xml/sel_fil.xml >arb_help2xml oldhelp/tags.hlp Xml/tags.xml >arb_help2xml oldhelp/probedesignresult.hlp Xml/probedesignresult.xml >arb_help2xml oldhelp/prompt/format_alignments.hlp Xml/prompt/format_alignments.xml >make[5]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/HELP_SOURCE' >--------------------------------------------------- >------------ Converting xml 2 hlp: >make help >make[5]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/HELP_SOURCE' >sabcmd to_help.xsl Xml/arb.xml ../lib/help/arb.hlp '$myname=arb.xml' '$xml_location=Xml' || rm ../lib/help/arb.hlp >sabcmd to_help.xsl Xml/agde_protml_sub_protml_doc.xml ../lib/help/agde_protml_sub_protml_doc.hlp '$myname=agde_protml_sub_protml_doc.xml' '$xml_location=Xml' || rm ../lib/help/agde_protml_sub_protml_doc.hlp >sabcmd to_help.xsl Xml/changes.xml ../lib/help/changes.hlp '$myname=changes.xml' '$xml_location=Xml' || rm ../lib/help/changes.hlp >sabcmd to_help.xsl Xml/agde_protml_sub_protml_cli_doc.xml ../lib/help/agde_protml_sub_protml_cli_doc.hlp '$myname=agde_protml_sub_protml_cli_doc.xml' '$xml_location=Xml' || rm ../lib/help/agde_protml_sub_protml_cli_doc.hlp >sabcmd to_help.xsl Xml/agde_DNAml_rates.xml ../lib/help/agde_DNAml_rates.hlp '$myname=agde_DNAml_rates.xml' '$xml_location=Xml' || rm ../lib/help/agde_DNAml_rates.hlp >sabcmd to_help.xsl Xml/agde_dnapars.xml ../lib/help/agde_dnapars.hlp '$myname=agde_dnapars.xml' '$xml_location=Xml' || rm ../lib/help/agde_dnapars.hlp >sabcmd to_help.xsl Xml/agde_proml.xml ../lib/help/agde_proml.hlp '$myname=agde_proml.xml' '$xml_location=Xml' || rm ../lib/help/agde_proml.hlp >sabcmd to_help.xsl Xml/agde_dnaml_sub_AxML_doc.xml ../lib/help/agde_dnaml_sub_AxML_doc.hlp '$myname=agde_dnaml_sub_AxML_doc.xml' '$xml_location=Xml' || rm ../lib/help/agde_dnaml_sub_AxML_doc.hlp >sabcmd to_help.xsl Xml/agde_dnaml_sub_fastDNAml_doc.xml ../lib/help/agde_dnaml_sub_fastDNAml_doc.hlp '$myname=agde_dnaml_sub_fastDNAml_doc.xml' '$xml_location=Xml' || rm ../lib/help/agde_dnaml_sub_fastDNAml_doc.hlp >sabcmd to_help.xsl Xml/agde_phylip_distance_sub_neighbor_doc.xml ../lib/help/agde_phylip_distance_sub_neighbor_doc.hlp '$myname=agde_phylip_distance_sub_neighbor_doc.xml' '$xml_location=Xml' || rm ../lib/help/agde_phylip_distance_sub_neighbor_doc.hlp >sabcmd to_help.xsl Xml/agde_lsadt.xml ../lib/help/agde_lsadt.hlp '$myname=agde_lsadt.xml' '$xml_location=Xml' || rm ../lib/help/agde_lsadt.hlp >sabcmd to_help.xsl Xml/agde_protml.xml ../lib/help/agde_protml.hlp '$myname=agde_protml.xml' '$xml_location=Xml' || rm ../lib/help/agde_protml.hlp >sabcmd to_help.xsl Xml/agde_readseq_sub_Formats.xml ../lib/help/agde_readseq_sub_Formats.hlp '$myname=agde_readseq_sub_Formats.xml' '$xml_location=Xml' || rm ../lib/help/agde_readseq_sub_Formats.hlp >sabcmd to_help.xsl Xml/agde_clustalw_sub_clustalw_help.xml ../lib/help/agde_clustalw_sub_clustalw_help.hlp '$myname=agde_clustalw_sub_clustalw_help.xml' '$xml_location=Xml' || rm ../lib/help/agde_clustalw_sub_clustalw_help.hlp >sabcmd to_help.xsl Xml/agde_treepuzzle.xml ../lib/help/agde_treepuzzle.hlp '$myname=agde_treepuzzle.xml' '$xml_location=Xml' || rm ../lib/help/agde_treepuzzle.hlp >sabcmd to_help.xsl Xml/agde_clustalw_sub_clustalw_doc.xml ../lib/help/agde_clustalw_sub_clustalw_doc.hlp '$myname=agde_clustalw_sub_clustalw_doc.xml' '$xml_location=Xml' || rm ../lib/help/agde_clustalw_sub_clustalw_doc.hlp >sabcmd to_help.xsl Xml/agde.xml ../lib/help/agde.hlp '$myname=agde.xml' '$xml_location=Xml' || rm ../lib/help/agde.hlp >sabcmd to_help.xsl Xml/agde_CAP2.xml ../lib/help/agde_CAP2.hlp '$myname=agde_CAP2.xml' '$xml_location=Xml' || rm ../lib/help/agde_CAP2.hlp >sabcmd to_help.xsl Xml/agde_protpars.xml ../lib/help/agde_protpars.hlp '$myname=agde_protpars.xml' '$xml_location=Xml' || rm ../lib/help/agde_protpars.hlp >sabcmd to_help.xsl Xml/agde_readseq.xml ../lib/help/agde_readseq.hlp '$myname=agde_readseq.xml' '$xml_location=Xml' || rm ../lib/help/agde_readseq.hlp >sabcmd to_help.xsl Xml/agde_phylip_distance_sub_fitch_doc.xml ../lib/help/agde_phylip_distance_sub_fitch_doc.hlp '$myname=agde_phylip_distance_sub_fitch_doc.xml' '$xml_location=Xml' || rm ../lib/help/agde_phylip_distance_sub_fitch_doc.hlp >sabcmd to_help.xsl Xml/agde_phylip_distance.xml ../lib/help/agde_phylip_distance.hlp '$myname=agde_phylip_distance.xml' '$xml_location=Xml' || rm ../lib/help/agde_phylip_distance.hlp >sabcmd to_help.xsl Xml/copyright.xml ../lib/help/copyright.hlp '$myname=copyright.xml' '$xml_location=Xml' || rm ../lib/help/copyright.hlp >sabcmd to_help.xsl Xml/agde_raxml.xml ../lib/help/agde_raxml.hlp '$myname=agde_raxml.xml' '$xml_location=Xml' || rm ../lib/help/agde_raxml.hlp >sabcmd to_help.xsl Xml/agde_phyml.xml ../lib/help/agde_phyml.hlp '$myname=agde_phyml.xml' '$xml_location=Xml' || rm ../lib/help/agde_phyml.hlp >sabcmd to_help.xsl Xml/agde_readseq_sub_Readseq_help.xml ../lib/help/agde_readseq_sub_Readseq_help.hlp '$myname=agde_readseq_sub_Readseq_help.xml' '$xml_location=Xml' || rm ../lib/help/agde_readseq_sub_Readseq_help.hlp >sabcmd to_help.xsl Xml/agde_phylip_distance_sub_dnadist_doc.xml ../lib/help/agde_phylip_distance_sub_dnadist_doc.hlp '$myname=agde_phylip_distance_sub_dnadist_doc.xml' '$xml_location=Xml' || rm ../lib/help/agde_phylip_distance_sub_dnadist_doc.hlp >sabcmd to_help.xsl Xml/agde_dnaml.xml ../lib/help/agde_dnaml.hlp '$myname=agde_dnaml.xml' '$xml_location=Xml' || rm ../lib/help/agde_dnaml.hlp >sabcmd to_help.xsl Xml/agde_phylip_distance_sub_kitsch_doc.xml ../lib/help/agde_phylip_distance_sub_kitsch_doc.hlp '$myname=agde_phylip_distance_sub_kitsch_doc.xml' '$xml_location=Xml' || rm ../lib/help/agde_phylip_distance_sub_kitsch_doc.hlp >sabcmd to_help.xsl Xml/agde_phylip_distance_sub_protdist_doc.xml ../lib/help/agde_phylip_distance_sub_protdist_doc.hlp '$myname=agde_phylip_distance_sub_protdist_doc.xml' '$xml_location=Xml' || rm ../lib/help/agde_phylip_distance_sub_protdist_doc.hlp >sabcmd to_help.xsl Xml/agde_readseq_sub_Readme.xml ../lib/help/agde_readseq_sub_Readme.hlp '$myname=agde_readseq_sub_Readme.xml' '$xml_location=Xml' || rm ../lib/help/agde_readseq_sub_Readme.hlp >sabcmd to_help.xsl Xml/agde_clustalw.xml ../lib/help/agde_clustalw.hlp '$myname=agde_clustalw.xml' '$xml_location=Xml' || rm ../lib/help/agde_clustalw.hlp >sabcmd to_help.xsl Xml/checkfield.xml ../lib/help/checkfield.hlp '$myname=checkfield.xml' '$xml_location=Xml' || rm ../lib/help/checkfield.hlp >sabcmd to_help.xsl Xml/set_protection.xml ../lib/help/set_protection.hlp '$myname=set_protection.xml' '$xml_location=Xml' || rm ../lib/help/set_protection.hlp >sabcmd to_help.xsl Xml/FAQS.xml ../lib/help/FAQS.hlp '$myname=FAQS.xml' '$xml_location=Xml' || rm ../lib/help/FAQS.hlp >sabcmd to_help.xsl Xml/pa_partial.xml ../lib/help/pa_partial.hlp '$myname=pa_partial.xml' '$xml_location=Xml' || rm ../lib/help/pa_partial.hlp >sabcmd to_help.xsl Xml/gde_ift.xml ../lib/help/gde_ift.hlp '$myname=gde_ift.xml' '$xml_location=Xml' || rm ../lib/help/gde_ift.hlp >sabcmd to_help.xsl Xml/mode_reset.xml ../lib/help/mode_reset.hlp '$myname=mode_reset.xml' '$xml_location=Xml' || rm ../lib/help/mode_reset.hlp >sabcmd to_help.xsl Xml/tbl_boot2len.xml ../lib/help/tbl_boot2len.hlp '$myname=tbl_boot2len.xml' '$xml_location=Xml' || rm ../lib/help/tbl_boot2len.hlp >sabcmd to_help.xsl Xml/props_frame.xml ../lib/help/props_frame.hlp '$myname=props_frame.xml' '$xml_location=Xml' || rm ../lib/help/props_frame.hlp >sabcmd to_help.xsl Xml/rna3d_mapSeqData.xml ../lib/help/rna3d_mapSeqData.hlp '$myname=rna3d_mapSeqData.xml' '$xml_location=Xml' || rm ../lib/help/rna3d_mapSeqData.hlp >sabcmd to_help.xsl Xml/treeadm.xml ../lib/help/treeadm.hlp '$myname=treeadm.xml' '$xml_location=Xml' || rm ../lib/help/treeadm.hlp >sabcmd to_help.xsl Xml/mode_set_root.xml ../lib/help/mode_set_root.hlp '$myname=mode_set_root.xml' '$xml_location=Xml' || rm ../lib/help/mode_set_root.hlp >sabcmd to_help.xsl Xml/seq_quality.xml ../lib/help/seq_quality.hlp '$myname=seq_quality.xml' '$xml_location=Xml' || rm ../lib/help/seq_quality.hlp >sabcmd to_help.xsl Xml/arb_export_nds.xml ../lib/help/arb_export_nds.hlp '$myname=arb_export_nds.xml' '$xml_location=Xml' || rm ../lib/help/arb_export_nds.hlp >sabcmd to_help.xsl Xml/gene_options.xml ../lib/help/gene_options.hlp '$myname=gene_options.xml' '$xml_location=Xml' || rm ../lib/help/gene_options.hlp >sabcmd to_help.xsl Xml/tr_jump.xml ../lib/help/tr_jump.hlp '$myname=tr_jump.xml' '$xml_location=Xml' || rm ../lib/help/tr_jump.hlp >sabcmd to_help.xsl Xml/mp_params.xml ../lib/help/mp_params.hlp '$myname=mp_params.xml' '$xml_location=Xml' || rm ../lib/help/mp_params.hlp >sabcmd to_help.xsl Xml/gene_species.xml ../lib/help/gene_species.hlp '$myname=gene_species.xml' '$xml_location=Xml' || rm ../lib/help/gene_species.hlp >sabcmd to_help.xsl Xml/glossary.xml ../lib/help/glossary.hlp '$myname=glossary.xml' '$xml_location=Xml' || rm ../lib/help/glossary.hlp >sabcmd to_help.xsl Xml/vn_delete.xml ../lib/help/vn_delete.hlp '$myname=vn_delete.xml' '$xml_location=Xml' || rm ../lib/help/vn_delete.hlp >sabcmd to_help.xsl Xml/exportcursor.xml ../lib/help/exportcursor.hlp '$myname=exportcursor.xml' '$xml_location=Xml' || rm ../lib/help/exportcursor.hlp >sabcmd to_help.xsl Xml/tbl_reset.xml ../lib/help/tbl_reset.hlp '$myname=tbl_reset.xml' '$xml_location=Xml' || rm ../lib/help/tbl_reset.hlp >sabcmd to_help.xsl Xml/markcolor.xml ../lib/help/markcolor.hlp '$myname=markcolor.xml' '$xml_location=Xml' || rm ../lib/help/markcolor.hlp >sabcmd to_help.xsl Xml/ne_pretty.xml ../lib/help/ne_pretty.hlp '$myname=ne_pretty.xml' '$xml_location=Xml' || rm ../lib/help/ne_pretty.hlp >sabcmd to_help.xsl Xml/mode.xml ../lib/help/mode.hlp '$myname=mode.xml' '$xml_location=Xml' || rm ../lib/help/mode.hlp >sabcmd to_help.xsl Xml/neprops.xml ../lib/help/neprops.hlp '$myname=neprops.xml' '$xml_location=Xml' || rm ../lib/help/neprops.hlp >sabcmd to_help.xsl Xml/macro.xml ../lib/help/macro.hlp '$myname=macro.xml' '$xml_location=Xml' || rm ../lib/help/macro.hlp >sabcmd to_help.xsl Xml/tr_type_irs.xml ../lib/help/tr_type_irs.hlp '$myname=tr_type_irs.xml' '$xml_location=Xml' || rm ../lib/help/tr_type_irs.hlp >sabcmd to_help.xsl Xml/help.xml ../lib/help/help.hlp '$myname=help.xml' '$xml_location=Xml' || rm ../lib/help/help.hlp >sabcmd to_help.xsl Xml/tbl_justify.xml ../lib/help/tbl_justify.hlp '$myname=tbl_justify.xml' '$xml_location=Xml' || rm ../lib/help/tbl_justify.hlp >sabcmd to_help.xsl Xml/merge_species.xml ../lib/help/merge_species.hlp '$myname=merge_species.xml' '$xml_location=Xml' || rm ../lib/help/merge_species.hlp >sabcmd to_help.xsl Xml/next_neighbours.xml ../lib/help/next_neighbours.hlp '$myname=next_neighbours.xml' '$xml_location=Xml' || rm ../lib/help/next_neighbours.hlp >sabcmd to_help.xsl Xml/probe_param.xml ../lib/help/probe_param.hlp '$myname=probe_param.xml' '$xml_location=Xml' || rm ../lib/help/probe_param.hlp >sabcmd to_help.xsl Xml/rna3d_dispMolecule.xml ../lib/help/rna3d_dispMolecule.hlp '$myname=rna3d_dispMolecule.xml' '$xml_location=Xml' || rm ../lib/help/rna3d_dispMolecule.hlp >sabcmd to_help.xsl Xml/next_neighbours_common.xml ../lib/help/next_neighbours_common.hlp '$myname=next_neighbours_common.xml' '$xml_location=Xml' || rm ../lib/help/next_neighbours_common.hlp >sabcmd to_help.xsl Xml/mg_species.xml ../lib/help/mg_species.hlp '$myname=mg_species.xml' '$xml_location=Xml' || rm ../lib/help/mg_species.hlp >sabcmd to_help.xsl Xml/importift.xml ../lib/help/importift.hlp '$myname=importift.xml' '$xml_location=Xml' || rm ../lib/help/importift.hlp >sabcmd to_help.xsl Xml/spaf_scandb.xml ../lib/help/spaf_scandb.hlp '$myname=spaf_scandb.xml' '$xml_location=Xml' || rm ../lib/help/spaf_scandb.hlp >sabcmd to_help.xsl Xml/user_matrix.xml ../lib/help/user_matrix.hlp '$myname=user_matrix.xml' '$xml_location=Xml' || rm ../lib/help/user_matrix.hlp >sabcmd to_help.xsl Xml/mode_rotate.xml ../lib/help/mode_rotate.hlp '$myname=mode_rotate.xml' '$xml_location=Xml' || rm ../lib/help/mode_rotate.hlp >sabcmd to_help.xsl Xml/neprops_data.xml ../lib/help/neprops_data.hlp '$myname=neprops_data.xml' '$xml_location=Xml' || rm ../lib/help/neprops_data.hlp >sabcmd to_help.xsl Xml/ad_align.xml ../lib/help/ad_align.hlp '$myname=ad_align.xml' '$xml_location=Xml' || rm ../lib/help/ad_align.hlp >sabcmd to_help.xsl Xml/arb_edit4.xml ../lib/help/arb_edit4.hlp '$myname=arb_edit4.xml' '$xml_location=Xml' || rm ../lib/help/arb_edit4.hlp >sabcmd to_help.xsl Xml/vn_import.xml ../lib/help/vn_import.hlp '$myname=vn_import.xml' '$xml_location=Xml' || rm ../lib/help/vn_import.hlp >sabcmd to_help.xsl Xml/consensus.xml ../lib/help/consensus.hlp '$myname=consensus.xml' '$xml_location=Xml' || rm ../lib/help/consensus.hlp >sabcmd to_help.xsl Xml/sp_del_mrkd.xml ../lib/help/sp_del_mrkd.hlp '$myname=sp_del_mrkd.xml' '$xml_location=Xml' || rm ../lib/help/sp_del_mrkd.hlp >sabcmd to_help.xsl Xml/probematch.xml ../lib/help/probematch.hlp '$myname=probematch.xml' '$xml_location=Xml' || rm ../lib/help/probematch.hlp >sabcmd to_help.xsl Xml/e4_block.xml ../lib/help/e4_block.hlp '$myname=e4_block.xml' '$xml_location=Xml' || rm ../lib/help/e4_block.hlp >sabcmd to_help.xsl Xml/input_mask.xml ../lib/help/input_mask.hlp '$myname=input_mask.xml' '$xml_location=Xml' || rm ../lib/help/input_mask.hlp >sabcmd to_help.xsl Xml/commands.xml ../lib/help/commands.hlp '$myname=commands.xml' '$xml_location=Xml' || rm ../lib/help/commands.hlp >sabcmd to_help.xsl Xml/arb_pars_init.xml ../lib/help/arb_pars_init.hlp '$myname=arb_pars_init.xml' '$xml_location=Xml' || rm ../lib/help/arb_pars_init.hlp >sabcmd to_help.xsl Xml/mg_preserve.xml ../lib/help/mg_preserve.hlp '$myname=mg_preserve.xml' '$xml_location=Xml' || rm ../lib/help/mg_preserve.hlp >sabcmd to_help.xsl Xml/pd_spec_param.xml ../lib/help/pd_spec_param.hlp '$myname=pd_spec_param.xml' '$xml_location=Xml' || rm ../lib/help/pd_spec_param.hlp >sabcmd to_help.xsl Xml/tree2prt.xml ../lib/help/tree2prt.hlp '$myname=tree2prt.xml' '$xml_location=Xml' || rm ../lib/help/tree2prt.hlp >sabcmd to_help.xsl Xml/primer_new.xml ../lib/help/primer_new.hlp '$myname=primer_new.xml' '$xml_location=Xml' || rm ../lib/help/primer_new.hlp >sabcmd to_help.xsl Xml/pa_bootstrap.xml ../lib/help/pa_bootstrap.hlp '$myname=pa_bootstrap.xml' '$xml_location=Xml' || rm ../lib/help/pa_bootstrap.hlp >sabcmd to_help.xsl Xml/st_ml.xml ../lib/help/st_ml.hlp '$myname=st_ml.xml' '$xml_location=Xml' || rm ../lib/help/st_ml.hlp >sabcmd to_help.xsl Xml/e4_options.xml ../lib/help/e4_options.hlp '$myname=e4_options.xml' '$xml_location=Xml' || rm ../lib/help/e4_options.hlp >sabcmd to_help.xsl Xml/sp_info.xml ../lib/help/sp_info.hlp '$myname=sp_info.xml' '$xml_location=Xml' || rm ../lib/help/sp_info.hlp >sabcmd to_help.xsl Xml/tgroupcolor.xml ../lib/help/tgroupcolor.hlp '$myname=tgroupcolor.xml' '$xml_location=Xml' || rm ../lib/help/tgroupcolor.hlp >sabcmd to_help.xsl Xml/tkeep_mrkd.xml ../lib/help/tkeep_mrkd.hlp '$myname=tkeep_mrkd.xml' '$xml_location=Xml' || rm ../lib/help/tkeep_mrkd.hlp >sabcmd to_help.xsl Xml/dewachter_ift.xml ../lib/help/dewachter_ift.hlp '$myname=dewachter_ift.xml' '$xml_location=Xml' || rm ../lib/help/dewachter_ift.hlp >sabcmd to_help.xsl Xml/ne_compl.xml ../lib/help/ne_compl.hlp '$myname=ne_compl.xml' '$xml_location=Xml' || rm ../lib/help/ne_compl.hlp >sabcmd to_help.xsl Xml/iupac-codes.xml ../lib/help/iupac-codes.hlp '$myname=iupac-codes.xml' '$xml_location=Xml' || rm ../lib/help/iupac-codes.hlp >sabcmd to_help.xsl Xml/awt_csp.xml ../lib/help/awt_csp.hlp '$myname=awt_csp.xml' '$xml_location=Xml' || rm ../lib/help/awt_csp.hlp >sabcmd to_help.xsl Xml/gene_info.xml ../lib/help/gene_info.hlp '$myname=gene_info.xml' '$xml_location=Xml' || rm ../lib/help/gene_info.hlp >sabcmd to_help.xsl Xml/sv_def.xml ../lib/help/sv_def.hlp '$myname=sv_def.xml' '$xml_location=Xml' || rm ../lib/help/sv_def.hlp >sabcmd to_help.xsl Xml/ad_extended.xml ../lib/help/ad_extended.hlp '$myname=ad_extended.xml' '$xml_location=Xml' || rm ../lib/help/ad_extended.hlp >sabcmd to_help.xsl Xml/extended.xml ../lib/help/extended.hlp '$myname=extended.xml' '$xml_location=Xml' || rm ../lib/help/extended.hlp >sabcmd to_help.xsl Xml/set_color_of_listed.xml ../lib/help/set_color_of_listed.hlp '$myname=set_color_of_listed.xml' '$xml_location=Xml' || rm ../lib/help/set_color_of_listed.hlp >sabcmd to_help.xsl Xml/mode_www.xml ../lib/help/mode_www.hlp '$myname=mode_www.xml' '$xml_location=Xml' || rm ../lib/help/mode_www.hlp >sabcmd to_help.xsl Xml/mode_kernlin.xml ../lib/help/mode_kernlin.hlp '$myname=mode_kernlin.xml' '$xml_location=Xml' || rm ../lib/help/mode_kernlin.hlp >sabcmd to_help.xsl Xml/sec_main.xml ../lib/help/sec_main.hlp '$myname=sec_main.xml' '$xml_location=Xml' || rm ../lib/help/sec_main.hlp >sabcmd to_help.xsl Xml/arb_merge.xml ../lib/help/arb_merge.hlp '$myname=arb_merge.xml' '$xml_location=Xml' || rm ../lib/help/arb_merge.hlp >sabcmd to_help.xsl Xml/ne_copy_sequence.xml ../lib/help/ne_copy_sequence.hlp '$myname=ne_copy_sequence.xml' '$xml_location=Xml' || rm ../lib/help/ne_copy_sequence.hlp >sabcmd to_help.xsl Xml/pa_quick_sel.xml ../lib/help/pa_quick_sel.hlp '$myname=pa_quick_sel.xml' '$xml_location=Xml' || rm ../lib/help/pa_quick_sel.hlp >sabcmd to_help.xsl Xml/nekey_map.xml ../lib/help/nekey_map.hlp '$myname=nekey_map.xml' '$xml_location=Xml' || rm ../lib/help/nekey_map.hlp >sabcmd to_help.xsl Xml/spaf_convert.xml ../lib/help/spaf_convert.hlp '$myname=spaf_convert.xml' '$xml_location=Xml' || rm ../lib/help/spaf_convert.hlp >sabcmd to_help.xsl Xml/rename.xml ../lib/help/rename.hlp '$myname=rename.xml' '$xml_location=Xml' || rm ../lib/help/rename.hlp >sabcmd to_help.xsl Xml/realign_dna.xml ../lib/help/realign_dna.hlp '$myname=realign_dna.xml' '$xml_location=Xml' || rm ../lib/help/realign_dna.hlp >sabcmd to_help.xsl Xml/tgroupnmrkd.xml ../lib/help/tgroupnmrkd.hlp '$myname=tgroupnmrkd.xml' '$xml_location=Xml' || rm ../lib/help/tgroupnmrkd.hlp >sabcmd to_help.xsl Xml/ae2_ift.xml ../lib/help/ae2_ift.hlp '$myname=ae2_ift.xml' '$xml_location=Xml' || rm ../lib/help/ae2_ift.hlp >sabcmd to_help.xsl Xml/spaf_delete.xml ../lib/help/spaf_delete.hlp '$myname=spaf_delete.xml' '$xml_location=Xml' || rm ../lib/help/spaf_delete.hlp >sabcmd to_help.xsl Xml/tungroupall.xml ../lib/help/tungroupall.hlp '$myname=tungroupall.xml' '$xml_location=Xml' || rm ../lib/help/tungroupall.hlp >sabcmd to_help.xsl Xml/e4.xml ../lib/help/e4.hlp '$myname=e4.xml' '$xml_location=Xml' || rm ../lib/help/e4.hlp >sabcmd to_help.xsl Xml/nt_align_select.xml ../lib/help/nt_align_select.hlp '$myname=nt_align_select.xml' '$xml_location=Xml' || rm ../lib/help/nt_align_select.hlp >sabcmd to_help.xsl Xml/ecoliref.xml ../lib/help/ecoliref.hlp '$myname=ecoliref.xml' '$xml_location=Xml' || rm ../lib/help/ecoliref.hlp >sabcmd to_help.xsl Xml/track_ali_changes.xml ../lib/help/track_ali_changes.hlp '$myname=track_ali_changes.xml' '$xml_location=Xml' || rm ../lib/help/track_ali_changes.hlp >sabcmd to_help.xsl Xml/mg_trees.xml ../lib/help/mg_trees.hlp '$myname=mg_trees.xml' '$xml_location=Xml' || rm ../lib/help/mg_trees.hlp >sabcmd to_help.xsl Xml/tbl_scale.xml ../lib/help/tbl_scale.hlp '$myname=tbl_scale.xml' '$xml_location=Xml' || rm ../lib/help/tbl_scale.hlp >sabcmd to_help.xsl Xml/mg_configs.xml ../lib/help/mg_configs.hlp '$myname=mg_configs.xml' '$xml_location=Xml' || rm ../lib/help/mg_configs.hlp >sabcmd to_help.xsl Xml/tree2file.xml ../lib/help/tree2file.hlp '$myname=tree2file.xml' '$xml_location=Xml' || rm ../lib/help/tree2file.hlp >sabcmd to_help.xsl Xml/gene_species_field_transfer.xml ../lib/help/gene_species_field_transfer.hlp '$myname=gene_species_field_transfer.xml' '$xml_location=Xml' || rm ../lib/help/gene_species_field_transfer.hlp >sabcmd to_help.xsl Xml/manual.xml ../lib/help/manual.hlp '$myname=manual.xml' '$xml_location=Xml' || rm ../lib/help/manual.hlp >sabcmd to_help.xsl Xml/multiproberesults.xml ../lib/help/multiproberesults.hlp '$myname=multiproberesults.xml' '$xml_location=Xml' || rm ../lib/help/multiproberesults.hlp >sabcmd to_help.xsl Xml/rst_log_zoom.xml ../lib/help/rst_log_zoom.hlp '$myname=rst_log_zoom.xml' '$xml_location=Xml' || rm ../lib/help/rst_log_zoom.hlp >sabcmd to_help.xsl Xml/spaf_reorder.xml ../lib/help/spaf_reorder.hlp '$myname=spaf_reorder.xml' '$xml_location=Xml' || rm ../lib/help/spaf_reorder.hlp >sabcmd to_help.xsl Xml/searching.xml ../lib/help/searching.hlp '$myname=searching.xml' '$xml_location=Xml' || rm ../lib/help/searching.hlp >sabcmd to_help.xsl Xml/trm_boot.xml ../lib/help/trm_boot.hlp '$myname=trm_boot.xml' '$xml_location=Xml' || rm ../lib/help/trm_boot.hlp >sabcmd to_help.xsl Xml/organisms.xml ../lib/help/organisms.hlp '$myname=organisms.xml' '$xml_location=Xml' || rm ../lib/help/organisms.hlp >sabcmd to_help.xsl Xml/tr_type_nds.xml ../lib/help/tr_type_nds.hlp '$myname=tr_type_nds.xml' '$xml_location=Xml' || rm ../lib/help/tr_type_nds.hlp >sabcmd to_help.xsl Xml/gde_flat_ift.xml ../lib/help/gde_flat_ift.hlp '$myname=gde_flat_ift.xml' '$xml_location=Xml' || rm ../lib/help/gde_flat_ift.hlp >sabcmd to_help.xsl Xml/helix.xml ../lib/help/helix.hlp '$myname=helix.xml' '$xml_location=Xml' || rm ../lib/help/helix.hlp >sabcmd to_help.xsl Xml/resorttree.xml ../lib/help/resorttree.hlp '$myname=resorttree.xml' '$xml_location=Xml' || rm ../lib/help/resorttree.hlp >sabcmd to_help.xsl Xml/concatenate.xml ../lib/help/concatenate.hlp '$myname=concatenate.xml' '$xml_location=Xml' || rm ../lib/help/concatenate.hlp >sabcmd to_help.xsl Xml/partial_sequences.xml ../lib/help/partial_sequences.hlp '$myname=partial_sequences.xml' '$xml_location=Xml' || rm ../lib/help/partial_sequences.hlp >sabcmd to_help.xsl Xml/primer_parameters.xml ../lib/help/primer_parameters.hlp '$myname=primer_parameters.xml' '$xml_location=Xml' || rm ../lib/help/primer_parameters.hlp >sabcmd to_help.xsl Xml/spa_create.xml ../lib/help/spa_create.hlp '$myname=spa_create.xml' '$xml_location=Xml' || rm ../lib/help/spa_create.hlp >sabcmd to_help.xsl Xml/vn_suggest.xml ../lib/help/vn_suggest.hlp '$myname=vn_suggest.xml' '$xml_location=Xml' || rm ../lib/help/vn_suggest.hlp >sabcmd to_help.xsl Xml/mode_info.xml ../lib/help/mode_info.hlp '$myname=mode_info.xml' '$xml_location=Xml' || rm ../lib/help/mode_info.hlp >sabcmd to_help.xsl Xml/selected_gene.xml ../lib/help/selected_gene.hlp '$myname=selected_gene.xml' '$xml_location=Xml' || rm ../lib/help/selected_gene.hlp >sabcmd to_help.xsl Xml/rdp_ift.xml ../lib/help/rdp_ift.hlp '$myname=rdp_ift.xml' '$xml_location=Xml' || rm ../lib/help/rdp_ift.hlp >sabcmd to_help.xsl Xml/ne_replace.xml ../lib/help/ne_replace.hlp '$myname=ne_replace.xml' '$xml_location=Xml' || rm ../lib/help/ne_replace.hlp >sabcmd to_help.xsl Xml/mg_alignment.xml ../lib/help/mg_alignment.hlp '$myname=mg_alignment.xml' '$xml_location=Xml' || rm ../lib/help/mg_alignment.hlp >sabcmd to_help.xsl Xml/mode_optimize.xml ../lib/help/mode_optimize.hlp '$myname=mode_optimize.xml' '$xml_location=Xml' || rm ../lib/help/mode_optimize.hlp >sabcmd to_help.xsl Xml/trm_del.xml ../lib/help/trm_del.hlp '$myname=trm_del.xml' '$xml_location=Xml' || rm ../lib/help/trm_del.hlp >sabcmd to_help.xsl Xml/props_www.xml ../lib/help/props_www.hlp '$myname=props_www.xml' '$xml_location=Xml' || rm ../lib/help/props_www.hlp >sabcmd to_help.xsl Xml/organism_mark.xml ../lib/help/organism_mark.hlp '$myname=organism_mark.xml' '$xml_location=Xml' || rm ../lib/help/organism_mark.hlp >sabcmd to_help.xsl Xml/tree_cmp.xml ../lib/help/tree_cmp.hlp '$myname=tree_cmp.xml' '$xml_location=Xml' || rm ../lib/help/tree_cmp.hlp >sabcmd to_help.xsl Xml/spa_delete.xml ../lib/help/spa_delete.hlp '$myname=spa_delete.xml' '$xml_location=Xml' || rm ../lib/help/spa_delete.hlp >sabcmd to_help.xsl Xml/security.xml ../lib/help/security.hlp '$myname=security.xml' '$xml_location=Xml' || rm ../lib/help/security.hlp >sabcmd to_help.xsl Xml/arb_ntree.xml ../lib/help/arb_ntree.hlp '$myname=arb_ntree.xml' '$xml_location=Xml' || rm ../lib/help/arb_ntree.hlp >sabcmd to_help.xsl Xml/gene_mode.xml ../lib/help/gene_mode.hlp '$myname=gene_mode.xml' '$xml_location=Xml' || rm ../lib/help/gene_mode.hlp >sabcmd to_help.xsl Xml/mark_list.xml ../lib/help/mark_list.hlp '$myname=mark_list.xml' '$xml_location=Xml' || rm ../lib/help/mark_list.hlp >sabcmd to_help.xsl Xml/arb_edit.xml ../lib/help/arb_edit.hlp '$myname=arb_edit.xml' '$xml_location=Xml' || rm ../lib/help/arb_edit.hlp >sabcmd to_help.xsl Xml/mg_spec_sel_field.xml ../lib/help/mg_spec_sel_field.hlp '$myname=mg_spec_sel_field.xml' '$xml_location=Xml' || rm ../lib/help/mg_spec_sel_field.hlp >sabcmd to_help.xsl Xml/nt_keys.xml ../lib/help/nt_keys.hlp '$myname=nt_keys.xml' '$xml_location=Xml' || rm ../lib/help/nt_keys.hlp >sabcmd to_help.xsl Xml/input_mask_format.xml ../lib/help/input_mask_format.hlp '$myname=input_mask_format.xml' '$xml_location=Xml' || rm ../lib/help/input_mask_format.hlp >sabcmd to_help.xsl Xml/tr_type_radial.xml ../lib/help/tr_type_radial.hlp '$myname=tr_type_radial.xml' '$xml_location=Xml' || rm ../lib/help/tr_type_radial.hlp >sabcmd to_help.xsl Xml/helixsym.xml ../lib/help/helixsym.hlp '$myname=helixsym.xml' '$xml_location=Xml' || rm ../lib/help/helixsym.hlp >sabcmd to_help.xsl Xml/input_mask_new.xml ../lib/help/input_mask_new.hlp '$myname=input_mask_new.xml' '$xml_location=Xml' || rm ../lib/help/input_mask_new.hlp >sabcmd to_help.xsl Xml/phyl.xml ../lib/help/phyl.hlp '$myname=phyl.xml' '$xml_location=Xml' || rm ../lib/help/phyl.hlp >sabcmd to_help.xsl Xml/sequence_colors.xml ../lib/help/sequence_colors.hlp '$myname=sequence_colors.xml' '$xml_location=Xml' || rm ../lib/help/sequence_colors.hlp >sabcmd to_help.xsl Xml/registration.xml ../lib/help/registration.hlp '$myname=registration.xml' '$xml_location=Xml' || rm ../lib/help/registration.hlp >sabcmd to_help.xsl Xml/pos_var_pars.xml ../lib/help/pos_var_pars.hlp '$myname=pos_var_pars.xml' '$xml_location=Xml' || rm ../lib/help/pos_var_pars.hlp >sabcmd to_help.xsl Xml/save.xml ../lib/help/save.hlp '$myname=save.xml' '$xml_location=Xml' || rm ../lib/help/save.hlp >sabcmd to_help.xsl Xml/sp_sort_fld.xml ../lib/help/sp_sort_fld.hlp '$myname=sp_sort_fld.xml' '$xml_location=Xml' || rm ../lib/help/sp_sort_fld.hlp >sabcmd to_help.xsl Xml/savedef.xml ../lib/help/savedef.hlp '$myname=savedef.xml' '$xml_location=Xml' || rm ../lib/help/savedef.hlp >sabcmd to_help.xsl Xml/sec_props.xml ../lib/help/sec_props.hlp '$myname=sec_props.xml' '$xml_location=Xml' || rm ../lib/help/sec_props.hlp >sabcmd to_help.xsl Xml/spa_rename.xml ../lib/help/spa_rename.hlp '$myname=spa_rename.xml' '$xml_location=Xml' || rm ../lib/help/spa_rename.hlp >sabcmd to_help.xsl Xml/pars.xml ../lib/help/pars.hlp '$myname=pars.xml' '$xml_location=Xml' || rm ../lib/help/pars.hlp >sabcmd to_help.xsl Xml/translate_dna_2_pro.xml ../lib/help/translate_dna_2_pro.hlp '$myname=translate_dna_2_pro.xml' '$xml_location=Xml' || rm ../lib/help/translate_dna_2_pro.hlp >sabcmd to_help.xsl Xml/mode_move.xml ../lib/help/mode_move.hlp '$myname=mode_move.xml' '$xml_location=Xml' || rm ../lib/help/mode_move.hlp >sabcmd to_help.xsl Xml/e4_consensus.xml ../lib/help/e4_consensus.hlp '$myname=e4_consensus.xml' '$xml_location=Xml' || rm ../lib/help/e4_consensus.hlp >sabcmd to_help.xsl Xml/arb_export.xml ../lib/help/arb_export.hlp '$myname=arb_export.xml' '$xml_location=Xml' || rm ../lib/help/arb_export.hlp >sabcmd to_help.xsl Xml/pa_add.xml ../lib/help/pa_add.hlp '$myname=pa_add.xml' '$xml_location=Xml' || rm ../lib/help/pa_add.hlp >sabcmd to_help.xsl Xml/sec_display.xml ../lib/help/sec_display.hlp '$myname=sec_display.xml' '$xml_location=Xml' || rm ../lib/help/sec_display.hlp >sabcmd to_help.xsl Xml/search_duplicates.xml ../lib/help/search_duplicates.hlp '$myname=search_duplicates.xml' '$xml_location=Xml' || rm ../lib/help/search_duplicates.hlp >sabcmd to_help.xsl Xml/parser.xml ../lib/help/parser.hlp '$myname=parser.xml' '$xml_location=Xml' || rm ../lib/help/parser.hlp >sabcmd to_help.xsl Xml/pa_add_sel.xml ../lib/help/pa_add_sel.hlp '$myname=pa_add_sel.xml' '$xml_location=Xml' || rm ../lib/help/pa_add_sel.hlp >sabcmd to_help.xsl Xml/mode_lzoom.xml ../lib/help/mode_lzoom.hlp '$myname=mode_lzoom.xml' '$xml_location=Xml' || rm ../lib/help/mode_lzoom.hlp >sabcmd to_help.xsl Xml/version.xml ../lib/help/version.hlp '$myname=version.xml' '$xml_location=Xml' || rm ../lib/help/version.hlp >sabcmd to_help.xsl Xml/galign_main.xml ../lib/help/galign_main.hlp '$myname=galign_main.xml' '$xml_location=Xml' || rm ../lib/help/galign_main.hlp >sabcmd to_help.xsl Xml/species_join.xml ../lib/help/species_join.hlp '$myname=species_join.xml' '$xml_location=Xml' || rm ../lib/help/species_join.hlp >sabcmd to_help.xsl Xml/pa_ranchlengths.xml ../lib/help/pa_ranchlengths.hlp '$myname=pa_ranchlengths.xml' '$xml_location=Xml' || rm ../lib/help/pa_ranchlengths.hlp >sabcmd to_help.xsl Xml/mark_long_branches.xml ../lib/help/mark_long_branches.hlp '$myname=mark_long_branches.xml' '$xml_location=Xml' || rm ../lib/help/mark_long_branches.hlp >sabcmd to_help.xsl Xml/sp_count_mrk.xml ../lib/help/sp_count_mrk.hlp '$myname=sp_count_mrk.xml' '$xml_location=Xml' || rm ../lib/help/sp_count_mrk.hlp >sabcmd to_help.xsl Xml/gene_map.xml ../lib/help/gene_map.hlp '$myname=gene_map.xml' '$xml_location=Xml' || rm ../lib/help/gene_map.hlp >sabcmd to_help.xsl Xml/gene_species_mark.xml ../lib/help/gene_species_mark.hlp '$myname=gene_species_mark.xml' '$xml_location=Xml' || rm ../lib/help/gene_species_mark.hlp >sabcmd to_help.xsl Xml/trees.xml ../lib/help/trees.hlp '$myname=trees.xml' '$xml_location=Xml' || rm ../lib/help/trees.hlp >sabcmd to_help.xsl Xml/insdelchar.xml ../lib/help/insdelchar.hlp '$myname=insdelchar.xml' '$xml_location=Xml' || rm ../lib/help/insdelchar.hlp >sabcmd to_help.xsl Xml/mode_pzoom.xml ../lib/help/mode_pzoom.hlp '$myname=mode_pzoom.xml' '$xml_location=Xml' || rm ../lib/help/mode_pzoom.hlp >sabcmd to_help.xsl Xml/mode_mark.xml ../lib/help/mode_mark.hlp '$myname=mode_mark.xml' '$xml_location=Xml' || rm ../lib/help/mode_mark.hlp >sabcmd to_help.xsl Xml/dssp_ift.xml ../lib/help/dssp_ift.hlp '$myname=dssp_ift.xml' '$xml_location=Xml' || rm ../lib/help/dssp_ift.hlp >sabcmd to_help.xsl Xml/color_props.xml ../lib/help/color_props.hlp '$myname=color_props.xml' '$xml_location=Xml' || rm ../lib/help/color_props.hlp >sabcmd to_help.xsl Xml/acisrt.xml ../lib/help/acisrt.hlp '$myname=acisrt.xml' '$xml_location=Xml' || rm ../lib/help/acisrt.hlp >sabcmd to_help.xsl Xml/genes.xml ../lib/help/genes.hlp '$myname=genes.xml' '$xml_location=Xml' || rm ../lib/help/genes.hlp >sabcmd to_help.xsl Xml/mode_nni.xml ../lib/help/mode_nni.hlp '$myname=mode_nni.xml' '$xml_location=Xml' || rm ../lib/help/mode_nni.hlp >sabcmd to_help.xsl Xml/mg_names.xml ../lib/help/mg_names.hlp '$myname=mg_names.xml' '$xml_location=Xml' || rm ../lib/help/mg_names.hlp >sabcmd to_help.xsl Xml/mode_width.xml ../lib/help/mode_width.hlp '$myname=mode_width.xml' '$xml_location=Xml' || rm ../lib/help/mode_width.hlp >sabcmd to_help.xsl Xml/trans_anal.xml ../lib/help/trans_anal.hlp '$myname=trans_anal.xml' '$xml_location=Xml' || rm ../lib/help/trans_anal.hlp >sabcmd to_help.xsl Xml/probeadmin.xml ../lib/help/probeadmin.hlp '$myname=probeadmin.xml' '$xml_location=Xml' || rm ../lib/help/probeadmin.hlp >sabcmd to_help.xsl Xml/color.xml ../lib/help/color.hlp '$myname=color.xml' '$xml_location=Xml' || rm ../lib/help/color.hlp >sabcmd to_help.xsl Xml/sp_sp_2_ext.xml ../lib/help/sp_sp_2_ext.hlp '$myname=sp_sp_2_ext.xml' '$xml_location=Xml' || rm ../lib/help/sp_sp_2_ext.hlp >sabcmd to_help.xsl Xml/pfold_sai.xml ../lib/help/pfold_sai.hlp '$myname=pfold_sai.xml' '$xml_location=Xml' || rm ../lib/help/pfold_sai.hlp >sabcmd to_help.xsl Xml/saveas.xml ../lib/help/saveas.hlp '$myname=saveas.xml' '$xml_location=Xml' || rm ../lib/help/saveas.hlp >sabcmd to_help.xsl Xml/bootstrap.xml ../lib/help/bootstrap.hlp '$myname=bootstrap.xml' '$xml_location=Xml' || rm ../lib/help/bootstrap.hlp >sabcmd to_help.xsl Xml/rna3d_general.xml ../lib/help/rna3d_general.hlp '$myname=rna3d_general.xml' '$xml_location=Xml' || rm ../lib/help/rna3d_general.hlp >sabcmd to_help.xsl Xml/search_equal_fields.xml ../lib/help/search_equal_fields.hlp '$myname=search_equal_fields.xml' '$xml_location=Xml' || rm ../lib/help/search_equal_fields.hlp >sabcmd to_help.xsl Xml/spaf_create.xml ../lib/help/spaf_create.hlp '$myname=spaf_create.xml' '$xml_location=Xml' || rm ../lib/help/spaf_create.hlp >sabcmd to_help.xsl Xml/nt_tree_select.xml ../lib/help/nt_tree_select.hlp '$myname=nt_tree_select.xml' '$xml_location=Xml' || rm ../lib/help/nt_tree_select.hlp >sabcmd to_help.xsl Xml/props_nds.xml ../lib/help/props_nds.hlp '$myname=props_nds.xml' '$xml_location=Xml' || rm ../lib/help/props_nds.hlp >sabcmd to_help.xsl Xml/checkgcg.xml ../lib/help/checkgcg.hlp '$myname=checkgcg.xml' '$xml_location=Xml' || rm ../lib/help/checkgcg.hlp >sabcmd to_help.xsl Xml/csp_2_gnuplot.xml ../lib/help/csp_2_gnuplot.hlp '$myname=csp_2_gnuplot.xml' '$xml_location=Xml' || rm ../lib/help/csp_2_gnuplot.hlp >sabcmd to_help.xsl Xml/ne_search.xml ../lib/help/ne_search.hlp '$myname=ne_search.xml' '$xml_location=Xml' || rm ../lib/help/ne_search.hlp >sabcmd to_help.xsl Xml/check_quality.xml ../lib/help/check_quality.hlp '$myname=check_quality.xml' '$xml_location=Xml' || rm ../lib/help/check_quality.hlp >sabcmd to_help.xsl Xml/asciiprint.xml ../lib/help/asciiprint.hlp '$myname=asciiprint.xml' '$xml_location=Xml' || rm ../lib/help/asciiprint.hlp >sabcmd to_help.xsl Xml/configuration.xml ../lib/help/configuration.hlp '$myname=configuration.xml' '$xml_location=Xml' || rm ../lib/help/configuration.hlp >sabcmd to_help.xsl Xml/mark_genes.xml ../lib/help/mark_genes.hlp '$myname=mark_genes.xml' '$xml_location=Xml' || rm ../lib/help/mark_genes.hlp >sabcmd to_help.xsl Xml/max_freq.xml ../lib/help/max_freq.hlp '$myname=max_freq.xml' '$xml_location=Xml' || rm ../lib/help/max_freq.hlp >sabcmd to_help.xsl Xml/arb_pars.xml ../lib/help/arb_pars.hlp '$myname=arb_pars.xml' '$xml_location=Xml' || rm ../lib/help/arb_pars.hlp >sabcmd to_help.xsl Xml/pt_server.xml ../lib/help/pt_server.hlp '$myname=pt_server.xml' '$xml_location=Xml' || rm ../lib/help/pt_server.hlp >sabcmd to_help.xsl Xml/save_matrix.xml ../lib/help/save_matrix.hlp '$myname=save_matrix.xml' '$xml_location=Xml' || rm ../lib/help/save_matrix.hlp >sabcmd to_help.xsl Xml/trm_mrkd.xml ../lib/help/trm_mrkd.hlp '$myname=trm_mrkd.xml' '$xml_location=Xml' || rm ../lib/help/trm_mrkd.hlp >sabcmd to_help.xsl Xml/ne_align_seq.xml ../lib/help/ne_align_seq.hlp '$myname=ne_align_seq.xml' '$xml_location=Xml' || rm ../lib/help/ne_align_seq.hlp >sabcmd to_help.xsl Xml/regexpr.xml ../lib/help/regexpr.hlp '$myname=regexpr.xml' '$xml_location=Xml' || rm ../lib/help/regexpr.hlp >sabcmd to_help.xsl Xml/arb_commands.xml ../lib/help/arb_commands.hlp '$myname=arb_commands.xml' '$xml_location=Xml' || rm ../lib/help/arb_commands.hlp >sabcmd to_help.xsl Xml/tr_type_list.xml ../lib/help/tr_type_list.hlp '$myname=tr_type_list.xml' '$xml_location=Xml' || rm ../lib/help/tr_type_list.hlp >sabcmd to_help.xsl Xml/tr_import.xml ../lib/help/tr_import.hlp '$myname=tr_import.xml' '$xml_location=Xml' || rm ../lib/help/tr_import.hlp >sabcmd to_help.xsl Xml/configurations.xml ../lib/help/configurations.hlp '$myname=configurations.xml' '$xml_location=Xml' || rm ../lib/help/configurations.hlp >sabcmd to_help.xsl Xml/sp_invert_mrk.xml ../lib/help/sp_invert_mrk.hlp '$myname=sp_invert_mrk.xml' '$xml_location=Xml' || rm ../lib/help/sp_invert_mrk.hlp >sabcmd to_help.xsl Xml/submission.xml ../lib/help/submission.hlp '$myname=submission.xml' '$xml_location=Xml' || rm ../lib/help/submission.hlp >sabcmd to_help.xsl Xml/set_meny_fields.xml ../lib/help/set_meny_fields.hlp '$myname=set_meny_fields.xml' '$xml_location=Xml' || rm ../lib/help/set_meny_fields.hlp >sabcmd to_help.xsl Xml/unmark_list.xml ../lib/help/unmark_list.hlp '$myname=unmark_list.xml' '$xml_location=Xml' || rm ../lib/help/unmark_list.hlp >sabcmd to_help.xsl Xml/arb_secedit.xml ../lib/help/arb_secedit.hlp '$myname=arb_secedit.xml' '$xml_location=Xml' || rm ../lib/help/arb_secedit.hlp >sabcmd to_help.xsl Xml/mod_field_list.xml ../lib/help/mod_field_list.hlp '$myname=mod_field_list.xml' '$xml_location=Xml' || rm ../lib/help/mod_field_list.hlp >sabcmd to_help.xsl Xml/pa_quick.xml ../lib/help/pa_quick.hlp '$myname=pa_quick.xml' '$xml_location=Xml' || rm ../lib/help/pa_quick.hlp >sabcmd to_help.xsl Xml/visualizeSAI.xml ../lib/help/visualizeSAI.hlp '$myname=visualizeSAI.xml' '$xml_location=Xml' || rm ../lib/help/visualizeSAI.hlp >sabcmd to_help.xsl Xml/write_field_list.xml ../lib/help/write_field_list.hlp '$myname=write_field_list.xml' '$xml_location=Xml' || rm ../lib/help/write_field_list.hlp >sabcmd to_help.xsl Xml/alignment.xml ../lib/help/alignment.hlp '$myname=alignment.xml' '$xml_location=Xml' || rm ../lib/help/alignment.hlp >sabcmd to_help.xsl Xml/gene_mark.xml ../lib/help/gene_mark.hlp '$myname=gene_mark.xml' '$xml_location=Xml' || rm ../lib/help/gene_mark.hlp >sabcmd to_help.xsl Xml/colorize.xml ../lib/help/colorize.hlp '$myname=colorize.xml' '$xml_location=Xml' || rm ../lib/help/colorize.hlp >sabcmd to_help.xsl Xml/consensus_def.xml ../lib/help/consensus_def.hlp '$myname=consensus_def.xml' '$xml_location=Xml' || rm ../lib/help/consensus_def.hlp >sabcmd to_help.xsl Xml/primer.xml ../lib/help/primer.hlp '$myname=primer.xml' '$xml_location=Xml' || rm ../lib/help/primer.hlp >sabcmd to_help.xsl Xml/del_list.xml ../lib/help/del_list.hlp '$myname=del_list.xml' '$xml_location=Xml' || rm ../lib/help/del_list.hlp >sabcmd to_help.xsl Xml/saiProbeHelp.xml ../lib/help/saiProbeHelp.hlp '$myname=saiProbeHelp.xml' '$xml_location=Xml' || rm ../lib/help/saiProbeHelp.hlp >sabcmd to_help.xsl Xml/ebi_ift.xml ../lib/help/ebi_ift.hlp '$myname=ebi_ift.xml' '$xml_location=Xml' || rm ../lib/help/ebi_ift.hlp >sabcmd to_help.xsl Xml/change_security.xml ../lib/help/change_security.hlp '$myname=change_security.xml' '$xml_location=Xml' || rm ../lib/help/change_security.hlp >sabcmd to_help.xsl Xml/sel_spec.xml ../lib/help/sel_spec.hlp '$myname=sel_spec.xml' '$xml_location=Xml' || rm ../lib/help/sel_spec.hlp >sabcmd to_help.xsl Xml/gde.xml ../lib/help/gde.hlp '$myname=gde.xml' '$xml_location=Xml' || rm ../lib/help/gde.hlp >sabcmd to_help.xsl Xml/mode_length.xml ../lib/help/mode_length.hlp '$myname=mode_length.xml' '$xml_location=Xml' || rm ../lib/help/mode_length.hlp >sabcmd to_help.xsl Xml/sec_keys.xml ../lib/help/sec_keys.hlp '$myname=sec_keys.xml' '$xml_location=Xml' || rm ../lib/help/sec_keys.hlp >sabcmd to_help.xsl Xml/gene_extract.xml ../lib/help/gene_extract.hlp '$myname=gene_extract.xml' '$xml_location=Xml' || rm ../lib/help/gene_extract.hlp >sabcmd to_help.xsl Xml/selected.xml ../lib/help/selected.hlp '$myname=selected.xml' '$xml_location=Xml' || rm ../lib/help/selected.hlp >sabcmd to_help.xsl Xml/spa_copy.xml ../lib/help/spa_copy.hlp '$myname=spa_copy.xml' '$xml_location=Xml' || rm ../lib/help/spa_copy.hlp >sabcmd to_help.xsl Xml/rst_phys_zoom.xml ../lib/help/rst_phys_zoom.hlp '$myname=rst_phys_zoom.xml' '$xml_location=Xml' || rm ../lib/help/rst_phys_zoom.hlp >sabcmd to_help.xsl Xml/sp_mrk_all.xml ../lib/help/sp_mrk_all.hlp '$myname=sp_mrk_all.xml' '$xml_location=Xml' || rm ../lib/help/sp_mrk_all.hlp >sabcmd to_help.xsl Xml/man_arb_edit4.xml ../lib/help/man_arb_edit4.hlp '$myname=man_arb_edit4.xml' '$xml_location=Xml' || rm ../lib/help/man_arb_edit4.hlp >sabcmd to_help.xsl Xml/probedesign.xml ../lib/help/probedesign.hlp '$myname=probedesign.xml' '$xml_location=Xml' || rm ../lib/help/probedesign.hlp >sabcmd to_help.xsl Xml/mode_group.xml ../lib/help/mode_group.hlp '$myname=mode_group.xml' '$xml_location=Xml' || rm ../lib/help/mode_group.hlp >sabcmd to_help.xsl Xml/islandhopping.xml ../lib/help/islandhopping.hlp '$myname=islandhopping.xml' '$xml_location=Xml' || rm ../lib/help/islandhopping.hlp >sabcmd to_help.xsl Xml/undo.xml ../lib/help/undo.hlp '$myname=undo.xml' '$xml_location=Xml' || rm ../lib/help/undo.hlp >sabcmd to_help.xsl Xml/missbase.xml ../lib/help/missbase.hlp '$myname=missbase.xml' '$xml_location=Xml' || rm ../lib/help/missbase.hlp >sabcmd to_help.xsl Xml/sel_box.xml ../lib/help/sel_box.hlp '$myname=sel_box.xml' '$xml_location=Xml' || rm ../lib/help/sel_box.hlp >sabcmd to_help.xsl Xml/pfold_props.xml ../lib/help/pfold_props.hlp '$myname=pfold_props.xml' '$xml_location=Xml' || rm ../lib/help/pfold_props.hlp >sabcmd to_help.xsl Xml/gene_search.xml ../lib/help/gene_search.hlp '$myname=gene_search.xml' '$xml_location=Xml' || rm ../lib/help/gene_search.hlp >sabcmd to_help.xsl Xml/quit.xml ../lib/help/quit.hlp '$myname=quit.xml' '$xml_location=Xml' || rm ../lib/help/quit.hlp >sabcmd to_help.xsl Xml/ph_export_markerline.xml ../lib/help/ph_export_markerline.hlp '$myname=ph_export_markerline.xml' '$xml_location=Xml' || rm ../lib/help/ph_export_markerline.hlp >sabcmd to_help.xsl Xml/tgroupall.xml ../lib/help/tgroupall.hlp '$myname=tgroupall.xml' '$xml_location=Xml' || rm ../lib/help/tgroupall.hlp >sabcmd to_help.xsl Xml/mg_extendeds.xml ../lib/help/mg_extendeds.hlp '$myname=mg_extendeds.xml' '$xml_location=Xml' || rm ../lib/help/mg_extendeds.hlp >sabcmd to_help.xsl Xml/scandb.xml ../lib/help/scandb.hlp '$myname=scandb.xml' '$xml_location=Xml' || rm ../lib/help/scandb.hlp >sabcmd to_help.xsl Xml/arb_db.xml ../lib/help/arb_db.hlp '$myname=arb_db.xml' '$xml_location=Xml' || rm ../lib/help/arb_db.hlp >sabcmd to_help.xsl Xml/arb_intro.xml ../lib/help/arb_intro.hlp '$myname=arb_intro.xml' '$xml_location=Xml' || rm ../lib/help/arb_intro.hlp >sabcmd to_help.xsl Xml/arb_gde.xml ../lib/help/arb_gde.hlp '$myname=arb_gde.xml' '$xml_location=Xml' || rm ../lib/help/arb_gde.hlp >sabcmd to_help.xsl Xml/universal_ift.xml ../lib/help/universal_ift.hlp '$myname=universal_ift.xml' '$xml_location=Xml' || rm ../lib/help/universal_ift.hlp >sabcmd to_help.xsl Xml/sp_mrk_tree.xml ../lib/help/sp_mrk_tree.hlp '$myname=sp_mrk_tree.xml' '$xml_location=Xml' || rm ../lib/help/sp_mrk_tree.hlp >sabcmd to_help.xsl Xml/sp_umrk_all.xml ../lib/help/sp_umrk_all.hlp '$myname=sp_umrk_all.xml' '$xml_location=Xml' || rm ../lib/help/sp_umrk_all.hlp >sabcmd to_help.xsl Xml/proteinViewer.xml ../lib/help/proteinViewer.hlp '$myname=proteinViewer.xml' '$xml_location=Xml' || rm ../lib/help/proteinViewer.hlp >sabcmd to_help.xsl Xml/vn_search.xml ../lib/help/vn_search.hlp '$myname=vn_search.xml' '$xml_location=Xml' || rm ../lib/help/vn_search.hlp >sabcmd to_help.xsl Xml/pfold.xml ../lib/help/pfold.hlp '$myname=pfold.xml' '$xml_location=Xml' || rm ../lib/help/pfold.hlp >sabcmd to_help.xsl Xml/secedit_imexport.xml ../lib/help/secedit_imexport.hlp '$myname=secedit_imexport.xml' '$xml_location=Xml' || rm ../lib/help/secedit_imexport.hlp >sabcmd to_help.xsl Xml/color_props_groups.xml ../lib/help/color_props_groups.hlp '$myname=color_props_groups.xml' '$xml_location=Xml' || rm ../lib/help/color_props_groups.hlp >sabcmd to_help.xsl Xml/export_format.xml ../lib/help/export_format.hlp '$myname=export_format.xml' '$xml_location=Xml' || rm ../lib/help/export_format.hlp >sabcmd to_help.xsl Xml/mode_swap.xml ../lib/help/mode_swap.hlp '$myname=mode_swap.xml' '$xml_location=Xml' || rm ../lib/help/mode_swap.hlp >sabcmd to_help.xsl Xml/rna3d_dispBases.xml ../lib/help/rna3d_dispBases.hlp '$myname=rna3d_dispBases.xml' '$xml_location=Xml' || rm ../lib/help/rna3d_dispBases.hlp >sabcmd to_help.xsl Xml/save_def.xml ../lib/help/save_def.hlp '$myname=save_def.xml' '$xml_location=Xml' || rm ../lib/help/save_def.hlp >sabcmd to_help.xsl Xml/ne_new_sequence.xml ../lib/help/ne_new_sequence.hlp '$myname=ne_new_sequence.xml' '$xml_location=Xml' || rm ../lib/help/ne_new_sequence.hlp >sabcmd to_help.xsl Xml/e4_replace.xml ../lib/help/e4_replace.hlp '$myname=e4_replace.xml' '$xml_location=Xml' || rm ../lib/help/e4_replace.hlp >sabcmd to_help.xsl Xml/gene_hide.xml ../lib/help/gene_hide.hlp '$myname=gene_hide.xml' '$xml_location=Xml' || rm ../lib/help/gene_hide.hlp >sabcmd to_help.xsl Xml/optimize.xml ../lib/help/optimize.hlp '$myname=optimize.xml' '$xml_location=Xml' || rm ../lib/help/optimize.hlp >sabcmd to_help.xsl Xml/mode_angle.xml ../lib/help/mode_angle.hlp '$myname=mode_angle.xml' '$xml_location=Xml' || rm ../lib/help/mode_angle.hlp >sabcmd to_help.xsl Xml/sp_rename.xml ../lib/help/sp_rename.hlp '$myname=sp_rename.xml' '$xml_location=Xml' || rm ../lib/help/sp_rename.hlp >sabcmd to_help.xsl Xml/sp_search.xml ../lib/help/sp_search.hlp '$myname=sp_search.xml' '$xml_location=Xml' || rm ../lib/help/sp_search.hlp >sabcmd to_help.xsl Xml/sp_umrk_tree.xml ../lib/help/sp_umrk_tree.hlp '$myname=sp_umrk_tree.xml' '$xml_location=Xml' || rm ../lib/help/sp_umrk_tree.hlp >sabcmd to_help.xsl Xml/sp_sort_phyl.xml ../lib/help/sp_sort_phyl.hlp '$myname=sp_sort_phyl.xml' '$xml_location=Xml' || rm ../lib/help/sp_sort_phyl.hlp >sabcmd to_help.xsl Xml/species.xml ../lib/help/species.hlp '$myname=species.xml' '$xml_location=Xml' || rm ../lib/help/species.hlp >sabcmd to_help.xsl Xml/nt_tree_settings.xml ../lib/help/nt_tree_settings.hlp '$myname=nt_tree_settings.xml' '$xml_location=Xml' || rm ../lib/help/nt_tree_settings.hlp >sabcmd to_help.xsl Xml/nt_props_data.xml ../lib/help/nt_props_data.hlp '$myname=nt_props_data.xml' '$xml_location=Xml' || rm ../lib/help/nt_props_data.hlp >sabcmd to_help.xsl Xml/sec_mode.xml ../lib/help/sec_mode.hlp '$myname=sec_mode.xml' '$xml_location=Xml' || rm ../lib/help/sec_mode.hlp >sabcmd to_help.xsl Xml/namesadmin.xml ../lib/help/namesadmin.hlp '$myname=namesadmin.xml' '$xml_location=Xml' || rm ../lib/help/namesadmin.hlp >sabcmd to_help.xsl Xml/faligner.xml ../lib/help/faligner.hlp '$myname=faligner.xml' '$xml_location=Xml' || rm ../lib/help/faligner.hlp >sabcmd to_help.xsl Xml/mark.xml ../lib/help/mark.hlp '$myname=mark.xml' '$xml_location=Xml' || rm ../lib/help/mark.hlp >sabcmd to_help.xsl Xml/mode_select.xml ../lib/help/mode_select.hlp '$myname=mode_select.xml' '$xml_location=Xml' || rm ../lib/help/mode_select.hlp >sabcmd to_help.xsl Xml/arb_import.xml ../lib/help/arb_import.hlp '$myname=arb_import.xml' '$xml_location=Xml' || rm ../lib/help/arb_import.hlp >sabcmd to_help.xsl Xml/rna3d_dispHelices.xml ../lib/help/rna3d_dispHelices.hlp '$myname=rna3d_dispHelices.xml' '$xml_location=Xml' || rm ../lib/help/rna3d_dispHelices.hlp >sabcmd to_help.xsl Xml/ed4_nds.xml ../lib/help/ed4_nds.hlp '$myname=ed4_nds.xml' '$xml_location=Xml' || rm ../lib/help/ed4_nds.hlp >sabcmd to_help.xsl Xml/no_tree.xml ../lib/help/no_tree.hlp '$myname=no_tree.xml' '$xml_location=Xml' || rm ../lib/help/no_tree.hlp >sabcmd to_help.xsl Xml/fasta_ift.xml ../lib/help/fasta_ift.hlp '$myname=fasta_ift.xml' '$xml_location=Xml' || rm ../lib/help/fasta_ift.hlp >sabcmd to_help.xsl Xml/exec_bug.xml ../lib/help/exec_bug.hlp '$myname=exec_bug.xml' '$xml_location=Xml' || rm ../lib/help/exec_bug.hlp >sabcmd to_help.xsl Xml/pa_optimizer.xml ../lib/help/pa_optimizer.hlp '$myname=pa_optimizer.xml' '$xml_location=Xml' || rm ../lib/help/pa_optimizer.hlp >sabcmd to_help.xsl Xml/result.xml ../lib/help/result.hlp '$myname=result.xml' '$xml_location=Xml' || rm ../lib/help/result.hlp >sabcmd to_help.xsl Xml/phylo.xml ../lib/help/phylo.hlp '$myname=phylo.xml' '$xml_location=Xml' || rm ../lib/help/phylo.hlp >sabcmd to_help.xsl Xml/e4_search.xml ../lib/help/e4_search.hlp '$myname=e4_search.xml' '$xml_location=Xml' || rm ../lib/help/e4_search.hlp >sabcmd to_help.xsl Xml/arb_envar.xml ../lib/help/arb_envar.hlp '$myname=arb_envar.xml' '$xml_location=Xml' || rm ../lib/help/arb_envar.hlp >sabcmd to_help.xsl Xml/multiprobe.xml ../lib/help/multiprobe.hlp '$myname=multiprobe.xml' '$xml_location=Xml' || rm ../lib/help/multiprobe.hlp >sabcmd to_help.xsl Xml/next_neighbours_listed.xml ../lib/help/next_neighbours_listed.hlp '$myname=next_neighbours_listed.xml' '$xml_location=Xml' || rm ../lib/help/next_neighbours_listed.hlp >sabcmd to_help.xsl Xml/align.xml ../lib/help/align.hlp '$myname=align.xml' '$xml_location=Xml' || rm ../lib/help/align.hlp >sabcmd to_help.xsl Xml/dist.xml ../lib/help/dist.hlp '$myname=dist.xml' '$xml_location=Xml' || rm ../lib/help/dist.hlp >sabcmd to_help.xsl Xml/cons_params.xml ../lib/help/cons_params.hlp '$myname=cons_params.xml' '$xml_location=Xml' || rm ../lib/help/cons_params.hlp >sabcmd to_help.xsl Xml/Protection.xml ../lib/help/Protection.hlp '$myname=Protection.xml' '$xml_location=Xml' || rm ../lib/help/Protection.hlp >sabcmd to_help.xsl Xml/ap_stack.xml ../lib/help/ap_stack.hlp '$myname=ap_stack.xml' '$xml_location=Xml' || rm ../lib/help/ap_stack.hlp >sabcmd to_help.xsl Xml/sel_fil.xml ../lib/help/sel_fil.hlp '$myname=sel_fil.xml' '$xml_location=Xml' || rm ../lib/help/sel_fil.hlp >sabcmd to_help.xsl Xml/tags.xml ../lib/help/tags.hlp '$myname=tags.xml' '$xml_location=Xml' || rm ../lib/help/tags.hlp >sabcmd to_help.xsl Xml/probedesignresult.xml ../lib/help/probedesignresult.hlp '$myname=probedesignresult.xml' '$xml_location=Xml' || rm ../lib/help/probedesignresult.hlp >sabcmd to_help.xsl Xml/prompt/format_alignments.xml ../lib/help/prompt/format_alignments.hlp '$myname=prompt/format_alignments.xml' '$xml_location=Xml' || rm ../lib/help/prompt/format_alignments.hlp >make[5]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/HELP_SOURCE' >make ../lib/help/FORM.hlp >make[5]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/HELP_SOURCE' >cp -p oldhelp/FORM.hlp ../lib/help/FORM.hlp >make[5]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/HELP_SOURCE' >--------------------------------------------------- >------------ Converting xml 2 html: >make html >make[5]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/HELP_SOURCE' >sabcmd to_html.xsl Xml/arb.xml ../lib/help_html/arb.html '$myname=arb.xml' '$xml_location=Xml' || (rm ../lib/help_html/arb.html && test -f ../lib/help_html/arb.html) >sabcmd to_html.xsl Xml/agde_protml_sub_protml_doc.xml ../lib/help_html/agde_protml_sub_protml_doc.html '$myname=agde_protml_sub_protml_doc.xml' '$xml_location=Xml' || (rm ../lib/help_html/agde_protml_sub_protml_doc.html && test -f ../lib/help_html/agde_protml_sub_protml_doc.html) >sabcmd to_html.xsl Xml/changes.xml ../lib/help_html/changes.html '$myname=changes.xml' '$xml_location=Xml' || (rm ../lib/help_html/changes.html && test -f ../lib/help_html/changes.html) >sabcmd to_html.xsl Xml/agde_protml_sub_protml_cli_doc.xml ../lib/help_html/agde_protml_sub_protml_cli_doc.html '$myname=agde_protml_sub_protml_cli_doc.xml' '$xml_location=Xml' || (rm ../lib/help_html/agde_protml_sub_protml_cli_doc.html && test -f ../lib/help_html/agde_protml_sub_protml_cli_doc.html) >sabcmd to_html.xsl Xml/agde_DNAml_rates.xml ../lib/help_html/agde_DNAml_rates.html '$myname=agde_DNAml_rates.xml' '$xml_location=Xml' || (rm ../lib/help_html/agde_DNAml_rates.html && test -f ../lib/help_html/agde_DNAml_rates.html) >sabcmd to_html.xsl Xml/agde_dnapars.xml ../lib/help_html/agde_dnapars.html '$myname=agde_dnapars.xml' '$xml_location=Xml' || (rm ../lib/help_html/agde_dnapars.html && test -f ../lib/help_html/agde_dnapars.html) >sabcmd to_html.xsl Xml/agde_proml.xml ../lib/help_html/agde_proml.html '$myname=agde_proml.xml' '$xml_location=Xml' || (rm ../lib/help_html/agde_proml.html && test -f ../lib/help_html/agde_proml.html) >sabcmd to_html.xsl Xml/agde_dnaml_sub_AxML_doc.xml ../lib/help_html/agde_dnaml_sub_AxML_doc.html '$myname=agde_dnaml_sub_AxML_doc.xml' '$xml_location=Xml' || (rm ../lib/help_html/agde_dnaml_sub_AxML_doc.html && test -f ../lib/help_html/agde_dnaml_sub_AxML_doc.html) >sabcmd to_html.xsl Xml/agde_dnaml_sub_fastDNAml_doc.xml ../lib/help_html/agde_dnaml_sub_fastDNAml_doc.html '$myname=agde_dnaml_sub_fastDNAml_doc.xml' '$xml_location=Xml' || (rm ../lib/help_html/agde_dnaml_sub_fastDNAml_doc.html && test -f ../lib/help_html/agde_dnaml_sub_fastDNAml_doc.html) >sabcmd to_html.xsl Xml/agde_phylip_distance_sub_neighbor_doc.xml ../lib/help_html/agde_phylip_distance_sub_neighbor_doc.html '$myname=agde_phylip_distance_sub_neighbor_doc.xml' '$xml_location=Xml' || (rm ../lib/help_html/agde_phylip_distance_sub_neighbor_doc.html && test -f ../lib/help_html/agde_phylip_distance_sub_neighbor_doc.html) >sabcmd to_html.xsl Xml/agde_lsadt.xml ../lib/help_html/agde_lsadt.html '$myname=agde_lsadt.xml' '$xml_location=Xml' || (rm ../lib/help_html/agde_lsadt.html && test -f ../lib/help_html/agde_lsadt.html) >sabcmd to_html.xsl Xml/agde_readseq_sub_Formats.xml ../lib/help_html/agde_readseq_sub_Formats.html '$myname=agde_readseq_sub_Formats.xml' '$xml_location=Xml' || (rm ../lib/help_html/agde_readseq_sub_Formats.html && test -f ../lib/help_html/agde_readseq_sub_Formats.html) >sabcmd to_html.xsl Xml/agde_protml.xml ../lib/help_html/agde_protml.html '$myname=agde_protml.xml' '$xml_location=Xml' || (rm ../lib/help_html/agde_protml.html && test -f ../lib/help_html/agde_protml.html) >sabcmd to_html.xsl Xml/agde_treepuzzle.xml ../lib/help_html/agde_treepuzzle.html '$myname=agde_treepuzzle.xml' '$xml_location=Xml' || (rm ../lib/help_html/agde_treepuzzle.html && test -f ../lib/help_html/agde_treepuzzle.html) >sabcmd to_html.xsl Xml/agde_clustalw_sub_clustalw_help.xml ../lib/help_html/agde_clustalw_sub_clustalw_help.html '$myname=agde_clustalw_sub_clustalw_help.xml' '$xml_location=Xml' || (rm ../lib/help_html/agde_clustalw_sub_clustalw_help.html && test -f ../lib/help_html/agde_clustalw_sub_clustalw_help.html) >sabcmd to_html.xsl Xml/agde_clustalw_sub_clustalw_doc.xml ../lib/help_html/agde_clustalw_sub_clustalw_doc.html '$myname=agde_clustalw_sub_clustalw_doc.xml' '$xml_location=Xml' || (rm ../lib/help_html/agde_clustalw_sub_clustalw_doc.html && test -f ../lib/help_html/agde_clustalw_sub_clustalw_doc.html) >sabcmd to_html.xsl Xml/agde.xml ../lib/help_html/agde.html '$myname=agde.xml' '$xml_location=Xml' || (rm ../lib/help_html/agde.html && test -f ../lib/help_html/agde.html) >sabcmd to_html.xsl Xml/agde_CAP2.xml ../lib/help_html/agde_CAP2.html '$myname=agde_CAP2.xml' '$xml_location=Xml' || (rm ../lib/help_html/agde_CAP2.html && test -f ../lib/help_html/agde_CAP2.html) >sabcmd to_html.xsl Xml/agde_phylip_distance_sub_fitch_doc.xml ../lib/help_html/agde_phylip_distance_sub_fitch_doc.html '$myname=agde_phylip_distance_sub_fitch_doc.xml' '$xml_location=Xml' || (rm ../lib/help_html/agde_phylip_distance_sub_fitch_doc.html && test -f ../lib/help_html/agde_phylip_distance_sub_fitch_doc.html) >sabcmd to_html.xsl Xml/agde_readseq.xml ../lib/help_html/agde_readseq.html '$myname=agde_readseq.xml' '$xml_location=Xml' || (rm ../lib/help_html/agde_readseq.html && test -f ../lib/help_html/agde_readseq.html) >sabcmd to_html.xsl Xml/agde_protpars.xml ../lib/help_html/agde_protpars.html '$myname=agde_protpars.xml' '$xml_location=Xml' || (rm ../lib/help_html/agde_protpars.html && test -f ../lib/help_html/agde_protpars.html) >sabcmd to_html.xsl Xml/agde_phylip_distance.xml ../lib/help_html/agde_phylip_distance.html '$myname=agde_phylip_distance.xml' '$xml_location=Xml' || (rm ../lib/help_html/agde_phylip_distance.html && test -f ../lib/help_html/agde_phylip_distance.html) >sabcmd to_html.xsl Xml/copyright.xml ../lib/help_html/copyright.html '$myname=copyright.xml' '$xml_location=Xml' || (rm ../lib/help_html/copyright.html && test -f ../lib/help_html/copyright.html) >sabcmd to_html.xsl Xml/agde_raxml.xml ../lib/help_html/agde_raxml.html '$myname=agde_raxml.xml' '$xml_location=Xml' || (rm ../lib/help_html/agde_raxml.html && test -f ../lib/help_html/agde_raxml.html) >sabcmd to_html.xsl Xml/agde_phyml.xml ../lib/help_html/agde_phyml.html '$myname=agde_phyml.xml' '$xml_location=Xml' || (rm ../lib/help_html/agde_phyml.html && test -f ../lib/help_html/agde_phyml.html) >sabcmd to_html.xsl Xml/agde_readseq_sub_Readseq_help.xml ../lib/help_html/agde_readseq_sub_Readseq_help.html '$myname=agde_readseq_sub_Readseq_help.xml' '$xml_location=Xml' || (rm ../lib/help_html/agde_readseq_sub_Readseq_help.html && test -f ../lib/help_html/agde_readseq_sub_Readseq_help.html) >sabcmd to_html.xsl Xml/agde_phylip_distance_sub_dnadist_doc.xml ../lib/help_html/agde_phylip_distance_sub_dnadist_doc.html '$myname=agde_phylip_distance_sub_dnadist_doc.xml' '$xml_location=Xml' || (rm ../lib/help_html/agde_phylip_distance_sub_dnadist_doc.html && test -f ../lib/help_html/agde_phylip_distance_sub_dnadist_doc.html) >sabcmd to_html.xsl Xml/agde_dnaml.xml ../lib/help_html/agde_dnaml.html '$myname=agde_dnaml.xml' '$xml_location=Xml' || (rm ../lib/help_html/agde_dnaml.html && test -f ../lib/help_html/agde_dnaml.html) >sabcmd to_html.xsl Xml/agde_phylip_distance_sub_kitsch_doc.xml ../lib/help_html/agde_phylip_distance_sub_kitsch_doc.html '$myname=agde_phylip_distance_sub_kitsch_doc.xml' '$xml_location=Xml' || (rm ../lib/help_html/agde_phylip_distance_sub_kitsch_doc.html && test -f ../lib/help_html/agde_phylip_distance_sub_kitsch_doc.html) >sabcmd to_html.xsl Xml/agde_phylip_distance_sub_protdist_doc.xml ../lib/help_html/agde_phylip_distance_sub_protdist_doc.html '$myname=agde_phylip_distance_sub_protdist_doc.xml' '$xml_location=Xml' || (rm ../lib/help_html/agde_phylip_distance_sub_protdist_doc.html && test -f ../lib/help_html/agde_phylip_distance_sub_protdist_doc.html) >sabcmd to_html.xsl Xml/agde_readseq_sub_Readme.xml ../lib/help_html/agde_readseq_sub_Readme.html '$myname=agde_readseq_sub_Readme.xml' '$xml_location=Xml' || (rm ../lib/help_html/agde_readseq_sub_Readme.html && test -f ../lib/help_html/agde_readseq_sub_Readme.html) >sabcmd to_html.xsl Xml/agde_clustalw.xml ../lib/help_html/agde_clustalw.html '$myname=agde_clustalw.xml' '$xml_location=Xml' || (rm ../lib/help_html/agde_clustalw.html && test -f ../lib/help_html/agde_clustalw.html) >sabcmd to_html.xsl Xml/checkfield.xml ../lib/help_html/checkfield.html '$myname=checkfield.xml' '$xml_location=Xml' || (rm ../lib/help_html/checkfield.html && test -f ../lib/help_html/checkfield.html) >sabcmd to_html.xsl Xml/set_protection.xml ../lib/help_html/set_protection.html '$myname=set_protection.xml' '$xml_location=Xml' || (rm ../lib/help_html/set_protection.html && test -f ../lib/help_html/set_protection.html) >sabcmd to_html.xsl Xml/FAQS.xml ../lib/help_html/FAQS.html '$myname=FAQS.xml' '$xml_location=Xml' || (rm ../lib/help_html/FAQS.html && test -f ../lib/help_html/FAQS.html) >sabcmd to_html.xsl Xml/pa_partial.xml ../lib/help_html/pa_partial.html '$myname=pa_partial.xml' '$xml_location=Xml' || (rm ../lib/help_html/pa_partial.html && test -f ../lib/help_html/pa_partial.html) >sabcmd to_html.xsl Xml/mode_reset.xml ../lib/help_html/mode_reset.html '$myname=mode_reset.xml' '$xml_location=Xml' || (rm ../lib/help_html/mode_reset.html && test -f ../lib/help_html/mode_reset.html) >sabcmd to_html.xsl Xml/gde_ift.xml ../lib/help_html/gde_ift.html '$myname=gde_ift.xml' '$xml_location=Xml' || (rm ../lib/help_html/gde_ift.html && test -f ../lib/help_html/gde_ift.html) >sabcmd to_html.xsl Xml/tbl_boot2len.xml ../lib/help_html/tbl_boot2len.html '$myname=tbl_boot2len.xml' '$xml_location=Xml' || (rm ../lib/help_html/tbl_boot2len.html && test -f ../lib/help_html/tbl_boot2len.html) >sabcmd to_html.xsl Xml/treeadm.xml ../lib/help_html/treeadm.html '$myname=treeadm.xml' '$xml_location=Xml' || (rm ../lib/help_html/treeadm.html && test -f ../lib/help_html/treeadm.html) >sabcmd to_html.xsl Xml/rna3d_mapSeqData.xml ../lib/help_html/rna3d_mapSeqData.html '$myname=rna3d_mapSeqData.xml' '$xml_location=Xml' || (rm ../lib/help_html/rna3d_mapSeqData.html && test -f ../lib/help_html/rna3d_mapSeqData.html) >sabcmd to_html.xsl Xml/props_frame.xml ../lib/help_html/props_frame.html '$myname=props_frame.xml' '$xml_location=Xml' || (rm ../lib/help_html/props_frame.html && test -f ../lib/help_html/props_frame.html) >sabcmd to_html.xsl Xml/mode_set_root.xml ../lib/help_html/mode_set_root.html '$myname=mode_set_root.xml' '$xml_location=Xml' || (rm ../lib/help_html/mode_set_root.html && test -f ../lib/help_html/mode_set_root.html) >sabcmd to_html.xsl Xml/seq_quality.xml ../lib/help_html/seq_quality.html '$myname=seq_quality.xml' '$xml_location=Xml' || (rm ../lib/help_html/seq_quality.html && test -f ../lib/help_html/seq_quality.html) >sabcmd to_html.xsl Xml/arb_export_nds.xml ../lib/help_html/arb_export_nds.html '$myname=arb_export_nds.xml' '$xml_location=Xml' || (rm ../lib/help_html/arb_export_nds.html && test -f ../lib/help_html/arb_export_nds.html) >sabcmd to_html.xsl Xml/gene_options.xml ../lib/help_html/gene_options.html '$myname=gene_options.xml' '$xml_location=Xml' || (rm ../lib/help_html/gene_options.html && test -f ../lib/help_html/gene_options.html) >sabcmd to_html.xsl Xml/tr_jump.xml ../lib/help_html/tr_jump.html '$myname=tr_jump.xml' '$xml_location=Xml' || (rm ../lib/help_html/tr_jump.html && test -f ../lib/help_html/tr_jump.html) >sabcmd to_html.xsl Xml/mp_params.xml ../lib/help_html/mp_params.html '$myname=mp_params.xml' '$xml_location=Xml' || (rm ../lib/help_html/mp_params.html && test -f ../lib/help_html/mp_params.html) >sabcmd to_html.xsl Xml/gene_species.xml ../lib/help_html/gene_species.html '$myname=gene_species.xml' '$xml_location=Xml' || (rm ../lib/help_html/gene_species.html && test -f ../lib/help_html/gene_species.html) >sabcmd to_html.xsl Xml/glossary.xml ../lib/help_html/glossary.html '$myname=glossary.xml' '$xml_location=Xml' || (rm ../lib/help_html/glossary.html && test -f ../lib/help_html/glossary.html) >sabcmd to_html.xsl Xml/vn_delete.xml ../lib/help_html/vn_delete.html '$myname=vn_delete.xml' '$xml_location=Xml' || (rm ../lib/help_html/vn_delete.html && test -f ../lib/help_html/vn_delete.html) >sabcmd to_html.xsl Xml/exportcursor.xml ../lib/help_html/exportcursor.html '$myname=exportcursor.xml' '$xml_location=Xml' || (rm ../lib/help_html/exportcursor.html && test -f ../lib/help_html/exportcursor.html) >sabcmd to_html.xsl Xml/tbl_reset.xml ../lib/help_html/tbl_reset.html '$myname=tbl_reset.xml' '$xml_location=Xml' || (rm ../lib/help_html/tbl_reset.html && test -f ../lib/help_html/tbl_reset.html) >sabcmd to_html.xsl Xml/markcolor.xml ../lib/help_html/markcolor.html '$myname=markcolor.xml' '$xml_location=Xml' || (rm ../lib/help_html/markcolor.html && test -f ../lib/help_html/markcolor.html) >sabcmd to_html.xsl Xml/mode.xml ../lib/help_html/mode.html '$myname=mode.xml' '$xml_location=Xml' || (rm ../lib/help_html/mode.html && test -f ../lib/help_html/mode.html) >sabcmd to_html.xsl Xml/ne_pretty.xml ../lib/help_html/ne_pretty.html '$myname=ne_pretty.xml' '$xml_location=Xml' || (rm ../lib/help_html/ne_pretty.html && test -f ../lib/help_html/ne_pretty.html) >sabcmd to_html.xsl Xml/neprops.xml ../lib/help_html/neprops.html '$myname=neprops.xml' '$xml_location=Xml' || (rm ../lib/help_html/neprops.html && test -f ../lib/help_html/neprops.html) >sabcmd to_html.xsl Xml/macro.xml ../lib/help_html/macro.html '$myname=macro.xml' '$xml_location=Xml' || (rm ../lib/help_html/macro.html && test -f ../lib/help_html/macro.html) >sabcmd to_html.xsl Xml/tr_type_irs.xml ../lib/help_html/tr_type_irs.html '$myname=tr_type_irs.xml' '$xml_location=Xml' || (rm ../lib/help_html/tr_type_irs.html && test -f ../lib/help_html/tr_type_irs.html) >sabcmd to_html.xsl Xml/help.xml ../lib/help_html/help.html '$myname=help.xml' '$xml_location=Xml' || (rm ../lib/help_html/help.html && test -f ../lib/help_html/help.html) >sabcmd to_html.xsl Xml/tbl_justify.xml ../lib/help_html/tbl_justify.html '$myname=tbl_justify.xml' '$xml_location=Xml' || (rm ../lib/help_html/tbl_justify.html && test -f ../lib/help_html/tbl_justify.html) >sabcmd to_html.xsl Xml/merge_species.xml ../lib/help_html/merge_species.html '$myname=merge_species.xml' '$xml_location=Xml' || (rm ../lib/help_html/merge_species.html && test -f ../lib/help_html/merge_species.html) >sabcmd to_html.xsl Xml/next_neighbours.xml ../lib/help_html/next_neighbours.html '$myname=next_neighbours.xml' '$xml_location=Xml' || (rm ../lib/help_html/next_neighbours.html && test -f ../lib/help_html/next_neighbours.html) >sabcmd to_html.xsl Xml/probe_param.xml ../lib/help_html/probe_param.html '$myname=probe_param.xml' '$xml_location=Xml' || (rm ../lib/help_html/probe_param.html && test -f ../lib/help_html/probe_param.html) >sabcmd to_html.xsl Xml/rna3d_dispMolecule.xml ../lib/help_html/rna3d_dispMolecule.html '$myname=rna3d_dispMolecule.xml' '$xml_location=Xml' || (rm ../lib/help_html/rna3d_dispMolecule.html && test -f ../lib/help_html/rna3d_dispMolecule.html) >sabcmd to_html.xsl Xml/next_neighbours_common.xml ../lib/help_html/next_neighbours_common.html '$myname=next_neighbours_common.xml' '$xml_location=Xml' || (rm ../lib/help_html/next_neighbours_common.html && test -f ../lib/help_html/next_neighbours_common.html) >sabcmd to_html.xsl Xml/mg_species.xml ../lib/help_html/mg_species.html '$myname=mg_species.xml' '$xml_location=Xml' || (rm ../lib/help_html/mg_species.html && test -f ../lib/help_html/mg_species.html) >sabcmd to_html.xsl Xml/importift.xml ../lib/help_html/importift.html '$myname=importift.xml' '$xml_location=Xml' || (rm ../lib/help_html/importift.html && test -f ../lib/help_html/importift.html) >sabcmd to_html.xsl Xml/spaf_scandb.xml ../lib/help_html/spaf_scandb.html '$myname=spaf_scandb.xml' '$xml_location=Xml' || (rm ../lib/help_html/spaf_scandb.html && test -f ../lib/help_html/spaf_scandb.html) >sabcmd to_html.xsl Xml/user_matrix.xml ../lib/help_html/user_matrix.html '$myname=user_matrix.xml' '$xml_location=Xml' || (rm ../lib/help_html/user_matrix.html && test -f ../lib/help_html/user_matrix.html) >sabcmd to_html.xsl Xml/mode_rotate.xml ../lib/help_html/mode_rotate.html '$myname=mode_rotate.xml' '$xml_location=Xml' || (rm ../lib/help_html/mode_rotate.html && test -f ../lib/help_html/mode_rotate.html) >sabcmd to_html.xsl Xml/neprops_data.xml ../lib/help_html/neprops_data.html '$myname=neprops_data.xml' '$xml_location=Xml' || (rm ../lib/help_html/neprops_data.html && test -f ../lib/help_html/neprops_data.html) >sabcmd to_html.xsl Xml/ad_align.xml ../lib/help_html/ad_align.html '$myname=ad_align.xml' '$xml_location=Xml' || (rm ../lib/help_html/ad_align.html && test -f ../lib/help_html/ad_align.html) >sabcmd to_html.xsl Xml/arb_edit4.xml ../lib/help_html/arb_edit4.html '$myname=arb_edit4.xml' '$xml_location=Xml' || (rm ../lib/help_html/arb_edit4.html && test -f ../lib/help_html/arb_edit4.html) >sabcmd to_html.xsl Xml/vn_import.xml ../lib/help_html/vn_import.html '$myname=vn_import.xml' '$xml_location=Xml' || (rm ../lib/help_html/vn_import.html && test -f ../lib/help_html/vn_import.html) >sabcmd to_html.xsl Xml/consensus.xml ../lib/help_html/consensus.html '$myname=consensus.xml' '$xml_location=Xml' || (rm ../lib/help_html/consensus.html && test -f ../lib/help_html/consensus.html) >sabcmd to_html.xsl Xml/sp_del_mrkd.xml ../lib/help_html/sp_del_mrkd.html '$myname=sp_del_mrkd.xml' '$xml_location=Xml' || (rm ../lib/help_html/sp_del_mrkd.html && test -f ../lib/help_html/sp_del_mrkd.html) >sabcmd to_html.xsl Xml/probematch.xml ../lib/help_html/probematch.html '$myname=probematch.xml' '$xml_location=Xml' || (rm ../lib/help_html/probematch.html && test -f ../lib/help_html/probematch.html) >sabcmd to_html.xsl Xml/e4_block.xml ../lib/help_html/e4_block.html '$myname=e4_block.xml' '$xml_location=Xml' || (rm ../lib/help_html/e4_block.html && test -f ../lib/help_html/e4_block.html) >sabcmd to_html.xsl Xml/input_mask.xml ../lib/help_html/input_mask.html '$myname=input_mask.xml' '$xml_location=Xml' || (rm ../lib/help_html/input_mask.html && test -f ../lib/help_html/input_mask.html) >sabcmd to_html.xsl Xml/arb_pars_init.xml ../lib/help_html/arb_pars_init.html '$myname=arb_pars_init.xml' '$xml_location=Xml' || (rm ../lib/help_html/arb_pars_init.html && test -f ../lib/help_html/arb_pars_init.html) >sabcmd to_html.xsl Xml/commands.xml ../lib/help_html/commands.html '$myname=commands.xml' '$xml_location=Xml' || (rm ../lib/help_html/commands.html && test -f ../lib/help_html/commands.html) >sabcmd to_html.xsl Xml/mg_preserve.xml ../lib/help_html/mg_preserve.html '$myname=mg_preserve.xml' '$xml_location=Xml' || (rm ../lib/help_html/mg_preserve.html && test -f ../lib/help_html/mg_preserve.html) >sabcmd to_html.xsl Xml/pd_spec_param.xml ../lib/help_html/pd_spec_param.html '$myname=pd_spec_param.xml' '$xml_location=Xml' || (rm ../lib/help_html/pd_spec_param.html && test -f ../lib/help_html/pd_spec_param.html) >sabcmd to_html.xsl Xml/tree2prt.xml ../lib/help_html/tree2prt.html '$myname=tree2prt.xml' '$xml_location=Xml' || (rm ../lib/help_html/tree2prt.html && test -f ../lib/help_html/tree2prt.html) >sabcmd to_html.xsl Xml/primer_new.xml ../lib/help_html/primer_new.html '$myname=primer_new.xml' '$xml_location=Xml' || (rm ../lib/help_html/primer_new.html && test -f ../lib/help_html/primer_new.html) >sabcmd to_html.xsl Xml/pa_bootstrap.xml ../lib/help_html/pa_bootstrap.html '$myname=pa_bootstrap.xml' '$xml_location=Xml' || (rm ../lib/help_html/pa_bootstrap.html && test -f ../lib/help_html/pa_bootstrap.html) >sabcmd to_html.xsl Xml/st_ml.xml ../lib/help_html/st_ml.html '$myname=st_ml.xml' '$xml_location=Xml' || (rm ../lib/help_html/st_ml.html && test -f ../lib/help_html/st_ml.html) >sabcmd to_html.xsl Xml/sp_info.xml ../lib/help_html/sp_info.html '$myname=sp_info.xml' '$xml_location=Xml' || (rm ../lib/help_html/sp_info.html && test -f ../lib/help_html/sp_info.html) >sabcmd to_html.xsl Xml/e4_options.xml ../lib/help_html/e4_options.html '$myname=e4_options.xml' '$xml_location=Xml' || (rm ../lib/help_html/e4_options.html && test -f ../lib/help_html/e4_options.html) >sabcmd to_html.xsl Xml/tgroupcolor.xml ../lib/help_html/tgroupcolor.html '$myname=tgroupcolor.xml' '$xml_location=Xml' || (rm ../lib/help_html/tgroupcolor.html && test -f ../lib/help_html/tgroupcolor.html) >sabcmd to_html.xsl Xml/tkeep_mrkd.xml ../lib/help_html/tkeep_mrkd.html '$myname=tkeep_mrkd.xml' '$xml_location=Xml' || (rm ../lib/help_html/tkeep_mrkd.html && test -f ../lib/help_html/tkeep_mrkd.html) >sabcmd to_html.xsl Xml/dewachter_ift.xml ../lib/help_html/dewachter_ift.html '$myname=dewachter_ift.xml' '$xml_location=Xml' || (rm ../lib/help_html/dewachter_ift.html && test -f ../lib/help_html/dewachter_ift.html) >sabcmd to_html.xsl Xml/ne_compl.xml ../lib/help_html/ne_compl.html '$myname=ne_compl.xml' '$xml_location=Xml' || (rm ../lib/help_html/ne_compl.html && test -f ../lib/help_html/ne_compl.html) >sabcmd to_html.xsl Xml/iupac-codes.xml ../lib/help_html/iupac-codes.html '$myname=iupac-codes.xml' '$xml_location=Xml' || (rm ../lib/help_html/iupac-codes.html && test -f ../lib/help_html/iupac-codes.html) >sabcmd to_html.xsl Xml/awt_csp.xml ../lib/help_html/awt_csp.html '$myname=awt_csp.xml' '$xml_location=Xml' || (rm ../lib/help_html/awt_csp.html && test -f ../lib/help_html/awt_csp.html) >sabcmd to_html.xsl Xml/gene_info.xml ../lib/help_html/gene_info.html '$myname=gene_info.xml' '$xml_location=Xml' || (rm ../lib/help_html/gene_info.html && test -f ../lib/help_html/gene_info.html) >sabcmd to_html.xsl Xml/sv_def.xml ../lib/help_html/sv_def.html '$myname=sv_def.xml' '$xml_location=Xml' || (rm ../lib/help_html/sv_def.html && test -f ../lib/help_html/sv_def.html) >sabcmd to_html.xsl Xml/ad_extended.xml ../lib/help_html/ad_extended.html '$myname=ad_extended.xml' '$xml_location=Xml' || (rm ../lib/help_html/ad_extended.html && test -f ../lib/help_html/ad_extended.html) >sabcmd to_html.xsl Xml/extended.xml ../lib/help_html/extended.html '$myname=extended.xml' '$xml_location=Xml' || (rm ../lib/help_html/extended.html && test -f ../lib/help_html/extended.html) >sabcmd to_html.xsl Xml/mode_www.xml ../lib/help_html/mode_www.html '$myname=mode_www.xml' '$xml_location=Xml' || (rm ../lib/help_html/mode_www.html && test -f ../lib/help_html/mode_www.html) >sabcmd to_html.xsl Xml/set_color_of_listed.xml ../lib/help_html/set_color_of_listed.html '$myname=set_color_of_listed.xml' '$xml_location=Xml' || (rm ../lib/help_html/set_color_of_listed.html && test -f ../lib/help_html/set_color_of_listed.html) >sabcmd to_html.xsl Xml/mode_kernlin.xml ../lib/help_html/mode_kernlin.html '$myname=mode_kernlin.xml' '$xml_location=Xml' || (rm ../lib/help_html/mode_kernlin.html && test -f ../lib/help_html/mode_kernlin.html) >sabcmd to_html.xsl Xml/sec_main.xml ../lib/help_html/sec_main.html '$myname=sec_main.xml' '$xml_location=Xml' || (rm ../lib/help_html/sec_main.html && test -f ../lib/help_html/sec_main.html) >sabcmd to_html.xsl Xml/arb_merge.xml ../lib/help_html/arb_merge.html '$myname=arb_merge.xml' '$xml_location=Xml' || (rm ../lib/help_html/arb_merge.html && test -f ../lib/help_html/arb_merge.html) >sabcmd to_html.xsl Xml/ne_copy_sequence.xml ../lib/help_html/ne_copy_sequence.html '$myname=ne_copy_sequence.xml' '$xml_location=Xml' || (rm ../lib/help_html/ne_copy_sequence.html && test -f ../lib/help_html/ne_copy_sequence.html) >sabcmd to_html.xsl Xml/pa_quick_sel.xml ../lib/help_html/pa_quick_sel.html '$myname=pa_quick_sel.xml' '$xml_location=Xml' || (rm ../lib/help_html/pa_quick_sel.html && test -f ../lib/help_html/pa_quick_sel.html) >sabcmd to_html.xsl Xml/nekey_map.xml ../lib/help_html/nekey_map.html '$myname=nekey_map.xml' '$xml_location=Xml' || (rm ../lib/help_html/nekey_map.html && test -f ../lib/help_html/nekey_map.html) >sabcmd to_html.xsl Xml/spaf_convert.xml ../lib/help_html/spaf_convert.html '$myname=spaf_convert.xml' '$xml_location=Xml' || (rm ../lib/help_html/spaf_convert.html && test -f ../lib/help_html/spaf_convert.html) >sabcmd to_html.xsl Xml/rename.xml ../lib/help_html/rename.html '$myname=rename.xml' '$xml_location=Xml' || (rm ../lib/help_html/rename.html && test -f ../lib/help_html/rename.html) >sabcmd to_html.xsl Xml/realign_dna.xml ../lib/help_html/realign_dna.html '$myname=realign_dna.xml' '$xml_location=Xml' || (rm ../lib/help_html/realign_dna.html && test -f ../lib/help_html/realign_dna.html) >sabcmd to_html.xsl Xml/tgroupnmrkd.xml ../lib/help_html/tgroupnmrkd.html '$myname=tgroupnmrkd.xml' '$xml_location=Xml' || (rm ../lib/help_html/tgroupnmrkd.html && test -f ../lib/help_html/tgroupnmrkd.html) >sabcmd to_html.xsl Xml/ae2_ift.xml ../lib/help_html/ae2_ift.html '$myname=ae2_ift.xml' '$xml_location=Xml' || (rm ../lib/help_html/ae2_ift.html && test -f ../lib/help_html/ae2_ift.html) >sabcmd to_html.xsl Xml/spaf_delete.xml ../lib/help_html/spaf_delete.html '$myname=spaf_delete.xml' '$xml_location=Xml' || (rm ../lib/help_html/spaf_delete.html && test -f ../lib/help_html/spaf_delete.html) >sabcmd to_html.xsl Xml/tungroupall.xml ../lib/help_html/tungroupall.html '$myname=tungroupall.xml' '$xml_location=Xml' || (rm ../lib/help_html/tungroupall.html && test -f ../lib/help_html/tungroupall.html) >sabcmd to_html.xsl Xml/e4.xml ../lib/help_html/e4.html '$myname=e4.xml' '$xml_location=Xml' || (rm ../lib/help_html/e4.html && test -f ../lib/help_html/e4.html) >sabcmd to_html.xsl Xml/nt_align_select.xml ../lib/help_html/nt_align_select.html '$myname=nt_align_select.xml' '$xml_location=Xml' || (rm ../lib/help_html/nt_align_select.html && test -f ../lib/help_html/nt_align_select.html) >sabcmd to_html.xsl Xml/ecoliref.xml ../lib/help_html/ecoliref.html '$myname=ecoliref.xml' '$xml_location=Xml' || (rm ../lib/help_html/ecoliref.html && test -f ../lib/help_html/ecoliref.html) >sabcmd to_html.xsl Xml/track_ali_changes.xml ../lib/help_html/track_ali_changes.html '$myname=track_ali_changes.xml' '$xml_location=Xml' || (rm ../lib/help_html/track_ali_changes.html && test -f ../lib/help_html/track_ali_changes.html) >sabcmd to_html.xsl Xml/mg_trees.xml ../lib/help_html/mg_trees.html '$myname=mg_trees.xml' '$xml_location=Xml' || (rm ../lib/help_html/mg_trees.html && test -f ../lib/help_html/mg_trees.html) >sabcmd to_html.xsl Xml/tbl_scale.xml ../lib/help_html/tbl_scale.html '$myname=tbl_scale.xml' '$xml_location=Xml' || (rm ../lib/help_html/tbl_scale.html && test -f ../lib/help_html/tbl_scale.html) >sabcmd to_html.xsl Xml/mg_configs.xml ../lib/help_html/mg_configs.html '$myname=mg_configs.xml' '$xml_location=Xml' || (rm ../lib/help_html/mg_configs.html && test -f ../lib/help_html/mg_configs.html) >sabcmd to_html.xsl Xml/tree2file.xml ../lib/help_html/tree2file.html '$myname=tree2file.xml' '$xml_location=Xml' || (rm ../lib/help_html/tree2file.html && test -f ../lib/help_html/tree2file.html) >sabcmd to_html.xsl Xml/gene_species_field_transfer.xml ../lib/help_html/gene_species_field_transfer.html '$myname=gene_species_field_transfer.xml' '$xml_location=Xml' || (rm ../lib/help_html/gene_species_field_transfer.html && test -f ../lib/help_html/gene_species_field_transfer.html) >sabcmd to_html.xsl Xml/manual.xml ../lib/help_html/manual.html '$myname=manual.xml' '$xml_location=Xml' || (rm ../lib/help_html/manual.html && test -f ../lib/help_html/manual.html) >sabcmd to_html.xsl Xml/multiproberesults.xml ../lib/help_html/multiproberesults.html '$myname=multiproberesults.xml' '$xml_location=Xml' || (rm ../lib/help_html/multiproberesults.html && test -f ../lib/help_html/multiproberesults.html) >sabcmd to_html.xsl Xml/rst_log_zoom.xml ../lib/help_html/rst_log_zoom.html '$myname=rst_log_zoom.xml' '$xml_location=Xml' || (rm ../lib/help_html/rst_log_zoom.html && test -f ../lib/help_html/rst_log_zoom.html) >sabcmd to_html.xsl Xml/spaf_reorder.xml ../lib/help_html/spaf_reorder.html '$myname=spaf_reorder.xml' '$xml_location=Xml' || (rm ../lib/help_html/spaf_reorder.html && test -f ../lib/help_html/spaf_reorder.html) >sabcmd to_html.xsl Xml/searching.xml ../lib/help_html/searching.html '$myname=searching.xml' '$xml_location=Xml' || (rm ../lib/help_html/searching.html && test -f ../lib/help_html/searching.html) >sabcmd to_html.xsl Xml/trm_boot.xml ../lib/help_html/trm_boot.html '$myname=trm_boot.xml' '$xml_location=Xml' || (rm ../lib/help_html/trm_boot.html && test -f ../lib/help_html/trm_boot.html) >sabcmd to_html.xsl Xml/organisms.xml ../lib/help_html/organisms.html '$myname=organisms.xml' '$xml_location=Xml' || (rm ../lib/help_html/organisms.html && test -f ../lib/help_html/organisms.html) >sabcmd to_html.xsl Xml/tr_type_nds.xml ../lib/help_html/tr_type_nds.html '$myname=tr_type_nds.xml' '$xml_location=Xml' || (rm ../lib/help_html/tr_type_nds.html && test -f ../lib/help_html/tr_type_nds.html) >sabcmd to_html.xsl Xml/gde_flat_ift.xml ../lib/help_html/gde_flat_ift.html '$myname=gde_flat_ift.xml' '$xml_location=Xml' || (rm ../lib/help_html/gde_flat_ift.html && test -f ../lib/help_html/gde_flat_ift.html) >sabcmd to_html.xsl Xml/helix.xml ../lib/help_html/helix.html '$myname=helix.xml' '$xml_location=Xml' || (rm ../lib/help_html/helix.html && test -f ../lib/help_html/helix.html) >sabcmd to_html.xsl Xml/resorttree.xml ../lib/help_html/resorttree.html '$myname=resorttree.xml' '$xml_location=Xml' || (rm ../lib/help_html/resorttree.html && test -f ../lib/help_html/resorttree.html) >sabcmd to_html.xsl Xml/concatenate.xml ../lib/help_html/concatenate.html '$myname=concatenate.xml' '$xml_location=Xml' || (rm ../lib/help_html/concatenate.html && test -f ../lib/help_html/concatenate.html) >sabcmd to_html.xsl Xml/partial_sequences.xml ../lib/help_html/partial_sequences.html '$myname=partial_sequences.xml' '$xml_location=Xml' || (rm ../lib/help_html/partial_sequences.html && test -f ../lib/help_html/partial_sequences.html) >sabcmd to_html.xsl Xml/primer_parameters.xml ../lib/help_html/primer_parameters.html '$myname=primer_parameters.xml' '$xml_location=Xml' || (rm ../lib/help_html/primer_parameters.html && test -f ../lib/help_html/primer_parameters.html) >sabcmd to_html.xsl Xml/spa_create.xml ../lib/help_html/spa_create.html '$myname=spa_create.xml' '$xml_location=Xml' || (rm ../lib/help_html/spa_create.html && test -f ../lib/help_html/spa_create.html) >sabcmd to_html.xsl Xml/vn_suggest.xml ../lib/help_html/vn_suggest.html '$myname=vn_suggest.xml' '$xml_location=Xml' || (rm ../lib/help_html/vn_suggest.html && test -f ../lib/help_html/vn_suggest.html) >sabcmd to_html.xsl Xml/mode_info.xml ../lib/help_html/mode_info.html '$myname=mode_info.xml' '$xml_location=Xml' || (rm ../lib/help_html/mode_info.html && test -f ../lib/help_html/mode_info.html) >sabcmd to_html.xsl Xml/selected_gene.xml ../lib/help_html/selected_gene.html '$myname=selected_gene.xml' '$xml_location=Xml' || (rm ../lib/help_html/selected_gene.html && test -f ../lib/help_html/selected_gene.html) >sabcmd to_html.xsl Xml/rdp_ift.xml ../lib/help_html/rdp_ift.html '$myname=rdp_ift.xml' '$xml_location=Xml' || (rm ../lib/help_html/rdp_ift.html && test -f ../lib/help_html/rdp_ift.html) >sabcmd to_html.xsl Xml/ne_replace.xml ../lib/help_html/ne_replace.html '$myname=ne_replace.xml' '$xml_location=Xml' || (rm ../lib/help_html/ne_replace.html && test -f ../lib/help_html/ne_replace.html) >sabcmd to_html.xsl Xml/mg_alignment.xml ../lib/help_html/mg_alignment.html '$myname=mg_alignment.xml' '$xml_location=Xml' || (rm ../lib/help_html/mg_alignment.html && test -f ../lib/help_html/mg_alignment.html) >sabcmd to_html.xsl Xml/mode_optimize.xml ../lib/help_html/mode_optimize.html '$myname=mode_optimize.xml' '$xml_location=Xml' || (rm ../lib/help_html/mode_optimize.html && test -f ../lib/help_html/mode_optimize.html) >sabcmd to_html.xsl Xml/trm_del.xml ../lib/help_html/trm_del.html '$myname=trm_del.xml' '$xml_location=Xml' || (rm ../lib/help_html/trm_del.html && test -f ../lib/help_html/trm_del.html) >sabcmd to_html.xsl Xml/props_www.xml ../lib/help_html/props_www.html '$myname=props_www.xml' '$xml_location=Xml' || (rm ../lib/help_html/props_www.html && test -f ../lib/help_html/props_www.html) >sabcmd to_html.xsl Xml/organism_mark.xml ../lib/help_html/organism_mark.html '$myname=organism_mark.xml' '$xml_location=Xml' || (rm ../lib/help_html/organism_mark.html && test -f ../lib/help_html/organism_mark.html) >sabcmd to_html.xsl Xml/tree_cmp.xml ../lib/help_html/tree_cmp.html '$myname=tree_cmp.xml' '$xml_location=Xml' || (rm ../lib/help_html/tree_cmp.html && test -f ../lib/help_html/tree_cmp.html) >sabcmd to_html.xsl Xml/spa_delete.xml ../lib/help_html/spa_delete.html '$myname=spa_delete.xml' '$xml_location=Xml' || (rm ../lib/help_html/spa_delete.html && test -f ../lib/help_html/spa_delete.html) >sabcmd to_html.xsl Xml/security.xml ../lib/help_html/security.html '$myname=security.xml' '$xml_location=Xml' || (rm ../lib/help_html/security.html && test -f ../lib/help_html/security.html) >sabcmd to_html.xsl Xml/arb_ntree.xml ../lib/help_html/arb_ntree.html '$myname=arb_ntree.xml' '$xml_location=Xml' || (rm ../lib/help_html/arb_ntree.html && test -f ../lib/help_html/arb_ntree.html) >sabcmd to_html.xsl Xml/gene_mode.xml ../lib/help_html/gene_mode.html '$myname=gene_mode.xml' '$xml_location=Xml' || (rm ../lib/help_html/gene_mode.html && test -f ../lib/help_html/gene_mode.html) >sabcmd to_html.xsl Xml/mark_list.xml ../lib/help_html/mark_list.html '$myname=mark_list.xml' '$xml_location=Xml' || (rm ../lib/help_html/mark_list.html && test -f ../lib/help_html/mark_list.html) >sabcmd to_html.xsl Xml/arb_edit.xml ../lib/help_html/arb_edit.html '$myname=arb_edit.xml' '$xml_location=Xml' || (rm ../lib/help_html/arb_edit.html && test -f ../lib/help_html/arb_edit.html) >sabcmd to_html.xsl Xml/mg_spec_sel_field.xml ../lib/help_html/mg_spec_sel_field.html '$myname=mg_spec_sel_field.xml' '$xml_location=Xml' || (rm ../lib/help_html/mg_spec_sel_field.html && test -f ../lib/help_html/mg_spec_sel_field.html) >sabcmd to_html.xsl Xml/nt_keys.xml ../lib/help_html/nt_keys.html '$myname=nt_keys.xml' '$xml_location=Xml' || (rm ../lib/help_html/nt_keys.html && test -f ../lib/help_html/nt_keys.html) >sabcmd to_html.xsl Xml/tr_type_radial.xml ../lib/help_html/tr_type_radial.html '$myname=tr_type_radial.xml' '$xml_location=Xml' || (rm ../lib/help_html/tr_type_radial.html && test -f ../lib/help_html/tr_type_radial.html) >sabcmd to_html.xsl Xml/input_mask_format.xml ../lib/help_html/input_mask_format.html '$myname=input_mask_format.xml' '$xml_location=Xml' || (rm ../lib/help_html/input_mask_format.html && test -f ../lib/help_html/input_mask_format.html) >sabcmd to_html.xsl Xml/input_mask_new.xml ../lib/help_html/input_mask_new.html '$myname=input_mask_new.xml' '$xml_location=Xml' || (rm ../lib/help_html/input_mask_new.html && test -f ../lib/help_html/input_mask_new.html) >sabcmd to_html.xsl Xml/helixsym.xml ../lib/help_html/helixsym.html '$myname=helixsym.xml' '$xml_location=Xml' || (rm ../lib/help_html/helixsym.html && test -f ../lib/help_html/helixsym.html) >sabcmd to_html.xsl Xml/phyl.xml ../lib/help_html/phyl.html '$myname=phyl.xml' '$xml_location=Xml' || (rm ../lib/help_html/phyl.html && test -f ../lib/help_html/phyl.html) >sabcmd to_html.xsl Xml/sequence_colors.xml ../lib/help_html/sequence_colors.html '$myname=sequence_colors.xml' '$xml_location=Xml' || (rm ../lib/help_html/sequence_colors.html && test -f ../lib/help_html/sequence_colors.html) >sabcmd to_html.xsl Xml/registration.xml ../lib/help_html/registration.html '$myname=registration.xml' '$xml_location=Xml' || (rm ../lib/help_html/registration.html && test -f ../lib/help_html/registration.html) >sabcmd to_html.xsl Xml/pos_var_pars.xml ../lib/help_html/pos_var_pars.html '$myname=pos_var_pars.xml' '$xml_location=Xml' || (rm ../lib/help_html/pos_var_pars.html && test -f ../lib/help_html/pos_var_pars.html) >sabcmd to_html.xsl Xml/save.xml ../lib/help_html/save.html '$myname=save.xml' '$xml_location=Xml' || (rm ../lib/help_html/save.html && test -f ../lib/help_html/save.html) >sabcmd to_html.xsl Xml/sp_sort_fld.xml ../lib/help_html/sp_sort_fld.html '$myname=sp_sort_fld.xml' '$xml_location=Xml' || (rm ../lib/help_html/sp_sort_fld.html && test -f ../lib/help_html/sp_sort_fld.html) >sabcmd to_html.xsl Xml/sec_props.xml ../lib/help_html/sec_props.html '$myname=sec_props.xml' '$xml_location=Xml' || (rm ../lib/help_html/sec_props.html && test -f ../lib/help_html/sec_props.html) >sabcmd to_html.xsl Xml/spa_rename.xml ../lib/help_html/spa_rename.html '$myname=spa_rename.xml' '$xml_location=Xml' || (rm ../lib/help_html/spa_rename.html && test -f ../lib/help_html/spa_rename.html) >sabcmd to_html.xsl Xml/savedef.xml ../lib/help_html/savedef.html '$myname=savedef.xml' '$xml_location=Xml' || (rm ../lib/help_html/savedef.html && test -f ../lib/help_html/savedef.html) >sabcmd to_html.xsl Xml/pars.xml ../lib/help_html/pars.html '$myname=pars.xml' '$xml_location=Xml' || (rm ../lib/help_html/pars.html && test -f ../lib/help_html/pars.html) >sabcmd to_html.xsl Xml/translate_dna_2_pro.xml ../lib/help_html/translate_dna_2_pro.html '$myname=translate_dna_2_pro.xml' '$xml_location=Xml' || (rm ../lib/help_html/translate_dna_2_pro.html && test -f ../lib/help_html/translate_dna_2_pro.html) >sabcmd to_html.xsl Xml/mode_move.xml ../lib/help_html/mode_move.html '$myname=mode_move.xml' '$xml_location=Xml' || (rm ../lib/help_html/mode_move.html && test -f ../lib/help_html/mode_move.html) >sabcmd to_html.xsl Xml/arb_export.xml ../lib/help_html/arb_export.html '$myname=arb_export.xml' '$xml_location=Xml' || (rm ../lib/help_html/arb_export.html && test -f ../lib/help_html/arb_export.html) >sabcmd to_html.xsl Xml/pa_add.xml ../lib/help_html/pa_add.html '$myname=pa_add.xml' '$xml_location=Xml' || (rm ../lib/help_html/pa_add.html && test -f ../lib/help_html/pa_add.html) >sabcmd to_html.xsl Xml/e4_consensus.xml ../lib/help_html/e4_consensus.html '$myname=e4_consensus.xml' '$xml_location=Xml' || (rm ../lib/help_html/e4_consensus.html && test -f ../lib/help_html/e4_consensus.html) >sabcmd to_html.xsl Xml/sec_display.xml ../lib/help_html/sec_display.html '$myname=sec_display.xml' '$xml_location=Xml' || (rm ../lib/help_html/sec_display.html && test -f ../lib/help_html/sec_display.html) >sabcmd to_html.xsl Xml/search_duplicates.xml ../lib/help_html/search_duplicates.html '$myname=search_duplicates.xml' '$xml_location=Xml' || (rm ../lib/help_html/search_duplicates.html && test -f ../lib/help_html/search_duplicates.html) >sabcmd to_html.xsl Xml/parser.xml ../lib/help_html/parser.html '$myname=parser.xml' '$xml_location=Xml' || (rm ../lib/help_html/parser.html && test -f ../lib/help_html/parser.html) >sabcmd to_html.xsl Xml/pa_add_sel.xml ../lib/help_html/pa_add_sel.html '$myname=pa_add_sel.xml' '$xml_location=Xml' || (rm ../lib/help_html/pa_add_sel.html && test -f ../lib/help_html/pa_add_sel.html) >sabcmd to_html.xsl Xml/mode_lzoom.xml ../lib/help_html/mode_lzoom.html '$myname=mode_lzoom.xml' '$xml_location=Xml' || (rm ../lib/help_html/mode_lzoom.html && test -f ../lib/help_html/mode_lzoom.html) >sabcmd to_html.xsl Xml/galign_main.xml ../lib/help_html/galign_main.html '$myname=galign_main.xml' '$xml_location=Xml' || (rm ../lib/help_html/galign_main.html && test -f ../lib/help_html/galign_main.html) >sabcmd to_html.xsl Xml/version.xml ../lib/help_html/version.html '$myname=version.xml' '$xml_location=Xml' || (rm ../lib/help_html/version.html && test -f ../lib/help_html/version.html) >sabcmd to_html.xsl Xml/species_join.xml ../lib/help_html/species_join.html '$myname=species_join.xml' '$xml_location=Xml' || (rm ../lib/help_html/species_join.html && test -f ../lib/help_html/species_join.html) >sabcmd to_html.xsl Xml/pa_ranchlengths.xml ../lib/help_html/pa_ranchlengths.html '$myname=pa_ranchlengths.xml' '$xml_location=Xml' || (rm ../lib/help_html/pa_ranchlengths.html && test -f ../lib/help_html/pa_ranchlengths.html) >sabcmd to_html.xsl Xml/sp_count_mrk.xml ../lib/help_html/sp_count_mrk.html '$myname=sp_count_mrk.xml' '$xml_location=Xml' || (rm ../lib/help_html/sp_count_mrk.html && test -f ../lib/help_html/sp_count_mrk.html) >sabcmd to_html.xsl Xml/mark_long_branches.xml ../lib/help_html/mark_long_branches.html '$myname=mark_long_branches.xml' '$xml_location=Xml' || (rm ../lib/help_html/mark_long_branches.html && test -f ../lib/help_html/mark_long_branches.html) >sabcmd to_html.xsl Xml/gene_map.xml ../lib/help_html/gene_map.html '$myname=gene_map.xml' '$xml_location=Xml' || (rm ../lib/help_html/gene_map.html && test -f ../lib/help_html/gene_map.html) >sabcmd to_html.xsl Xml/gene_species_mark.xml ../lib/help_html/gene_species_mark.html '$myname=gene_species_mark.xml' '$xml_location=Xml' || (rm ../lib/help_html/gene_species_mark.html && test -f ../lib/help_html/gene_species_mark.html) >sabcmd to_html.xsl Xml/trees.xml ../lib/help_html/trees.html '$myname=trees.xml' '$xml_location=Xml' || (rm ../lib/help_html/trees.html && test -f ../lib/help_html/trees.html) >sabcmd to_html.xsl Xml/insdelchar.xml ../lib/help_html/insdelchar.html '$myname=insdelchar.xml' '$xml_location=Xml' || (rm ../lib/help_html/insdelchar.html && test -f ../lib/help_html/insdelchar.html) >sabcmd to_html.xsl Xml/mode_pzoom.xml ../lib/help_html/mode_pzoom.html '$myname=mode_pzoom.xml' '$xml_location=Xml' || (rm ../lib/help_html/mode_pzoom.html && test -f ../lib/help_html/mode_pzoom.html) >sabcmd to_html.xsl Xml/mode_mark.xml ../lib/help_html/mode_mark.html '$myname=mode_mark.xml' '$xml_location=Xml' || (rm ../lib/help_html/mode_mark.html && test -f ../lib/help_html/mode_mark.html) >sabcmd to_html.xsl Xml/dssp_ift.xml ../lib/help_html/dssp_ift.html '$myname=dssp_ift.xml' '$xml_location=Xml' || (rm ../lib/help_html/dssp_ift.html && test -f ../lib/help_html/dssp_ift.html) >sabcmd to_html.xsl Xml/color_props.xml ../lib/help_html/color_props.html '$myname=color_props.xml' '$xml_location=Xml' || (rm ../lib/help_html/color_props.html && test -f ../lib/help_html/color_props.html) >sabcmd to_html.xsl Xml/acisrt.xml ../lib/help_html/acisrt.html '$myname=acisrt.xml' '$xml_location=Xml' || (rm ../lib/help_html/acisrt.html && test -f ../lib/help_html/acisrt.html) >sabcmd to_html.xsl Xml/genes.xml ../lib/help_html/genes.html '$myname=genes.xml' '$xml_location=Xml' || (rm ../lib/help_html/genes.html && test -f ../lib/help_html/genes.html) >sabcmd to_html.xsl Xml/mode_nni.xml ../lib/help_html/mode_nni.html '$myname=mode_nni.xml' '$xml_location=Xml' || (rm ../lib/help_html/mode_nni.html && test -f ../lib/help_html/mode_nni.html) >sabcmd to_html.xsl Xml/mg_names.xml ../lib/help_html/mg_names.html '$myname=mg_names.xml' '$xml_location=Xml' || (rm ../lib/help_html/mg_names.html && test -f ../lib/help_html/mg_names.html) >sabcmd to_html.xsl Xml/mode_width.xml ../lib/help_html/mode_width.html '$myname=mode_width.xml' '$xml_location=Xml' || (rm ../lib/help_html/mode_width.html && test -f ../lib/help_html/mode_width.html) >sabcmd to_html.xsl Xml/trans_anal.xml ../lib/help_html/trans_anal.html '$myname=trans_anal.xml' '$xml_location=Xml' || (rm ../lib/help_html/trans_anal.html && test -f ../lib/help_html/trans_anal.html) >sabcmd to_html.xsl Xml/probeadmin.xml ../lib/help_html/probeadmin.html '$myname=probeadmin.xml' '$xml_location=Xml' || (rm ../lib/help_html/probeadmin.html && test -f ../lib/help_html/probeadmin.html) >sabcmd to_html.xsl Xml/color.xml ../lib/help_html/color.html '$myname=color.xml' '$xml_location=Xml' || (rm ../lib/help_html/color.html && test -f ../lib/help_html/color.html) >sabcmd to_html.xsl Xml/sp_sp_2_ext.xml ../lib/help_html/sp_sp_2_ext.html '$myname=sp_sp_2_ext.xml' '$xml_location=Xml' || (rm ../lib/help_html/sp_sp_2_ext.html && test -f ../lib/help_html/sp_sp_2_ext.html) >sabcmd to_html.xsl Xml/pfold_sai.xml ../lib/help_html/pfold_sai.html '$myname=pfold_sai.xml' '$xml_location=Xml' || (rm ../lib/help_html/pfold_sai.html && test -f ../lib/help_html/pfold_sai.html) >sabcmd to_html.xsl Xml/saveas.xml ../lib/help_html/saveas.html '$myname=saveas.xml' '$xml_location=Xml' || (rm ../lib/help_html/saveas.html && test -f ../lib/help_html/saveas.html) >sabcmd to_html.xsl Xml/bootstrap.xml ../lib/help_html/bootstrap.html '$myname=bootstrap.xml' '$xml_location=Xml' || (rm ../lib/help_html/bootstrap.html && test -f ../lib/help_html/bootstrap.html) >sabcmd to_html.xsl Xml/rna3d_general.xml ../lib/help_html/rna3d_general.html '$myname=rna3d_general.xml' '$xml_location=Xml' || (rm ../lib/help_html/rna3d_general.html && test -f ../lib/help_html/rna3d_general.html) >sabcmd to_html.xsl Xml/search_equal_fields.xml ../lib/help_html/search_equal_fields.html '$myname=search_equal_fields.xml' '$xml_location=Xml' || (rm ../lib/help_html/search_equal_fields.html && test -f ../lib/help_html/search_equal_fields.html) >sabcmd to_html.xsl Xml/spaf_create.xml ../lib/help_html/spaf_create.html '$myname=spaf_create.xml' '$xml_location=Xml' || (rm ../lib/help_html/spaf_create.html && test -f ../lib/help_html/spaf_create.html) >sabcmd to_html.xsl Xml/nt_tree_select.xml ../lib/help_html/nt_tree_select.html '$myname=nt_tree_select.xml' '$xml_location=Xml' || (rm ../lib/help_html/nt_tree_select.html && test -f ../lib/help_html/nt_tree_select.html) >sabcmd to_html.xsl Xml/props_nds.xml ../lib/help_html/props_nds.html '$myname=props_nds.xml' '$xml_location=Xml' || (rm ../lib/help_html/props_nds.html && test -f ../lib/help_html/props_nds.html) >sabcmd to_html.xsl Xml/checkgcg.xml ../lib/help_html/checkgcg.html '$myname=checkgcg.xml' '$xml_location=Xml' || (rm ../lib/help_html/checkgcg.html && test -f ../lib/help_html/checkgcg.html) >sabcmd to_html.xsl Xml/csp_2_gnuplot.xml ../lib/help_html/csp_2_gnuplot.html '$myname=csp_2_gnuplot.xml' '$xml_location=Xml' || (rm ../lib/help_html/csp_2_gnuplot.html && test -f ../lib/help_html/csp_2_gnuplot.html) >sabcmd to_html.xsl Xml/ne_search.xml ../lib/help_html/ne_search.html '$myname=ne_search.xml' '$xml_location=Xml' || (rm ../lib/help_html/ne_search.html && test -f ../lib/help_html/ne_search.html) >sabcmd to_html.xsl Xml/check_quality.xml ../lib/help_html/check_quality.html '$myname=check_quality.xml' '$xml_location=Xml' || (rm ../lib/help_html/check_quality.html && test -f ../lib/help_html/check_quality.html) >sabcmd to_html.xsl Xml/asciiprint.xml ../lib/help_html/asciiprint.html '$myname=asciiprint.xml' '$xml_location=Xml' || (rm ../lib/help_html/asciiprint.html && test -f ../lib/help_html/asciiprint.html) >sabcmd to_html.xsl Xml/configuration.xml ../lib/help_html/configuration.html '$myname=configuration.xml' '$xml_location=Xml' || (rm ../lib/help_html/configuration.html && test -f ../lib/help_html/configuration.html) >sabcmd to_html.xsl Xml/mark_genes.xml ../lib/help_html/mark_genes.html '$myname=mark_genes.xml' '$xml_location=Xml' || (rm ../lib/help_html/mark_genes.html && test -f ../lib/help_html/mark_genes.html) >sabcmd to_html.xsl Xml/max_freq.xml ../lib/help_html/max_freq.html '$myname=max_freq.xml' '$xml_location=Xml' || (rm ../lib/help_html/max_freq.html && test -f ../lib/help_html/max_freq.html) >sabcmd to_html.xsl Xml/save_matrix.xml ../lib/help_html/save_matrix.html '$myname=save_matrix.xml' '$xml_location=Xml' || (rm ../lib/help_html/save_matrix.html && test -f ../lib/help_html/save_matrix.html) >sabcmd to_html.xsl Xml/arb_pars.xml ../lib/help_html/arb_pars.html '$myname=arb_pars.xml' '$xml_location=Xml' || (rm ../lib/help_html/arb_pars.html && test -f ../lib/help_html/arb_pars.html) >sabcmd to_html.xsl Xml/trm_mrkd.xml ../lib/help_html/trm_mrkd.html '$myname=trm_mrkd.xml' '$xml_location=Xml' || (rm ../lib/help_html/trm_mrkd.html && test -f ../lib/help_html/trm_mrkd.html) >sabcmd to_html.xsl Xml/pt_server.xml ../lib/help_html/pt_server.html '$myname=pt_server.xml' '$xml_location=Xml' || (rm ../lib/help_html/pt_server.html && test -f ../lib/help_html/pt_server.html) >sabcmd to_html.xsl Xml/ne_align_seq.xml ../lib/help_html/ne_align_seq.html '$myname=ne_align_seq.xml' '$xml_location=Xml' || (rm ../lib/help_html/ne_align_seq.html && test -f ../lib/help_html/ne_align_seq.html) >sabcmd to_html.xsl Xml/regexpr.xml ../lib/help_html/regexpr.html '$myname=regexpr.xml' '$xml_location=Xml' || (rm ../lib/help_html/regexpr.html && test -f ../lib/help_html/regexpr.html) >sabcmd to_html.xsl Xml/arb_commands.xml ../lib/help_html/arb_commands.html '$myname=arb_commands.xml' '$xml_location=Xml' || (rm ../lib/help_html/arb_commands.html && test -f ../lib/help_html/arb_commands.html) >sabcmd to_html.xsl Xml/tr_type_list.xml ../lib/help_html/tr_type_list.html '$myname=tr_type_list.xml' '$xml_location=Xml' || (rm ../lib/help_html/tr_type_list.html && test -f ../lib/help_html/tr_type_list.html) >sabcmd to_html.xsl Xml/tr_import.xml ../lib/help_html/tr_import.html '$myname=tr_import.xml' '$xml_location=Xml' || (rm ../lib/help_html/tr_import.html && test -f ../lib/help_html/tr_import.html) >sabcmd to_html.xsl Xml/sp_invert_mrk.xml ../lib/help_html/sp_invert_mrk.html '$myname=sp_invert_mrk.xml' '$xml_location=Xml' || (rm ../lib/help_html/sp_invert_mrk.html && test -f ../lib/help_html/sp_invert_mrk.html) >sabcmd to_html.xsl Xml/configurations.xml ../lib/help_html/configurations.html '$myname=configurations.xml' '$xml_location=Xml' || (rm ../lib/help_html/configurations.html && test -f ../lib/help_html/configurations.html) >sabcmd to_html.xsl Xml/submission.xml ../lib/help_html/submission.html '$myname=submission.xml' '$xml_location=Xml' || (rm ../lib/help_html/submission.html && test -f ../lib/help_html/submission.html) >sabcmd to_html.xsl Xml/set_meny_fields.xml ../lib/help_html/set_meny_fields.html '$myname=set_meny_fields.xml' '$xml_location=Xml' || (rm ../lib/help_html/set_meny_fields.html && test -f ../lib/help_html/set_meny_fields.html) >sabcmd to_html.xsl Xml/unmark_list.xml ../lib/help_html/unmark_list.html '$myname=unmark_list.xml' '$xml_location=Xml' || (rm ../lib/help_html/unmark_list.html && test -f ../lib/help_html/unmark_list.html) >sabcmd to_html.xsl Xml/arb_secedit.xml ../lib/help_html/arb_secedit.html '$myname=arb_secedit.xml' '$xml_location=Xml' || (rm ../lib/help_html/arb_secedit.html && test -f ../lib/help_html/arb_secedit.html) >sabcmd to_html.xsl Xml/mod_field_list.xml ../lib/help_html/mod_field_list.html '$myname=mod_field_list.xml' '$xml_location=Xml' || (rm ../lib/help_html/mod_field_list.html && test -f ../lib/help_html/mod_field_list.html) >sabcmd to_html.xsl Xml/pa_quick.xml ../lib/help_html/pa_quick.html '$myname=pa_quick.xml' '$xml_location=Xml' || (rm ../lib/help_html/pa_quick.html && test -f ../lib/help_html/pa_quick.html) >sabcmd to_html.xsl Xml/visualizeSAI.xml ../lib/help_html/visualizeSAI.html '$myname=visualizeSAI.xml' '$xml_location=Xml' || (rm ../lib/help_html/visualizeSAI.html && test -f ../lib/help_html/visualizeSAI.html) >sabcmd to_html.xsl Xml/write_field_list.xml ../lib/help_html/write_field_list.html '$myname=write_field_list.xml' '$xml_location=Xml' || (rm ../lib/help_html/write_field_list.html && test -f ../lib/help_html/write_field_list.html) >sabcmd to_html.xsl Xml/alignment.xml ../lib/help_html/alignment.html '$myname=alignment.xml' '$xml_location=Xml' || (rm ../lib/help_html/alignment.html && test -f ../lib/help_html/alignment.html) >sabcmd to_html.xsl Xml/gene_mark.xml ../lib/help_html/gene_mark.html '$myname=gene_mark.xml' '$xml_location=Xml' || (rm ../lib/help_html/gene_mark.html && test -f ../lib/help_html/gene_mark.html) >sabcmd to_html.xsl Xml/colorize.xml ../lib/help_html/colorize.html '$myname=colorize.xml' '$xml_location=Xml' || (rm ../lib/help_html/colorize.html && test -f ../lib/help_html/colorize.html) >sabcmd to_html.xsl Xml/consensus_def.xml ../lib/help_html/consensus_def.html '$myname=consensus_def.xml' '$xml_location=Xml' || (rm ../lib/help_html/consensus_def.html && test -f ../lib/help_html/consensus_def.html) >sabcmd to_html.xsl Xml/primer.xml ../lib/help_html/primer.html '$myname=primer.xml' '$xml_location=Xml' || (rm ../lib/help_html/primer.html && test -f ../lib/help_html/primer.html) >sabcmd to_html.xsl Xml/del_list.xml ../lib/help_html/del_list.html '$myname=del_list.xml' '$xml_location=Xml' || (rm ../lib/help_html/del_list.html && test -f ../lib/help_html/del_list.html) >sabcmd to_html.xsl Xml/saiProbeHelp.xml ../lib/help_html/saiProbeHelp.html '$myname=saiProbeHelp.xml' '$xml_location=Xml' || (rm ../lib/help_html/saiProbeHelp.html && test -f ../lib/help_html/saiProbeHelp.html) >sabcmd to_html.xsl Xml/ebi_ift.xml ../lib/help_html/ebi_ift.html '$myname=ebi_ift.xml' '$xml_location=Xml' || (rm ../lib/help_html/ebi_ift.html && test -f ../lib/help_html/ebi_ift.html) >sabcmd to_html.xsl Xml/change_security.xml ../lib/help_html/change_security.html '$myname=change_security.xml' '$xml_location=Xml' || (rm ../lib/help_html/change_security.html && test -f ../lib/help_html/change_security.html) >sabcmd to_html.xsl Xml/gde.xml ../lib/help_html/gde.html '$myname=gde.xml' '$xml_location=Xml' || (rm ../lib/help_html/gde.html && test -f ../lib/help_html/gde.html) >sabcmd to_html.xsl Xml/mode_length.xml ../lib/help_html/mode_length.html '$myname=mode_length.xml' '$xml_location=Xml' || (rm ../lib/help_html/mode_length.html && test -f ../lib/help_html/mode_length.html) >sabcmd to_html.xsl Xml/sel_spec.xml ../lib/help_html/sel_spec.html '$myname=sel_spec.xml' '$xml_location=Xml' || (rm ../lib/help_html/sel_spec.html && test -f ../lib/help_html/sel_spec.html) >sabcmd to_html.xsl Xml/sec_keys.xml ../lib/help_html/sec_keys.html '$myname=sec_keys.xml' '$xml_location=Xml' || (rm ../lib/help_html/sec_keys.html && test -f ../lib/help_html/sec_keys.html) >sabcmd to_html.xsl Xml/gene_extract.xml ../lib/help_html/gene_extract.html '$myname=gene_extract.xml' '$xml_location=Xml' || (rm ../lib/help_html/gene_extract.html && test -f ../lib/help_html/gene_extract.html) >sabcmd to_html.xsl Xml/selected.xml ../lib/help_html/selected.html '$myname=selected.xml' '$xml_location=Xml' || (rm ../lib/help_html/selected.html && test -f ../lib/help_html/selected.html) >sabcmd to_html.xsl Xml/spa_copy.xml ../lib/help_html/spa_copy.html '$myname=spa_copy.xml' '$xml_location=Xml' || (rm ../lib/help_html/spa_copy.html && test -f ../lib/help_html/spa_copy.html) >sabcmd to_html.xsl Xml/rst_phys_zoom.xml ../lib/help_html/rst_phys_zoom.html '$myname=rst_phys_zoom.xml' '$xml_location=Xml' || (rm ../lib/help_html/rst_phys_zoom.html && test -f ../lib/help_html/rst_phys_zoom.html) >sabcmd to_html.xsl Xml/sp_mrk_all.xml ../lib/help_html/sp_mrk_all.html '$myname=sp_mrk_all.xml' '$xml_location=Xml' || (rm ../lib/help_html/sp_mrk_all.html && test -f ../lib/help_html/sp_mrk_all.html) >sabcmd to_html.xsl Xml/man_arb_edit4.xml ../lib/help_html/man_arb_edit4.html '$myname=man_arb_edit4.xml' '$xml_location=Xml' || (rm ../lib/help_html/man_arb_edit4.html && test -f ../lib/help_html/man_arb_edit4.html) >sabcmd to_html.xsl Xml/probedesign.xml ../lib/help_html/probedesign.html '$myname=probedesign.xml' '$xml_location=Xml' || (rm ../lib/help_html/probedesign.html && test -f ../lib/help_html/probedesign.html) >sabcmd to_html.xsl Xml/mode_group.xml ../lib/help_html/mode_group.html '$myname=mode_group.xml' '$xml_location=Xml' || (rm ../lib/help_html/mode_group.html && test -f ../lib/help_html/mode_group.html) >sabcmd to_html.xsl Xml/undo.xml ../lib/help_html/undo.html '$myname=undo.xml' '$xml_location=Xml' || (rm ../lib/help_html/undo.html && test -f ../lib/help_html/undo.html) >sabcmd to_html.xsl Xml/islandhopping.xml ../lib/help_html/islandhopping.html '$myname=islandhopping.xml' '$xml_location=Xml' || (rm ../lib/help_html/islandhopping.html && test -f ../lib/help_html/islandhopping.html) >sabcmd to_html.xsl Xml/sel_box.xml ../lib/help_html/sel_box.html '$myname=sel_box.xml' '$xml_location=Xml' || (rm ../lib/help_html/sel_box.html && test -f ../lib/help_html/sel_box.html) >sabcmd to_html.xsl Xml/missbase.xml ../lib/help_html/missbase.html '$myname=missbase.xml' '$xml_location=Xml' || (rm ../lib/help_html/missbase.html && test -f ../lib/help_html/missbase.html) >sabcmd to_html.xsl Xml/pfold_props.xml ../lib/help_html/pfold_props.html '$myname=pfold_props.xml' '$xml_location=Xml' || (rm ../lib/help_html/pfold_props.html && test -f ../lib/help_html/pfold_props.html) >sabcmd to_html.xsl Xml/gene_search.xml ../lib/help_html/gene_search.html '$myname=gene_search.xml' '$xml_location=Xml' || (rm ../lib/help_html/gene_search.html && test -f ../lib/help_html/gene_search.html) >sabcmd to_html.xsl Xml/quit.xml ../lib/help_html/quit.html '$myname=quit.xml' '$xml_location=Xml' || (rm ../lib/help_html/quit.html && test -f ../lib/help_html/quit.html) >sabcmd to_html.xsl Xml/ph_export_markerline.xml ../lib/help_html/ph_export_markerline.html '$myname=ph_export_markerline.xml' '$xml_location=Xml' || (rm ../lib/help_html/ph_export_markerline.html && test -f ../lib/help_html/ph_export_markerline.html) >sabcmd to_html.xsl Xml/mg_extendeds.xml ../lib/help_html/mg_extendeds.html '$myname=mg_extendeds.xml' '$xml_location=Xml' || (rm ../lib/help_html/mg_extendeds.html && test -f ../lib/help_html/mg_extendeds.html) >sabcmd to_html.xsl Xml/tgroupall.xml ../lib/help_html/tgroupall.html '$myname=tgroupall.xml' '$xml_location=Xml' || (rm ../lib/help_html/tgroupall.html && test -f ../lib/help_html/tgroupall.html) >sabcmd to_html.xsl Xml/scandb.xml ../lib/help_html/scandb.html '$myname=scandb.xml' '$xml_location=Xml' || (rm ../lib/help_html/scandb.html && test -f ../lib/help_html/scandb.html) >sabcmd to_html.xsl Xml/arb_db.xml ../lib/help_html/arb_db.html '$myname=arb_db.xml' '$xml_location=Xml' || (rm ../lib/help_html/arb_db.html && test -f ../lib/help_html/arb_db.html) >sabcmd to_html.xsl Xml/arb_intro.xml ../lib/help_html/arb_intro.html '$myname=arb_intro.xml' '$xml_location=Xml' || (rm ../lib/help_html/arb_intro.html && test -f ../lib/help_html/arb_intro.html) >sabcmd to_html.xsl Xml/arb_gde.xml ../lib/help_html/arb_gde.html '$myname=arb_gde.xml' '$xml_location=Xml' || (rm ../lib/help_html/arb_gde.html && test -f ../lib/help_html/arb_gde.html) >sabcmd to_html.xsl Xml/universal_ift.xml ../lib/help_html/universal_ift.html '$myname=universal_ift.xml' '$xml_location=Xml' || (rm ../lib/help_html/universal_ift.html && test -f ../lib/help_html/universal_ift.html) >sabcmd to_html.xsl Xml/sp_mrk_tree.xml ../lib/help_html/sp_mrk_tree.html '$myname=sp_mrk_tree.xml' '$xml_location=Xml' || (rm ../lib/help_html/sp_mrk_tree.html && test -f ../lib/help_html/sp_mrk_tree.html) >sabcmd to_html.xsl Xml/sp_umrk_all.xml ../lib/help_html/sp_umrk_all.html '$myname=sp_umrk_all.xml' '$xml_location=Xml' || (rm ../lib/help_html/sp_umrk_all.html && test -f ../lib/help_html/sp_umrk_all.html) >sabcmd to_html.xsl Xml/vn_search.xml ../lib/help_html/vn_search.html '$myname=vn_search.xml' '$xml_location=Xml' || (rm ../lib/help_html/vn_search.html && test -f ../lib/help_html/vn_search.html) >sabcmd to_html.xsl Xml/proteinViewer.xml ../lib/help_html/proteinViewer.html '$myname=proteinViewer.xml' '$xml_location=Xml' || (rm ../lib/help_html/proteinViewer.html && test -f ../lib/help_html/proteinViewer.html) >sabcmd to_html.xsl Xml/pfold.xml ../lib/help_html/pfold.html '$myname=pfold.xml' '$xml_location=Xml' || (rm ../lib/help_html/pfold.html && test -f ../lib/help_html/pfold.html) >sabcmd to_html.xsl Xml/secedit_imexport.xml ../lib/help_html/secedit_imexport.html '$myname=secedit_imexport.xml' '$xml_location=Xml' || (rm ../lib/help_html/secedit_imexport.html && test -f ../lib/help_html/secedit_imexport.html) >sabcmd to_html.xsl Xml/color_props_groups.xml ../lib/help_html/color_props_groups.html '$myname=color_props_groups.xml' '$xml_location=Xml' || (rm ../lib/help_html/color_props_groups.html && test -f ../lib/help_html/color_props_groups.html) >sabcmd to_html.xsl Xml/export_format.xml ../lib/help_html/export_format.html '$myname=export_format.xml' '$xml_location=Xml' || (rm ../lib/help_html/export_format.html && test -f ../lib/help_html/export_format.html) >sabcmd to_html.xsl Xml/mode_swap.xml ../lib/help_html/mode_swap.html '$myname=mode_swap.xml' '$xml_location=Xml' || (rm ../lib/help_html/mode_swap.html && test -f ../lib/help_html/mode_swap.html) >sabcmd to_html.xsl Xml/rna3d_dispBases.xml ../lib/help_html/rna3d_dispBases.html '$myname=rna3d_dispBases.xml' '$xml_location=Xml' || (rm ../lib/help_html/rna3d_dispBases.html && test -f ../lib/help_html/rna3d_dispBases.html) >sabcmd to_html.xsl Xml/save_def.xml ../lib/help_html/save_def.html '$myname=save_def.xml' '$xml_location=Xml' || (rm ../lib/help_html/save_def.html && test -f ../lib/help_html/save_def.html) >sabcmd to_html.xsl Xml/ne_new_sequence.xml ../lib/help_html/ne_new_sequence.html '$myname=ne_new_sequence.xml' '$xml_location=Xml' || (rm ../lib/help_html/ne_new_sequence.html && test -f ../lib/help_html/ne_new_sequence.html) >sabcmd to_html.xsl Xml/e4_replace.xml ../lib/help_html/e4_replace.html '$myname=e4_replace.xml' '$xml_location=Xml' || (rm ../lib/help_html/e4_replace.html && test -f ../lib/help_html/e4_replace.html) >sabcmd to_html.xsl Xml/gene_hide.xml ../lib/help_html/gene_hide.html '$myname=gene_hide.xml' '$xml_location=Xml' || (rm ../lib/help_html/gene_hide.html && test -f ../lib/help_html/gene_hide.html) >sabcmd to_html.xsl Xml/optimize.xml ../lib/help_html/optimize.html '$myname=optimize.xml' '$xml_location=Xml' || (rm ../lib/help_html/optimize.html && test -f ../lib/help_html/optimize.html) >sabcmd to_html.xsl Xml/mode_angle.xml ../lib/help_html/mode_angle.html '$myname=mode_angle.xml' '$xml_location=Xml' || (rm ../lib/help_html/mode_angle.html && test -f ../lib/help_html/mode_angle.html) >sabcmd to_html.xsl Xml/sp_rename.xml ../lib/help_html/sp_rename.html '$myname=sp_rename.xml' '$xml_location=Xml' || (rm ../lib/help_html/sp_rename.html && test -f ../lib/help_html/sp_rename.html) >sabcmd to_html.xsl Xml/sp_search.xml ../lib/help_html/sp_search.html '$myname=sp_search.xml' '$xml_location=Xml' || (rm ../lib/help_html/sp_search.html && test -f ../lib/help_html/sp_search.html) >sabcmd to_html.xsl Xml/sp_umrk_tree.xml ../lib/help_html/sp_umrk_tree.html '$myname=sp_umrk_tree.xml' '$xml_location=Xml' || (rm ../lib/help_html/sp_umrk_tree.html && test -f ../lib/help_html/sp_umrk_tree.html) >sabcmd to_html.xsl Xml/sp_sort_phyl.xml ../lib/help_html/sp_sort_phyl.html '$myname=sp_sort_phyl.xml' '$xml_location=Xml' || (rm ../lib/help_html/sp_sort_phyl.html && test -f ../lib/help_html/sp_sort_phyl.html) >sabcmd to_html.xsl Xml/species.xml ../lib/help_html/species.html '$myname=species.xml' '$xml_location=Xml' || (rm ../lib/help_html/species.html && test -f ../lib/help_html/species.html) >sabcmd to_html.xsl Xml/nt_tree_settings.xml ../lib/help_html/nt_tree_settings.html '$myname=nt_tree_settings.xml' '$xml_location=Xml' || (rm ../lib/help_html/nt_tree_settings.html && test -f ../lib/help_html/nt_tree_settings.html) >sabcmd to_html.xsl Xml/nt_props_data.xml ../lib/help_html/nt_props_data.html '$myname=nt_props_data.xml' '$xml_location=Xml' || (rm ../lib/help_html/nt_props_data.html && test -f ../lib/help_html/nt_props_data.html) >sabcmd to_html.xsl Xml/sec_mode.xml ../lib/help_html/sec_mode.html '$myname=sec_mode.xml' '$xml_location=Xml' || (rm ../lib/help_html/sec_mode.html && test -f ../lib/help_html/sec_mode.html) >sabcmd to_html.xsl Xml/namesadmin.xml ../lib/help_html/namesadmin.html '$myname=namesadmin.xml' '$xml_location=Xml' || (rm ../lib/help_html/namesadmin.html && test -f ../lib/help_html/namesadmin.html) >sabcmd to_html.xsl Xml/faligner.xml ../lib/help_html/faligner.html '$myname=faligner.xml' '$xml_location=Xml' || (rm ../lib/help_html/faligner.html && test -f ../lib/help_html/faligner.html) >sabcmd to_html.xsl Xml/mark.xml ../lib/help_html/mark.html '$myname=mark.xml' '$xml_location=Xml' || (rm ../lib/help_html/mark.html && test -f ../lib/help_html/mark.html) >sabcmd to_html.xsl Xml/mode_select.xml ../lib/help_html/mode_select.html '$myname=mode_select.xml' '$xml_location=Xml' || (rm ../lib/help_html/mode_select.html && test -f ../lib/help_html/mode_select.html) >sabcmd to_html.xsl Xml/arb_import.xml ../lib/help_html/arb_import.html '$myname=arb_import.xml' '$xml_location=Xml' || (rm ../lib/help_html/arb_import.html && test -f ../lib/help_html/arb_import.html) >sabcmd to_html.xsl Xml/ed4_nds.xml ../lib/help_html/ed4_nds.html '$myname=ed4_nds.xml' '$xml_location=Xml' || (rm ../lib/help_html/ed4_nds.html && test -f ../lib/help_html/ed4_nds.html) >sabcmd to_html.xsl Xml/rna3d_dispHelices.xml ../lib/help_html/rna3d_dispHelices.html '$myname=rna3d_dispHelices.xml' '$xml_location=Xml' || (rm ../lib/help_html/rna3d_dispHelices.html && test -f ../lib/help_html/rna3d_dispHelices.html) >sabcmd to_html.xsl Xml/no_tree.xml ../lib/help_html/no_tree.html '$myname=no_tree.xml' '$xml_location=Xml' || (rm ../lib/help_html/no_tree.html && test -f ../lib/help_html/no_tree.html) >sabcmd to_html.xsl Xml/fasta_ift.xml ../lib/help_html/fasta_ift.html '$myname=fasta_ift.xml' '$xml_location=Xml' || (rm ../lib/help_html/fasta_ift.html && test -f ../lib/help_html/fasta_ift.html) >sabcmd to_html.xsl Xml/exec_bug.xml ../lib/help_html/exec_bug.html '$myname=exec_bug.xml' '$xml_location=Xml' || (rm ../lib/help_html/exec_bug.html && test -f ../lib/help_html/exec_bug.html) >sabcmd to_html.xsl Xml/pa_optimizer.xml ../lib/help_html/pa_optimizer.html '$myname=pa_optimizer.xml' '$xml_location=Xml' || (rm ../lib/help_html/pa_optimizer.html && test -f ../lib/help_html/pa_optimizer.html) >sabcmd to_html.xsl Xml/result.xml ../lib/help_html/result.html '$myname=result.xml' '$xml_location=Xml' || (rm ../lib/help_html/result.html && test -f ../lib/help_html/result.html) >sabcmd to_html.xsl Xml/phylo.xml ../lib/help_html/phylo.html '$myname=phylo.xml' '$xml_location=Xml' || (rm ../lib/help_html/phylo.html && test -f ../lib/help_html/phylo.html) >sabcmd to_html.xsl Xml/e4_search.xml ../lib/help_html/e4_search.html '$myname=e4_search.xml' '$xml_location=Xml' || (rm ../lib/help_html/e4_search.html && test -f ../lib/help_html/e4_search.html) >sabcmd to_html.xsl Xml/multiprobe.xml ../lib/help_html/multiprobe.html '$myname=multiprobe.xml' '$xml_location=Xml' || (rm ../lib/help_html/multiprobe.html && test -f ../lib/help_html/multiprobe.html) >sabcmd to_html.xsl Xml/arb_envar.xml ../lib/help_html/arb_envar.html '$myname=arb_envar.xml' '$xml_location=Xml' || (rm ../lib/help_html/arb_envar.html && test -f ../lib/help_html/arb_envar.html) >sabcmd to_html.xsl Xml/next_neighbours_listed.xml ../lib/help_html/next_neighbours_listed.html '$myname=next_neighbours_listed.xml' '$xml_location=Xml' || (rm ../lib/help_html/next_neighbours_listed.html && test -f ../lib/help_html/next_neighbours_listed.html) >sabcmd to_html.xsl Xml/cons_params.xml ../lib/help_html/cons_params.html '$myname=cons_params.xml' '$xml_location=Xml' || (rm ../lib/help_html/cons_params.html && test -f ../lib/help_html/cons_params.html) >sabcmd to_html.xsl Xml/align.xml ../lib/help_html/align.html '$myname=align.xml' '$xml_location=Xml' || (rm ../lib/help_html/align.html && test -f ../lib/help_html/align.html) >sabcmd to_html.xsl Xml/Protection.xml ../lib/help_html/Protection.html '$myname=Protection.xml' '$xml_location=Xml' || (rm ../lib/help_html/Protection.html && test -f ../lib/help_html/Protection.html) >sabcmd to_html.xsl Xml/ap_stack.xml ../lib/help_html/ap_stack.html '$myname=ap_stack.xml' '$xml_location=Xml' || (rm ../lib/help_html/ap_stack.html && test -f ../lib/help_html/ap_stack.html) >sabcmd to_html.xsl Xml/dist.xml ../lib/help_html/dist.html '$myname=dist.xml' '$xml_location=Xml' || (rm ../lib/help_html/dist.html && test -f ../lib/help_html/dist.html) >sabcmd to_html.xsl Xml/sel_fil.xml ../lib/help_html/sel_fil.html '$myname=sel_fil.xml' '$xml_location=Xml' || (rm ../lib/help_html/sel_fil.html && test -f ../lib/help_html/sel_fil.html) >sabcmd to_html.xsl Xml/probedesignresult.xml ../lib/help_html/probedesignresult.html '$myname=probedesignresult.xml' '$xml_location=Xml' || (rm ../lib/help_html/probedesignresult.html && test -f ../lib/help_html/probedesignresult.html) >sabcmd to_html.xsl Xml/tags.xml ../lib/help_html/tags.html '$myname=tags.xml' '$xml_location=Xml' || (rm ../lib/help_html/tags.html && test -f ../lib/help_html/tags.html) >sabcmd to_html.xsl Xml/prompt/format_alignments.xml ../lib/help_html/prompt/format_alignments.html '$myname=prompt/format_alignments.xml' '$xml_location=Xml' || (rm ../lib/help_html/prompt/format_alignments.html && test -f ../lib/help_html/prompt/format_alignments.html) >cp -p Logo_25wht.gif ../lib/help_html/Logo_25wht.gif >make[5]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/HELP_SOURCE' >make html_index >make[5]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/HELP_SOURCE' >find ../lib/help_html -name "*.html" >html.list >echo '<HTML><HEAD><TITLE>Arb-Help Index</TITLE></HEAD>' >_index.html >echo '<BODY>' >>_index.html >cat html.list | sed -e 's/^\(.*\)$/<A href="\1">\1<\/A> /' >>_index.html >echo '</BODY></HTML>' >>_index.html >make[5]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/HELP_SOURCE' >make[4]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213/HELP_SOURCE' >make[3]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213' >make[2]: *** [arb] Error 2 >make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213' >make[1]: *** [all] Error 2 >make[1]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213' >make: *** [rebuild] Error 2 >emake failed > * ERROR: sci-biology/arb-5.1-r1 failed: > * (no error message) > * > * Call stack: > * ebuild.sh, line 56: Called src_compile > * environment, line 2503: Called die > * The specific snippet of code: > * emake ARBHOME="${S}" PATH="${PATH}:${S}/bin" LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:${S}/lib" tarfile || die; > * > * If you need support, post the output of 'emerge --info =sci-biology/arb-5.1-r1', > * the complete build log and the output of 'emerge -pqv =sci-biology/arb-5.1-r1'. > * The complete build log is located at '/var/log/portage/build/sci-biology/arb-5.1-r1:20101011-125451.log'. > * The ebuild environment file is located at '/var/tmp/portage/sci-biology/arb-5.1-r1/temp/environment'. > * S: '/var/tmp/portage/sci-biology/arb-5.1-r1/work/arbsrc_6213'
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