>>> Unpacking source... >>> Unpacking arb-5.1.tgz to /var/tmp/portage/sci-biology/arb-5.1/work >>> Source unpacked in /var/tmp/portage/sci-biology/arb-5.1/work >>> Preparing source in /var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213 ... make -j14 ARBHOME=/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213 links SOURCE_TOOLS/generate_all_links.sh make[1]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/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/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/work/arbsrc_6213 ... >>> Source configured. >>> Compiling source in /var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213 ... make -j14 ARBHOME=/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213 PATH=/usr/lib/ccache/bin:/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/4.4.2:/opt/intel/Compiler/11.1/056/bin/ia32:/opt/intel/fc/10.1.018/bin:/opt/SunStudioExpress/bin:/opt/intel/idb/10.1.018/bin:/opt/stuffit/bin:/opt/xxe:/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/qt/3/bin:/usr/qt/3-embedded/bin:/usr/i686-pc-linux-gnu/gnat-gcc-bin/4.3:/usr/libexec/gnat-gcc/i686-pc-linux-gnu/4.3:/usr/libexec/gpc/i686-pc-linux-gnu/3.4:/opt/flexlm/bin:/opt/vmware/server/bin:/opt/vmware/server/console/bin:/opt/vmware/vix/bin:/opt/coccinella:/opt/cuda/bin:/usr/GNUstep/System/Tools:/usr/GNUstep/Local/Tools:/var/qmail/bin:/usr/ti-linux-gnu/tigcc-bin/4.1.2:/usr/ti-linux-gnu/bin:/var/vpopmail/bin:/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/bin LD_LIBRARY_PATH=:/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/lib tarfile make clean2 make[1]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213' make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/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/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/work/arbsrc_6213/AISC_MKPTPS' rm -f mkptypes.o aisc_mkpt make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/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]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/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]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/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]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/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]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/AISC_MKPTPS' make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/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/work/arbsrc_6213/AISC' make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/AWTC' rm -f AWTC_constructSequence.o AWTC_next_neighbours.o AWTC_seq_search.o AWTC_submission.o *.a make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/PROBE' make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/ARB_GDE' make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/AWTI' rm -f AWTI_import.o AWTI_export.o *.a make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/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/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/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/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/work/arbsrc_6213/bin/arb_convert_aln make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/ARBDBS' make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/AWTC' make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/AWTI' make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/ALIV3' make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/ARBDB' make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/ARBDBPP' make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/AWT' make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/CONVERTALN' make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/DBSERVER' rm -f db_server.o *.a make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/CONSENSUS_TREE' make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/ARBDB2' make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/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]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/EDIT' rm -f edit.o edit_naligner.o edit_tools.o ed_conf.o *.a make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/EISPACK' rm -f eispack.o d_sign.o *.a make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/DBSERVER' make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/GDE' make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/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/work/arbsrc_6213/EDIT' make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/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]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/DIST' make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/GENOM_IMPORT' rm *.o make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/EISPACK' make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/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-5.1/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/work/arbsrc_6213/bin/clustalv make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/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/work/arbsrc_6213/GL' make[3]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/GDE/SUPPORT' rm -f /var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/bin/CAP2 /var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/bin/Restriction /var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/bin/Zuk_to_gen /var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/bin/count /var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/bin/findall /var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/bin/lsadt /var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/bin/sho_helix /var/tmp/portage/sci-biology/arb-5.1/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/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 make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/GENOM' make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/EDIT4' make[3]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/GDE/SUPPORT' make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/ISLAND_HOPPING' make[3]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/GDE/AxML' rm -f axml.o /var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/bin/axml make[3]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/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/work/arbsrc_6213/bin/raxmlHPC make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/MERGE' make[3]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/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[3]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/GL/glpng' rm -f glpng.o *.a make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/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[3]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/GDE/AxML' make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/NAMES' rm -f names.o *.a make[3]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/GDE/CLUSTAL' 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/work/arbsrc_6213/GDE/RAxML' make[3]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/GDE/MOLPHY' make[3]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/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/work/arbsrc_6213/bin/phyml make[3]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/GDE/CLUSTALW' rm -f *.o /var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/bin/clustalw make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/NAMES_COM' make[3]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/GL/glpng' make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/NALIGNER' make[3]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/GL/glAW' rm -f GLwMDrawA.o AW_window_ogl.o *.a make[3]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/NAMES_COM' rm -f *.[ao] make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/MULTI_PROBE' make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/NAMES' make[3]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/GDE/PHYLIP' rm -f /var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/bin/clique /var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/bin/consense /var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/bin/contml /var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/bin/contrast /var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/bin/dnacomp /var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/bin/dnadist /var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/bin/dnainvar /var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/bin/dnaml /var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/bin/dnamlk /var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/bin/dnamove /var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/bin/dnapars /var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/bin/dnapenny /var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/bin/dolmove /var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/bin/dollop /var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/bin/dolpenny /var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/bin/factor /var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/bin/fitch /var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/bin/gendist /var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/bin/kitsch /var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/bin/mix /var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/bin/move /var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/bin/neighbor /var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/bin/pars /var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/bin/penny /var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/bin/proml /var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/bin/promlk /var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/bin/protdist /var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/bin/protpars /var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/bin/restdist /var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/bin/restml /var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/bin/retree /var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/bin/seqboot /var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/bin/treedist /var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/bin/drawgram /var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/bin/drawtree *.o make[3]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/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/work/arbsrc_6213/bin/puzzle make[3]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/GDE/FASTDNAML' rm -f fastDNAml.o /var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/bin/fastdnaml make[3]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/GDE/PHYML' rm -f */*.[ao] make[3]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/GDE/FASTDNAML' make[3]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/GDE/CLUSTALW' rm: cannot remove `*.bak': No such file or directory make[3]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/GL/glAW' make[2]: [clean] Error 1 (ignored) rm *~ make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/GL' make[3]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/GDE/TREEPUZZLE' make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/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[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/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[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/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 rm -f GENH/* make[3]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/GDE/PHYLIP' make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/GDE' make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/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 rm: cannot remove `*~': No such file or directory make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/PROBE_COM' make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/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 make[2]: [clean] Error 1 (ignored) rm *# make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/NTREE' make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/PARSIMONY' make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/PGT' make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/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 rm -f GENC/* make[3]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/PROBE_COM' rm -f *.[ao] make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/PHYLO' make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/PROBE_DESIGN' rm -f probe_design.o SaiProbeVisualization.o probe_match_parser.o *.a rm -f /var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/PROBE_SET/bin/ps_show_result /var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/PROBE_SET/bin/ps_arb2asciipaths /var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/PROBE_SET/bin/ps_my2asciipaths /var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/PROBE_SET/bin/ps_my2ascii /var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/PROBE_SET/bin/ps_get_probes /var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/PROBE_SET/bin/ps_eval /var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/PROBE_SET/bin/ps_find /var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/PROBE_SET/bin/ps_detect /var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/PROBE_SET/bin/ps_merge /var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/PROBE_SET/bin/ps_convert /var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/PROBE_SET/bin/fb_test rm: cannot remove `*#': No such file or directory make[2]: [clean] Error 1 (ignored) rm *\% make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/READSEQ' rm -f readseq.o ureadseq.o /var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/bin/arb_readseq make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/PRIMER_DESIGN' make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/PROBE_SET' make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/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]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/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/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/work/arbsrc_6213/PROBE_DESIGN' rm -f */*.[ao] 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/work/arbsrc_6213/GENOM_IMPORT' make[3]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/NAMES_COM' make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/NAMES_COM' make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/SERVERCNTRL' rm -f servercntrl.o *.a make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/READSEQ' make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/STAT' rm -f ST_quality.o ST_ml.o ST_window.o *.a make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/RNA3D' make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/SECEDIT' rm -f GENH/* make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/TOOLS' rm -f /var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/bin/arb_2_ascii /var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/bin/arb_2_bin /var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/bin/arb_a2ps /var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/bin/arb_count_chars /var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/bin/arb_dnarates /var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/bin/arb_export_rates /var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/bin/arb_export_tree /var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/bin/arb_gene_probe /var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/bin/arb_message /var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/bin/arb_notify /var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/bin/arb_primer /var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/bin/arb_probe /var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/bin/arb_proto_2_xsub /var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/bin/arb_read_tree /var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/bin/arb_replace /var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/bin/arb_swap_rnastr make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/SEQ_QUALITY' make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/SL' make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/STAT' make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/SERVERCNTRL' 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]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/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/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/work/arbsrc_6213/WETC' rm -f WETC_main.o *.a make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/XML' rm -f xml.o *.a rm -f GENC/* make[3]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/SL/TREE_WRITE' rm -f TreeWrite.o *.a make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/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 make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/GDEHELP' rm -f MENUS/align.genmenu MENUS/desoete.genmenu MENUS/dnamlrates.genmenu MENUS/export.genmenu MENUS/fastdnaml.genmenu MENUS/import.genmenu MENUS/inc_fastdnaml.genmenu MENUS/molphy.genmenu MENUS/phylip_dist.genmenu MENUS/phylip_dist_org.genmenu MENUS/phylip_help.genmenu MENUS/phylip_ml.genmenu MENUS/phylip_pars.genmenu MENUS/pretty_print.genmenu MENUS/puzzle.genmenu MENUS/raxml.genmenu MENUS/start_arb.genmenu MENUS/warning.genmenu ARB_GDEmenus helpfiles.lst make[3]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/SL/TREE_READ' make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/TREEGEN' make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/TOOLS' make[3]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/SL/HELIX' rm -f BI_helix.o *.a make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/SOURCE_TOOLS' rm -f generate_all_links.stamp make[3]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/SL/TREE_WRITE' make[3]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/SL/AW_HELIX' rm -f AW_helix.o *.a make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/WETC' make[3]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/PROBE_COM' make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/WINDOW' make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/PROBE_COM' make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/SOURCE_TOOLS' make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/bin' make[3]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/SL/HELIX' find . -type l -exec rm {} \; make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/XML' make[3]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/SL/AW_NAME' rm -f AW_rename.o AW_names_admin.o *.a make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/PERL2ARB' test -f Makefile && make clean make[3]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/SL/DB_SCANNER' rm -f db_scanner.o *.a make[3]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/SL/AW_HELIX' make[3]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/SL/FILE_BUFFER' cat: rm -f FileBuffer.o *.a helpfiles.lst: No such file or directory make[3]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/SL/REGEXPR' rm -f RegExpr.o *.a make[3]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/GDEHELP' rm -f ./HELP_GEN/*.help make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/HELP_SOURCE' rm -f arb_help2xml.o /var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/bin/arb_help2xml 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/work/arbsrc_6213/lib/ARB.pm /var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/lib/ARB.so make[3]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/SL/FAST_ALIGNER' rm -f ClustalV.o fast_aligner.o *.a rm -f _index.html `find ../lib/help -name "*.hlp"` make[3]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/SL/AW_NAME' make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/PERL2ARB' make[3]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/SL/DB_SCANNER' rm -f ./HELP_DOC_GEN/*.doc make[3]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/SL/REGEXPR' make[3]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/SL/FILE_BUFFER' make[3]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/SL/FAST_ALIGNER' make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/SL' rm -f html.list `find ../lib/help_html -name "*.html"` make[3]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/GDEHELP' make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/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/work/arbsrc_6213/HELP_SOURCE/genhelp' rm -f *.hlp make[3]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/HELP_SOURCE/genhelp' make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/HELP_SOURCE' find . -type f -perm -100 -exec rm {} \; make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/bin' rm -f *.last_gcc make[1]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213' make all make[1]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213' make links make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213' SOURCE_TOOLS/generate_all_links.sh make[3]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/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/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/work/arbsrc_6213' make com make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213' -------------------------------------------------------------------------------- Make everything in AISC_MKPTPS make[3]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/AISC_MKPTPS' 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_AISC_MKPTPS -c mkptypes.c 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_AISC_MKPTPS -o aisc_mkpt mkptypes.o make[3]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/AISC_MKPTPS' -------------------------------------------------------------------------------- Make everything in AISC make[3]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/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/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-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/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-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/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-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/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-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/work/arbsrc_6213/AISC' -------------------------------------------------------------------------------- Make everything in NAMES_COM make[3]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/NAMES_COM' make[4]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/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 33): cannot find include file "stddef.h" not in GENH/stddef.h not in C/stddef.h not in /usr/include/stddef.h makedepend: warning: C/aisc_extern.c, 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/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/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/work/arbsrc_6213/NAMES_COM' make[4]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/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 ../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/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_NAMES_COM -I/var/tmp/portage/sci-biology/arb-5.1/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/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/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/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_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-5.1/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 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/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/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/work/arbsrc_6213/INCLUDE -fno-strict-aliasing -Wno-unused -c -o names_extern.o names_extern.c -IGENH -I. -IC -DAISC_SAVE_YES C/debug.c: In function 'const char* aisc_debug_local(aisc_com*, int, long int, char*, ...)': C/debug.c:115: warning: ignoring return value of 'size_t fwrite(const void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result ld -O99 --strip-all --export-dynamic -r -o client.a O/client.o O/debug.o GENC/aisc_debug_globals.o ld -O99 --strip-all --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/work/arbsrc_6213/NAMES_COM' make[3]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/NAMES_COM' -------------------------------------------------------------------------------- Make everything in PROBE_COM make[3]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/PROBE_COM' make[4]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/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 33): cannot find include file "stddef.h" not in GENH/stddef.h not in C/stddef.h not in /usr/include/stddef.h makedepend: warning: C/aisc_extern.c, 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/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/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/work/arbsrc_6213/PROBE_COM' make[4]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/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/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/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/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/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/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 rm -f GENH/aisc_server_proto.h echo GENH/import_proto.h ../MAKEBIN/aisc_mkpt -C GENC/aisc_server.c >GENH/aisc_server_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/work/arbsrc_6213/INCLUDE -fno-strict-aliasing -Wno-unused -c -o GENC/aisc_debug_globals.o GENC/aisc_debug_globals.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/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/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/work/arbsrc_6213/INCLUDE -fno-strict-aliasing -Wno-unused -c -o PT_extern.o PT_extern.c -IGENH -I. -IC -DAISC_SAVE_NO C/debug.c: In function 'const char* aisc_debug_local(aisc_com*, int, long int, char*, ...)': C/debug.c:115: warning: ignoring return value of 'size_t fwrite(const void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result ld -O99 --strip-all --export-dynamic -r -o client.a O/client.o O/debug.o GENC/aisc_debug_globals.o ld -O99 --strip-all --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/work/arbsrc_6213/PROBE_COM' make[3]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/PROBE_COM' make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213' make arb make[2]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213' (cd lib;make all) make[3]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/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/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/work/arbsrc_6213/lib/nas' make[3]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/lib' make arbbasic2 make[3]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213' -------------------------------------------------------------------------------- Make everything in AISC_MKPTPS make[4]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/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/work/arbsrc_6213/AISC_MKPTPS' -------------------------------------------------------------------------------- Make everything in AISC make[4]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/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/work/arbsrc_6213/AISC' -------------------------------------------------------------------------------- Make everything in NAMES_COM make[4]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/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/work/arbsrc_6213/NAMES_COM' -------------------------------------------------------------------------------- Make everything in NAMES_COM make[4]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/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/work/arbsrc_6213/NAMES_COM' -------------------------------------------------------------------------------- Make everything in PROBE_COM make[4]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/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/work/arbsrc_6213/PROBE_COM' make SL/SL.dummy -------------------------------------------------------------------------------- Make everything in TEMPLATES make[4]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/TEMPLATES' ../SOURCE_TOOLS/build_info.pl make[4]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/TEMPLATES' make[4]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213' -------------------------------------------------------------------------------- Make everything in GL make[4]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/GL' make[5]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/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/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include make[5]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/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/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-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/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include -I/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/WINDOW ld -O99 --strip-all --export-dynamic -r -o libglAW.a GLwMDrawA.o AW_window_ogl.o make[5]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/GL/glAW' glpng.c: In function 'pngLoadRawF': glpng.c:280: warning: ignoring return value of 'fread', declared with attribute warn_unused_result glpng.c: In function 'pngLoadF': glpng.c:385: warning: ignoring return value of 'fread', declared with attribute warn_unused_result ld -O99 --strip-all --export-dynamic -r -o libglpng_arb.a glpng.o make[5]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/GL/glpng' make[4]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/GL' -------------------------------------------------------------------------------- Make everything in SL make[5]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/SL' make[6]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/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/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-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/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include ld -O99 --strip-all --export-dynamic -r -o TREE_READ.a TreeRead.o TreeTools.o make[6]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/SL/TREE_READ' make[6]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/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/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include ld -O99 --strip-all --export-dynamic -r -o REGEXPR.a RegExpr.o make[6]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/SL/REGEXPR' make[6]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/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/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include FileBuffer.cxx: In member function 'void FileBuffer::rewind()': FileBuffer.cxx:122: error: 'rewind' is not a member of 'std' make[6]: *** [FileBuffer.o] Error 1 make[6]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/SL/FILE_BUFFER' make[5]: *** [FILE_BUFFER/FILE_BUFFER.dummy] Error 1 make[5]: *** Waiting for unfinished jobs.... make[6]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/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/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include ld -O99 --strip-all --export-dynamic -r -o AW_HELIX.a AW_helix.o make[6]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/SL/AW_HELIX' make[6]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/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/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include ld -O99 --strip-all --export-dynamic -r -o DB_SCANNER.a db_scanner.o make[6]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/SL/DB_SCANNER' make[6]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/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/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include ld -O99 --strip-all --export-dynamic -r -o HELIX.a BI_helix.o make[6]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/SL/HELIX' make[6]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/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/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include ld -O99 --strip-all --export-dynamic -r -o TREE_WRITE.a TreeWrite.o make[6]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/SL/TREE_WRITE' make[6]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/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/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-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/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include ld -O99 --strip-all --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/work/arbsrc_6213/SL/AW_NAME' make[6]: Entering directory `/var/tmp/portage/sci-biology/arb-5.1/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 ClustalV.cxx -I. -I/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include i686-pc-linux-gnu-g++ -O2 -pipe -O4 -pipe -fmessage-length=0 -funit-at-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/work/arbsrc_6213/INCLUDE -I/usr/X11R6/include ClustalV.cxx: In function 'int AWTC_baseMatch(char, char)': ClustalV.cxx:289: error: invalid conversion from 'const char*' to 'char*' ClustalV.cxx:290: error: invalid conversion from 'const char*' to 'char*' make[6]: *** [ClustalV.o] Error 1 make[6]: *** Waiting for unfinished jobs.... 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: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/INCLUDE/ad_t_prot.h:108) fast_aligner.cxx:1254: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated (declared at /var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/INCLUDE/ad_t_prot.h:108) make[6]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/SL/FAST_ALIGNER' make[5]: *** [FAST_ALIGNER/FAST_ALIGNER.dummy] Error 1 make[5]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213/SL' make[4]: *** [SL/SL.dummy] Error 1 make[4]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213' make[3]: *** [sl] Error 2 make[3]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213' make[2]: *** [arbbasic] Error 2 make[2]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213' make[1]: *** [all] Error 2 make[1]: Leaving directory `/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213' make: *** [rebuild] Error 2 * ERROR: sci-biology/arb-5.1 failed: * (no error message) * * Call stack: * ebuild.sh, line 55: Called src_compile * environment, line 2482: 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', * the complete build log and the output of 'emerge -pqv =sci-biology/arb-5.1'. * The complete build log is located at '/var/log/portage/build/sci-biology/arb-5.1:20091127-150152.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-biology/arb-5.1/temp/environment'. * S: '/var/tmp/portage/sci-biology/arb-5.1/work/arbsrc_6213'