Build log

arb-5.2:20110808-155917.log (text/plain), 70.67 KB, created by Diego Elio Pettenò (RETIRED) on 2011-08-08 16:08:32 UTC

 * Package:    sci-biology/arb-5.2
 * Repository: gentoo
 * Maintainer: [e-mail] [e-mail]
 * USE:        elibc_glibc kernel_linux opengl test userland_GNU x86
 * FEATURES:   sandbox test userpriv usersandbox
>>> Unpacking source...
>>> Unpacking arb-5.2.tgz to /var/tmp/portage/sci-biology/arb-5.2/work
>>> Unpacking arb-5.2-linker.patch.bz2 to /var/tmp/portage/sci-biology/arb-5.2/work
>>> Source unpacked in /var/tmp/portage/sci-biology/arb-5.2/work
>>> Preparing source in /var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2 ...
 * Applying arb-5.2-linker.patch ...
 [ ok ]
 * Applying 5.1-libs.patch ...
 [ ok ]
 * Applying 5.1-bfr-overflow.patch ...
 [ ok ]
make -j14 ARBHOME=/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2 links 
SOURCE_TOOLS/generate_all_links.sh
make[1]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/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-5.2/work/arb-5.2/bin'
generate_all_links.sh done.
touch SOURCE_TOOLS/generate_all_links.stamp
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2 ...
>>> Source configured.
>>> Compiling source in /var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2 ...
make -j14 ARBHOME=/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2 PATH=/usr/lib/portage/bin/ebuild-helpers/4:/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/4.6.0:/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:/opt/c3-4:/opt/hp/hpacucli:/usr/libexec/gpc/i686-pc-linux-gnu/3.4:/opt/firebird/bin:/opt/tivoli/tsm/client/ba/bin:/opt/eagle-5.11.0/bin:/opt/flexlm/bin:/opt/vmware/vix/bin:/opt/cuda/bin:/opt/ec2-api-tools/bin:/usr/ti-linux-gnu/tigcc-bin/4.1.2:/usr/ti-linux-gnu/bin:/var/vpopmail/bin:/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin LD_LIBRARY_PATH=:/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/lib tarfile 
make clean2
make[1]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2'
make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/AISC_MKPTPS'
rm -f mkptypes.o aisc_mkpt
make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/AISC'
rm -f aisc.o aisc_commands.o aisc_var_ref.o aisc_mix.o aisc
make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/AISC_MKPTPS'
make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/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-5.2/work/arb-5.2/ALIV3'
rm -f a3.o a3_seq.o a3_ptree1.o a3_ptree2.o a3_helix.o a3_darray.o a3_ali.o a3_matrix.o a3_arbdb.o a3_basen.o  *.a
make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/ARBDBPP'
rm -f adtsequence.o adt_edit.o adtali.o adextended.o adseq.o adspecies.o admain.o adali.o  liste.o *.a *.so
make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/ARBDB'
rm -f adsort.o adlang1.o adstring.o admatch.o arbdb.o ad_core.o admath.o adoptimize.o adsystem.o adindex.o adperl.o adlink.o adsocket.o adcomm.o adhash.o adquery.o ad_save_load.o adcompr.o admalloc.o ad_load.o admap.o adTest.o adtune.o adGene.o adtcp.o adhashtools.o adExperiment.o adtools.o adseqcompr.o adtables.o adRevCompl.o adChangeKey.o adali.o adcolumns.o adtree.o adname.o aditem.o arbdbpp.o ad_config.o *.a *.so
make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/ARBDB2'
rm -f adsort.o adlang1.o adstring.o admatch.o arbdb.o ad_core.o admath.o adoptimize.o adsystem.o adindex.o adperl.o adlink.o adsocket.o adcomm.o adhash.o adquery.o ad_save_load.o adcompr.o admalloc.o ad_load.o admap.o adTest.o adtune.o adGene.o adtcp.o adhashtools.o adExperiment.o adtools.o adseqcompr.o adtables.o adRevCompl.o adChangeKey.o adali.o adcolumns.o adtree.o adname.o aditem.o ad_config.o *.a *.so
make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/AISC'
make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/AWTC'
rm -f AWTC_next_neighbours.o AWTC_constructSequence.o AWTC_seq_search.o AWTC_submission.o *.a
make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/ARB_GDE'
rm -f GDE_ParseMenu.o GDE.o GDE_event.o GDE_arbdb_io.o  GDE_HGLfile.o GDE_Genbank.o GDE_FileIO.o *.a 
make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/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-5.2/work/arb-5.2/AWTI'
rm -f AWTI_import.o AWTI_export.o  *.a
make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/ALIV3'
make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/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-5.2/work/arb-5.2/ARBDBS'
rm -f adsort.o adlang1.o adstring.o admatch.o arbdb.o ad_core.o admath.o adoptimize.o adsystem.o adindex.o adperl.o adlink.o adsocket.o adcomm.o adhash.o adquery.o ad_save_load.o adcompr.o admalloc.o ad_load.o admap.o adTest.o adtune.o adGene.o adtcp.o adhashtools.o adExperiment.o adtools.o adseqcompr.o adtables.o adRevCompl.o adChangeKey.o adali.o adcolumns.o adtree.o adname.o aditem.o arbdbpp.o ad_config.o *.a
make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/PROBE'
make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/CONSENSUS_TREE'
make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/AWTI'
make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/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-5.2/work/arb-5.2/bin/arb_convert_aln
make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/AWTC'
make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/ARBDBPP'
make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/DBSERVER'
rm -f db_server.o *.a
make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/CONVERTALN'
make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/ARB_GDE'
make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/ARBDB2'
make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/AWT'
make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/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-5.2/work/arb-5.2/DBSERVER'
make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/GDE'
make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/ARBDBS'
make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/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]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/EISPACK'
rm -f eispack.o d_sign.o *.a
make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/EDIT'
make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/ARBDB'
make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/GL'
make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/GENOM'
rm -f GEN_interface.o GEN_map.o GEN_graphic.o GEN_gene.o GEN_nds.o GEN_color_groups.o GEN_translations.o EXP_interface.o EXP_main.o  *.a
make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/EISPACK'
make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/DIST'
make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/EDIT4'
rm -f ED4_protein_2nd_structure.o ED4_ProteinViewer.o ED4_search.o ED4_cursor.o ED4_dump.o ED4_nds.o ED4_secedit.o ED4_RNA3D.o ED4_main.o ED4_mini_classes.o ED4_edit_string.o ED4_base.o ED4_manager.o ED4_terminal.o ED4_root.o EDB_root_bact.o ED4_window.o ED4_members.o ED4_no_class.o ED4_list.o ED4_text_terminals.o ED4_tools.o ED4_block.o ED4_visualizeSAI.o edit_naligner.o graph_aligner_gui.o ED4_dots.o  *.a
make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/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-5.2/work/arb-5.2/GENOM_IMPORT'
make[3]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/GL/glpng'
rm -f glpng.o *.a
rm *.o
make[3]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/GL/glAW'
rm -f GLwMDrawA.o AW_window_ogl.o *.a
make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/MULTI_PROBE'
rm -f MP_main.o MP_Window.o MP_noclass.o MP_sonde.o MP_sondentopf.o MP_mo_liste.o MP_probe.o MP_GenerationDuplicates.o MP_Generation.o MP_probe_combi_statistic.o MP_probe_tabs.o MP_permute.o *.a
make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/GENOM'
make[3]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/GDE/CLUSTAL'
make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/ISLAND_HOPPING'
rm -f island_hopping.o i-hopper.o align.o memory.o trnsprob.o *.a
make[3]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/GDE/SUPPORT'
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-5.2/work/arb-5.2/bin/clustalv
make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/EDIT4'
make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/MERGE'
rm -f /var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/CAP2 /var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/Restriction /var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/Zuk_to_gen /var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/count /var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/findall /var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/lsadt /var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/sho_helix /var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/varpos
make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/NALIGNER'
rm -f ali_aligner.o ali_arbdb.o ali_global.o ali_main.o ali_pathmap.o ali_prealigner.o ali_profile.o ali_pt.o ali_sequence.o ali_solution.o  *.a
make[3]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/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]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/NAMES'
make[3]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/GDE/SUPPORT'
make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/ISLAND_HOPPING'
rm: cannot remove `*.o': No such file or directory
rm -f names.o *.a
make[2]: [clean] Error 1 (ignored)
rm *.a
make[3]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/GL/glAW'
make[3]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/GL/glpng'
make[3]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/GDE/CLUSTAL'
make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/GL'
make[3]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/GDE/MOLPHY'
make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/NAMES_COM'
make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/MULTI_PROBE'
make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/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
rm: make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/NALIGNER'
make[3]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/GDE/AxML'
rm -f axml.o /var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/axml
cannot remove `*.a': No such file or directory
make[2]: [clean] Error 1 (ignored)
rm *.bak
make[3]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/NAMES_COM'
rm -f *.[ao]
make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/NAMES'
make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/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-5.2/work/arb-5.2/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-5.2/work/arb-5.2/GDE/AxML'
make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/PHYLO'
rm -f PH_data.o PH_root.o PH_main.o PH_filt.o PH_display.o PH_matr.o *.a
make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/PRIMER_DESIGN'
rm -f PRD_Pair.o PRD_Item.o PRD_Node.o PRD_Range.o PRD_SequenceIterator.o PRD_SearchFIFO.o PRD_Design.o primer_design.o  *.a
make[3]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/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-5.2/work/arb-5.2/bin/raxmlHPC
make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/PROBE_COM'
make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/PGT'
make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/PROBE_DESIGN'
rm -f probe_design.o SaiProbeVisualization.o probe_match_parser.o *.a
rm -f */*.[ao]
make[3]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/GDE/RAxML'
make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/PARSIMONY'
make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/PRIMER_DESIGN'
make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/PHYLO'
make[3]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/PROBE_COM'
rm -f *.[ao]
make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/READSEQ'
rm -f readseq.o ureadseq.o /var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/arb_readseq 
make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/NTREE'
make[3]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/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-5.2/work/arb-5.2/bin/phyml
rm: cannot remove `*.bak': No such file or directory
make[2]: [clean] Error 1 (ignored)
rm *~
make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/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]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/READSEQ'
make[3]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/GDE/PHYML'
rm -f GENH/*
make[3]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/GDE/CLUSTALW'
rm -f *.o /var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/clustalw
rm -f /var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/PROBE_SET/bin/ps_show_result /var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/PROBE_SET/bin/ps_arb2asciipaths /var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/PROBE_SET/bin/ps_my2asciipaths /var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/PROBE_SET/bin/ps_my2ascii /var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/PROBE_SET/bin/ps_get_probes /var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/PROBE_SET/bin/ps_eval /var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/PROBE_SET/bin/ps_find /var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/PROBE_SET/bin/ps_detect /var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/PROBE_SET/bin/ps_merge /var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/PROBE_SET/bin/ps_convert /var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/PROBE_SET/bin/fb_test 
make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/PROBE_DESIGN'
make[3]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/GDE/PHYLIP'
rm -f /var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/clique /var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/consense /var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/contml /var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/contrast /var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/dnacomp /var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/dnadist /var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/dnainvar /var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/dnaml /var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/dnamlk /var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/dnamove /var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/dnapars /var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/dnapenny /var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/dolmove /var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/dollop /var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/dolpenny /var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/factor /var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/fitch /var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/gendist /var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/kitsch /var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/mix /var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/move /var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/neighbor /var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/pars /var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/penny /var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/proml /var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/promlk /var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/protdist /var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/protpars /var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/restdist /var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/restml /var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/retree /var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/seqboot /var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/treedist /var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/drawgram /var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/drawtree *.o
make[3]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/GDE/FASTDNAML'
rm -f fastDNAml.o /var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/fastdnaml
rm -f */*.[ao]
make[3]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/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-5.2/work/arb-5.2/bin/puzzle
make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/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]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/RNA3D'
make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/PROBE_SET'
make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/SERVERCNTRL'
make[3]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/GDE/FASTDNAML'
rm -f servercntrl.o *.a
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
rm -f GENC/*
make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/SEQ_QUALITY'
rm -f SQ_main.o SQ_functions.o SQ_GroupData.o *.a
make[3]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/GDE/CLUSTALW'
make[3]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/GDE/TREEPUZZLE'
rm: cannot remove `*~': No such file or directory
make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/SL'
make[3]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/GDE/PHYLIP'
make[2]: [clean] Error 1 (ignored)
rm *#
make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/GDE'
rm -f GENH/*
make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/SECEDIT'
make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/RNA3D'
rm: cannot remove `*#': No such file or directory
make[2]: [clean] Error 1 (ignored)
rm *\%
make[3]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/SL/TREE_READ'
rm -f  TreeRead.o TreeTools.o *.a
make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/STAT'
rm -f ST_quality.o ST_ml.o ST_window.o *.a
make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/SEQ_QUALITY'
rm -f .depends
make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/SERVERCNTRL'
make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/WETC'
rm -f WETC_main.o *.a
make[3]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/SL/TREE_WRITE'
rm -f  TreeWrite.o *.a
make[3]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/SL/TREE_READ'
make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/TOOLS'
make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/TREEGEN'
rm -f GENC/*
rm -f  base.o defines.o frand.o readcfg.o rns.o sim.o simcfg.o spreadin.o *.a
rm -f /var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/arb_2_ascii /var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/arb_2_bin /var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/arb_a2ps /var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/arb_count_chars /var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/arb_dnarates /var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/arb_export_rates /var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/arb_export_tree /var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/arb_gene_probe /var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/arb_message /var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/arb_notify /var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/arb_primer /var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/arb_probe /var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/arb_proto_2_xsub /var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/arb_read_tree /var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/arb_replace /var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/arb_swap_rnastr
make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/XML'
rm -f xml.o *.a
make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/STAT'
rm: cannot remove `*%': No such file or directory
make[2]: [clean] Error 1 (ignored)
make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/GENOM_IMPORT'
make[3]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/NAMES_COM'
make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/NAMES_COM'
make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/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
make[3]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/SL/TREE_WRITE'
make[3]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/SL/AW_HELIX'
rm -f  AW_helix.o *.a
make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/WETC'
make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/WINDOW'
rm -f AW_position.o AW_Xm.o AW_at.o AW_button.o AW_click.o AW_debug.o AW_device.o AW_font_group.o AW_global_awars.o AW_nawar.o AW_preset.o AW_print.o AW_question.o AW_size.o AW_status.o AW_window.o AW_xfig.o AW_xfigfont.o AW_xfont.o AW_xkey.o AW_window_Xm_interface.o  *.a *.so
make[3]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/SL/HELIX'
rm -f  BI_helix.o *.a
rm -f arb_2_ascii.o arb_2_bin.o arb_a2ps.o arb_count_chars.o arb_dnarates.o arb_export_rates.o arb_export_tree.o arb_gene_probe.o arb_message.o arb_notify.o arb_primer.o arb_probe.o arb_proto_2_xsub.o arb_read_tree.o arb_replace.o arb_swap_rnastr.o
make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/XML'
rm -f .depends
make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/TREEGEN'
make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/SOURCE_TOOLS'
rm -f generate_all_links.stamp
make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/TOOLS'
make[3]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/SL/HELIX'
make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin'
find . -type l            -exec rm {} \;
make[3]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/SL/DB_SCANNER'
rm -f  db_scanner.o  *.a
make[3]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/SL/AW_NAME'
rm -f  AW_rename.o AW_names_admin.o  *.a
make[3]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/SL/FILE_BUFFER'
rm -f  FileBuffer.o  *.a
make[3]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/SL/AW_HELIX'
make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/WINDOW'
make[3]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/PROBE_COM'
make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/SOURCE_TOOLS'
make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/PROBE_COM'
make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/PERL2ARB'
test -f Makefile && make clean
make[3]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/SL/REGEXPR'
rm -f  RegExpr.o *.a
make[3]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/SL/FAST_ALIGNER'
rm -f  fast_aligner.o ClustalV.o *.a
make[3]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/SL/FILE_BUFFER'
make[3]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/SL/DB_SCANNER'
make[3]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/SL/AW_NAME'
cat: helpfiles.lst: No such file or directory
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-5.2/work/arb-5.2/lib/ARB.pm /var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/lib/ARB.so	
make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/HELP_SOURCE'
rm -f arb_help2xml.o /var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/arb_help2xml
make[3]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/GDEHELP'
rm -f ./HELP_GEN/*.help
make[3]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/SL/REGEXPR'
make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/PERL2ARB'
rm -f _index.html `find ../lib/help -name "*.hlp"`
make[3]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/SL/FAST_ALIGNER'
make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/SL'
rm -f ./HELP_DOC_GEN/*.doc
rm -f html.list `find ../lib/help_html -name "*.html"`
make[3]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/GDEHELP'
make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/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-5.2/work/arb-5.2/HELP_SOURCE/genhelp'
rm -f *.hlp
make[3]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/HELP_SOURCE/genhelp'
make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/HELP_SOURCE'
find . -type f -perm -100 -exec rm {} \;
make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin'
rm -f *.last_gcc
make[1]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2'
make all
make[1]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2'
make links
make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2'
SOURCE_TOOLS/generate_all_links.sh
make[3]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/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-5.2/work/arb-5.2/bin'
generate_all_links.sh done.
touch SOURCE_TOOLS/generate_all_links.stamp
make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2'
make com
make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2'
-------------------------------------------------------------------------------- Make everything in AISC_MKPTPS
make[3]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/AISC_MKPTPS'
cc -O4 -pipe -fmessage-length=0 -funit-at-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.c 
i686-pc-linux-gnu-g++ -O2 -pipe -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu   -Wl,--export-dynamic  -rdynamic -o aisc_mkpt mkptypes.o
make[3]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/AISC_MKPTPS'
-------------------------------------------------------------------------------- Make everything in AISC
make[3]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/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-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
i686-pc-linux-gnu-g++ -O2 -pipe  -O4 -pipe -fmessage-length=0 -funit-at-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-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
i686-pc-linux-gnu-g++ -O2 -pipe  -O4 -pipe -fmessage-length=0 -funit-at-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-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
i686-pc-linux-gnu-g++ -O2 -pipe  -O4 -pipe -fmessage-length=0 -funit-at-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-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
aisc_commands.c: In function ‘int do_com_next(const char*)’:
aisc_commands.c:906:21: warning: variable ‘p’ set but not used [-Wunused-but-set-variable]
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-5.2/work/arb-5.2/AISC'
-------------------------------------------------------------------------------- Make everything in NAMES_COM
make[3]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/NAMES_COM'
make[4]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/NAMES_COM'
AISC/Makefile:95: .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-5.2/work/arb-5.2/SOURCE_TOOLS/mv_if_diff .depends_new .depends
.depends created.
make[4]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/NAMES_COM'
make[4]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/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
../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-5.2/work/arb-5.2/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_NAMES_COM -I/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/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-5.2/work/arb-5.2/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-5.2/work/arb-5.2/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-5.2/work/arb-5.2/INCLUDE -fno-strict-aliasing -Wno-unused -c -o O/aisc_extern.o C/aisc_extern.c -IGENH -I. -IC
../MAKEBIN/aisc AISC/aisc_debug_globals.pa names.aisc GENC/aisc_debug_globals.c GENH/aisc_server_extern.aisc GENH/import_proto.h
../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
i686-pc-linux-gnu-g++ -O2 -pipe  -O4 -pipe -fmessage-length=0 -funit-at-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-5.2/work/arb-5.2/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 [-Wunused-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-5.2/work/arb-5.2/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-5.2/work/arb-5.2/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-5.2/work/arb-5.2/INCLUDE -fno-strict-aliasing -Wno-unused -c -o names_extern.o names_extern.c -IGENH -I. -IC -DAISC_SAVE_YES
ld -r -o client.a O/client.o O/debug.o GENC/aisc_debug_globals.o
ld -r -o server.a O/server.o O/struct_man.o O/aisc_extern.o GENC/aisc_global.o GENC/aisc_server.o names_extern.o
make[4]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/NAMES_COM'
make[3]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/NAMES_COM'
-------------------------------------------------------------------------------- Make everything in PROBE_COM
make[3]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/PROBE_COM'
make[4]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/PROBE_COM'
AISC/Makefile:95: .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-5.2/work/arb-5.2/SOURCE_TOOLS/mv_if_diff .depends_new .depends
.depends created.
make[4]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/PROBE_COM'
make[4]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/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-5.2/work/arb-5.2/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-5.2/work/arb-5.2/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-5.2/work/arb-5.2/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-5.2/work/arb-5.2/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-5.2/work/arb-5.2/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-5.2/work/arb-5.2/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 [-Wunused-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-5.2/work/arb-5.2/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-5.2/work/arb-5.2/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-5.2/work/arb-5.2/INCLUDE -fno-strict-aliasing -Wno-unused -c -o PT_extern.o PT_extern.c -IGENH -I. -IC -DAISC_SAVE_NO
ld -r -o client.a O/client.o O/debug.o GENC/aisc_debug_globals.o
ld -r -o server.a O/server.o O/struct_man.o O/aisc_extern.o GENC/aisc_global.o GENC/aisc_server.o PT_extern.o
make[4]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/PROBE_COM'
make[3]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/PROBE_COM'
make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2'
make arb
make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2'
(cd lib;make all)
make[3]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/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-5.2/work/arb-5.2/lib/nas'
rm -f names.dat
cp names.dat.template names.dat
rm -f *%
make[4]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/lib/nas'
make[3]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/lib'
make arbbasic2
make[3]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2'
-------------------------------------------------------------------------------- Make everything in AISC_MKPTPS
make[4]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/AISC_MKPTPS'
make[4]: Nothing to be done for `dummy.a'.
make[4]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/AISC_MKPTPS'
-------------------------------------------------------------------------------- Make everything in AISC
make[4]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/AISC'
make[4]: Nothing to be done for `dummy.a'.
make[4]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/AISC'
-------------------------------------------------------------------------------- Make everything in NAMES_COM
make[4]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/NAMES_COM'
make[4]: `server.a' is up to date.
make[4]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/NAMES_COM'
-------------------------------------------------------------------------------- Make everything in PROBE_COM
make[4]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/PROBE_COM'
make[4]: `server.a' is up to date.
make[4]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/PROBE_COM'
-------------------------------------------------------------------------------- Make everything in NAMES_COM
make[4]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/NAMES_COM'
make[4]: `server.a' is up to date.
make[4]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/NAMES_COM'
-------------------------------------------------------------------------------- Make everything in TEMPLATES
make[4]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/TEMPLATES'
../SOURCE_TOOLS/build_info.pl 
make[4]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/TEMPLATES'
make SL/SL.dummy
make[4]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2'
-------------------------------------------------------------------------------- Make everything in GL
make[4]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/GL'
make[5]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/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-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include 
make[5]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/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-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include 
i686-pc-linux-gnu-g++ -O2 -pipe  -O4 -pipe -fmessage-length=0 -funit-at-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-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include -I/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/WINDOW 
In file included from glpng.c:38:0:
/usr/include/png.h:839:9: error: expected identifier or ‘(’ before ‘-’ token
/usr/include/png.h:840:9: error: expected identifier or ‘(’ before ‘-’ token
/usr/include/png.h:841:9: error: expected identifier or ‘(’ before ‘-’ token
/usr/include/png.h:842:9: error: expected identifier or ‘(’ before ‘-’ token
/usr/include/png.h:844:9: error: expected identifier or ‘(’ before ‘-’ token
/usr/include/png.h:848:9: error: expected identifier or ‘(’ before ‘-’ token
/usr/include/png.h:849:9: error: expected identifier or ‘(’ before ‘-’ token
/usr/include/png.h:861:9: error: expected identifier or ‘(’ before ‘-’ token
/usr/include/png.h:864:9: error: expected identifier or ‘(’ before ‘-’ token
/usr/include/png.h:871:9: error: expected identifier or ‘(’ before ‘-’ token
/usr/include/png.h:876:9: error: expected identifier or ‘(’ before ‘-’ token
/usr/include/png.h:880:9: error: expected identifier or ‘(’ before ‘-’ token
/usr/include/png.h:932:9: error: expected identifier or ‘(’ before ‘-’ token
/usr/include/png.h:934:9: error: expected identifier or ‘(’ before ‘-’ token
/usr/include/png.h:989:1: error: unknown type name ‘png_error_ptr’
/usr/include/png.h:989:1: error: unknown type name ‘png_error_ptr’
/usr/include/png.h:995:1: error: unknown type name ‘png_error_ptr’
/usr/include/png.h:995:1: error: unknown type name ‘png_error_ptr’
/usr/include/png.h:1040:1: error: unknown type name ‘png_error_ptr’
/usr/include/png.h:1040:1: error: unknown type name ‘png_error_ptr’
/usr/include/png.h:1040:1: error: unknown type name ‘png_malloc_ptr’
/usr/include/png.h:1040:1: error: unknown type name ‘png_free_ptr’
/usr/include/png.h:1045:1: error: unknown type name ‘png_error_ptr’
/usr/include/png.h:1045:1: error: unknown type name ‘png_error_ptr’
/usr/include/png.h:1045:1: error: unknown type name ‘png_malloc_ptr’
/usr/include/png.h:1045:1: error: unknown type name ‘png_free_ptr’
/usr/include/png.h:1739:1: error: unknown type name ‘png_error_ptr’
/usr/include/png.h:1739:1: error: unknown type name ‘png_error_ptr’
/usr/include/png.h:1756:1: error: unknown type name ‘png_rw_ptr’
/usr/include/png.h:1756:1: error: unknown type name ‘png_flush_ptr’
/usr/include/png.h:1760:1: error: unknown type name ‘png_rw_ptr’
/usr/include/png.h:1766:1: error: unknown type name ‘png_read_status_ptr’
/usr/include/png.h:1769:1: error: unknown type name ‘png_write_status_ptr’
/usr/include/png.h:1774:1: error: unknown type name ‘png_malloc_ptr’
/usr/include/png.h:1774:1: error: unknown type name ‘png_free_ptr’
/usr/include/png.h:1781:1: error: unknown type name ‘png_user_transform_ptr’
/usr/include/png.h:1786:1: error: unknown type name ‘png_user_transform_ptr’
/usr/include/png.h:1816:1: error: unknown type name ‘png_user_chunk_ptr’
/usr/include/png.h:1825:1: error: unknown type name ‘png_progressive_info_ptr’
/usr/include/png.h:1825:1: error: unknown type name ‘png_progressive_row_ptr’
/usr/include/png.h:1825:1: error: unknown type name ‘png_progressive_end_ptr’
/usr/include/png.h:1829:1: error: unknown type name ‘png_progressive_frame_ptr’
/usr/include/png.h:1829:1: error: unknown type name ‘png_progressive_frame_ptr’
glpng.c: In function ‘DefaultAlphaCallback’:
glpng.c:45:57: warning: parameter ‘red’ set but not used [-Wunused-but-set-parameter]
glpng.c: In function ‘pngLoadRawF’:
glpng.c:283:5: warning: implicit declaration of function ‘png_create_read_struct’ [-Wimplicit-function-declaration]
glpng.c:283:9: warning: assignment makes pointer from integer without a cast [enabled by default]
glpng.c:288:9: error: dereferencing pointer to incomplete type
glpng.c: In function ‘pngLoadF’:
glpng.c:388:9: warning: assignment makes pointer from integer without a cast [enabled by default]
glpng.c:393:9: error: dereferencing pointer to incomplete type
glpng.c:385:10: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
glpng.c: In function ‘pngLoadRawF’:
glpng.c:280:10: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
make[5]: *** [glpng.o] Error 1
make[5]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/GL/glpng'
make[4]: *** [glpng/libglpng_arb.dummy] Error 2
make[4]: *** Waiting for unfinished jobs....
ld -r -o libglAW.a GLwMDrawA.o AW_window_ogl.o
make[5]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/GL/glAW'
make[4]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/GL'
make[3]: *** [GL/GL.dummy] Error 1
make[3]: *** Waiting for unfinished jobs....
-------------------------------------------------------------------------------- Make everything in SL
make[5]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/SL'
make[6]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/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-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
ld -r -o FILE_BUFFER.a  FileBuffer.o 
make[6]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/SL/FILE_BUFFER'
make[6]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/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-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
ld -r -o AW_HELIX.a  AW_helix.o
make[6]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/SL/AW_HELIX'
make[6]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/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-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
i686-pc-linux-gnu-g++ -O2 -pipe  -O4 -pipe -fmessage-length=0 -funit-at-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-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
ld -r -o TREE_READ.a  TreeRead.o TreeTools.o
make[6]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/SL/TREE_READ'
make[6]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/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-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
ld -r -o REGEXPR.a  RegExpr.o
make[6]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/SL/REGEXPR'
make[6]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/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-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
ld -r -o HELIX.a  BI_helix.o
make[6]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/SL/HELIX'
make[6]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/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-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
ld -r -o DB_SCANNER.a  db_scanner.o 
make[6]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/SL/DB_SCANNER'
make[6]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/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-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
ld -r -o TREE_WRITE.a  TreeWrite.o
make[6]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/SL/TREE_WRITE'
make[6]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/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-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
i686-pc-linux-gnu-g++ -O2 -pipe  -O4 -pipe -fmessage-length=0 -funit-at-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-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
ld -r -o AW_NAME.a  AW_rename.o AW_names_admin.o 
make[6]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/SL/AW_NAME'
make[6]: Entering directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/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-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
i686-pc-linux-gnu-g++ -O2 -pipe  -O4 -pipe -fmessage-length=0 -funit-at-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-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
fast_aligner.cxx: In function ‘const char* alignCompactedTo(AWTC_CompactedSubSequence*, const AWTC_FastSearchSequence*, int, GB_CSTR, long int, GBDATA*, GBDATA*, const AlignParams&)’:
fast_aligner.cxx:1254:31: warning: ‘GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)’ is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE/ad_t_prot.h:108) [-Wdeprecated-declarations]
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-5.2/work/arb-5.2/INCLUDE/ad_t_prot.h:108) [-Wdeprecated-declarations]
ld -r -o FAST_ALIGNER.a  fast_aligner.o ClustalV.o
make[6]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/SL/FAST_ALIGNER'
make[5]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/SL'
make[4]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2'
make[3]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2'
make[2]: *** [arbbasic] Error 2
make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2'
make[1]: *** [all] Error 2
make[1]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2'
make: *** [rebuild] Error 2
 * ERROR: sci-biology/arb-5.2 failed (compile phase):
 *   emake failed
 * 
 * If you need support, post the output of 'emerge --info =sci-biology/arb-5.2',
 * the complete build log and the output of 'emerge -pqv =sci-biology/arb-5.2'.
/usr/lib/portage/bin/isolated-functions.sh: line 209: tinderbox_mask_pkg: command not found
 * The complete build log is located at '/var/log/portage/build/sci-biology/arb-5.2:20110808-155917.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-biology/arb-5.2/temp/environment'.
 * S: '/var/tmp/portage/sci-biology/arb-5.2/work/arb-5.2'