* 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 ‘const char* aisc_debug_local(aisc_com*, int, long int, char*, ...)’:
C/debug.c:115:37: warning: ignoring return value of ‘size_t fwrite(const void*, size_t, size_t, FILE*)’, 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 ‘const char* aisc_debug_local(aisc_com*, int, long int, char*, ...)’:
C/debug.c:115:37: warning: ignoring return value of ‘size_t fwrite(const void*, size_t, size_t, FILE*)’, 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 ‘pngLoadRawF’:
glpng.c:288:5: warning: ‘jmpbuf’ is deprecated (declared at /usr/include/png.h:1098)
glpng.c: In function ‘pngLoadF’:
glpng.c:393:5: warning: ‘jmpbuf’ is deprecated (declared at /usr/include/png.h:1098)
glpng.c:385:10: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
glpng.c: In function ‘pngLoadRawF’:
glpng.c:280:10: warning: ignoring return value of ‘fread’, 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 ‘const char* alignCompactedTo(AWTC_CompactedSubSequence*, const AWTC_FastSearchSequence*, int, const char*, long int, GBDATA*, GBDATA*, const AlignParams&)’:
fast_aligner.cxx:1254:31: warning: ‘GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)’ is deprecated (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: ‘GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)’ 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 ‘AD_ERR* AD_CONT::create(AD_SPECIES*, AD_ALI*)’:
adseq.cxx:1012:20: warning: ‘GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)’ is deprecated (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: ‘GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)’ 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 ‘const char* export_species_using_form(FILE*, GBDATA*, const char*)’:
AWTI_export.cxx:511:32: warning: ignoring return value of ‘size_t fwrite(const void*, size_t, size_t, FILE*)’, 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 ‘void gen_extract_gene_2_pseudoSpecies(GBDATA*, GBDATA*, EG2PS_data*)’:
GEN_map.cxx:882:39: warning: ‘GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)’ is deprecated (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: ‘GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)’ 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 ‘selected_range’
i686-pc-linux-gnu-g++ -O2 -pipe  -O4 -pipe -fmessage-length=0 -funit-at-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 ‘arb_look_and_start_server’:
servercntrl.c:202:35: warning: ignoring return value of ‘system’, declared with attribute warn_unused_result
servercntrl.c: In function ‘arb_start_server’:
servercntrl.c:145:68: warning: ignoring return value of ‘system’, 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 ‘const char* SQ_reset_quality_calcstate(GBDATA*)’:
SQ_functions.cxx:82:21: warning: ‘const char* GB_get_error()’ 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: ‘const char* GB_get_error()’ 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: ‘const char* GB_get_error()’ 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: ‘const char* GB_get_error()’ 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 ‘const char* SQ_evaluate(GBDATA*, const SQ_weights&, bool)’:
SQ_functions.cxx:239:21: warning: ‘const char* GB_get_error()’ 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: ‘const char* GB_get_error()’ 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 ‘const char* SQ_pass1(SQ_GroupData*, GBDATA*, GBT_TREE*, AP_filter*)’:
SQ_functions.cxx:450:17: warning: ‘const char* GB_get_error()’ 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: ‘const char* GB_get_error()’ 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: ‘const char* GB_get_error()’ 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: ‘const char* GB_get_error()’ 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: ‘const char* GB_get_error()’ 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: ‘const char* GB_get_error()’ 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 ‘const char* SQ_pass1_no_tree(SQ_GroupData*, GBDATA*, AP_filter*)’:
SQ_functions.cxx:554:21: warning: ‘const char* GB_get_error()’ 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: ‘const char* GB_get_error()’ 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: ‘const char* GB_get_error()’ 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: ‘const char* GB_get_error()’ 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: ‘const char* GB_get_error()’ 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: ‘const char* GB_get_error()’ 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 ‘const char* SQ_pass2(const SQ_GroupData*, GBDATA*, GBT_TREE*, AP_filter*)’:
SQ_functions.cxx:649:17: warning: ‘const char* GB_get_error()’ is deprecated (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: ‘const char* GB_get_error()’ 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: ‘const char* GB_get_error()’ 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: ‘const char* GB_get_error()’ 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: ‘const char* GB_get_error()’ 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: ‘const char* GB_get_error()’ 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: ‘const char* GB_get_error()’ 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: ‘const char* GB_get_error()’ 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: ‘const char* GB_get_error()’ 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: ‘const char* GB_get_error()’ 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 ‘const char* SQ_pass2_no_tree(const SQ_GroupData*, GBDATA*, AP_filter*)’:
SQ_functions.cxx:889:21: warning: ‘const char* GB_get_error()’ is deprecated (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: ‘const char* GB_get_error()’ 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: ‘const char* GB_get_error()’ 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: ‘const char* GB_get_error()’ 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: ‘const char* GB_get_error()’ 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: ‘const char* GB_get_error()’ 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: ‘const char* GB_get_error()’ 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: ‘const char* GB_get_error()’ 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: ‘const char* GB_get_error()’ 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: ‘const char* GB_get_error()’ 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 ‘const char* SQ_count_nr_of_species(GBDATA*)’:
SQ_functions.cxx:1120:21: warning: ‘const char* GB_get_error()’ 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: ‘const char* GB_get_error()’ 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: ‘const char* GB_get_error()’ 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: ‘const char* GB_get_error()’ 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 ‘void Node::print()’:
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 ‘void st_ml_add_quality_string_to_species(GBDATA*, const char*, const char*, int, int, GB_HASH*, st_report_enum, const char*)’:
ST_quality.cxx:168:33: warning: ‘GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)’ is deprecated (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: ‘GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)’ 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 ‘void DBwriter::writeSequence(const SequenceBuffer&)’:
DBwriter.cxx:226:23: warning: ‘GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)’ 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: ‘GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)’ 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 ‘quotedText’
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 ‘const char* detect_bitmap_size(const char*, int*, int*)’:
AW_button.cxx:398:47: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result
AW_button.cxx:417:51: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result
AW_button.cxx:418:51: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, 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 ‘AW_awar* AW_root::awar_pointer(const char*, void*, GBDATA*)’:
AW_nawar.cxx:193:111: warning: passing NULL to non-pointer argument 4 of ‘AW_awar::AW_awar(AW_VARIABLE_TYPE, const char*, const char*, double, GBDATA*, AW_root*)’
i686-pc-linux-gnu-g++ -O2 -pipe   -O4 -pipe -fmessage-length=0 -funit-at-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 ‘int aw_status_read_int(int, int)’:
AW_status.cxx:281:19: warning: dereferencing type-punned pointer will break strict-aliasing rules
AW_status.cxx: In function ‘void aw_help_edit_help(AW_window*)’:
AW_status.cxx:1746:25: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result
AW_status.cxx: In function ‘void aw_status_timer_event(AW_root*, AW_CL, AW_CL)’:
AW_status.cxx:419:28: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result
i686-pc-linux-gnu-g++ -O2 -pipe   -O4 -pipe -fmessage-length=0 -funit-at-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 ‘GBS_string_eval’:
admatch.c:763:37: warning: ignoring return value of ‘gbs_build_replace_string’, declared with attribute warn_unused_result
arbdb.c: In function ‘GB_copy_with_protection’:
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 ‘GB_get_full_path’:
adsocket.c:1256:21: warning: ignoring return value of ‘realpath’, declared with attribute warn_unused_result
adsocket.c:1260:21: warning: ignoring return value of ‘realpath’, 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 ‘gb_search’:
adquery.c:449:28: warning: comparison between ‘GB_TYPES’ and ‘enum gb_search_enum’
adquery.c:455:28: warning: comparison between ‘GB_TYPES’ and ‘enum gb_search_enum’
adquery.c:526:31: warning: comparison between ‘GB_TYPES’ and ‘enum gb_search_enum’
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 ‘gb_write_bin_rek’:
ad_save_load.c:799:13: warning: null argument where non-null required (argument 1)
ad_save_load.c: In function ‘GB_save_as’:
ad_save_load.c:1079:5: warning: ‘GB_get_error’ is deprecated (declared at ./ad_prot.h:43)
ad_save_load.c: In function ‘GB_save_quick_as’:
ad_save_load.c:1122:5: warning: ‘GB_get_error’ is deprecated (declared at ./ad_prot.h:43)
ad_save_load.c:1123:5: warning: ‘GB_get_error’ is deprecated (declared at ./ad_prot.h:43)
ad_save_load.c:1145:9: warning: ‘GB_get_error’ is deprecated (declared at ./ad_prot.h:43)
ad_save_load.c:1170:9: warning: ‘GB_get_error’ is deprecated (declared at ./ad_prot.h:43)
ad_save_load.c:1181:9: warning: ‘GB_get_error’ is deprecated (declared at ./ad_prot.h:43)
ad_save_load.c: In function ‘GB_save_quick’:
ad_save_load.c:1206:5: warning: ‘GB_get_error’ is deprecated (declared at ./ad_prot.h:43)
ad_save_load.c:1207:5: warning: ‘GB_get_error’ is deprecated (declared at ./ad_prot.h:43)
ad_save_load.c:1228:9: warning: ‘GB_get_error’ is deprecated (declared at ./ad_prot.h:43)
ad_save_load.c:1261:5: warning: ‘GB_get_error’ is deprecated (declared at ./ad_prot.h:43)
ad_save_load.c: In function ‘gb_check_saveable’:
ad_save_load.c:1301:9: warning: ‘GB_get_error’ is deprecated (declared at ./ad_prot.h:43)
ad_save_load.c:1306:9: warning: ‘GB_get_error’ is deprecated (declared at ./ad_prot.h:43)
ad_save_load.c: In function ‘gb_write_bin’:
ad_save_load.c:824:11: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
ad_save_load.c:827:11: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
ad_save_load.c:842:11: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
ad_save_load.c:850:11: warning: ignoring return value of ‘fwrite’, 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 ‘GB_login’:
ad_load.c:1380:34: warning: ignoring return value of ‘gb_scan_directory’, declared with attribute warn_unused_result
admap.c: In function ‘gb_is_valid_mapfile’:
admap.c:722:14: warning: ignoring return value of ‘fread’, 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 ‘GBT_check_arb_file’:
adtools.c:74:10: warning: ignoring return value of ‘fgets’, 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 ‘GBT_create_sequence_data’:
adali.c:597:5: warning: ‘GBT_add_data’ 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 ‘void aed_start_naligning(AW_window*)’:
edit_naligner.cxx:102:19: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result
i686-pc-linux-gnu-g++ -O2 -pipe  -O4 -pipe -fmessage-length=0 -funit-at-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 ‘GBS_string_eval’:
admatch.c:763:37: warning: ignoring return value of ‘gbs_build_replace_string’, 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 ‘GB_copy_with_protection’:
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 ‘GB_get_full_path’:
adsocket.c:1256:21: warning: ignoring return value of ‘realpath’, declared with attribute warn_unused_result
adsocket.c:1260:21: warning: ignoring return value of ‘realpath’, 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 ‘gb_search’:
adquery.c:449:28: warning: comparison between ‘GB_TYPES’ and ‘enum gb_search_enum’
adquery.c:455:28: warning: comparison between ‘GB_TYPES’ and ‘enum gb_search_enum’
adquery.c:526:31: warning: comparison between ‘GB_TYPES’ and ‘enum gb_search_enum’
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 ‘gb_write_bin_rek’:
ad_save_load.c:799:13: warning: null argument where non-null required (argument 1)
ad_save_load.c: In function ‘GB_save_as’:
ad_save_load.c:1079:5: warning: ‘GB_get_error’ is deprecated (declared at ./ad_prot.h:43)
ad_save_load.c: In function ‘GB_save_quick_as’:
ad_save_load.c:1122:5: warning: ‘GB_get_error’ is deprecated (declared at ./ad_prot.h:43)
ad_save_load.c:1123:5: warning: ‘GB_get_error’ is deprecated (declared at ./ad_prot.h:43)
ad_save_load.c:1145:9: warning: ‘GB_get_error’ is deprecated (declared at ./ad_prot.h:43)
ad_save_load.c:1170:9: warning: ‘GB_get_error’ is deprecated (declared at ./ad_prot.h:43)
ad_save_load.c:1181:9: warning: ‘GB_get_error’ is deprecated (declared at ./ad_prot.h:43)
ad_save_load.c: In function ‘GB_save_quick’:
ad_save_load.c:1206:5: warning: ‘GB_get_error’ is deprecated (declared at ./ad_prot.h:43)
ad_save_load.c:1207:5: warning: ‘GB_get_error’ is deprecated (declared at ./ad_prot.h:43)
ad_save_load.c:1228:9: warning: ‘GB_get_error’ is deprecated (declared at ./ad_prot.h:43)
ad_save_load.c:1261:5: warning: ‘GB_get_error’ is deprecated (declared at ./ad_prot.h:43)
ad_save_load.c: In function ‘gb_check_saveable’:
ad_save_load.c:1301:9: warning: ‘GB_get_error’ is deprecated (declared at ./ad_prot.h:43)
ad_save_load.c:1306:9: warning: ‘GB_get_error’ is deprecated (declared at ./ad_prot.h:43)
ad_save_load.c: In function ‘gb_write_bin’:
ad_save_load.c:824:11: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
ad_save_load.c:827:11: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
ad_save_load.c:842:11: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
ad_save_load.c:850:11: warning: ignoring return value of ‘fwrite’, 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 ‘GB_login’:
ad_load.c:1380:34: warning: ignoring return value of ‘gb_scan_directory’, 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 ‘gb_is_valid_mapfile’:
admap.c:722:14: warning: ignoring return value of ‘fread’, 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 ‘GBT_check_arb_file’:
adtools.c:74:10: warning: ignoring return value of ‘fgets’, 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 ‘GBT_create_sequence_data’:
adali.c:597:5: warning: ‘GBT_add_data’ 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 ‘GBS_string_eval’:
admatch.c:763:37: warning: ignoring return value of ‘gbs_build_replace_string’, 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 ‘GB_copy_with_protection’:
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 ‘GB_get_full_path’:
adsocket.c:1256:21: warning: ignoring return value of ‘realpath’, declared with attribute warn_unused_result
adsocket.c:1260:21: warning: ignoring return value of ‘realpath’, 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 ‘gb_search’:
adquery.c:449:28: warning: comparison between ‘GB_TYPES’ and ‘enum gb_search_enum’
adquery.c:455:28: warning: comparison between ‘GB_TYPES’ and ‘enum gb_search_enum’
adquery.c:526:31: warning: comparison between ‘GB_TYPES’ and ‘enum gb_search_enum’
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 ‘gb_write_bin_rek’:
ad_save_load.c:799:13: warning: null argument where non-null required (argument 1)
ad_save_load.c: In function ‘GB_save_as’:
ad_save_load.c:1079:5: warning: ‘GB_get_error’ is deprecated (declared at ./ad_prot.h:43)
ad_save_load.c: In function ‘GB_save_quick_as’:
ad_save_load.c:1122:5: warning: ‘GB_get_error’ is deprecated (declared at ./ad_prot.h:43)
ad_save_load.c:1123:5: warning: ‘GB_get_error’ is deprecated (declared at ./ad_prot.h:43)
ad_save_load.c:1145:9: warning: ‘GB_get_error’ is deprecated (declared at ./ad_prot.h:43)
ad_save_load.c:1170:9: warning: ‘GB_get_error’ is deprecated (declared at ./ad_prot.h:43)
ad_save_load.c:1181:9: warning: ‘GB_get_error’ is deprecated (declared at ./ad_prot.h:43)
ad_save_load.c: In function ‘GB_save_quick’:
ad_save_load.c:1206:5: warning: ‘GB_get_error’ is deprecated (declared at ./ad_prot.h:43)
ad_save_load.c:1207:5: warning: ‘GB_get_error’ is deprecated (declared at ./ad_prot.h:43)
ad_save_load.c:1228:9: warning: ‘GB_get_error’ is deprecated (declared at ./ad_prot.h:43)
ad_save_load.c:1261:5: warning: ‘GB_get_error’ is deprecated (declared at ./ad_prot.h:43)
ad_save_load.c: In function ‘gb_check_saveable’:
ad_save_load.c:1301:9: warning: ‘GB_get_error’ is deprecated (declared at ./ad_prot.h:43)
ad_save_load.c:1306:9: warning: ‘GB_get_error’ is deprecated (declared at ./ad_prot.h:43)
ad_save_load.c: In function ‘gb_write_bin’:
ad_save_load.c:824:11: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
ad_save_load.c:827:11: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
ad_save_load.c:842:11: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
ad_save_load.c:850:11: warning: ignoring return value of ‘fwrite’, 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 ‘GB_login’:
ad_load.c:1380:34: warning: ignoring return value of ‘gb_scan_directory’, 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 ‘gb_is_valid_mapfile’:
admap.c:722:14: warning: ignoring return value of ‘fread’, 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 ‘GBT_check_arb_file’:
adtools.c:74:10: warning: ignoring return value of ‘fgets’, 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 ‘GBT_create_sequence_data’:
adali.c:597:5: warning: ‘GBT_add_data’ 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 ‘newIsland’:
align.c:312:49: warning: ‘iii’ may be used uninitialized in this function
align.c:312:53: warning: ‘jjj’ 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 ‘updateTrnsprob’:
trnsprob.c:217:14: warning: ‘a’ may be used uninitialized in this function
trnsprob.c:217:16: warning: ‘b’ may be used uninitialized in this function
trnsprob.c:217:18: warning: ‘c’ may be used uninitialized in this function
trnsprob.c:217:20: warning: ‘d’ may be used uninitialized in this function
trnsprob.c:217:22: warning: ‘e’ may be used uninitialized in this function
trnsprob.c:217:24: warning: ‘f’ 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 ‘void awt_aps_go(AW_window*)’:
AWT_asciiprint.cxx:228:86: warning: ignoring return value of ‘size_t fwrite(const void*, size_t, size_t, FILE*)’, 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 ‘void AWT_print_tree_to_file_xfig(AW_window*, AW_CL)’:
AWT_canio.cxx:268:53: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result
i686-pc-linux-gnu-g++ -O2 -pipe   -O4 -pipe -fmessage-length=0 -funit-at-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 ‘int main(int, char**)’:
DI_main.cxx:71:63: warning: ignoring return value of ‘const char* ARB_init_global_awars(AW_root*, GBDATA*, GBDATA*)’, declared with attribute warn_unused_result
DI_matr.cxx: In member function ‘char* DI_MATRIX::load(char*, AP_filter*, AP_weights*, LoadWhat, const char*, bool, GBDATA**)’:
DI_matr.cxx:278:9: warning: ‘no_of_species’ may be used uninitialized in this function
DI_matr.cxx:270:13: warning: ‘gb_species’ 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 ‘const char* CON_export(char*, char*, int**, char*, int*, char*, int, long int, long int, int, int, int, double, double, int, int)’:
AP_consensus.cxx:409:23: warning: ‘GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)’ is deprecated (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: ‘GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)’ 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: ‘GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)’ 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: ‘GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)’ 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: ‘GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)’ 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: ‘GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)’ 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 ‘void CON_calc_max_freq_cb(AW_window*)’:
AP_consensus.cxx:962:27: warning: ‘GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)’ is deprecated (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: ‘GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)’ 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: ‘GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)’ 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: ‘GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)’ 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: ‘GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)’ 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: ‘GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)’ 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 ‘void AP_conservProfile2Gnuplot_callback(AW_window*)’:
AP_conservProfile2Gnuplot.cxx:58:42: warning: ignoring return value of ‘const char* GB_xcmd(const char*, GB_BOOL, GB_BOOL)’, declared with attribute warn_unused_result
AP_cprofile.cxx: In function ‘void CPRO_condense_cb(AW_window*, AW_CL)’:
AP_cprofile.cxx:1420:14: warning: ‘GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)’ is deprecated (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: ‘GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)’ 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: ‘GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)’ 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: ‘GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)’ 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 ‘char* get_overlay_files(AW_root*, const char*, const char*&)’:
AP_csp_2_gnuplot.cxx:92:50: warning: ‘const char* GB_get_error()’ is deprecated (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: ‘const char* GB_get_error()’ 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: ‘const char* GB_get_error()’ 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: ‘const char* GB_get_error()’ 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 ‘void AP_csp_2_gnuplot_cb(AW_window*, AW_CL, AW_CL)’:
AP_csp_2_gnuplot.cxx:388:62: warning: ignoring return value of ‘const char* GB_xcmd(const char*, GB_BOOL, GB_BOOL)’, declared with attribute warn_unused_result
i686-pc-linux-gnu-g++ -O2 -pipe  -O4 -pipe -fmessage-length=0 -funit-at-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 ‘void NT_system_cb2(AW_window*, AW_CL, AW_CL)’:
NT_cb.cxx:128:35: warning: ignoring return value of ‘const char* GB_xcmd(const char*, GB_BOOL, GB_BOOL)’, declared with attribute warn_unused_result
i686-pc-linux-gnu-g++ -O2 -pipe  -O4 -pipe -fmessage-length=0 -funit-at-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 ‘const char* displayAlignmentInfo(GBDATA*, const char*, char*, char*)’:
NT_concatenate.cxx:310:37: warning: ‘GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)’ 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: ‘GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)’ 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 ‘void concatenateAlignments(AW_window*)’:
NT_concatenate.cxx:415:39: warning: ‘GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)’ 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: ‘GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)’ 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 ‘GBDATA* concatenateFieldsCreateNewSpecies(AW_window*, GBDATA*, SPECIES_ConcatenateList*)’:
NT_concatenate.cxx:664:39: warning: ‘GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)’ 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: ‘GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)’ 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 ‘int main(int, char**)’:
NT_main.cxx:399:50: warning: ignoring return value of ‘int system(const char*)’, 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 ‘void ad_field_convert_commit_cb(AW_window*, AW_CL)’:
ad_spec.cxx:729:29: warning: unused variable ‘selector’
ad_transpro.cxx: In function ‘const char* arb_r2a(GBDATA*, bool, bool, int, bool, const char*, const char*)’:
ad_transpro.cxx:159:48: warning: ‘GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)’ is deprecated (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: ‘GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)’ 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 ‘char* readXmlTree(char*)’:
ad_trees.cxx:418:44: warning: ignoring return value of ‘const char* GB_xcmd(const char*, GB_BOOL, GB_BOOL)’, declared with attribute warn_unused_result
ad_trees.cxx:422:44: warning: ignoring return value of ‘const char* GB_xcmd(const char*, GB_BOOL, GB_BOOL)’, declared with attribute warn_unused_result
-------------------- 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 ‘const char* PHDATA::calculate_matrix(const char*, double, PH_TRANSFORMATION)’:
PH_data.cxx:201:5: warning: ‘options_vector[0]’ may be used uninitialized in this function
PH_data.cxx:210:5: warning: ‘options_vector[1]’ may be used uninitialized in this function
PH_data.cxx:219:5: warning: ‘options_vector[2]’ 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 ‘const char* PH_create_ml_multiline_SAI(const char*, int, GBDATA**)’:
PH_main.cxx:157:31: warning: ‘GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)’ 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: ‘GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)’ 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: ‘GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)’ 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: ‘GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)’ 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 ‘void PH_save_ml_cb(AW_window*)’:
PH_main.cxx:330:31: warning: ‘GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)’ is deprecated (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: ‘GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)’ 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: ‘GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)’ 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: ‘GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)’ 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 ‘int main(int, char**)’:
PH_main.cxx:576:63: warning: ignoring return value of ‘const char* ARB_init_global_awars(AW_root*, GBDATA*, GBDATA*)’, 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 ‘void RNA3D_StartApplication(AW_root*)’:
RNA3D_Main.cxx:73:32: warning: ‘const char* GB_get_error()’ 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: ‘const char* GB_get_error()’ 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 ‘void initExtensions()’:
RNA3D_OpenGLEngine.cxx:125:44: warning: ignoring return value of ‘int scanf(const char*, ...)’, declared with attribute warn_unused_result
RNA3D_Interface.cxx: In function ‘AW_window* CreateDisplayHelices_window(AW_root*)’:
RNA3D_Interface.cxx:469:25: warning: ‘helixRange’ 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 ‘void Structure3D::ReadCoOrdinateFile()’:
RNA3D_StructureData.cxx:222:18: warning: ‘pos’ may be used uninitialized in this function
RNA3D_StructureData.cxx: In member function ‘void Structure3D::GetSecondaryStructureInfo()’:
RNA3D_StructureData.cxx:327:25: warning: array subscript is above array bounds
RNA3D_StructureData.cxx:326:9: warning: ‘pos’ may be used uninitialized in this function
RNA3D_StructureData.cxx:326:14: warning: ‘helixNr’ may be used uninitialized in this function
RNA3D_StructureData.cxx: In member function ‘void Structure3D::MapSearchStringsToEcoliTemplate(AW_root*)’:
RNA3D_StructureData.cxx:1542:61: warning: ‘vLastPt.Vector3::y’ may be used uninitialized in this function
RNA3D_StructureData.cxx:1542:61: warning: ‘vLastPt.Vector3::z’ may be used uninitialized in this function
RNA3D_StructureData.cxx:1542:61: warning: ‘vLastPt.Vector3::x’ 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 ‘const char* SEC_region::read(std::istream&, SEC_root*, int)’:
SEC_read.cxx:133:17: warning: ‘seq_start’ may be used uninitialized in this function
SEC_read.cxx:133:28: warning: ‘seq_end’ 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 ‘gb_main’
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 ‘void set_AWAR(const char*, char*)’:
arb_interface.cxx:722:18: warning: unused variable ‘error’
arb_interface.cxx: In function ‘void set_CONFIG(const char*, const char*)’:
arb_interface.cxx:764:18: warning: unused variable ‘error’
i686-pc-linux-gnu-g++ -O2 -pipe  -O4 -pipe -fmessage-length=0 -funit-at-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 ‘void imageDialog::set_ARB_image_path(const char*)’:
image_dialog.cxx:1189:18: warning: unused variable ‘error’
i686-pc-linux-gnu-g++ -O2 -pipe  -O4 -pipe -fmessage-length=0 -funit-at-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 ‘void GDE_export(NA_Alignment*, char*, long int)’:
GDE_event.cxx:305:39: warning: ‘GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)’ is deprecated (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: ‘GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)’ 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: ‘GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)’ 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: ‘GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)’ 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: ‘GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)’ 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: ‘GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)’ 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 ‘void GDE_startaction_cb(AW_window*, GmenuItem*, AW_CL)’:
GDE_event.cxx:557:23: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result
i686-pc-linux-gnu-g++ -O2 -pipe  -O4 -pipe -fmessage-length=0 -funit-at-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 ‘char* strncpy(char*, const char*, size_t)’,
    inlined from ‘void ReadGDE(char*, NA_Alignment*, int)’ 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 ‘void ReadCMask(const char*)’:
GDE_FileIO.cxx:837:48: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result
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 ‘void PV_WriteTranslatedSequenceToDB(ED4_AA_sequence_terminal*, char*)’:
ED4_ProteinViewer.cxx:498:44: warning: ‘GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)’ is deprecated (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: ‘GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)’ 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 ‘void load_search_paras_from_file(AW_window*, AW_CL)’:
ED4_search.cxx:1616:38: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result
i686-pc-linux-gnu-g++ -O2 -pipe  -O4 -pipe -fmessage-length=0 -funit-at-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 ‘void sina_start(AW_window*, AW_CL)’:
graph_aligner_gui.cxx:171:63: warning: ignoring return value of ‘size_t fwrite(const void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result
graph_aligner_gui.cxx:172:42: warning: ignoring return value of ‘size_t fwrite(const void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result
graph_aligner_gui.cxx:189:55: warning: ignoring return value of ‘size_t fwrite(const void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result
graph_aligner_gui.cxx:190:46: warning: ignoring return value of ‘size_t fwrite(const void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result
graph_aligner_gui.cxx:204:55: warning: ignoring return value of ‘size_t fwrite(const void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result
graph_aligner_gui.cxx:205:46: warning: ignoring return value of ‘size_t fwrite(const void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result
edit_naligner.cxx: In function ‘void aed_start_naligning(AW_window*)’:
edit_naligner.cxx:102:19: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result
ED4_dots.cxx: In function ‘void dot_missing_bases(AW_window*)’:
ED4_dots.cxx:151:21: warning: ‘sai_len’ 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 ‘char* AWTC_constructSequence(int, const char**, int, char**)’:
AWTC_constructSequence.cxx:507:11: warning: unused variable ‘resultSeq’
AWTC_constructSequence.cxx:509:9: warning: unused variable ‘off’
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 ‘int PTD(POS_TREE*)’:
PT_prefixtree.cxx:174:5: warning: dereferencing type-punned pointer will break strict-aliasing rules
PT_prefixtree.cxx: In function ‘POS_TREE* PT_change_leaf_to_node(PTM2*, POS_TREE*)’:
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 ‘POS_TREE* PT_leaf_to_chain(PTM2*, POS_TREE*)’:
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 ‘POS_TREE* PT_create_leaf(PTM2*, POS_TREE**, PT_BASES, int, int, int)’:
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 ‘void PTD_clear_fathers(PTM2*, POS_TREE*)’:
PT_prefixtree.cxx:389:5: warning: dereferencing type-punned pointer will break strict-aliasing rules
PT_prefixtree.cxx: In function ‘void PTD_put_int(FILE*, ULONG)’:
PT_prefixtree.cxx:424:5: warning: dereferencing type-punned pointer will break strict-aliasing rules
PT_prefixtree.cxx: In function ‘void PTD_put_short(FILE*, ULONG)’:
PT_prefixtree.cxx:436:5: warning: dereferencing type-punned pointer will break strict-aliasing rules
PT_prefixtree.cxx: In function ‘void PTD_set_object_to_saved_status(POS_TREE*, long int, int)’:
PT_prefixtree.cxx:443:5: warning: dereferencing type-punned pointer will break strict-aliasing rules
PT_prefixtree.cxx: In function ‘long int PTD_write_leafs_to_disk(FILE*, PTM2*, POS_TREE*, long int, long int*, int*)’:
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 ‘void pd_query_pt_server(AW_window*)’:
probe_design.cxx:1769:35: warning: ignoring return value of ‘const char* GB_xcmd(const char*, GB_BOOL, GB_BOOL)’, declared with attribute warn_unused_result
i686-pc-linux-gnu-g++ -O2 -pipe  -O4 -pipe -fmessage-length=0 -funit-at-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 ‘int ALI_ARBDB::put_SAI(const char*, char*)’:
ali_arbdb.cxx:157:27: warning: ‘GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)’ is deprecated (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: ‘GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)’ 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'