1. * Package: sci-biology/arb-5.2
  2. * Repository: gentoo
  3. * Maintainer: weaver@gentoo.org sci-biology@gentoo.org
  4. * USE: amd64 elibc_glibc kernel_linux multilib opengl test userland_GNU
  5. * FEATURES: sandbox test userpriv usersandbox
  6. >>> Unpacking source...
  7. >>> Unpacking arb-5.2.tgz to /tmp/portage/sci-biology/arb-5.2/work
  8. >>> Unpacking arb-5.2-linker.patch.bz2 to /tmp/portage/sci-biology/arb-5.2/work
  9. >>> Source unpacked in /tmp/portage/sci-biology/arb-5.2/work
  10. >>> Preparing source in /tmp/portage/sci-biology/arb-5.2/work/arb-5.2 ...
  11. * Applying arb-5.2-linker.patch ...
  12. [ ok ]
  13. * Applying 5.1-libs.patch ...
  14. [ ok ]
  15. * Applying 5.1-bfr-overflow.patch ...
  16. [ ok ]
  17. * Applying 5.2-libpng15.patch ...
  18. [ ok ]
  19. make -j24 ARBHOME=/tmp/portage/sci-biology/arb-5.2/work/arb-5.2 links
  20. SOURCE_TOOLS/generate_all_links.sh
  21. make[1]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin'
  22. make[1]: warning: jobserver unavailable: using -j1. Add `+' to parent make rule.
  23. find . -type l -exec rm {} \;
  24. ln -s -f `find ../SH ../PERL_SCRIPTS -perm -100 ! -type d ! -name 'config*' -print` .
  25. make[1]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin'
  26. generate_all_links.sh done.
  27. touch SOURCE_TOOLS/generate_all_links.stamp
  28. >>> Source prepared.
  29. >>> Configuring source in /tmp/portage/sci-biology/arb-5.2/work/arb-5.2 ...
  30. >>> Source configured.
  31. >>> Compiling source in /tmp/portage/sci-biology/arb-5.2/work/arb-5.2 ...
  32. make -j24 ARBHOME=/tmp/portage/sci-biology/arb-5.2/work/arb-5.2 PATH=/usr/lib64/portage/bin/ebuild-helpers/4:/usr/lib64/portage/bin/ebuild-helpers:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/opt/bin:/usr/x86_64-pc-linux-gnu/gcc-bin/4.7.1:/opt/dmd/bin:/opt/hp/hpacucli:/usr/x86_64-pc-linux-gnu/gnat-gcc-bin/4.4:/usr/libexec/gnat-gcc/x86_64-pc-linux-gnu/4.4:/usr/libexec/gpc/x86_64-pc-linux-gnu/3.4:/opt/tivoli/tsm/client/ba/bin:/opt/eagle-5.11.0/bin:/opt/flexlm/bin:/opt/vmware/bin:/opt/aws-as-tools/bin:/opt/aws-elb-tools/bin:/opt/aws-iam-tools/bin:/opt/aws-rds-tools/bin:/usr/bin/cdsclient:/opt/cuda/bin:/opt/ec2-ami-tools/bin:/opt/ec2-api-tools/bin:/usr/ti-linux-gnu/tigcc-bin/4.1.2:/usr/ti-linux-gnu/bin:/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin LD_LIBRARY_PATH=:/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/lib tarfile
  33. make clean2
  34. make[1]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2'
  35. make[2]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/PROBE'
  36. 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
  37. make[2]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/AISC'
  38. rm -f aisc.o aisc_commands.o aisc_var_ref.o aisc_mix.o aisc
  39. make[2]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/AISC_MKPTPS'
  40. rm -f mkptypes.o aisc_mkpt
  41. make[2]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/ALIV3'
  42. 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
  43. make[2]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/AISC_MKPTPS'
  44. make[2]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/AISC'
  45. make[2]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/ARBDB2'
  46. 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
  47. make[2]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/ARBDB'
  48. 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
  49. make[2]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/ARBDBPP'
  50. rm -f adtsequence.o adt_edit.o adtali.o adextended.o adseq.o adspecies.o admain.o adali.o liste.o *.a *.so
  51. make[2]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/ARB_GDE'
  52. rm -f GDE_ParseMenu.o GDE.o GDE_event.o GDE_arbdb_io.o GDE_HGLfile.o GDE_Genbank.o GDE_FileIO.o *.a
  53. make[2]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/ARBDBS'
  54. 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
  55. make[2]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/AWTC'
  56. rm -f AWTC_next_neighbours.o AWTC_constructSequence.o AWTC_seq_search.o AWTC_submission.o *.a
  57. make[2]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/CONSENSUS_TREE'
  58. rm -f CT_part.o CT_hash.o CT_ntree.o CT_rbtree.o CT_dtree.o CT_ctree.o CT_mem.o *.a
  59. make[2]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/AWTI'
  60. rm -f AWTI_import.o AWTI_export.o *.a
  61. make[2]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/CONVERTALN'
  62. 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 /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/arb_convert_aln
  63. make[2]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/AWT'
  64. 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
  65. make[2]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/DBSERVER'
  66. rm -f db_server.o *.a
  67. make[2]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/DIST'
  68. 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
  69. make[2]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/EDIT'
  70. rm -f edit.o edit_naligner.o edit_tools.o ed_conf.o *.a
  71. make[2]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/EISPACK'
  72. rm -f eispack.o d_sign.o *.a
  73. make[2]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/PROBE'
  74. make[2]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/EDIT4'
  75. 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
  76. make[2]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/GDE'
  77. make[2]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/GENOM'
  78. 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
  79. make[2]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/ALIV3'
  80. make[2]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/GENOM_IMPORT'
  81. rm *.o
  82. make[2]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/GL'
  83. make[2]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/ISLAND_HOPPING'
  84. rm -f island_hopping.o i-hopper.o align.o memory.o trnsprob.o *.a
  85. make[2]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/ARBDBPP'
  86. make[2]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/ARB_GDE'
  87. make[2]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/MERGE'
  88. 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
  89. make[2]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/CONVERTALN'
  90. make[2]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/AWTI'
  91. make[2]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/AWTC'
  92. make[2]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/DBSERVER'
  93. make[2]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/MULTI_PROBE'
  94. 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
  95. make[2]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/CONSENSUS_TREE'
  96. make[3]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/GL/glpng'
  97. rm -f glpng.o *.a
  98. make[2]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/EISPACK'
  99. make[2]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/ARBDB2'
  100. make[2]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/EDIT'
  101. make[2]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/ARBDB'
  102. make[2]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/DIST'
  103. make[2]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/NALIGNER'
  104. 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
  105. make[3]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/GDE/CLUSTAL'
  106. rm -f clustalv.o amenu.o myers.o sequence.o showpair.o upgma.o util.o trees.o gcgcheck.o /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/clustalv
  107. make[2]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/NAMES'
  108. rm -f names.o *.a
  109. rm: cannot remove '*.o': No such file or directory
  110. make[2]: [clean] Error 1 (ignored)
  111. rm *.a
  112. make[2]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/GENOM'
  113. make[2]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/ARBDBS'
  114. make[3]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/GL/glAW'
  115. rm -f GLwMDrawA.o AW_window_ogl.o *.a
  116. make[3]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/GDE/SUPPORT'
  117. rm -f /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/CAP2 /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/Restriction /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/Zuk_to_gen /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/count /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/findall /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/lsadt /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/sho_helix /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/varpos
  118. make[2]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/ISLAND_HOPPING'
  119. make[2]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/AWT'
  120. make[3]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/GDE/MOLPHY'
  121. 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
  122. make[2]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/MERGE'
  123. make[2]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/EDIT4'
  124. make[3]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/GDE/AxML'
  125. rm -f axml.o /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/axml
  126. make[3]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/GL/glpng'
  127. make[3]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/GDE/RAxML'
  128. 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 /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/raxmlHPC
  129. make[3]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/GDE/CLUSTAL'
  130. make[2]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/MULTI_PROBE'
  131. make[2]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/NAMES_COM'
  132. make[3]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/GDE/PHYML'
  133. rm -f main.o utilities.o optimiz.o lk.o bionj.o models.o free.o options.o simu.o eigen.o /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/phyml
  134. make[2]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/PARSIMONY'
  135. 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
  136. make[2]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/NALIGNER'
  137. make[3]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/GDE/SUPPORT'
  138. make[2]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/NTREE'
  139. 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
  140. make[3]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/GDE/CLUSTALW'
  141. rm -f *.o /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/clustalw
  142. rm: cannot remove '*.a': No such file or directory
  143. make[2]: [clean] Error 1 (ignored)
  144. rm *.bak
  145. make[2]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/NAMES'
  146. make[3]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/GDE/AxML'
  147. make[2]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/PGT'
  148. 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
  149. make[3]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/GL/glAW'
  150. make[2]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/GL'
  151. make[3]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/NAMES_COM'
  152. rm -f *.[ao]
  153. make[3]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/GDE/TREEPUZZLE'
  154. 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 /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/puzzle
  155. make[3]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/GDE/RAxML'
  156. make[3]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/GDE/PHYLIP'
  157. rm -f /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/clique /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/consense /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/contml /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/contrast /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/dnacomp /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/dnadist /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/dnainvar /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/dnaml /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/dnamlk /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/dnamove /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/dnapars /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/dnapenny /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/dolmove /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/dollop /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/dolpenny /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/factor /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/fitch /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/gendist /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/kitsch /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/mix /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/move /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/neighbor /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/pars /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/penny /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/proml /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/promlk /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/protdist /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/protpars /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/restdist /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/restml /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/retree /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/seqboot /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/treedist /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/drawgram /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/drawtree *.o
  158. make[3]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/GDE/FASTDNAML'
  159. rm -f fastDNAml.o /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/fastdnaml
  160. make[2]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/PHYLO'
  161. rm -f PH_data.o PH_root.o PH_main.o PH_filt.o PH_display.o PH_matr.o *.a
  162. make[3]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/GDE/MOLPHY'
  163. make[2]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/PRIMER_DESIGN'
  164. 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
  165. make[3]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/GDE/PHYML'
  166. make[2]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/PROBE_DESIGN'
  167. rm -f probe_design.o SaiProbeVisualization.o probe_match_parser.o *.a
  168. make[2]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/PROBE_COM'
  169. make[2]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/PROBE_SET'
  170. 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
  171. make[2]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/READSEQ'
  172. rm -f readseq.o ureadseq.o /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/arb_readseq
  173. make[3]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/GDE/CLUSTALW'
  174. rm: cannot remove '*.bak': No such file or directory
  175. make[2]: [clean] Error 1 (ignored)
  176. rm *~
  177. make[3]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/GDE/FASTDNAML'
  178. make[2]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/RNA3D'
  179. 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
  180. make[2]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/SECEDIT'
  181. 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
  182. make[2]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/PARSIMONY'
  183. make[2]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/SEQ_QUALITY'
  184. rm -f SQ_main.o SQ_functions.o SQ_GroupData.o *.a
  185. make[2]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/SERVERCNTRL'
  186. rm -f servercntrl.o *.a
  187. make[3]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/GDE/TREEPUZZLE'
  188. rm -f */*.[ao]
  189. make[2]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/STAT'
  190. rm -f ST_quality.o ST_ml.o ST_window.o *.a
  191. make[2]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/SL'
  192. make[2]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/TOOLS'
  193. rm -f /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/arb_2_ascii /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/arb_2_bin /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/arb_a2ps /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/arb_count_chars /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/arb_dnarates /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/arb_export_rates /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/arb_export_tree /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/arb_gene_probe /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/arb_message /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/arb_notify /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/arb_primer /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/arb_probe /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/arb_proto_2_xsub /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/arb_read_tree /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/arb_replace /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/arb_swap_rnastr
  194. make[3]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/PROBE_COM'
  195. rm -f *.[ao]
  196. make[2]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/PGT'
  197. make[2]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/READSEQ'
  198. make[2]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/NTREE'
  199. make[2]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/TREEGEN'
  200. rm -f base.o defines.o frand.o readcfg.o rns.o sim.o simcfg.o spreadin.o *.a
  201. make[2]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/PHYLO'
  202. make[2]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/WETC'
  203. rm -f WETC_main.o *.a
  204. make[2]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/PRIMER_DESIGN'
  205. rm -f /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/PROBE_SET/bin/ps_show_result /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/PROBE_SET/bin/ps_arb2asciipaths /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/PROBE_SET/bin/ps_my2asciipaths /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/PROBE_SET/bin/ps_my2ascii /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/PROBE_SET/bin/ps_get_probes /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/PROBE_SET/bin/ps_eval /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/PROBE_SET/bin/ps_find /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/PROBE_SET/bin/ps_detect /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/PROBE_SET/bin/ps_merge /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/PROBE_SET/bin/ps_convert /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/PROBE_SET/bin/fb_test
  206. make[2]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/PROBE_DESIGN'
  207. rm: cannot remove '*~': No such file or directory
  208. make[2]: [clean] Error 1 (ignored)
  209. rm *#
  210. make[3]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/SL/TREE_READ'
  211. rm -f TreeRead.o TreeTools.o *.a
  212. make[2]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/WINDOW'
  213. 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
  214. make[2]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/XML'
  215. rm -f xml.o *.a
  216. make[2]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/SEQ_QUALITY'
  217. make[2]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/SERVERCNTRL'
  218. make[3]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/SL/TREE_WRITE'
  219. rm -f TreeWrite.o *.a
  220. make[2]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/STAT'
  221. make[2]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/RNA3D'
  222. rm -f GENH/*
  223. make[2]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/GDEHELP'
  224. 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
  225. make[3]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/SL/HELIX'
  226. rm -f BI_helix.o *.a
  227. make[2]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/SECEDIT'
  228. rm -f */*.[ao]
  229. make[2]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/SOURCE_TOOLS'
  230. rm -f generate_all_links.stamp
  231. make[2]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin'
  232. find . -type l -exec rm {} \;
  233. make[2]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/WETC'
  234. 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
  235. make[2]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/PERL2ARB'
  236. test -f Makefile && make clean
  237. make[2]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/TREEGEN'
  238. make[3]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/SL/AW_HELIX'
  239. rm -f AW_helix.o *.a
  240. rm: cannot remove '*#': No such file or directory
  241. make[2]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/PROBE_SET'
  242. make[2]: [clean] Error 1 (ignored)
  243. rm *\%
  244. make[3]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/SL/AW_NAME'
  245. rm -f AW_rename.o AW_names_admin.o *.a
  246. make[3]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/GDE/PHYLIP'
  247. make[3]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/SL/TREE_READ'
  248. make[2]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/GDE'
  249. make[2]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/XML'
  250. make[2]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/SOURCE_TOOLS'
  251. make[3]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/SL/DB_SCANNER'
  252. rm -f db_scanner.o *.a
  253. make[3]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/SL/TREE_WRITE'
  254. rm -f GENC/*
  255. make[3]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/SL/FILE_BUFFER'
  256. rm -f FileBuffer.o *.a
  257. make[2]: [clean] Error 1 (ignored)
  258. rm -f Makefile.old proto.h debug.h ARB.c ARB.xs .depends depends.stamp Makefile.PL /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/lib/ARB.pm /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/lib/ARB.so
  259. make[2]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/WINDOW'
  260. make[2]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/TOOLS'
  261. make[3]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/SL/HELIX'
  262. rm -f GENH/*
  263. make[3]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/SL/REGEXPR'
  264. rm -f RegExpr.o *.a
  265. make[3]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/SL/FAST_ALIGNER'
  266. rm -f fast_aligner.o ClustalV.o *.a
  267. rm: cannot remove '*%': No such file or directory
  268. make[2]: [clean] Error 1 (ignored)
  269. make[2]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/GENOM_IMPORT'
  270. make[3]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/SL/AW_HELIX'
  271. make[2]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/PERL2ARB'
  272. make[3]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/SL/AW_NAME'
  273. rm -f .depends
  274. make[3]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/SL/DB_SCANNER'
  275. make[3]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/SL/FILE_BUFFER'
  276. make[2]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/HELP_SOURCE'
  277. rm -f arb_help2xml.o /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin/arb_help2xml
  278. rm -f GENC/*
  279. cat: helpfiles.lst: No such file or directory
  280. make[3]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/NAMES_COM'
  281. make[2]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/NAMES_COM'
  282. make[3]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/SL/REGEXPR'
  283. make[3]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/SL/FAST_ALIGNER'
  284. make[3]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/GDEHELP'
  285. rm -f ./HELP_GEN/*.help
  286. make[2]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/SL'
  287. rm -f _index.html `find ../lib/help -name "*.hlp"`
  288. rm -f .depends
  289. rm -f ./HELP_DOC_GEN/*.doc
  290. make[3]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/PROBE_COM'
  291. make[2]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/PROBE_COM'
  292. rm -f html.list `find ../lib/help_html -name "*.html"`
  293. make[3]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/GDEHELP'
  294. make[2]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/GDEHELP'
  295. find: `../lib/help_html': No such file or directory
  296. rm -f xml.stamp dummy `find Xml -name "*.xml"`
  297. find: `Xml': No such file or directory
  298. make -C genhelp clean
  299. make[3]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/HELP_SOURCE/genhelp'
  300. rm -f *.hlp
  301. make[3]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/HELP_SOURCE/genhelp'
  302. make[2]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/HELP_SOURCE'
  303. find . -type f -perm -100 -exec rm {} \;
  304. make[2]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin'
  305. rm -f *.last_gcc
  306. make[1]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2'
  307. make all
  308. make[1]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2'
  309. make links
  310. make[2]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2'
  311. SOURCE_TOOLS/generate_all_links.sh
  312. make[3]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin'
  313. make[3]: warning: jobserver unavailable: using -j1. Add `+' to parent make rule.
  314. find . -type l -exec rm {} \;
  315. ln -s -f `find ../SH ../PERL_SCRIPTS -perm -100 ! -type d ! -name 'config*' -print` .
  316. make[3]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin'
  317. generate_all_links.sh done.
  318. touch SOURCE_TOOLS/generate_all_links.stamp
  319. make[2]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2'
  320. make com
  321. make[2]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2'
  322. -------------------------------------------------------------------------------- Make everything in AISC_MKPTPS
  323. make[3]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/AISC_MKPTPS'
  324. cc -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AISC_MKPTPS -c mkptypes.c
  325. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -Wl,-O1 -Wl,--as-needed -Wl,--export-dynamic -rdynamic -o aisc_mkpt mkptypes.o
  326. make[3]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/AISC_MKPTPS'
  327. -------------------------------------------------------------------------------- Make everything in AISC
  328. make[3]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/AISC'
  329. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AISC -c aisc.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  330. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AISC -c aisc_commands.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  331. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AISC -c aisc_var_ref.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  332. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AISC -c aisc_mix.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  333. aisc_commands.c: In function 'int do_com_next(const char*)':
  334. aisc_commands.c:906:21: warning: variable 'p' set but not used [-Wunused-but-set-variable]
  335. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -Wl,-O1 -Wl,--as-needed -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AISC -o aisc aisc.o aisc_commands.o aisc_var_ref.o aisc_mix.o
  336. make[3]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/AISC'
  337. -------------------------------------------------------------------------------- Make everything in NAMES_COM
  338. make[3]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/NAMES_COM'
  339. make[4]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/NAMES_COM'
  340. AISC/Makefile:95: .depends: No such file or directory
  341. umask 002;makedepend C/*.c GENC/*.c -I GENH -I C -f- -w1 | grep -v ' /usr' | sed -e 's/^C/O/ig' > .depends_new
  342. makedepend: warning: C/aisc_extern.c (reading /usr/include/stdio.h, line 33): cannot find include file "stddef.h"
  343. not in GENH/stddef.h
  344. not in C/stddef.h
  345. not in /usr/include/stddef.h
  346. makedepend: warning: C/aisc_extern.c (reading /usr/include/_G_config.h, line 15): cannot find include file "stddef.h"
  347. not in GENH/stddef.h
  348. not in C/stddef.h
  349. not in /usr/include/stddef.h
  350. makedepend: warning: C/aisc_extern.c (reading /usr/include/wchar.h, line 39): cannot find include file "stdarg.h"
  351. not in GENH/stdarg.h
  352. not in C/stdarg.h
  353. not in /usr/include/stdarg.h
  354. makedepend: warning: C/aisc_extern.c (reading /usr/include/wchar.h, line 51): cannot find include file "stddef.h"
  355. not in GENH/stddef.h
  356. not in C/stddef.h
  357. not in /usr/include/stddef.h
  358. makedepend: warning: C/aisc_extern.c (reading /usr/include/libio.h, line 53): cannot find include file "stdarg.h"
  359. not in GENH/stdarg.h
  360. not in C/stdarg.h
  361. not in /usr/include/stdarg.h
  362. makedepend: warning: C/aisc_extern.c (reading /usr/include/string.h, line 32): cannot find include file "stddef.h"
  363. not in GENH/stddef.h
  364. not in C/stddef.h
  365. not in /usr/include/stddef.h
  366. makedepend: warning: C/aisc_extern.c, line 3: cannot find include file "aisc.h"
  367. not in GENH/aisc.h
  368. not in C/aisc.h
  369. not in /usr/include/aisc.h
  370. makedepend: warning: C/aisc_extern.c (reading C/aisc_extern_privat.h, line 19): cannot find include file "attributes.h"
  371. not in GENH/attributes.h
  372. not in C/attributes.h
  373. not in /usr/include/attributes.h
  374. makedepend: warning: C/client.c (reading /usr/include/stdlib.h, line 32): cannot find include file "stddef.h"
  375. not in GENH/stddef.h
  376. not in C/stddef.h
  377. not in /usr/include/stddef.h
  378. makedepend: warning: C/client.c (reading /usr/include/sys/types.h, line 146): cannot find include file "stddef.h"
  379. not in GENH/stddef.h
  380. not in C/stddef.h
  381. not in /usr/include/stddef.h
  382. makedepend: warning: C/client.c (reading /usr/include/alloca.h, line 24): cannot find include file "stddef.h"
  383. not in GENH/stddef.h
  384. not in C/stddef.h
  385. not in /usr/include/stddef.h
  386. makedepend: warning: C/client.c (reading /usr/include/unistd.h, line 226): cannot find include file "stddef.h"
  387. not in GENH/stddef.h
  388. not in C/stddef.h
  389. not in /usr/include/stddef.h
  390. makedepend: warning: C/client.c (reading C/ad_varargs.h, line 1): cannot find include file "stdarg.h"
  391. not in GENH/stdarg.h
  392. not in C/stdarg.h
  393. not in /usr/include/stdarg.h
  394. makedepend: warning: C/client.c (reading /usr/include/sys/socket.h, line 29): cannot find include file "stddef.h"
  395. not in GENH/stddef.h
  396. not in C/stddef.h
  397. not in /usr/include/stddef.h
  398. makedepend: warning: C/client.c (reading /usr/include/bits/socket.h, line 28): cannot find include file "stddef.h"
  399. not in GENH/stddef.h
  400. not in C/stddef.h
  401. not in /usr/include/stddef.h
  402. makedepend: warning: C/client.c (reading /usr/include/rpc/netdb.h, line 42): cannot find include file "stddef.h"
  403. not in GENH/stddef.h
  404. not in C/stddef.h
  405. not in /usr/include/stddef.h
  406. makedepend: warning: C/client.c (reading /usr/include/signal.h, line 348): cannot find include file "stddef.h"
  407. not in GENH/stddef.h
  408. not in C/stddef.h
  409. not in /usr/include/stddef.h
  410. makedepend: warning: C/client.c (reading C/client.h, line 22): cannot find include file "attributes.h"
  411. not in GENH/attributes.h
  412. not in C/attributes.h
  413. not in /usr/include/attributes.h
  414. makedepend: warning: C/debug.c, line 6: cannot find include file "aisc_com.h"
  415. not in GENH/aisc_com.h
  416. not in C/aisc_com.h
  417. not in /usr/include/aisc_com.h
  418. makedepend: warning: C/server.c (reading /usr/include/limits.h, line 124): cannot find include file "limits.h"
  419. makedepend: warning: C/server.c, line 33: cannot find include file "aisc_com.h"
  420. not in aisc_com.h
  421. not in C/aisc_com.h
  422. not in GENH/aisc_com.h
  423. not in C/aisc_com.h
  424. not in /usr/include/aisc_com.h
  425. makedepend: warning: C/server.c (reading C/server.h, line 22): cannot find include file "attributes.h"
  426. not in GENH/attributes.h
  427. not in C/attributes.h
  428. not in /usr/include/attributes.h
  429. makedepend: warning: C/server.c (reading ../INCLUDE/arb_assert.h), line 33: # error Neither DEBUG nor NDEBUG is defined!
  430. makedepend: warning: C/server.c (reading ../INCLUDE/arb_assert.h, line 183): cannot find include file "arbdb_base.h"
  431. not in GENH/arbdb_base.h
  432. not in C/arbdb_base.h
  433. not in /usr/include/arbdb_base.h
  434. makedepend: warning: C/struct_man.c, line 5: cannot find include file "aisc.h"
  435. not in aisc.h
  436. not in C/aisc.h
  437. not in GENH/aisc.h
  438. not in C/aisc.h
  439. not in /usr/include/aisc.h
  440. makedepend: warning: C/struct_man.c (reading C/struct_man.h, line 19): cannot find include file "attributes.h"
  441. not in GENH/attributes.h
  442. not in C/attributes.h
  443. not in /usr/include/attributes.h
  444. makedepend: warning: cannot open "GENC/*.c"
  445. /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/SOURCE_TOOLS/mv_if_diff .depends_new .depends
  446. .depends created.
  447. make[4]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/NAMES_COM'
  448. make[4]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/NAMES_COM'
  449. ../MAKEBIN/aisc AISC/aisc.pa names.aisc GENH/aisc.h
  450. ../MAKEBIN/aisc AISC/aisc_com.pa names.aisc GENH/aisc_com.h
  451. rm -f GENH/aisc_server_extern.aisc
  452. rm -f GENH/aisc_server_extern.h
  453. ../MAKEBIN/aisc_mkpt -a C/aisc_extern.c names_extern.c >GENH/aisc_server_extern.aisc
  454. ../MAKEBIN/aisc_mkpt -C C/aisc_extern.c names_extern.c >GENH/aisc_server_extern.h
  455. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NAMES_COM -I/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
  456. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NAMES_COM -I/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
  457. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NAMES_COM -I/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
  458. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NAMES_COM -I/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
  459. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NAMES_COM -I/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
  460. ../MAKEBIN/aisc AISC/aisc_debug_globals.pa names.aisc GENC/aisc_debug_globals.c GENH/aisc_server_extern.aisc GENH/import_proto.h
  461. ../MAKEBIN/aisc AISC/aisc_server.pa names.aisc GENC/aisc_server.c GENH/aisc_server_extern.aisc GENH/import_proto.h
  462. ../MAKEBIN/aisc AISC/aisc_global.pa names.aisc GENC/aisc_global.c GENH/aisc_server_extern.aisc GENH/import_proto.h
  463. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NAMES_COM -I/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
  464. rm -f GENH/aisc_server_proto.h
  465. echo GENH/import_proto.h
  466. ../MAKEBIN/aisc_mkpt -C GENC/aisc_server.c >GENH/aisc_server_proto.h
  467. GENH/import_proto.h
  468. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NAMES_COM -I/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
  469. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NAMES_COM -I/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
  470. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NAMES_COM -I/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
  471. ld -r -o client.a O/client.o O/debug.o GENC/aisc_debug_globals.o
  472. 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
  473. make[4]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/NAMES_COM'
  474. make[3]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/NAMES_COM'
  475. -------------------------------------------------------------------------------- Make everything in PROBE_COM
  476. make[3]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/PROBE_COM'
  477. make[4]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/PROBE_COM'
  478. AISC/Makefile:95: .depends: No such file or directory
  479. umask 002;makedepend C/*.c GENC/*.c -I GENH -I C -f- -w1 | grep -v ' /usr' | sed -e 's/^C/O/ig' > .depends_new
  480. makedepend: warning: C/aisc_extern.c (reading /usr/include/stdio.h, line 33): cannot find include file "stddef.h"
  481. not in GENH/stddef.h
  482. not in C/stddef.h
  483. not in /usr/include/stddef.h
  484. makedepend: warning: C/aisc_extern.c (reading /usr/include/_G_config.h, line 15): cannot find include file "stddef.h"
  485. not in GENH/stddef.h
  486. not in C/stddef.h
  487. not in /usr/include/stddef.h
  488. makedepend: warning: C/aisc_extern.c (reading /usr/include/wchar.h, line 39): cannot find include file "stdarg.h"
  489. not in GENH/stdarg.h
  490. not in C/stdarg.h
  491. not in /usr/include/stdarg.h
  492. makedepend: warning: C/aisc_extern.c (reading /usr/include/wchar.h, line 51): cannot find include file "stddef.h"
  493. not in GENH/stddef.h
  494. not in C/stddef.h
  495. not in /usr/include/stddef.h
  496. makedepend: warning: C/aisc_extern.c (reading /usr/include/libio.h, line 53): cannot find include file "stdarg.h"
  497. not in GENH/stdarg.h
  498. not in C/stdarg.h
  499. not in /usr/include/stdarg.h
  500. makedepend: warning: C/aisc_extern.c (reading /usr/include/string.h, line 32): cannot find include file "stddef.h"
  501. not in GENH/stddef.h
  502. not in C/stddef.h
  503. not in /usr/include/stddef.h
  504. makedepend: warning: C/aisc_extern.c, line 3: cannot find include file "aisc.h"
  505. not in GENH/aisc.h
  506. not in C/aisc.h
  507. not in /usr/include/aisc.h
  508. makedepend: warning: C/aisc_extern.c (reading C/aisc_extern_privat.h, line 19): cannot find include file "attributes.h"
  509. not in GENH/attributes.h
  510. not in C/attributes.h
  511. not in /usr/include/attributes.h
  512. makedepend: warning: C/client.c (reading /usr/include/stdlib.h, line 32): cannot find include file "stddef.h"
  513. not in GENH/stddef.h
  514. not in C/stddef.h
  515. not in /usr/include/stddef.h
  516. makedepend: warning: C/client.c (reading /usr/include/sys/types.h, line 146): cannot find include file "stddef.h"
  517. not in GENH/stddef.h
  518. not in C/stddef.h
  519. not in /usr/include/stddef.h
  520. makedepend: warning: C/client.c (reading /usr/include/alloca.h, line 24): cannot find include file "stddef.h"
  521. not in GENH/stddef.h
  522. not in C/stddef.h
  523. not in /usr/include/stddef.h
  524. makedepend: warning: C/client.c (reading /usr/include/unistd.h, line 226): cannot find include file "stddef.h"
  525. not in GENH/stddef.h
  526. not in C/stddef.h
  527. not in /usr/include/stddef.h
  528. makedepend: warning: C/client.c (reading C/ad_varargs.h, line 1): cannot find include file "stdarg.h"
  529. not in GENH/stdarg.h
  530. not in C/stdarg.h
  531. not in /usr/include/stdarg.h
  532. makedepend: warning: C/client.c (reading /usr/include/sys/socket.h, line 29): cannot find include file "stddef.h"
  533. not in GENH/stddef.h
  534. not in C/stddef.h
  535. not in /usr/include/stddef.h
  536. makedepend: warning: C/client.c (reading /usr/include/bits/socket.h, line 28): cannot find include file "stddef.h"
  537. not in GENH/stddef.h
  538. not in C/stddef.h
  539. not in /usr/include/stddef.h
  540. makedepend: warning: C/client.c (reading /usr/include/rpc/netdb.h, line 42): cannot find include file "stddef.h"
  541. not in GENH/stddef.h
  542. not in C/stddef.h
  543. not in /usr/include/stddef.h
  544. makedepend: warning: C/client.c (reading /usr/include/signal.h, line 348): cannot find include file "stddef.h"
  545. not in GENH/stddef.h
  546. not in C/stddef.h
  547. not in /usr/include/stddef.h
  548. makedepend: warning: C/client.c (reading C/client.h, line 22): cannot find include file "attributes.h"
  549. not in GENH/attributes.h
  550. not in C/attributes.h
  551. not in /usr/include/attributes.h
  552. makedepend: warning: C/debug.c, line 6: cannot find include file "aisc_com.h"
  553. not in GENH/aisc_com.h
  554. not in C/aisc_com.h
  555. not in /usr/include/aisc_com.h
  556. makedepend: warning: C/server.c (reading /usr/include/limits.h, line 124): cannot find include file "limits.h"
  557. makedepend: warning: C/server.c, line 33: cannot find include file "aisc_com.h"
  558. not in aisc_com.h
  559. not in C/aisc_com.h
  560. not in GENH/aisc_com.h
  561. not in C/aisc_com.h
  562. not in /usr/include/aisc_com.h
  563. makedepend: warning: C/server.c (reading C/server.h, line 22): cannot find include file "attributes.h"
  564. not in GENH/attributes.h
  565. not in C/attributes.h
  566. not in /usr/include/attributes.h
  567. makedepend: warning: C/server.c (reading ../INCLUDE/arb_assert.h), line 33: # error Neither DEBUG nor NDEBUG is defined!
  568. makedepend: warning: C/server.c (reading ../INCLUDE/arb_assert.h, line 183): cannot find include file "arbdb_base.h"
  569. not in GENH/arbdb_base.h
  570. not in C/arbdb_base.h
  571. not in /usr/include/arbdb_base.h
  572. makedepend: warning: C/struct_man.c, line 5: cannot find include file "aisc.h"
  573. not in aisc.h
  574. not in C/aisc.h
  575. not in GENH/aisc.h
  576. not in C/aisc.h
  577. not in /usr/include/aisc.h
  578. makedepend: warning: C/struct_man.c (reading C/struct_man.h, line 19): cannot find include file "attributes.h"
  579. not in GENH/attributes.h
  580. not in C/attributes.h
  581. not in /usr/include/attributes.h
  582. makedepend: warning: cannot open "GENC/*.c"
  583. /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/SOURCE_TOOLS/mv_if_diff .depends_new .depends
  584. .depends created.
  585. make[4]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/PROBE_COM'
  586. make[4]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/PROBE_COM'
  587. ../MAKEBIN/aisc AISC/aisc.pa PT.aisc GENH/aisc.h
  588. ../MAKEBIN/aisc AISC/aisc_com.pa PT.aisc GENH/aisc_com.h
  589. rm -f GENH/aisc_server_extern.aisc
  590. rm -f GENH/aisc_server_extern.h
  591. ../MAKEBIN/aisc_mkpt -a C/aisc_extern.c PT_extern.c >GENH/aisc_server_extern.aisc
  592. ../MAKEBIN/aisc_mkpt -C C/aisc_extern.c PT_extern.c >GENH/aisc_server_extern.h
  593. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PROBE_COM -I/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
  594. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PROBE_COM -I/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
  595. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PROBE_COM -I/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
  596. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PROBE_COM -I/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
  597. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PROBE_COM -I/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
  598. ../MAKEBIN/aisc AISC/aisc_debug_globals.pa PT.aisc GENC/aisc_debug_globals.c GENH/aisc_server_extern.aisc GENH/import_proto.h
  599. ../MAKEBIN/aisc AISC/aisc_server.pa PT.aisc GENC/aisc_server.c GENH/aisc_server_extern.aisc GENH/import_proto.h
  600. ../MAKEBIN/aisc AISC/aisc_global.pa PT.aisc GENC/aisc_global.c GENH/aisc_server_extern.aisc GENH/import_proto.h
  601. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PROBE_COM -I/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
  602. rm -f GENH/aisc_server_proto.h
  603. echo GENH/import_proto.h
  604. GENH/import_proto.h
  605. ../MAKEBIN/aisc_mkpt -C GENC/aisc_server.c >GENH/aisc_server_proto.h
  606. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PROBE_COM -I/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
  607. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PROBE_COM -I/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
  608. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_PROBE_COM -I/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
  609. ld -r -o client.a O/client.o O/debug.o GENC/aisc_debug_globals.o
  610. 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
  611. make[4]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/PROBE_COM'
  612. make[3]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/PROBE_COM'
  613. make[2]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2'
  614. make arb
  615. make[2]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2'
  616. (cd lib;make all)
  617. make[3]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/lib'
  618. test -e arb_tcp.dat || cp -p arb_tcp_org.dat arb_tcp.dat
  619. test -L nas && echo "lib/nas is a link - skipped" || \
  620. (cd nas;make all)
  621. make[4]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/lib/nas'
  622. rm -f names.dat
  623. cp names.dat.template names.dat
  624. rm -f *%
  625. make[4]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/lib/nas'
  626. make[3]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/lib'
  627. make arbbasic2
  628. make[3]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2'
  629. -------------------------------------------------------------------------------- Make everything in AISC_MKPTPS
  630. make[4]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/AISC_MKPTPS'
  631. make[4]: Nothing to be done for `dummy.a'.
  632. make[4]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/AISC_MKPTPS'
  633. -------------------------------------------------------------------------------- Make everything in AISC
  634. make[4]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/AISC'
  635. make[4]: Nothing to be done for `dummy.a'.
  636. make[4]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/AISC'
  637. -------------------------------------------------------------------------------- Make everything in TEMPLATES
  638. make[4]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/TEMPLATES'
  639. ../SOURCE_TOOLS/build_info.pl
  640. make[4]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/TEMPLATES'
  641. -------------------------------------------------------------------------------- Make everything in NAMES_COM
  642. make[4]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/NAMES_COM'
  643. make[4]: `server.a' is up to date.
  644. make[4]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/NAMES_COM'
  645. -------------------------------------------------------------------------------- Make everything in NAMES_COM
  646. make[4]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/NAMES_COM'
  647. make[4]: `server.a' is up to date.
  648. make[4]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/NAMES_COM'
  649. -------------------------------------------------------------------------------- Make everything in PROBE_COM
  650. make[4]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/PROBE_COM'
  651. make[4]: `server.a' is up to date.
  652. make[4]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/PROBE_COM'
  653. make SL/SL.dummy
  654. make[4]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2'
  655. -------------------------------------------------------------------------------- Make everything in GL
  656. make[4]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/GL'
  657. make[5]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/GL/glpng'
  658. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GL -DIN_ARB_glpng -c glpng.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  659. make[5]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/GL/glAW'
  660. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GL -DIN_ARB_glAW -c GLwMDrawA.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  661. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GL -DIN_ARB_glAW -c AW_window_ogl.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/WINDOW
  662. glpng.c: In function 'DefaultAlphaCallback':
  663. glpng.c:45:57: warning: parameter 'red' set but not used [-Wunused-but-set-parameter]
  664. glpng.c: In function 'pngLoadF':
  665. glpng.c:385:10: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
  666. glpng.c: In function 'pngLoadRawF':
  667. glpng.c:280:10: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
  668. ld -r -o libglAW.a GLwMDrawA.o AW_window_ogl.o
  669. make[5]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/GL/glAW'
  670. ld -r -o libglpng_arb.a glpng.o
  671. make[5]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/GL/glpng'
  672. make[4]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/GL'
  673. -------------------------------------------------------------------------------- Make everything in SL
  674. make[5]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/SL'
  675. make[6]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/SL/TREE_READ'
  676. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_SL -DIN_ARB_TREE_READ -c TreeRead.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  677. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_SL -DIN_ARB_TREE_READ -c TreeTools.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  678. ld -r -o TREE_READ.a TreeRead.o TreeTools.o
  679. make[6]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/SL/TREE_READ'
  680. make[6]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/SL/REGEXPR'
  681. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_SL -DIN_ARB_REGEXPR -c RegExpr.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  682. ld -r -o REGEXPR.a RegExpr.o
  683. make[6]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/SL/REGEXPR'
  684. make[6]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/SL/AW_HELIX'
  685. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_SL -DIN_ARB_AW_HELIX -c AW_helix.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  686. ld -r -o AW_HELIX.a AW_helix.o
  687. make[6]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/SL/AW_HELIX'
  688. make[6]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/SL/FILE_BUFFER'
  689. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_SL -DIN_ARB_FILE_BUFFER -c FileBuffer.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  690. ld -r -o FILE_BUFFER.a FileBuffer.o
  691. make[6]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/SL/FILE_BUFFER'
  692. make[6]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/SL/HELIX'
  693. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_SL -DIN_ARB_HELIX -c BI_helix.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  694. ld -r -o HELIX.a BI_helix.o
  695. make[6]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/SL/HELIX'
  696. make[6]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/SL/DB_SCANNER'
  697. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_SL -DIN_ARB_DB_SCANNER -c db_scanner.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  698. ld -r -o DB_SCANNER.a db_scanner.o
  699. make[6]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/SL/DB_SCANNER'
  700. make[6]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/SL/TREE_WRITE'
  701. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_SL -DIN_ARB_TREE_WRITE -c TreeWrite.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  702. ld -r -o TREE_WRITE.a TreeWrite.o
  703. make[6]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/SL/TREE_WRITE'
  704. make[6]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/SL/AW_NAME'
  705. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_SL -DIN_ARB_AW_NAME -c AW_rename.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  706. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_SL -DIN_ARB_AW_NAME -c AW_names_admin.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  707. ld -r -o AW_NAME.a AW_rename.o AW_names_admin.o
  708. make[6]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/SL/AW_NAME'
  709. make[6]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/SL/FAST_ALIGNER'
  710. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_SL -DIN_ARB_FAST_ALIGNER -c fast_aligner.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  711. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_SL -DIN_ARB_FAST_ALIGNER -c ClustalV.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  712. fast_aligner.cxx: In function 'const char* alignCompactedTo(AWTC_CompactedSubSequence*, const AWTC_FastSearchSequence*, int, GB_CSTR, long int, GBDATA*, GBDATA*, const AlignParams&)':
  713. fast_aligner.cxx:1254:31: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated (declared at /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE/ad_t_prot.h:108) [-Wdeprecated-declarations]
  714. fast_aligner.cxx:1254:84: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated (declared at /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE/ad_t_prot.h:108) [-Wdeprecated-declarations]
  715. fast_aligner.cxx: In function 'void AWTC_start_faligning(AW_window*, AW_CL)':
  716. fast_aligner.cxx:2368:58: warning: narrowing conversion of 'root->AW_root::awar(((const char*)"faligner/next_relatives"))->AW_awar::read_int()' from 'long int' to 'int' inside { } is ill-formed in C++11 [-Wnarrowing]
  717. fast_aligner.cxx:2369:53: warning: narrowing conversion of 'root->AW_root::awar(((const char*)"next_neighbours/oligo_len"))->AW_awar::read_int()' from 'long int' to 'int' inside { } is ill-formed in C++11 [-Wnarrowing]
  718. fast_aligner.cxx:2370:54: warning: narrowing conversion of 'root->AW_root::awar(((const char*)"next_neighbours/mismatches"))->AW_awar::read_int()' from 'long int' to 'int' inside { } is ill-formed in C++11 [-Wnarrowing]
  719. fast_aligner.cxx:2371:53: warning: narrowing conversion of 'root->AW_root::awar(((const char*)"next_neighbours/fast_mode"))->AW_awar::read_int()' from 'long int' to 'bool' inside { } is ill-formed in C++11 [-Wnarrowing]
  720. fast_aligner.cxx:2372:55: warning: narrowing conversion of 'root->AW_root::awar(((const char*)"next_neighbours/rel_matches"))->AW_awar::read_int()' from 'long int' to 'bool' inside { } is ill-formed in C++11 [-Wnarrowing]
  721. fast_aligner.cxx:2377:62: warning: narrowing conversion of 'root->AW_root::awar(((const char*)"faligner/show_gaps"))->AW_awar::read_int()' from 'long int' to 'bool' inside { } is ill-formed in C++11 [-Wnarrowing]
  722. ld -r -o FAST_ALIGNER.a fast_aligner.o ClustalV.o
  723. make[6]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/SL/FAST_ALIGNER'
  724. make[5]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/SL'
  725. make[4]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2'
  726. make[3]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2'
  727. make arbshared arbapplications help
  728. make[3]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2'
  729. make -C bin all
  730. make[4]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin'
  731. find . -type l -exec rm {} \;
  732. -------------------------------------------------------------------------------- Building prototyper
  733. make AISC_MKPTPS/AISC_MKPTPS.dummy
  734. -------------------------------------------------------------------------------- Make everything in AISC_MKPTPS
  735. make[4]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/AISC_MKPTPS'
  736. make[4]: Nothing to be done for `dummy.a'.
  737. make[4]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/AISC_MKPTPS'
  738. -------------------------------------------------------------------------------- Make everything in AISC
  739. make[4]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/AISC'
  740. make[4]: Nothing to be done for `dummy.a'.
  741. make[4]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/AISC'
  742. make[4]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2'
  743. -------------------------------------------------------------------------------- Make everything in AISC_MKPTPS
  744. make[5]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/AISC_MKPTPS'
  745. make[5]: Nothing to be done for `AISC_MKPTPS.a'.
  746. make[5]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/AISC_MKPTPS'
  747. make[4]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2'
  748. ln -s -f `find ../SH ../PERL_SCRIPTS -perm -100 ! -type d ! -name 'config*' -print` .
  749. make[4]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/bin'
  750. -------------------------------------------------------------------------------- Make everything in AWTI
  751. make[4]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/AWTI'
  752. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWTI -c AWTI_import.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  753. AWTI_import.cxx: In function 'void AWTC_import_go_cb(AW_window*)':
  754. AWTI_import.cxx:1174:16: error: 'sleep' was not declared in this scope
  755. make[4]: *** [AWTI_import.o] Error 1
  756. make[4]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/AWTI'
  757. make[3]: *** [AWTI/AWTI.dummy] Error 1
  758. make[3]: *** Waiting for unfinished jobs....
  759. -------------------------------------------------------------------------------- Make everything in ARBDBPP
  760. make[4]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/ARBDBPP'
  761. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBPP -c adtsequence.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  762. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBPP -c adt_edit.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  763. adt_edit.cxx: In member function 'AD_ERR* ADT_SEQUENCE::show_edit_search(ADT_SEARCH*, ADT_EDIT*)':
  764. adt_edit.cxx:581:13: warning: variable 'seq_empty_var' set but not used [-Wunused-but-set-variable]
  765. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBPP -c adtali.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  766. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBPP -c adextended.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  767. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBPP -c adseq.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  768. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBPP -c adspecies.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  769. adseq.cxx: In member function 'AD_ERR* AD_CONT::create(AD_SPECIES*, AD_ALI*)':
  770. adseq.cxx:1012:20: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated (declared at /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE/ad_t_prot.h:108) [-Wdeprecated-declarations]
  771. adseq.cxx:1012:84: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated (declared at /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE/ad_t_prot.h:108) [-Wdeprecated-declarations]
  772. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBPP -c admain.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  773. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBPP -c adali.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  774. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBPP -c liste.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  775. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -Wl,-O1 -Wl,--as-needed -Wl,--export-dynamic -shared -o libARBDBPP.so adtsequence.o adt_edit.o adtali.o adextended.o adseq.o adspecies.o admain.o adali.o liste.o
  776. touch libARBDBPP.a
  777. make[4]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/ARBDBPP'
  778. -------------------------------------------------------------------------------- Make everything in GENOM
  779. make[4]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/GENOM'
  780. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GENOM -c GEN_interface.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  781. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GENOM -c GEN_map.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  782. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GENOM -c GEN_graphic.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  783. GEN_graphic.cxx:158:12: warning: unused parameter 'selected_range' [-Wunused-parameter]
  784. GEN_map.cxx: In function 'void gen_extract_gene_2_pseudoSpecies(GBDATA*, GBDATA*, EG2PS_data*)':
  785. GEN_map.cxx:882:39: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated (declared at /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE/ad_t_prot.h:108) [-Wdeprecated-declarations]
  786. GEN_map.cxx:882:93: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated (declared at /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE/ad_t_prot.h:108) [-Wdeprecated-declarations]
  787. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GENOM -c GEN_gene.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  788. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GENOM -c GEN_nds.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  789. GEN_nds.cxx:307:2: warning: #warning make this function more general like AWT_popup_select_species_field_window [-Wcpp]
  790. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GENOM -c GEN_color_groups.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  791. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GENOM -c GEN_translations.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  792. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GENOM -c EXP_interface.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  793. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GENOM -c EXP_main.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  794. ld -r -o GENOM.a GEN_interface.o GEN_map.o GEN_graphic.o GEN_gene.o GEN_nds.o GEN_color_groups.o GEN_translations.o EXP_interface.o EXP_main.o
  795. make[4]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/GENOM'
  796. -------------------------------------------------------------------------------- Make everything in MERGE
  797. make[4]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/MERGE'
  798. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_MERGE -c MG_checkfield.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  799. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_MERGE -c MG_main.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  800. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_MERGE -c MG_trees.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  801. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_MERGE -c MG_alignment.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  802. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_MERGE -c MG_species.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  803. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_MERGE -c MG_extendeds.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  804. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_MERGE -c MG_names.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  805. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_MERGE -c MG_gene_species.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  806. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_MERGE -c MG_configs.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  807. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_MERGE -c MG_preserves.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  808. ld -r -o MERGE.a MG_checkfield.o MG_main.o MG_trees.o MG_alignment.o MG_species.o MG_extendeds.o MG_names.o MG_gene_species.o MG_configs.o MG_preserves.o
  809. make[4]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/MERGE'
  810. -------------------------------------------------------------------------------- Make everything in GENOM_IMPORT
  811. make[4]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/GENOM_IMPORT'
  812. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GENOM_IMPORT -c GenomeImport.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  813. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GENOM_IMPORT -c Importer.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  814. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GENOM_IMPORT -c DBwriter.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  815. DBwriter.cxx: In member function 'void DBwriter::writeSequence(const SequenceBuffer&)':
  816. DBwriter.cxx:226:23: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated (declared at /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE/ad_t_prot.h:108) [-Wdeprecated-declarations]
  817. DBwriter.cxx:226:76: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated (declared at /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE/ad_t_prot.h:108) [-Wdeprecated-declarations]
  818. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GENOM_IMPORT -c SequenceBuffer.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  819. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GENOM_IMPORT -c MetaInfo.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  820. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GENOM_IMPORT -c Feature.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  821. SequenceBuffer.cxx: In member function 'void BaseCounter::checkOverallCounter() const':
  822. SequenceBuffer.cxx:55:67: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'size_t {aka long unsigned int}' [-Wformat]
  823. SequenceBuffer.cxx:55:67: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'size_t {aka long unsigned int}' [-Wformat]
  824. SequenceBuffer.cxx: In member function 'void BaseCounter::expectEqual(const BaseCounter&) const':
  825. SequenceBuffer.cxx:116:114: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'size_t {aka long unsigned int}' [-Wformat]
  826. SequenceBuffer.cxx:116:114: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'size_t {aka long unsigned int}' [-Wformat]
  827. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GENOM_IMPORT -c Location.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  828. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GENOM_IMPORT -c tools.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  829. -------------------- Checking GENOM_IMPORT.a
  830. Target 'GENOM_IMPORT.a' not found
  831. -> rebuilding GENOM_IMPORT.a (Wed Dec 31 23:59:59 1969)
  832. ld -r -o GENOM_IMPORT.a GenomeImport.o Importer.o DBwriter.o SequenceBuffer.o MetaInfo.o Feature.o Location.o tools.o
  833. make[4]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/GENOM_IMPORT'
  834. -------------------------------------------------------------------------------- Make everything in WINDOW
  835. make[4]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/WINDOW'
  836. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_WINDOW -c AW_position.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  837. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_WINDOW -c AW_Xm.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  838. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_WINDOW -c AW_at.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  839. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_WINDOW -c AW_button.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  840. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_WINDOW -c AW_click.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  841. AW_button.cxx: In function 'void AW_variable_update_callback(Widget, XtPointer, XtPointer)':
  842. AW_button.cxx:199:37: warning: variable 'found' set but not used [-Wunused-but-set-variable]
  843. AW_button.cxx: In member function 'int AW_window::get_index_of_element(AW_selection_list*, const char*)':
  844. AW_button.cxx:1617:17: warning: variable 'found_index' set but not used [-Wunused-but-set-variable]
  845. AW_button.cxx: In function 'const char* detect_bitmap_size(const char*, int*, int*)':
  846. AW_button.cxx:398:47: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
  847. AW_button.cxx:417:51: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
  848. AW_button.cxx:418:51: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
  849. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_WINDOW -c AW_debug.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  850. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_WINDOW -c AW_device.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  851. AW_device.cxx: In member function 'int AW_device::text_overlay(int, const char*, long int, AW_pos, AW_pos, AW_pos, AW_bitset, AW_CL, AW_CL, AW_CL, AW_pos, AW_pos, int (*)(AW_device*, int, const char*, size_t, size_t, size_t, AW_pos, AW_pos, AW_pos, AW_pos, AW_CL, AW_CL, AW_CL))':
  852. AW_device.cxx:721:22: warning: variable 'yi' set but not used [-Wunused-but-set-variable]
  853. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_WINDOW -c AW_font_group.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  854. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_WINDOW -c AW_global_awars.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  855. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_WINDOW -c AW_nawar.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  856. AW_nawar.cxx: In member function 'AW_awar* AW_root::awar_pointer(const char*, void*, AW_default)':
  857. AW_nawar.cxx:193:111: warning: passing NULL to non-pointer argument 4 of 'AW_awar::AW_awar(AW_VARIABLE_TYPE, const char*, const char*, double, AW_default, AW_root*)' [-Wconversion-null]
  858. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_WINDOW -c AW_preset.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  859. AW_preset.cxx: In function 'void* AW_manage_GC(AW_window*, AW_device*, int, int, AW_GCM_AREA, void (*)(AW_window*, AW_CL, AW_CL), AW_CL, AW_CL, bool, const char*, ...)':
  860. AW_preset.cxx:613:18: warning: variable 'flag_no_color_selector' set but not used [-Wunused-but-set-variable]
  861. AW_preset.cxx:614:18: warning: variable 'flag_append_in_same_line' set but not used [-Wunused-but-set-variable]
  862. AW_preset.cxx: In function 'bool aw_insert_gcs(AW_root*, AW_window_simple*, aw_gc_manager*, bool)':
  863. AW_preset.cxx:786:17: warning: variable 'first' set but not used [-Wunused-but-set-variable]
  864. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_WINDOW -c AW_print.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  865. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_WINDOW -c AW_question.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  866. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_WINDOW -c AW_size.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  867. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_WINDOW -c AW_status.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  868. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_WINDOW -c AW_window.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  869. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_WINDOW -c AW_xfig.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  870. AW_status.cxx: In function 'int aw_status_read_int(int, int)':
  871. AW_status.cxx:281:19: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
  872. AW_status.cxx: In function 'void aw_help_edit_help(AW_window*)':
  873. AW_status.cxx:1746:25: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
  874. AW_window.cxx: In member function 'void AW_window::insert_separator()':
  875. AW_window.cxx:3002:12: warning: variable 'separator' set but not used [-Wunused-but-set-variable]
  876. AW_window.cxx: In member function 'void AW_window::insert_separator_help()':
  877. AW_window.cxx:3011:12: warning: variable 'separator' set but not used [-Wunused-but-set-variable]
  878. AW_status.cxx: In function 'void aw_status_timer_event(AW_root*, AW_CL, AW_CL)':
  879. AW_status.cxx:419:28: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
  880. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_WINDOW -c AW_xfigfont.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  881. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_WINDOW -c AW_xfont.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  882. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_WINDOW -c AW_xkey.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  883. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_WINDOW -c AW_window_Xm_interface.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  884. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -Wl,-O1 -Wl,--as-needed -Wl,--export-dynamic -shared -o libAW.so AW_position.o AW_Xm.o AW_at.o AW_button.o AW_click.o AW_debug.o AW_device.o AW_font_group.o AW_global_awars.o AW_nawar.o AW_preset.o AW_print.o AW_question.o AW_size.o AW_status.o AW_window.o AW_xfig.o AW_xfigfont.o AW_xfont.o AW_xkey.o AW_window_Xm_interface.o
  885. touch libAW.a
  886. make[4]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/WINDOW'
  887. -------------------------------------------------------------------------------- Make everything in ARBDBS
  888. make[4]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/ARBDBS'
  889. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c adsort.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  890. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c adlang1.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  891. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c adstring.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  892. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c admatch.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  893. admatch.c: In function 'GBS_string_eval':
  894. admatch.c:763:37: warning: ignoring return value of 'gbs_build_replace_string', declared with attribute warn_unused_result [-Wunused-result]
  895. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c arbdb.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  896. arbdb.c: In function 'GB_copy_with_protection':
  897. arbdb.c:1469:13: warning: null argument where non-null required (argument 2) [-Wnonnull]
  898. arbdb.c:1469:13: warning: null argument where non-null required (argument 2) [-Wnonnull]
  899. arbdb.c:1469:13: warning: null argument where non-null required (argument 2) [-Wnonnull]
  900. arbdb.c:1469:13: warning: null argument where non-null required (argument 2) [-Wnonnull]
  901. arbdb.c: In function 'gb_remove_callback':
  902. arbdb.c:2239:13: warning: variable 'removed' set but not used [-Wunused-but-set-variable]
  903. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c ad_core.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  904. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c admath.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  905. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c adoptimize.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  906. ad_core.c: In function 'ad_use':
  907. ad_core.c:11:17: warning: parameter 'dummy' set but not used [-Wunused-but-set-parameter]
  908. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c adsystem.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  909. adsystem.c: In function 'gb_load_single_key_data':
  910. adsystem.c:141:101: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
  911. adsystem.c:159:123: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
  912. adsystem.c:160:123: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
  913. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c adindex.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  914. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c adperl.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  915. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c adlink.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  916. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c adsocket.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  917. adsocket.c: In function 'GB_get_full_path':
  918. adsocket.c:1256:21: warning: ignoring return value of 'realpath', declared with attribute warn_unused_result [-Wunused-result]
  919. adsocket.c:1260:21: warning: ignoring return value of 'realpath', declared with attribute warn_unused_result [-Wunused-result]
  920. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c adcomm.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  921. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c adhash.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  922. adcomm.c: In function 'gbcms_write_updated':
  923. adcomm.c:303:23: warning: variable 'hs' set but not used [-Wunused-but-set-variable]
  924. adcomm.c: In function 'gbcms_talking_init_transaction':
  925. adcomm.c:533:14: warning: variable 'buffer' set but not used [-Wunused-but-set-variable]
  926. adcomm.c: In function 'gbcm_read_bin':
  927. adcomm.c:1231:27: warning: variable 'flags3' set but not used [-Wunused-but-set-variable]
  928. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c adquery.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  929. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c ad_save_load.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  930. adquery.c: In function 'gb_search':
  931. adquery.c:449:28: warning: comparison between 'GB_TYPES' and 'enum gb_search_enum' [-Wenum-compare]
  932. adquery.c:455:28: warning: comparison between 'GB_TYPES' and 'enum gb_search_enum' [-Wenum-compare]
  933. adquery.c:526:31: warning: comparison between 'GB_TYPES' and 'enum gb_search_enum' [-Wenum-compare]
  934. adquery.c: In function 'GB_command_interpreter':
  935. adquery.c:861:19: warning: variable 'len' set but not used [-Wunused-but-set-variable]
  936. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c adcompr.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  937. ad_save_load.c: In function 'gb_write_bin_rek':
  938. ad_save_load.c:799:13: warning: null argument where non-null required (argument 1) [-Wnonnull]
  939. ad_save_load.c: In function 'GB_save_as':
  940. ad_save_load.c:1079:5: warning: 'GB_get_error' is deprecated (declared at ./ad_prot.h:43) [-Wdeprecated-declarations]
  941. ad_save_load.c: In function 'GB_save_quick_as':
  942. ad_save_load.c:1126:5: warning: 'GB_get_error' is deprecated (declared at ./ad_prot.h:43) [-Wdeprecated-declarations]
  943. ad_save_load.c:1148:9: warning: 'GB_get_error' is deprecated (declared at ./ad_prot.h:43) [-Wdeprecated-declarations]
  944. ad_save_load.c:1173:9: warning: 'GB_get_error' is deprecated (declared at ./ad_prot.h:43) [-Wdeprecated-declarations]
  945. ad_save_load.c:1184:9: warning: 'GB_get_error' is deprecated (declared at ./ad_prot.h:43) [-Wdeprecated-declarations]
  946. ad_save_load.c: In function 'GB_save_quick':
  947. ad_save_load.c:1213:5: warning: 'GB_get_error' is deprecated (declared at ./ad_prot.h:43) [-Wdeprecated-declarations]
  948. ad_save_load.c:1234:9: warning: 'GB_get_error' is deprecated (declared at ./ad_prot.h:43) [-Wdeprecated-declarations]
  949. ad_save_load.c:1267:5: warning: 'GB_get_error' is deprecated (declared at ./ad_prot.h:43) [-Wdeprecated-declarations]
  950. ad_save_load.c: In function 'gb_check_saveable':
  951. ad_save_load.c:1307:9: warning: 'GB_get_error' is deprecated (declared at ./ad_prot.h:43) [-Wdeprecated-declarations]
  952. ad_save_load.c:1312:9: warning: 'GB_get_error' is deprecated (declared at ./ad_prot.h:43) [-Wdeprecated-declarations]
  953. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c admalloc.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  954. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c ad_load.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  955. ad_load.c: In function 'GB_login':
  956. ad_load.c:1380:34: warning: ignoring return value of 'gb_scan_directory', declared with attribute warn_unused_result [-Wunused-result]
  957. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c admap.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  958. admap.c: In function 'gb_save_mapfile':
  959. admap.c:636:9: warning: variable 'writeOffset' set but not used [-Wunused-but-set-variable]
  960. admap.c:635:10: warning: variable 'calcOffset' set but not used [-Wunused-but-set-variable]
  961. admap.c: In function 'gb_is_valid_mapfile':
  962. admap.c:722:14: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
  963. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c adTest.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  964. adTest.c: In function 'testData':
  965. adTest.c:36:9: warning: variable 'err' set but not used [-Wunused-but-set-variable]
  966. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c adtune.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  967. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c adGene.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  968. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c adtcp.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  969. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c adhashtools.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  970. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c adExperiment.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  971. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c adtools.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  972. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c adseqcompr.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  973. adtools.c: In function 'GBT_check_arb_file':
  974. adtools.c:74:10: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
  975. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c adtables.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  976. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c adRevCompl.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  977. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c adChangeKey.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  978. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c adali.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  979. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c adcolumns.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  980. adali.c: In function 'GBT_create_sequence_data':
  981. adali.c:597:5: warning: 'GBT_add_data' is deprecated (declared at adali.c:568) [-Wdeprecated-declarations]
  982. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c adtree.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  983. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c adname.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  984. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c aditem.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  985. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c arbdbpp.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  986. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDBS -c ad_config.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  987. ld -r -o libARBDB.a adsort.o adlang1.o adstring.o admatch.o arbdb.o ad_core.o admath.o adoptimize.o adsystem.o adindex.o adperl.o adlink.o adsocket.o adcomm.o adhash.o adquery.o ad_save_load.o adcompr.o admalloc.o ad_load.o admap.o adTest.o adtune.o adGene.o adtcp.o adhashtools.o adExperiment.o adtools.o adseqcompr.o adtables.o adRevCompl.o adChangeKey.o adali.o adcolumns.o adtree.o adname.o aditem.o arbdbpp.o ad_config.o
  988. make[4]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/ARBDBS'
  989. -------------------------------------------------------------------------------- Make everything in ARBDB2
  990. make[4]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/ARBDB2'
  991. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c adsort.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  992. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c adlang1.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  993. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c adstring.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  994. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c admatch.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  995. admatch.c: In function 'GBS_string_eval':
  996. admatch.c:763:37: warning: ignoring return value of 'gbs_build_replace_string', declared with attribute warn_unused_result [-Wunused-result]
  997. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c arbdb.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  998. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c ad_core.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  999. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c admath.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1000. ad_core.c: In function 'ad_use':
  1001. ad_core.c:11:17: warning: parameter 'dummy' set but not used [-Wunused-but-set-parameter]
  1002. arbdb.c: In function 'GB_copy_with_protection':
  1003. arbdb.c:1469:13: warning: null argument where non-null required (argument 2) [-Wnonnull]
  1004. arbdb.c:1469:13: warning: null argument where non-null required (argument 2) [-Wnonnull]
  1005. arbdb.c:1469:13: warning: null argument where non-null required (argument 2) [-Wnonnull]
  1006. arbdb.c:1469:13: warning: null argument where non-null required (argument 2) [-Wnonnull]
  1007. arbdb.c: In function 'gb_remove_callback':
  1008. arbdb.c:2239:13: warning: variable 'removed' set but not used [-Wunused-but-set-variable]
  1009. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c adoptimize.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1010. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c adsystem.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1011. adsystem.c: In function 'gb_load_single_key_data':
  1012. adsystem.c:141:101: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
  1013. adsystem.c:159:123: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
  1014. adsystem.c:160:123: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
  1015. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c adindex.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1016. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c adperl.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1017. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c adlink.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1018. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c adsocket.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1019. adsocket.c: In function 'GB_get_full_path':
  1020. adsocket.c:1256:21: warning: ignoring return value of 'realpath', declared with attribute warn_unused_result [-Wunused-result]
  1021. adsocket.c:1260:21: warning: ignoring return value of 'realpath', declared with attribute warn_unused_result [-Wunused-result]
  1022. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c adcomm.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1023. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c adhash.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1024. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c adquery.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1025. adcomm.c: In function 'gbcms_write_updated':
  1026. adcomm.c:303:23: warning: variable 'hs' set but not used [-Wunused-but-set-variable]
  1027. adcomm.c: In function 'gbcms_talking_init_transaction':
  1028. adcomm.c:533:14: warning: variable 'buffer' set but not used [-Wunused-but-set-variable]
  1029. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c ad_save_load.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1030. adcomm.c: In function 'gbcm_read_bin':
  1031. adcomm.c:1231:27: warning: variable 'flags3' set but not used [-Wunused-but-set-variable]
  1032. adquery.c: In function 'gb_search':
  1033. adquery.c:449:28: warning: comparison between 'GB_TYPES' and 'enum gb_search_enum' [-Wenum-compare]
  1034. adquery.c:455:28: warning: comparison between 'GB_TYPES' and 'enum gb_search_enum' [-Wenum-compare]
  1035. adquery.c:526:31: warning: comparison between 'GB_TYPES' and 'enum gb_search_enum' [-Wenum-compare]
  1036. adquery.c: In function 'GB_command_interpreter':
  1037. adquery.c:861:19: warning: variable 'len' set but not used [-Wunused-but-set-variable]
  1038. ad_save_load.c: In function 'gb_write_bin_rek':
  1039. ad_save_load.c:799:13: warning: null argument where non-null required (argument 1) [-Wnonnull]
  1040. ad_save_load.c: In function 'GB_save_as':
  1041. ad_save_load.c:1079:5: warning: 'GB_get_error' is deprecated (declared at ./ad_prot.h:43) [-Wdeprecated-declarations]
  1042. ad_save_load.c: In function 'GB_save_quick_as':
  1043. ad_save_load.c:1126:5: warning: 'GB_get_error' is deprecated (declared at ./ad_prot.h:43) [-Wdeprecated-declarations]
  1044. ad_save_load.c:1148:9: warning: 'GB_get_error' is deprecated (declared at ./ad_prot.h:43) [-Wdeprecated-declarations]
  1045. ad_save_load.c:1173:9: warning: 'GB_get_error' is deprecated (declared at ./ad_prot.h:43) [-Wdeprecated-declarations]
  1046. ad_save_load.c:1184:9: warning: 'GB_get_error' is deprecated (declared at ./ad_prot.h:43) [-Wdeprecated-declarations]
  1047. ad_save_load.c: In function 'GB_save_quick':
  1048. ad_save_load.c:1213:5: warning: 'GB_get_error' is deprecated (declared at ./ad_prot.h:43) [-Wdeprecated-declarations]
  1049. ad_save_load.c:1234:9: warning: 'GB_get_error' is deprecated (declared at ./ad_prot.h:43) [-Wdeprecated-declarations]
  1050. ad_save_load.c:1267:5: warning: 'GB_get_error' is deprecated (declared at ./ad_prot.h:43) [-Wdeprecated-declarations]
  1051. ad_save_load.c: In function 'gb_check_saveable':
  1052. ad_save_load.c:1307:9: warning: 'GB_get_error' is deprecated (declared at ./ad_prot.h:43) [-Wdeprecated-declarations]
  1053. ad_save_load.c:1312:9: warning: 'GB_get_error' is deprecated (declared at ./ad_prot.h:43) [-Wdeprecated-declarations]
  1054. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c adcompr.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1055. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c admalloc.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1056. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c ad_load.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1057. ad_load.c: In function 'GB_login':
  1058. ad_load.c:1380:34: warning: ignoring return value of 'gb_scan_directory', declared with attribute warn_unused_result [-Wunused-result]
  1059. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c admap.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1060. admap.c: In function 'gb_save_mapfile':
  1061. admap.c:636:9: warning: variable 'writeOffset' set but not used [-Wunused-but-set-variable]
  1062. admap.c:635:10: warning: variable 'calcOffset' set but not used [-Wunused-but-set-variable]
  1063. admap.c: In function 'gb_is_valid_mapfile':
  1064. admap.c:722:14: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
  1065. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c adTest.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1066. adTest.c: In function 'testData':
  1067. adTest.c:36:9: warning: variable 'err' set but not used [-Wunused-but-set-variable]
  1068. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c adtune.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1069. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c adGene.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1070. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c adtcp.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1071. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c adhashtools.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1072. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c adExperiment.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1073. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c adtools.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1074. adtools.c: In function 'GBT_check_arb_file':
  1075. adtools.c:74:10: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
  1076. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c adseqcompr.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1077. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c adtables.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1078. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c adRevCompl.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1079. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c adChangeKey.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1080. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c adali.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1081. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c adcolumns.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1082. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c adtree.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1083. adali.c: In function 'GBT_create_sequence_data':
  1084. adali.c:597:5: warning: 'GBT_add_data' is deprecated (declared at adali.c:568) [-Wdeprecated-declarations]
  1085. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c adname.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1086. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c aditem.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1087. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB2 -c ad_config.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1088. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -Wl,-O1 -Wl,--as-needed -Wl,--export-dynamic -shared -o libARBDB.so adsort.o adlang1.o adstring.o admatch.o arbdb.o ad_core.o admath.o adoptimize.o adsystem.o adindex.o adperl.o adlink.o adsocket.o adcomm.o adhash.o adquery.o ad_save_load.o adcompr.o admalloc.o ad_load.o admap.o adTest.o adtune.o adGene.o adtcp.o adhashtools.o adExperiment.o adtools.o adseqcompr.o adtables.o adRevCompl.o adChangeKey.o adali.o adcolumns.o adtree.o adname.o aditem.o ad_config.o
  1089. touch libARBDB.a
  1090. make[4]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/ARBDB2'
  1091. -------------------------------------------------------------------------------- Make everything in ARBDB
  1092. make[4]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/ARBDB'
  1093. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c adsort.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1094. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c adlang1.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1095. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c adstring.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1096. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c admatch.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1097. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c arbdb.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1098. admatch.c: In function 'GBS_string_eval':
  1099. admatch.c:763:37: warning: ignoring return value of 'gbs_build_replace_string', declared with attribute warn_unused_result [-Wunused-result]
  1100. arbdb.c: In function 'GB_copy_with_protection':
  1101. arbdb.c:1469:13: warning: null argument where non-null required (argument 2) [-Wnonnull]
  1102. arbdb.c:1469:13: warning: null argument where non-null required (argument 2) [-Wnonnull]
  1103. arbdb.c:1469:13: warning: null argument where non-null required (argument 2) [-Wnonnull]
  1104. arbdb.c:1469:13: warning: null argument where non-null required (argument 2) [-Wnonnull]
  1105. arbdb.c: In function 'gb_remove_callback':
  1106. arbdb.c:2239:13: warning: variable 'removed' set but not used [-Wunused-but-set-variable]
  1107. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c ad_core.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1108. ad_core.c: In function 'ad_use':
  1109. ad_core.c:11:17: warning: parameter 'dummy' set but not used [-Wunused-but-set-parameter]
  1110. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c admath.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1111. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c adoptimize.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1112. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c adsystem.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1113. adsystem.c: In function 'gb_load_single_key_data':
  1114. adsystem.c:141:101: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
  1115. adsystem.c:159:123: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
  1116. adsystem.c:160:123: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
  1117. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c adindex.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1118. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c adperl.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1119. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c adlink.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1120. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c adsocket.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1121. adsocket.c: In function 'GB_get_full_path':
  1122. adsocket.c:1256:21: warning: ignoring return value of 'realpath', declared with attribute warn_unused_result [-Wunused-result]
  1123. adsocket.c:1260:21: warning: ignoring return value of 'realpath', declared with attribute warn_unused_result [-Wunused-result]
  1124. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c adcomm.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1125. adcomm.c: In function 'gbcms_write_updated':
  1126. adcomm.c:303:23: warning: variable 'hs' set but not used [-Wunused-but-set-variable]
  1127. adcomm.c: In function 'gbcms_talking_init_transaction':
  1128. adcomm.c:533:14: warning: variable 'buffer' set but not used [-Wunused-but-set-variable]
  1129. adcomm.c: In function 'gbcm_read_bin':
  1130. adcomm.c:1231:27: warning: variable 'flags3' set but not used [-Wunused-but-set-variable]
  1131. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c adhash.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1132. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c adquery.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1133. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c ad_save_load.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1134. adquery.c: In function 'gb_search':
  1135. adquery.c:449:28: warning: comparison between 'GB_TYPES' and 'enum gb_search_enum' [-Wenum-compare]
  1136. adquery.c:455:28: warning: comparison between 'GB_TYPES' and 'enum gb_search_enum' [-Wenum-compare]
  1137. adquery.c:526:31: warning: comparison between 'GB_TYPES' and 'enum gb_search_enum' [-Wenum-compare]
  1138. adquery.c: In function 'GB_command_interpreter':
  1139. adquery.c:861:19: warning: variable 'len' set but not used [-Wunused-but-set-variable]
  1140. ad_save_load.c: In function 'gb_write_bin_rek':
  1141. ad_save_load.c:799:13: warning: null argument where non-null required (argument 1) [-Wnonnull]
  1142. ad_save_load.c: In function 'GB_save_as':
  1143. ad_save_load.c:1079:5: warning: 'GB_get_error' is deprecated (declared at ./ad_prot.h:43) [-Wdeprecated-declarations]
  1144. ad_save_load.c: In function 'GB_save_quick_as':
  1145. ad_save_load.c:1126:5: warning: 'GB_get_error' is deprecated (declared at ./ad_prot.h:43) [-Wdeprecated-declarations]
  1146. ad_save_load.c:1148:9: warning: 'GB_get_error' is deprecated (declared at ./ad_prot.h:43) [-Wdeprecated-declarations]
  1147. ad_save_load.c:1173:9: warning: 'GB_get_error' is deprecated (declared at ./ad_prot.h:43) [-Wdeprecated-declarations]
  1148. ad_save_load.c:1184:9: warning: 'GB_get_error' is deprecated (declared at ./ad_prot.h:43) [-Wdeprecated-declarations]
  1149. ad_save_load.c: In function 'GB_save_quick':
  1150. ad_save_load.c:1213:5: warning: 'GB_get_error' is deprecated (declared at ./ad_prot.h:43) [-Wdeprecated-declarations]
  1151. ad_save_load.c:1234:9: warning: 'GB_get_error' is deprecated (declared at ./ad_prot.h:43) [-Wdeprecated-declarations]
  1152. ad_save_load.c:1267:5: warning: 'GB_get_error' is deprecated (declared at ./ad_prot.h:43) [-Wdeprecated-declarations]
  1153. ad_save_load.c: In function 'gb_check_saveable':
  1154. ad_save_load.c:1307:9: warning: 'GB_get_error' is deprecated (declared at ./ad_prot.h:43) [-Wdeprecated-declarations]
  1155. ad_save_load.c:1312:9: warning: 'GB_get_error' is deprecated (declared at ./ad_prot.h:43) [-Wdeprecated-declarations]
  1156. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c adcompr.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1157. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c admalloc.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1158. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c ad_load.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1159. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c admap.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1160. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c adTest.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1161. ad_load.c: In function 'GB_login':
  1162. ad_load.c:1380:34: warning: ignoring return value of 'gb_scan_directory', declared with attribute warn_unused_result [-Wunused-result]
  1163. admap.c: In function 'gb_save_mapfile':
  1164. admap.c:636:9: warning: variable 'writeOffset' set but not used [-Wunused-but-set-variable]
  1165. admap.c:635:10: warning: variable 'calcOffset' set but not used [-Wunused-but-set-variable]
  1166. adTest.c: In function 'testData':
  1167. adTest.c:36:9: warning: variable 'err' set but not used [-Wunused-but-set-variable]
  1168. admap.c: In function 'gb_is_valid_mapfile':
  1169. admap.c:722:14: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
  1170. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c adtune.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1171. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c adGene.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1172. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c adtcp.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1173. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c adhashtools.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1174. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c adExperiment.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1175. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c adtools.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1176. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c adseqcompr.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1177. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c adtables.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1178. adtools.c: In function 'GBT_check_arb_file':
  1179. adtools.c:74:10: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
  1180. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c adRevCompl.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1181. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c adChangeKey.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1182. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c adali.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1183. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c adcolumns.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1184. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c adtree.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1185. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c adname.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1186. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c aditem.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1187. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c arbdbpp.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1188. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_ARBDB -c ad_config.c -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1189. adali.c: In function 'GBT_create_sequence_data':
  1190. adali.c:597:5: warning: 'GBT_add_data' is deprecated (declared at adali.c:568) [-Wdeprecated-declarations]
  1191. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -Wl,-O1 -Wl,--as-needed -Wl,--export-dynamic -shared -o libARBDB.so adsort.o adlang1.o adstring.o admatch.o arbdb.o ad_core.o admath.o adoptimize.o adsystem.o adindex.o adperl.o adlink.o adsocket.o adcomm.o adhash.o adquery.o ad_save_load.o adcompr.o admalloc.o ad_load.o admap.o adTest.o adtune.o adGene.o adtcp.o adhashtools.o adExperiment.o adtools.o adseqcompr.o adtables.o adRevCompl.o adChangeKey.o adali.o adcolumns.o adtree.o adname.o aditem.o arbdbpp.o ad_config.o
  1192. touch libARBDB.a
  1193. make[4]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/ARBDB'
  1194. -------------------------------------------------------------------------------- Make everything in NTREE
  1195. make[4]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/NTREE'
  1196. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NTREE -c AP_consensus.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1197. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NTREE -c AP_conservProfile2Gnuplot.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1198. AP_consensus.cxx: In function 'const char* CON_export(char*, char*, int**, char*, int*, char*, int, long int, long int, int, int, int, double, double, int, int)':
  1199. AP_consensus.cxx:409:23: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated (declared at /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE/ad_t_prot.h:108) [-Wdeprecated-declarations]
  1200. AP_consensus.cxx:409:72: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated (declared at /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE/ad_t_prot.h:108) [-Wdeprecated-declarations]
  1201. AP_consensus.cxx:411:25: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated (declared at /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE/ad_t_prot.h:108) [-Wdeprecated-declarations]
  1202. AP_consensus.cxx:411:75: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated (declared at /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE/ad_t_prot.h:108) [-Wdeprecated-declarations]
  1203. AP_consensus.cxx:465:28: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated (declared at /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE/ad_t_prot.h:108) [-Wdeprecated-declarations]
  1204. AP_consensus.cxx:465:80: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated (declared at /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE/ad_t_prot.h:108) [-Wdeprecated-declarations]
  1205. AP_consensus.cxx: In function 'void CON_calc_max_freq_cb(AW_window*)':
  1206. AP_consensus.cxx:962:27: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated (declared at /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE/ad_t_prot.h:108) [-Wdeprecated-declarations]
  1207. AP_consensus.cxx:962:76: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated (declared at /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE/ad_t_prot.h:108) [-Wdeprecated-declarations]
  1208. AP_consensus.cxx:963:27: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated (declared at /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE/ad_t_prot.h:108) [-Wdeprecated-declarations]
  1209. AP_consensus.cxx:963:76: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated (declared at /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE/ad_t_prot.h:108) [-Wdeprecated-declarations]
  1210. AP_consensus.cxx:966:27: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated (declared at /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE/ad_t_prot.h:108) [-Wdeprecated-declarations]
  1211. AP_consensus.cxx:966:77: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated (declared at /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE/ad_t_prot.h:108) [-Wdeprecated-declarations]
  1212. AP_conservProfile2Gnuplot.cxx: In function 'void AP_conservProfile2Gnuplot_callback(AW_window*)':
  1213. AP_conservProfile2Gnuplot.cxx:58:42: warning: ignoring return value of 'const char* GB_xcmd(const char*, GB_BOOL, GB_BOOL)', declared with attribute warn_unused_result [-Wunused-result]
  1214. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NTREE -c AP_cprofile.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1215. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NTREE -c AP_csp_2_gnuplot.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1216. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NTREE -c AP_pos_var_pars.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1217. AP_csp_2_gnuplot.cxx: In function 'char* get_overlay_files(AW_root*, const char*, const char*&)':
  1218. AP_csp_2_gnuplot.cxx:92:50: warning: 'const char* GB_get_error()' is deprecated (declared at /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE/ad_prot.h:43) [-Wdeprecated-declarations]
  1219. AP_csp_2_gnuplot.cxx:92:63: warning: 'const char* GB_get_error()' is deprecated (declared at /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE/ad_prot.h:43) [-Wdeprecated-declarations]
  1220. AP_csp_2_gnuplot.cxx:100:55: warning: 'const char* GB_get_error()' is deprecated (declared at /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE/ad_prot.h:43) [-Wdeprecated-declarations]
  1221. AP_csp_2_gnuplot.cxx:100:68: warning: 'const char* GB_get_error()' is deprecated (declared at /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE/ad_prot.h:43) [-Wdeprecated-declarations]
  1222. AP_csp_2_gnuplot.cxx: In function 'void AP_csp_2_gnuplot_cb(AW_window*, AW_CL, AW_CL)':
  1223. AP_csp_2_gnuplot.cxx:388:62: warning: ignoring return value of 'const char* GB_xcmd(const char*, GB_BOOL, GB_BOOL)', declared with attribute warn_unused_result [-Wunused-result]
  1224. AP_cprofile.cxx: In function 'void CPRO_workupstatistic(unsigned char)':
  1225. AP_cprofile.cxx:234:17: warning: variable 'colmax' set but not used [-Wunused-but-set-variable]
  1226. AP_cprofile.cxx: In function 'void CPRO_memrequirement_cb(AW_root*)':
  1227. AP_cprofile.cxx:663:10: warning: variable 'versus' set but not used [-Wunused-but-set-variable]
  1228. AP_cprofile.cxx: In function 'void CPRO_condense_cb(AW_window*, AW_CL)':
  1229. AP_cprofile.cxx:1420:14: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated (declared at /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE/ad_t_prot.h:108) [-Wdeprecated-declarations]
  1230. AP_cprofile.cxx:1420:62: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated (declared at /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE/ad_t_prot.h:108) [-Wdeprecated-declarations]
  1231. AP_cprofile.cxx:1423:23: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated (declared at /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE/ad_t_prot.h:108) [-Wdeprecated-declarations]
  1232. AP_cprofile.cxx:1423:72: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated (declared at /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE/ad_t_prot.h:108) [-Wdeprecated-declarations]
  1233. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NTREE -c NT_cb.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1234. NT_cb.cxx: In function 'void NT_system_cb2(AW_window*, AW_CL, AW_CL)':
  1235. NT_cb.cxx:128:35: warning: ignoring return value of 'const char* GB_xcmd(const char*, GB_BOOL, GB_BOOL)', declared with attribute warn_unused_result [-Wunused-result]
  1236. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NTREE -c NT_concatenate.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1237. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NTREE -c NT_dbrepair.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1238. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NTREE -c NT_edconf.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1239. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NTREE -c NT_extern.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1240. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NTREE -c NT_import.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1241. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NTREE -c NT_ins_col.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1242. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NTREE -c NT_join.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1243. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NTREE -c NT_main.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1244. NT_concatenate.cxx: In function 'const char* displayAlignmentInfo(GBDATA*, GB_ERROR, char*, char*)':
  1245. NT_concatenate.cxx:310:37: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated (declared at /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE/ad_t_prot.h:108) [-Wdeprecated-declarations]
  1246. NT_concatenate.cxx:310:93: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated (declared at /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE/ad_t_prot.h:108) [-Wdeprecated-declarations]
  1247. NT_concatenate.cxx: In function 'void concatenateAlignments(AW_window*)':
  1248. NT_concatenate.cxx:415:39: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated (declared at /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE/ad_t_prot.h:108) [-Wdeprecated-declarations]
  1249. NT_concatenate.cxx:415:95: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated (declared at /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE/ad_t_prot.h:108) [-Wdeprecated-declarations]
  1250. NT_concatenate.cxx: In function 'GBDATA* concatenateFieldsCreateNewSpecies(AW_window*, GBDATA*, speciesConcatenateList)':
  1251. NT_concatenate.cxx:664:39: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated (declared at /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE/ad_t_prot.h:108) [-Wdeprecated-declarations]
  1252. NT_concatenate.cxx:664:114: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated (declared at /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE/ad_t_prot.h:108) [-Wdeprecated-declarations]
  1253. NT_import.cxx: In function 'void NT_import_sequences(AW_window*, AW_CL, AW_CL)':
  1254. NT_import.cxx:52:30: warning: variable 'gb_merge_is_genom_db' set but not used [-Wunused-but-set-variable]
  1255. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NTREE -c NT_sort.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1256. NT_main.cxx: In function 'int main(int, char**)':
  1257. NT_main.cxx:399:50: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
  1258. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NTREE -c NT_trackAliChanges.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1259. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NTREE -c NT_validManual.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1260. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NTREE -c NT_validNameParser.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1261. NT_validNameParser.cxx: In function 'validNames::Desco validNames::determineType(const string&)':
  1262. NT_validNameParser.cxx:89:14: warning: variable 'isSee' set but not used [-Wunused-but-set-variable]
  1263. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NTREE -c NT_validNames.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1264. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NTREE -c ad_ali.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1265. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NTREE -c ad_ext.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1266. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NTREE -c ad_spec.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1267. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NTREE -c ad_transpro.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1268. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_NTREE -c ad_trees.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1269. ad_spec.cxx: In function 'void ad_field_convert_commit_cb(AW_window*, AW_CL)':
  1270. ad_spec.cxx:729:29: warning: unused variable 'selector' [-Wunused-variable]
  1271. ad_transpro.cxx: In function 'const char* arb_r2a(GBDATA*, bool, bool, int, bool, const char*, const char*)':
  1272. ad_transpro.cxx:159:48: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated (declared at /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE/ad_t_prot.h:108) [-Wdeprecated-declarations]
  1273. ad_transpro.cxx:159:100: warning: 'GBDATA* GBT_add_data(GBDATA*, const char*, const char*, GB_TYPES)' is deprecated (declared at /tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE/ad_t_prot.h:108) [-Wdeprecated-declarations]
  1274. ad_trees.cxx: In function 'char* readXmlTree(char*)':
  1275. ad_trees.cxx:418:44: warning: ignoring return value of 'const char* GB_xcmd(const char*, GB_BOOL, GB_BOOL)', declared with attribute warn_unused_result [-Wunused-result]
  1276. ad_trees.cxx:422:44: warning: ignoring return value of 'const char* GB_xcmd(const char*, GB_BOOL, GB_BOOL)', declared with attribute warn_unused_result [-Wunused-result]
  1277. -------------------- Checking NTREE.a
  1278. Target 'NTREE.a' not found
  1279. -> rebuilding NTREE.a (Wed Dec 31 23:59:59 1969)
  1280. ld -r -o NTREE.a AP_consensus.o AP_conservProfile2Gnuplot.o AP_cprofile.o AP_csp_2_gnuplot.o AP_pos_var_pars.o NT_cb.o NT_concatenate.o NT_dbrepair.o NT_edconf.o NT_extern.o NT_import.o NT_ins_col.o NT_join.o NT_main.o NT_sort.o NT_trackAliChanges.o NT_validManual.o NT_validNameParser.o NT_validNames.o ad_ali.o ad_ext.o ad_spec.o ad_transpro.o ad_trees.o
  1281. make[4]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/NTREE'
  1282. -------------------------------------------------------------------------------- Make everything in AWT
  1283. make[4]: Entering directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/AWT'
  1284. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_input_mask.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1285. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_hotkeys.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1286. AWT_input_mask.cxx: In function 'void create_new_mask_cb(AW_window*)':
  1287. AWT_input_mask.cxx:2242:18: warning: variable 'closeWindow' set but not used [-Wunused-but-set-variable]
  1288. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_www.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1289. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_tables.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1290. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_irstree.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1291. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_asciiprint.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1292. AWT_tables.cxx: In function 'void ad_table_field_reorder_cb(AW_window*, awt_table*)':
  1293. AWT_tables.cxx:25:14: warning: variable 'warning' set but not used [-Wunused-but-set-variable]
  1294. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_map_key.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1295. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_tree_cmp.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1296. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_seq_colors.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1297. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_pro_a_nucs.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1298. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_csp.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1299. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_canvas.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1300. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_dtree.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1301. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_tree.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1302. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_tree_cb.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1303. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_nei.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1304. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_filter.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1305. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_sel_boxes.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1306. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_canio.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1307. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_nds.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1308. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_query_and_functions.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1309. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_file_selection.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1310. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_preset.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1311. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_seq_dna.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1312. AWT_canio.cxx: In function 'void AWT_print_tree_to_file_xfig(AW_window*, AW_CL)':
  1313. AWT_canio.cxx:268:53: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
  1314. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_seq_protein.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1315. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_seq_simple_pro.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1316. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_codon_table.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1317. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_iupac.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1318. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_config_manager.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1319. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_advice.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1320. AWT_codon_table.cxx: In function 'bool AWT_is_codon(char, const char*, const AWT_allowedCode&, AWT_allowedCode&, const char**)':
  1321. AWT_codon_table.cxx:518:18: warning: variable 'correct_disallowed_translation' set but not used [-Wunused-but-set-variable]
  1322. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_db_browser.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1323. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_attributes.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1324. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_changekey.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1325. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_item_sel_list.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1326. AWT_config_manager.cxx: In function 'void AWT_start_config_manager(AW_window*, AW_CL)':
  1327. AWT_config_manager.cxx:119:24: warning: variable 'reopen' set but not used [-Wunused-but-set-variable]
  1328. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_macro.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1329. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fPIC -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -W -Wall -DNDEBUG -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_AWT -c AWT_translate.cxx -I. -I/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/INCLUDE -I/usr/X11R6/include
  1330. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -Wl,-O1 -Wl,--as-needed -Wl,--export-dynamic -shared -o libAWT.so AWT_input_mask.o AWT_hotkeys.o AWT_www.o AWT_tables.o AWT_irstree.o AWT_asciiprint.o AWT_map_key.o AWT_tree_cmp.o AWT_seq_colors.o AWT_pro_a_nucs.o AWT_csp.o AWT_canvas.o AWT_dtree.o AWT_tree.o AWT_tree_cb.o AWT_nei.o AWT_filter.o AWT_sel_boxes.o AWT_canio.o AWT_nds.o AWT_query_and_functions.o AWT_file_selection.o AWT_preset.o AWT_seq_dna.o AWT_seq_protein.o AWT_seq_simple_pro.o AWT_codon_table.o AWT_iupac.o AWT_config_manager.o AWT_advice.o AWT_db_browser.o AWT_attributes.o AWT_changekey.o AWT_item_sel_list.o AWT_macro.o AWT_translate.o
  1331. touch libAWT.a
  1332. make[4]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2/AWT'
  1333. make[3]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2'
  1334. make[2]: *** [arb] Error 2
  1335. make[2]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2'
  1336. make[1]: *** [all] Error 2
  1337. make[1]: Leaving directory `/tmp/portage/sci-biology/arb-5.2/work/arb-5.2'
  1338. make: *** [rebuild] Error 2
  1339. * ERROR: sci-biology/arb-5.2 failed (compile phase):
  1340. * emake failed
  1341. *
  1342. * If you need support, post the output of `emerge --info '=sci-biology/arb-5.2'`,
  1343. * the complete build log and the output of `emerge -pqv '=sci-biology/arb-5.2'`.
  1344. * The complete build log is located at '/var/log/portage/sci-biology:arb-5.2:20120813-044524.log'.
  1345. * For convenience, a symlink to the build log is located at '/tmp/portage/sci-biology/arb-5.2/temp/build.log'.
  1346. * The ebuild environment file is located at '/tmp/portage/sci-biology/arb-5.2/temp/environment'.
  1347. * Working directory: '/tmp/portage/sci-biology/arb-5.2/work/arb-5.2'
  1348. * S: '/tmp/portage/sci-biology/arb-5.2/work/arb-5.2'