printf ' ' | fink --no-use-binary-dist --yes --build-as-nobody rebuild ncbitools 2>&1 The package 'ncbitools' will be built without being installed. Reading build dependency for ncbitools-20080302-1... Reading dependency for ncbitools-20080302-1... Reading dependency for ncbitools-dev-20080302-1... Reading build conflict for ncbitools-20080302-1... The following package will be rebuilt: ncbitools curl --connect-timeout 30 -f -L -A 'fink/0.37.0' -o ncbitools-20080302.tar.gz http://distfiles.master.finkmirrors.net/distfiles/ncbitools-20080302.tar.gz % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 0 16.4M 0 1202 0 0 4908 0 0:58:43 --:--:-- 0:58:43 4906 2 16.4M 2 501k 0 0 399k 0 0:00:42 0:00:01 0:00:41 399k 5 16.4M 5 959k 0 0 397k 0 0:00:42 0:00:02 0:00:40 397k 8 16.4M 8 1471k 0 0 451k 0 0:00:37 0:00:03 0:00:34 451k 12 16.4M 12 2068k 0 0 488k 0 0:00:34 0:00:04 0:00:30 487k 16 16.4M 16 2767k 0 0 525k 0 0:00:32 0:00:05 0:00:27 551k 19 16.4M 19 3312k 0 0 516k 0 0:00:32 0:00:06 0:00:26 545k 22 16.4M 22 3807k 0 0 526k 0 0:00:32 0:00:07 0:00:25 590k 26 16.4M 26 4476k 0 0 543k 0 0:00:31 0:00:08 0:00:23 603k 30 16.4M 30 5170k 0 0 558k 0 0:00:30 0:00:09 0:00:21 618k 34 16.4M 34 5759k 0 0 553k 0 0:00:30 0:00:10 0:00:20 582k 36 16.4M 36 6208k 0 0 552k 0 0:00:30 0:00:11 0:00:19 600k 39 16.4M 39 6678k 0 0 545k 0 0:00:30 0:00:12 0:00:18 574k 42 16.4M 42 7116k 0 0 537k 0 0:00:31 0:00:13 0:00:18 526k 43 16.4M 43 7405k 0 0 510k 0 0:00:33 0:00:14 0:00:19 425k 45 16.4M 45 7767k 0 0 509k 0 0:00:33 0:00:15 0:00:18 415k 49 16.4M 49 8296k 0 0 510k 0 0:00:33 0:00:16 0:00:17 416k 53 16.4M 53 8966k 0 0 520k 0 0:00:32 0:00:17 0:00:15 456k 56 16.4M 56 9574k 0 0 520k 0 0:00:32 0:00:18 0:00:14 478k 60 16.4M 60 10.0M 0 0 534k 0 0:00:31 0:00:19 0:00:12 607k 66 16.4M 66 11.0M 0 0 557k 0 0:00:30 0:00:20 0:00:10 701k 72 16.4M 72 11.9M 0 0 576k 0 0:00:29 0:00:21 0:00:08 785k 77 16.4M 77 12.7M 0 0 586k 0 0:00:28 0:00:22 0:00:06 814k 81 16.4M 81 13.3M 0 0 589k 0 0:00:28 0:00:23 0:00:05 848k 85 16.4M 85 14.1M 0 0 597k 0 0:00:28 0:00:24 0:00:04 839k 90 16.4M 90 14.9M 0 0 607k 0 0:00:27 0:00:25 0:00:02 809k 93 16.4M 93 15.3M 0 0 593k 0 0:00:28 0:00:26 0:00:02 664k 96 16.4M 96 15.8M 0 0 595k 0 0:00:28 0:00:27 0:00:01 637k 100 16.4M 100 16.4M 0 0 599k 0 0:00:28 0:00:28 --:--:-- 651k curl --connect-timeout 30 -f -L -A 'fink/0.37.0' -O http://distfiles.master.finkmirrors.net/distfiles/vector.Z % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 0 1006k 0 1201 0 0 1259 0 0:13:38 --:--:-- 0:13:38 1258 45 1006k 45 456k 0 0 266k 0 0:00:03 0:00:01 0:00:02 266k 100 1006k 100 1006k 0 0 436k 0 0:00:02 0:00:02 --:--:-- 436k Setting runtime build-lock... dpkg-deb -b /sw/build.build/root-fink-buildlock-ncbitools-20080302-1 /sw/build.build dpkg-deb: building package `fink-buildlock-ncbitools-20080302-1' in `/sw/build.build/fink-buildlock-ncbitools-20080302-1_2014.07.31-00.11.20_darwin-x86_64.deb'. Installing build-lock package... /sw/bin/dpkg-lockwait -i /sw/build.build/fink-buildlock-ncbitools-20080302-1_2014.07.31-00.11.20_darwin-x86_64.deb Selecting previously deselected package fink-buildlock-ncbitools-20080302-1. (Reading database ... 4296 files and directories currently installed.) Unpacking fink-buildlock-ncbitools-20080302-1 (from .../fink-buildlock-ncbitools-20080302-1_2014.07.31-00.11.20_darwin-x86_64.deb) ... Setting up fink-buildlock-ncbitools-20080302-1 (2014.07.31-00.11.20) ... sudo -u fink-bld [ENV] sh -c /tmp/fink.PrG9K env LANG=C LC_ALL=C /sw/bin/tar --no-same-owner --no-same-permissions -xvf /sw/src/ncbitools-20080302.tar.gz ncbi/ ncbi/checkout.date ncbi/README.htm ncbi/access/ ncbi/access/cddapi.c ncbi/access/cddapi.h ncbi/access/egkludge.h ncbi/access/ent2api.c ncbi/access/ent2api.h ncbi/access/entrez2.asn ncbi/access/entrezgene.asn ncbi/access/makeacc.unx ncbi/access/mim.asn ncbi/access/mimapi.c ncbi/access/mimapi.h ncbi/access/mla2.asn ncbi/access/mla2api.c ncbi/access/mla2api.h ncbi/access/mlkludge.h ncbi/access/objegkludge.c ncbi/access/objegkludge.h ncbi/access/objent2.c ncbi/access/objent2.h ncbi/access/objentgene.c ncbi/access/objentgene.h ncbi/access/objmim.c ncbi/access/objmim.h ncbi/access/objmla2.c ncbi/access/objmla2.h ncbi/access/objtax3.c ncbi/access/objtax3.h ncbi/access/pmfapi.c ncbi/access/pmfapi.h ncbi/access/qblastapi.c ncbi/access/qblastapi.h ncbi/access/strucapi.c ncbi/access/strucapi.h ncbi/access/tax3api.c ncbi/access/tax3api.h ncbi/access/taxon3.asn ncbi/access/vecscnapi.c ncbi/access/vecscnapi.h ncbi/algo/ ncbi/algo/blast/ ncbi/algo/blast/api/ ncbi/algo/blast/api/blast_api.c ncbi/algo/blast/api/blast_api.h ncbi/algo/blast/api/blast_format.c ncbi/algo/blast/api/blast_format.h ncbi/algo/blast/api/blast_input.c ncbi/algo/blast/api/blast_input.h ncbi/algo/blast/api/blast_message_api.c ncbi/algo/blast/api/blast_message_api.h ncbi/algo/blast/api/blast_mtlock.c ncbi/algo/blast/api/blast_mtlock.h ncbi/algo/blast/api/blast_options_api.c ncbi/algo/blast/api/blast_options_api.h ncbi/algo/blast/api/blast_prelim.c ncbi/algo/blast/api/blast_prelim.h ncbi/algo/blast/api/blast_returns.c ncbi/algo/blast/api/blast_returns.h ncbi/algo/blast/api/blast_seq.c ncbi/algo/blast/api/blast_seq.h ncbi/algo/blast/api/blast_seqalign.c ncbi/algo/blast/api/blast_seqalign.h ncbi/algo/blast/api/blast_tabular.c ncbi/algo/blast/api/blast_tabular.h ncbi/algo/blast/api/dust_filter.c ncbi/algo/blast/api/dust_filter.h ncbi/algo/blast/api/hspstream_queue.c ncbi/algo/blast/api/hspstream_queue.h ncbi/algo/blast/api/repeats_filter.c ncbi/algo/blast/api/repeats_filter.h ncbi/algo/blast/api/seqsrc_multiseq.c ncbi/algo/blast/api/seqsrc_multiseq.h ncbi/algo/blast/api/seqsrc_readdb.c ncbi/algo/blast/api/seqsrc_readdb.h ncbi/algo/blast/api/twoseq_api.c ncbi/algo/blast/api/twoseq_api.h ncbi/algo/blast/composition_adjustment/ ncbi/algo/blast/composition_adjustment/compo_heap.c ncbi/algo/blast/composition_adjustment/compo_heap.h ncbi/algo/blast/composition_adjustment/compo_mode_condition.c ncbi/algo/blast/composition_adjustment/compo_mode_condition.h ncbi/algo/blast/composition_adjustment/composition_adjustment.c ncbi/algo/blast/composition_adjustment/composition_adjustment.h ncbi/algo/blast/composition_adjustment/composition_constants.h ncbi/algo/blast/composition_adjustment/matrix_frequency_data.c ncbi/algo/blast/composition_adjustment/matrix_frequency_data.h ncbi/algo/blast/composition_adjustment/nlm_linear_algebra.c ncbi/algo/blast/composition_adjustment/nlm_linear_algebra.h ncbi/algo/blast/composition_adjustment/optimize_target_freq.c ncbi/algo/blast/composition_adjustment/optimize_target_freq.h ncbi/algo/blast/composition_adjustment/redo_alignment.c ncbi/algo/blast/composition_adjustment/redo_alignment.h ncbi/algo/blast/composition_adjustment/smith_waterman.c ncbi/algo/blast/composition_adjustment/smith_waterman.h ncbi/algo/blast/composition_adjustment/unified_pvalues.c ncbi/algo/blast/composition_adjustment/unified_pvalues.h ncbi/algo/blast/core/ ncbi/algo/blast/core/aa_ungapped.c ncbi/algo/blast/core/aa_ungapped.h ncbi/algo/blast/core/blast_aalookup.c ncbi/algo/blast/core/blast_aalookup.h ncbi/algo/blast/core/blast_aascan.c ncbi/algo/blast/core/blast_aascan.h ncbi/algo/blast/core/blast_def.h ncbi/algo/blast/core/blast_diagnostics.c ncbi/algo/blast/core/blast_diagnostics.h ncbi/algo/blast/core/blast_dynarray.c ncbi/algo/blast/core/blast_dynarray.h ncbi/algo/blast/core/blast_encoding.c ncbi/algo/blast/core/blast_encoding.h ncbi/algo/blast/core/blast_engine.c ncbi/algo/blast/core/blast_engine.h ncbi/algo/blast/core/blast_export.h ncbi/algo/blast/core/blast_extend.c ncbi/algo/blast/core/blast_extend.h ncbi/algo/blast/core/blast_filter.c ncbi/algo/blast/core/blast_filter.h ncbi/algo/blast/core/blast_gapalign.c ncbi/algo/blast/core/blast_gapalign.h ncbi/algo/blast/core/blast_gapalign_priv.h ncbi/algo/blast/core/blast_hits.c ncbi/algo/blast/core/blast_hits.h ncbi/algo/blast/core/blast_hits_priv.h ncbi/algo/blast/core/blast_hspstream.c ncbi/algo/blast/core/blast_hspstream.h ncbi/algo/blast/core/blast_itree.c ncbi/algo/blast/core/blast_itree.h ncbi/algo/blast/core/blast_kappa.c ncbi/algo/blast/core/blast_kappa.h ncbi/algo/blast/core/blast_lookup.c ncbi/algo/blast/core/blast_lookup.h ncbi/algo/blast/core/blast_message.c ncbi/algo/blast/core/blast_message.h ncbi/algo/blast/core/blast_nalookup.c ncbi/algo/blast/core/blast_nalookup.h ncbi/algo/blast/core/blast_nascan.c ncbi/algo/blast/core/blast_nascan.h ncbi/algo/blast/core/blast_options.c ncbi/algo/blast/core/blast_options.h ncbi/algo/blast/core/blast_parameters.c ncbi/algo/blast/core/blast_parameters.h ncbi/algo/blast/core/blast_posit.c ncbi/algo/blast/core/blast_posit.h ncbi/algo/blast/core/blast_program.c ncbi/algo/blast/core/blast_program.h ncbi/algo/blast/core/blast_psi.c ncbi/algo/blast/core/blast_psi.h ncbi/algo/blast/core/blast_psi_priv.c ncbi/algo/blast/core/blast_psi_priv.h ncbi/algo/blast/core/blast_query_info.c ncbi/algo/blast/core/blast_query_info.h ncbi/algo/blast/core/blast_rps.h ncbi/algo/blast/core/blast_seg.c ncbi/algo/blast/core/blast_seg.h ncbi/algo/blast/core/blast_seqsrc.c ncbi/algo/blast/core/blast_seqsrc.h ncbi/algo/blast/core/blast_seqsrc_impl.h ncbi/algo/blast/core/blast_setup.c ncbi/algo/blast/core/blast_setup.h ncbi/algo/blast/core/blast_stat.c ncbi/algo/blast/core/blast_stat.h ncbi/algo/blast/core/blast_sw.c ncbi/algo/blast/core/blast_sw.h ncbi/algo/blast/core/blast_toolkit.h ncbi/algo/blast/core/blast_traceback.c ncbi/algo/blast/core/blast_traceback.h ncbi/algo/blast/core/blast_tune.c ncbi/algo/blast/core/blast_tune.h ncbi/algo/blast/core/blast_util.c ncbi/algo/blast/core/blast_util.h ncbi/algo/blast/core/gapinfo.c ncbi/algo/blast/core/gapinfo.h ncbi/algo/blast/core/gencode_singleton.c ncbi/algo/blast/core/gencode_singleton.h ncbi/algo/blast/core/greedy_align.c ncbi/algo/blast/core/greedy_align.h ncbi/algo/blast/core/hspstream_collector.c ncbi/algo/blast/core/hspstream_collector.h ncbi/algo/blast/core/index_ungapped.c ncbi/algo/blast/core/index_ungapped.h ncbi/algo/blast/core/link_hsps.c ncbi/algo/blast/core/link_hsps.h ncbi/algo/blast/core/lookup_util.c ncbi/algo/blast/core/lookup_util.h ncbi/algo/blast/core/lookup_wrap.c ncbi/algo/blast/core/lookup_wrap.h ncbi/algo/blast/core/matrix_freq_ratios.c ncbi/algo/blast/core/matrix_freq_ratios.h ncbi/algo/blast/core/mb_indexed_lookup.h ncbi/algo/blast/core/na_ungapped.c ncbi/algo/blast/core/na_ungapped.h ncbi/algo/blast/core/ncbi_math.c ncbi/algo/blast/core/ncbi_math.h ncbi/algo/blast/core/ncbi_std.c ncbi/algo/blast/core/ncbi_std.h ncbi/algo/blast/core/pattern.c ncbi/algo/blast/core/pattern.h ncbi/algo/blast/core/pattern_priv.h ncbi/algo/blast/core/phi_extend.c ncbi/algo/blast/core/phi_extend.h ncbi/algo/blast/core/phi_gapalign.c ncbi/algo/blast/core/phi_gapalign.h ncbi/algo/blast/core/phi_lookup.c ncbi/algo/blast/core/phi_lookup.h ncbi/algo/blast/core/split_query.c ncbi/algo/blast/core/split_query.h ncbi/api/ ncbi/api/a2ferr.h ncbi/api/a2ferr.msg ncbi/api/a2ferrdf.h ncbi/api/a2fstruc.h ncbi/api/alignmgr.c ncbi/api/alignmgr.h ncbi/api/alignmgr2.c ncbi/api/alignmgr2.h ncbi/api/alignval.c ncbi/api/alignval.h ncbi/api/aliparse.c ncbi/api/aliparse.h ncbi/api/aliread.c ncbi/api/aliread.h ncbi/api/asn2ff.h ncbi/api/asn2ff1.c ncbi/api/asn2ff2.c ncbi/api/asn2ff3.c ncbi/api/asn2ff4.c ncbi/api/asn2ff5.c ncbi/api/asn2ff6.c ncbi/api/asn2ff6.h ncbi/api/asn2ffg.h ncbi/api/asn2ffp.h ncbi/api/asn2gnb1.c ncbi/api/asn2gnb2.c ncbi/api/asn2gnb3.c ncbi/api/asn2gnb4.c ncbi/api/asn2gnb5.c ncbi/api/asn2gnb6.c ncbi/api/asn2gnbi.h ncbi/api/asn2gnbk.h ncbi/api/asn2gnbp.h ncbi/api/blocks.c ncbi/api/blocks.h ncbi/api/codon.c ncbi/api/codon.h ncbi/api/ddvcolor.c ncbi/api/ddvcolor.h ncbi/api/edutil.c ncbi/api/edutil.h ncbi/api/errdefn.h ncbi/api/explore.h ncbi/api/fastadl.asn ncbi/api/fastadl.h ncbi/api/fdlKludge.h ncbi/api/fdlobj.c ncbi/api/fdlobj.h ncbi/api/ffprint.c ncbi/api/ffprint.h ncbi/api/findrepl.c ncbi/api/findrepl.h ncbi/api/ftusrstr.c ncbi/api/ftusrstr.h ncbi/api/gather.c ncbi/api/gather.h ncbi/api/gbfeat.c ncbi/api/gbfeat.h ncbi/api/gbftdef.h ncbi/api/gbftglob.c ncbi/api/gbparint.c ncbi/api/gbparlex.h ncbi/api/jsavlt.c ncbi/api/jsavlt.h ncbi/api/jzcoll.c ncbi/api/jzcoll.h ncbi/api/jzmisc.c ncbi/api/jzmisc.h ncbi/api/lsqfetch.c ncbi/api/lsqfetch.h ncbi/api/macroapi.c ncbi/api/macroapi.h ncbi/api/maputil.c ncbi/api/maputil.h ncbi/api/mconsist.c ncbi/api/mconsist.h ncbi/api/needleman.c ncbi/api/needleman.h ncbi/api/objmgr.c ncbi/api/objmgr.h ncbi/api/parsegb.h ncbi/api/pgppop.c ncbi/api/pgppop.h ncbi/api/prtutil.c ncbi/api/prtutil.h ncbi/api/puberr.h ncbi/api/salpacc.c ncbi/api/salpacc.h ncbi/api/salpedit.c ncbi/api/salpedit.h ncbi/api/salprop.c ncbi/api/salprop.h ncbi/api/salpstat.c ncbi/api/salpstat.h ncbi/api/salsa.h ncbi/api/salsap.c ncbi/api/salsap.h ncbi/api/salstruc.c ncbi/api/salstruc.h ncbi/api/salutil.c ncbi/api/salutil.h ncbi/api/samutil.c ncbi/api/samutil.h ncbi/api/satutil.c ncbi/api/satutil.h ncbi/api/seqmgr.c ncbi/api/seqmgr.h ncbi/api/seqport.c ncbi/api/seqport.h ncbi/api/sequtil.c ncbi/api/sequtil.h ncbi/api/simple.c ncbi/api/simple.h ncbi/api/sqnutil1.c ncbi/api/sqnutil2.c ncbi/api/sqnutil3.c ncbi/api/sqnutil4.c ncbi/api/sqnutils.h ncbi/api/subutil.c ncbi/api/subutil.h ncbi/api/tofasta.c ncbi/api/tofasta.h ncbi/api/tofile.c ncbi/api/tofile.h ncbi/api/tomedlin.c ncbi/api/tomedlin.h ncbi/api/txalign.c ncbi/api/txalign.h ncbi/api/udvdef.h ncbi/api/udvseq.c ncbi/api/udvseq.h ncbi/api/undefwin.h ncbi/api/utilpars.c ncbi/api/utilpars.h ncbi/api/utilpub.c ncbi/api/utilpub.h ncbi/api/valid.c ncbi/api/valid.h ncbi/api/valid.msg ncbi/api/validatr.h ncbi/api/validatr.msg ncbi/api/validerr.h ncbi/api/viewmgr.c ncbi/api/viewmgr.h ncbi/api/wprint.c ncbi/asn/ ncbi/asn/asn.all ncbi/asn/.cvsignore ncbi/asn/access.asn ncbi/asn/all.bat ncbi/asn/all.mac ncbi/asn/all.unx ncbi/asn/allpub.bat ncbi/asn/allpub.mac ncbi/asn/allpub.unx ncbi/asn/biblio.asn ncbi/asn/change.txt ncbi/asn/dumpidl.unx ncbi/asn/featdef.asn ncbi/asn/gbseq.asn ncbi/asn/general.asn ncbi/asn/head.all ncbi/asn/insdseq.asn ncbi/asn/makeload.bat ncbi/asn/makeload.unx ncbi/asn/makestat.bat ncbi/asn/makestat.mac ncbi/asn/makestat.unx ncbi/asn/medlars.asn ncbi/asn/medline.asn ncbi/asn/ncbimime.asn ncbi/asn/objprt.asn ncbi/asn/proj.asn ncbi/asn/pub.asn ncbi/asn/pubmed.asn ncbi/asn/scoremat.asn ncbi/asn/seq.asn ncbi/asn/seqalign.asn ncbi/asn/seqblock.asn ncbi/asn/seqcode.asn ncbi/asn/seqfeat.asn ncbi/asn/seqloc.asn ncbi/asn/seqres.asn ncbi/asn/seqset.asn ncbi/asn/seqtable.asn ncbi/asn/submit.asn ncbi/asn/tinyseq.asn ncbi/asn/asnpub.all ncbi/asnlib/ ncbi/asnlib/asn.h ncbi/asnlib/asnbufo.c ncbi/asnlib/asnbuild.h ncbi/asnlib/asncode.c ncbi/asnlib/asndebin.c ncbi/asnlib/asndebin.h ncbi/asnlib/asnenbin.c ncbi/asnlib/asnenbin.h ncbi/asnlib/asngen.c ncbi/asnlib/asngenob.c ncbi/asnlib/asnio.c ncbi/asnlib/asnio.h ncbi/asnlib/asnlex.c ncbi/asnlib/asnlex.h ncbi/asnlib/asnlext.c ncbi/asnlib/asnlext.h ncbi/asnlib/asnout.c ncbi/asnlib/asnout.h ncbi/asnlib/asnprint.c ncbi/asnlib/asnprint.h ncbi/asnlib/asntool.c ncbi/asnlib/asntool.h ncbi/asnlib/asntypes.c ncbi/asnlib/asntypes.h ncbi/biostruc/ ncbi/biostruc/RESEARCH/ ncbi/biostruc/RESEARCH/iucrabs.html ncbi/biostruc/RESEARCH/res.html ncbi/biostruc/RESEARCH/res.shtml ncbi/biostruc/RESEARCH/threading.shtml ncbi/biostruc/Entrez.scr ncbi/biostruc/Entrez_active.scr ncbi/biostruc/Installing.README ncbi/biostruc/PubStruct.scr ncbi/biostruc/PubStructAsn.h ncbi/biostruc/PubStruct_proc.scr ncbi/biostruc/bsannotvs.c ncbi/biostruc/corematx.c ncbi/biostruc/corematx.h ncbi/biostruc/dvncode.c ncbi/biostruc/dvncode.h ncbi/biostruc/getmmdb.c ncbi/biostruc/loader_check.sh ncbi/biostruc/make-tool.sh ncbi/biostruc/make.mmdbsrv ncbi/biostruc/make.vastsrv ncbi/biostruc/mkbioseq.h ncbi/biostruc/mkbioseqA.c ncbi/biostruc/mkbioseqB.c ncbi/biostruc/mkbioseq_vs.c ncbi/biostruc/mmdb1.asn ncbi/biostruc/mmdb2.asn ncbi/biostruc/mmdb3.asn ncbi/biostruc/mmdbFF.c ncbi/biostruc/mmdb_pubstruct.c ncbi/biostruc/mmdbapi.c ncbi/biostruc/mmdbapi.doc ncbi/biostruc/mmdbapi.h ncbi/biostruc/mmdbapi1.c ncbi/biostruc/mmdbapi1.h ncbi/biostruc/mmdbapi2.c ncbi/biostruc/mmdbapi2.h ncbi/biostruc/mmdbapi3.c ncbi/biostruc/mmdbapi3.h ncbi/biostruc/mmdbapi4.c 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ncbi/make/msvc800_prj/vibrant/vibrant/vibrant.vcproj ncbi/make/msvc800_prj/vibrant/vibrant_ogl/ ncbi/make/msvc800_prj/vibrant/vibrant_ogl/vibrant_ogl.vcproj ncbi/make/msvc_prj/ ncbi/make/msvc_prj/algo/ ncbi/make/msvc_prj/algo/blast/ ncbi/make/msvc_prj/algo/blast/api/ ncbi/make/msvc_prj/algo/blast/api/blastapi.dsp ncbi/make/msvc_prj/algo/blast/composition_adjustment/ ncbi/make/msvc_prj/algo/blast/composition_adjustment/blastcompadj.dsp ncbi/make/msvc_prj/algo/blast/core/ ncbi/make/msvc_prj/algo/blast/core/blast.dsp ncbi/make/msvc_prj/all.bat ncbi/make/msvc_prj/all.dsp ncbi/make/msvc_prj/all2one.sh ncbi/make/msvc_prj/all_demo.dsp ncbi/make/msvc_prj/all_exe.dsp ncbi/make/msvc_prj/all_lib.dsp ncbi/make/msvc_prj/all_ncbi.bat ncbi/make/msvc_prj/all_ncbi.dsp ncbi/make/msvc_prj/install.bat ncbi/make/msvc_prj/install.sh ncbi/make/msvc_prj/ncbi.dsw ncbi/make/msvc_prj/one2all.sh ncbi/make/msvc_prj/one2all_r.sh ncbi/make/msvc_prj/one2one.sh ncbi/make/msvc_prj/asnlib/ ncbi/make/msvc_prj/asnlib/asntool/ ncbi/make/msvc_prj/asnlib/asntool/exe_asntool.dsp ncbi/make/msvc_prj/biostruc/ ncbi/make/msvc_prj/biostruc/ncbimmdb.dsp ncbi/make/msvc_prj/cdromlib/ ncbi/make/msvc_prj/cdromlib/ncbiacc/ ncbi/make/msvc_prj/cdromlib/ncbiacc/ncbiacc.dsp ncbi/make/msvc_prj/cdromlib/ncbicdr/ ncbi/make/msvc_prj/cdromlib/ncbicdr/ncbicdr.dsp ncbi/make/msvc_prj/cdromlib/ncbinacc/ ncbi/make/msvc_prj/cdromlib/ncbinacc/ncbinacc.dsp ncbi/make/msvc_prj/cn3d/ ncbi/make/msvc_prj/cn3d/cn3d/ ncbi/make/msvc_prj/cn3d/cn3d/exe_cn3d.dsp ncbi/make/msvc_prj/cn3d/ncbicn3d/ ncbi/make/msvc_prj/cn3d/ncbicn3d/ncbicn3d.dsp ncbi/make/msvc_prj/cn3d/ncbicn3d_ogl/ ncbi/make/msvc_prj/cn3d/ncbicn3d_ogl/ncbicn3d_ogl.dsp ncbi/make/msvc_prj/connect/ ncbi/make/msvc_prj/connect/test/ ncbi/make/msvc_prj/connect/test/http_connector_hit/ ncbi/make/msvc_prj/connect/test/http_connector_hit/http_connector_hit.dsp ncbi/make/msvc_prj/connect/test/xconntest.dsp ncbi/make/msvc_prj/connect/test/socket_io_bouncer/ ncbi/make/msvc_prj/connect/test/socket_io_bouncer/socket_io_bouncer.dsp ncbi/make/msvc_prj/connect/test/test_ncbi_buffer/ ncbi/make/msvc_prj/connect/test/test_ncbi_buffer/test_ncbi_buffer.dsp ncbi/make/msvc_prj/connect/test/test_ncbi_connutil_hit/ ncbi/make/msvc_prj/connect/test/test_ncbi_connutil_hit/test_ncbi_connutil_hit.dsp ncbi/make/msvc_prj/connect/test/test_ncbi_connutil_misc/ ncbi/make/msvc_prj/connect/test/test_ncbi_connutil_misc/test_ncbi_connutil_misc.dsp ncbi/make/msvc_prj/connect/test/test_ncbi_core/ ncbi/make/msvc_prj/connect/test/test_ncbi_core/test_ncbi_core.dsp ncbi/make/msvc_prj/connect/test/test_ncbi_disp/ ncbi/make/msvc_prj/connect/test/test_ncbi_disp/test_ncbi_disp.dsp ncbi/make/msvc_prj/connect/test/test_ncbi_dsock/ ncbi/make/msvc_prj/connect/test/test_ncbi_dsock/test_ncbi_dsock.dsp ncbi/make/msvc_prj/connect/test/test_ncbi_file_connector/ ncbi/make/msvc_prj/connect/test/test_ncbi_file_connector/test_ncbi_file_connector.dsp ncbi/make/msvc_prj/connect/test/test_ncbi_ftp_connector/ ncbi/make/msvc_prj/connect/test/test_ncbi_ftp_connector/test_ncbi_ftp_connector.dsp ncbi/make/msvc_prj/connect/test/test_ncbi_http_connector/ ncbi/make/msvc_prj/connect/test/test_ncbi_http_connector/test_ncbi_http_connector.dsp ncbi/make/msvc_prj/connect/test/test_ncbi_http_get/ ncbi/make/msvc_prj/connect/test/test_ncbi_http_get/test_ncbi_http_get.dsp ncbi/make/msvc_prj/connect/test/test_ncbi_memory_connector/ ncbi/make/msvc_prj/connect/test/test_ncbi_memory_connector/test_ncbi_memory_connector.dsp ncbi/make/msvc_prj/connect/test/test_ncbi_sendmail/ ncbi/make/msvc_prj/connect/test/test_ncbi_sendmail/test_ncbi_sendmail.dsp ncbi/make/msvc_prj/connect/test/test_ncbi_service_connector/ ncbi/make/msvc_prj/connect/test/test_ncbi_service_connector/test_ncbi_service_connector.dsp ncbi/make/msvc_prj/connect/test/test_ncbi_socket/ ncbi/make/msvc_prj/connect/test/test_ncbi_socket/test_ncbi_socket.dsp ncbi/make/msvc_prj/connect/test/test_ncbi_socket_connector/ ncbi/make/msvc_prj/connect/test/test_ncbi_socket_connector/test_ncbi_socket_connector.dsp ncbi/make/msvc_prj/connect/connect.dsp ncbi/make/msvc_prj/corelib/ ncbi/make/msvc_prj/corelib/ncbi/ ncbi/make/msvc_prj/corelib/ncbi/ncbi.dsp ncbi/make/msvc_prj/corelib/ncbiconfig.dsp ncbi/make/msvc_prj/corelib/ncbimain/ ncbi/make/msvc_prj/corelib/ncbimain/ncbimain.dsp ncbi/make/msvc_prj/ddv/ ncbi/make/msvc_prj/ddv/ddv/ ncbi/make/msvc_prj/ddv/ddv/exe_ddv.dsp ncbi/make/msvc_prj/ddv/ddvlib/ ncbi/make/msvc_prj/ddv/ddvlib/ddvlib.dsp ncbi/make/msvc_prj/demo/ ncbi/make/msvc_prj/demo/asn2all/ ncbi/make/msvc_prj/demo/asn2all/demo_asn2all.dsp ncbi/make/msvc_prj/demo/asn2ff/ ncbi/make/msvc_prj/demo/asn2ff/demo_asn2ff.dsp ncbi/make/msvc_prj/demo/asn2fsa/ ncbi/make/msvc_prj/demo/asn2fsa/demo_asn2fsa.dsp ncbi/make/msvc_prj/demo/asn2fsa/demo_asnval.dsp ncbi/make/msvc_prj/demo/asn2gb/ ncbi/make/msvc_prj/demo/asn2gb/demo_asn2gb.dsp ncbi/make/msvc_prj/demo/asn2idx/ ncbi/make/msvc_prj/demo/asn2idx/demo_asn2idx.dsp ncbi/make/msvc_prj/demo/asn2xml/ ncbi/make/msvc_prj/demo/asn2xml/demo_asn2xml.dsp ncbi/make/msvc_prj/demo/asnbarval/ ncbi/make/msvc_prj/demo/asnbarval/demo_asnbarval.dsp ncbi/make/msvc_prj/demo/asndhuff/ ncbi/make/msvc_prj/demo/asndhuff/demo_asndhuff.dsp ncbi/make/msvc_prj/demo/asndisc/ ncbi/make/msvc_prj/demo/asndisc/demo_asndisc.dsp ncbi/make/msvc_prj/demo/asnmacro/ ncbi/make/msvc_prj/demo/asnmacro/demo_asnmacro.dsp ncbi/make/msvc_prj/demo/asnstrip/ ncbi/make/msvc_prj/demo/asnstrip/demo_asnstrip.dsp ncbi/make/msvc_prj/demo/asnval/ ncbi/make/msvc_prj/demo/asnval/demo_asnval.dsp ncbi/make/msvc_prj/demo/bl2seq/ ncbi/make/msvc_prj/demo/bl2seq/demo_bl2seq.dsp ncbi/make/msvc_prj/demo/blast/ ncbi/make/msvc_prj/demo/blast/demo_blast.dsp ncbi/make/msvc_prj/demo/blastall/ ncbi/make/msvc_prj/demo/blastall/demo_blastall.dsp ncbi/make/msvc_prj/demo/blastclust/ ncbi/make/msvc_prj/demo/blastclust/demo_blastclust.dsp ncbi/make/msvc_prj/demo/blastpgp/ ncbi/make/msvc_prj/demo/blastpgp/demo_blastpgp.dsp ncbi/make/msvc_prj/demo/ccp/ ncbi/make/msvc_prj/demo/ccp/demo_ccp.dsp ncbi/make/msvc_prj/demo/ccpv/ ncbi/make/msvc_prj/demo/ccpv/demo_ccpv.dsp ncbi/make/msvc_prj/demo/cdscan/ ncbi/make/msvc_prj/demo/cdscan/demo_cdscan.dsp ncbi/make/msvc_prj/demo/checksub/ ncbi/make/msvc_prj/demo/checksub/demo_checksub.dsp ncbi/make/msvc_prj/demo/cleanasn/ ncbi/make/msvc_prj/demo/cleanasn/demo_cleanasn.dsp ncbi/make/msvc_prj/demo/cnsgn/ ncbi/make/msvc_prj/demo/cnsgn/demo_cnsgn.dsp ncbi/make/msvc_prj/demo/cnsgnv/ ncbi/make/msvc_prj/demo/cnsgnv/demo_cnsgnv.dsp ncbi/make/msvc_prj/demo/cnsrt/ ncbi/make/msvc_prj/demo/cnsrt/demo_cnsrt.dsp ncbi/make/msvc_prj/demo/cnsrtv/ ncbi/make/msvc_prj/demo/cnsrtv/demo_cnsrtv.dsp ncbi/make/msvc_prj/demo/copymat/ ncbi/make/msvc_prj/demo/copymat/demo_copymat.dsp ncbi/make/msvc_prj/demo/cspeedtest/ ncbi/make/msvc_prj/demo/cspeedtest/demo_cspeedtest.dsp ncbi/make/msvc_prj/demo/dosimple/ ncbi/make/msvc_prj/demo/dosimple/demo_dosimple.dsp ncbi/make/msvc_prj/demo/dust/ ncbi/make/msvc_prj/demo/dust/demo_dust.dsp ncbi/make/msvc_prj/demo/dustv/ ncbi/make/msvc_prj/demo/dustv/demo_dustv.dsp ncbi/make/msvc_prj/demo/entrez2/ ncbi/make/msvc_prj/demo/entrez2/demo_entrez2.dsp ncbi/make/msvc_prj/demo/epi/ ncbi/make/msvc_prj/demo/epi/demo_epi.dsp ncbi/make/msvc_prj/demo/epiv/ ncbi/make/msvc_prj/demo/epiv/demo_epiv.dsp ncbi/make/msvc_prj/demo/fa2htgs/ ncbi/make/msvc_prj/demo/fa2htgs/demo_fa2htgs.dsp ncbi/make/msvc_prj/demo/fastacmd/ ncbi/make/msvc_prj/demo/fastacmd/demo_fastacmd.dsp ncbi/make/msvc_prj/demo/flint/ ncbi/make/msvc_prj/demo/flint/demo_flint.dsp ncbi/make/msvc_prj/demo/formatdb/ ncbi/make/msvc_prj/demo/formatdb/demo_formatdb.dsp ncbi/make/msvc_prj/demo/formatrpsdb/ ncbi/make/msvc_prj/demo/formatrpsdb/demo_formatrpsdb.dsp ncbi/make/msvc_prj/demo/gbseqget/ ncbi/make/msvc_prj/demo/gbseqget/demo_gbseqget.dsp ncbi/make/msvc_prj/demo/gene2xml/ ncbi/make/msvc_prj/demo/gene2xml/demo_gene2xml.dsp ncbi/make/msvc_prj/demo/getfeat/ ncbi/make/msvc_prj/demo/getfeat/demo_getfeat.dsp ncbi/make/msvc_prj/demo/getmesh/ ncbi/make/msvc_prj/demo/getmesh/demo_getmesh.dsp ncbi/make/msvc_prj/demo/getpub/ ncbi/make/msvc_prj/demo/getpub/demo_getpub.dsp ncbi/make/msvc_prj/demo/gil2bin/ ncbi/make/msvc_prj/demo/gil2bin/demo_gil2bin.dsp ncbi/make/msvc_prj/demo/impala/ ncbi/make/msvc_prj/demo/impala/demo_impala.dsp ncbi/make/msvc_prj/demo/indexpub/ ncbi/make/msvc_prj/demo/indexpub/demo_indexpub.dsp ncbi/make/msvc_prj/demo/insdseqget/ ncbi/make/msvc_prj/demo/insdseqget/demo_insdseqget.dsp ncbi/make/msvc_prj/demo/makemat/ ncbi/make/msvc_prj/demo/makemat/demo_makemat.dsp ncbi/make/msvc_prj/demo/megablast/ ncbi/make/msvc_prj/demo/megablast/demo_megablast.dsp ncbi/make/msvc_prj/demo/nentrez/ ncbi/make/msvc_prj/demo/nentrez/demo_nentrez.dsp ncbi/make/msvc_prj/demo/nentrez_ogl/ ncbi/make/msvc_prj/demo/nentrez_ogl/demo_nentrez_ogl.dsp ncbi/make/msvc_prj/demo/netentcf/ ncbi/make/msvc_prj/demo/netentcf/demo_netentcf.dsp ncbi/make/msvc_prj/demo/raw2delt/ ncbi/make/msvc_prj/demo/raw2delt/demo_raw2delt.dsp ncbi/make/msvc_prj/demo/rpsblast/ ncbi/make/msvc_prj/demo/rpsblast/demo_rpsblast.dsp ncbi/make/msvc_prj/demo/searchv/ ncbi/make/msvc_prj/demo/searchv/demo_searchv.dsp ncbi/make/msvc_prj/demo/seedtop/ ncbi/make/msvc_prj/demo/seedtop/demo_seedtop.dsp ncbi/make/msvc_prj/demo/seqtest/ ncbi/make/msvc_prj/demo/seqtest/demo_seqtest.dsp ncbi/make/msvc_prj/demo/sigme/ ncbi/make/msvc_prj/demo/sigme/demo_sigme.dsp ncbi/make/msvc_prj/demo/sigmev/ ncbi/make/msvc_prj/demo/sigmev/demo_sigmev.dsp ncbi/make/msvc_prj/demo/spidey/ ncbi/make/msvc_prj/demo/spidey/demo_spidey.dsp ncbi/make/msvc_prj/demo/srchaa/ ncbi/make/msvc_prj/demo/srchaa/demo_srchaa.dsp ncbi/make/msvc_prj/demo/srchnt/ ncbi/make/msvc_prj/demo/srchnt/demo_srchnt.dsp ncbi/make/msvc_prj/demo/tbl2asn/ ncbi/make/msvc_prj/demo/tbl2asn/demo_tbl2asn.dsp ncbi/make/msvc_prj/demo/testcore/ ncbi/make/msvc_prj/demo/testcore/demo_testcore.dsp ncbi/make/msvc_prj/demo/testobj/ ncbi/make/msvc_prj/demo/testobj/demo_testobj.dsp ncbi/make/msvc_prj/demo/twop/ ncbi/make/msvc_prj/demo/twop/demo_twop.dsp ncbi/make/msvc_prj/demo/twopv/ ncbi/make/msvc_prj/demo/twopv/demo_twopv.dsp ncbi/make/msvc_prj/demo/udv/ ncbi/make/msvc_prj/demo/udv/demo_udv.dsp ncbi/make/msvc_prj/demo/vecscreen/ ncbi/make/msvc_prj/demo/vecscreen/demo_vecscreen.dsp ncbi/make/msvc_prj/desktop/ ncbi/make/msvc_prj/desktop/ncbidesk.dsp ncbi/make/msvc_prj/gif/ ncbi/make/msvc_prj/gif/vibgif.dsp ncbi/make/msvc_prj/internal/ ncbi/make/msvc_prj/internal/smart/ ncbi/make/msvc_prj/internal/smart/smartnet/ ncbi/make/msvc_prj/internal/smart/smartnet/smartnet.dsp ncbi/make/msvc_prj/internal/all_internal.dsp ncbi/make/msvc_prj/network/ ncbi/make/msvc_prj/network/blast3/ ncbi/make/msvc_prj/network/blast3/blastcl3/ ncbi/make/msvc_prj/network/blast3/blastcl3/exe_blastcl3.dsp ncbi/make/msvc_prj/network/blast3/netblast/ ncbi/make/msvc_prj/network/blast3/netblast/netblast.dsp ncbi/make/msvc_prj/network/entrez/ ncbi/make/msvc_prj/network/entrez/client/ ncbi/make/msvc_prj/network/entrez/client/netentr.dsp ncbi/make/msvc_prj/network/id1arch/ ncbi/make/msvc_prj/network/id1arch/ncbiid1.dsp ncbi/make/msvc_prj/network/idfetch/ ncbi/make/msvc_prj/network/idfetch/exe_idfetch.dsp ncbi/make/msvc_prj/network/medarch/ ncbi/make/msvc_prj/network/medarch/client/ ncbi/make/msvc_prj/network/medarch/client/medarch.dsp ncbi/make/msvc_prj/network/nsclilib/ ncbi/make/msvc_prj/network/nsclilib/netcli.dsp ncbi/make/msvc_prj/network/spell/ ncbi/make/msvc_prj/network/spell/client/ ncbi/make/msvc_prj/network/spell/client/ncbispel.dsp ncbi/make/msvc_prj/network/taxon1/ ncbi/make/msvc_prj/network/taxon1/taxon2/ ncbi/make/msvc_prj/network/taxon1/taxon2/ncbitxc2.dsp ncbi/make/msvc_prj/network/vibnet/ ncbi/make/msvc_prj/network/vibnet/vibnet.dsp ncbi/make/msvc_prj/object/ ncbi/make/msvc_prj/object/ncbiobj.dsp ncbi/make/msvc_prj/regexp/ ncbi/make/msvc_prj/regexp/demo/ ncbi/make/msvc_prj/regexp/demo/demo_regexp.dsp ncbi/make/msvc_prj/regexp/demo/demo_regexp_grep.dsp ncbi/make/msvc_prj/regexp/regexp.dsp ncbi/make/msvc_prj/regexp/test/ ncbi/make/msvc_prj/regexp/test/test_regexp.dsp ncbi/make/msvc_prj/sequin/ ncbi/make/msvc_prj/sequin/sbtedit/ ncbi/make/msvc_prj/sequin/sbtedit/exe_sbtedit.dsp ncbi/make/msvc_prj/sequin/sequin/ ncbi/make/msvc_prj/sequin/sequin/exe_sequin.dsp ncbi/make/msvc_prj/sequin/sequin_ogl/ ncbi/make/msvc_prj/sequin/sequin_ogl/exe_sequin_ogl.dsp ncbi/make/msvc_prj/sequin/ssequin/ ncbi/make/msvc_prj/sequin/ssequin/exe_ssequin.dsp ncbi/make/msvc_prj/tools/ ncbi/make/msvc_prj/tools/ncbitool.dsp ncbi/make/msvc_prj/vibrant/ ncbi/make/msvc_prj/vibrant/vibrant/ ncbi/make/msvc_prj/vibrant/vibrant/vibrant.dsp ncbi/make/msvc_prj/vibrant/vibrant_ogl/ ncbi/make/msvc_prj/vibrant/vibrant_ogl/vibrant_ogl.dsp ncbi/make/xCode/ ncbi/make/xCode/NCBI.xcode/ ncbi/make/xCode/NCBI.xcode/project.pbxproj ncbi/make/xCode/ncbicguiapp/ ncbi/make/xCode/ncbicguiapp/English.lproj/ ncbi/make/xCode/ncbicguiapp/English.lproj/InfoPlist.strings ncbi/make/xCode/ncbicguiapp/Entrez-Info.plist ncbi/make/xCode/ncbicguiapp/Sequin-Info.plist ncbi/make/xCode/ncbicguiapp/main.c ncbi/make/xCode/ncbicguiapp/ncbi.icns ncbi/make/xCode/ncbicguiapp/ncbicguiapp.xcodeproj/ ncbi/make/xCode/ncbicguiapp/ncbicguiapp.xcodeproj/project.pbxproj ncbi/make/xCode/ncbictoolkit/ ncbi/make/xCode/ncbictoolkit/English.lproj/ ncbi/make/xCode/ncbictoolkit/English.lproj/InfoPlist.strings ncbi/make/xCode/ncbictoolkit/Info.plist ncbi/make/xCode/ncbictoolkit/ncbictoolkit.xcodeproj/ ncbi/make/xCode/ncbictoolkit/ncbictoolkit.xcodeproj/project.pbxproj ncbi/make/makedis.csh ncbi/make/makeallchives ncbi/network/ ncbi/network/apple/ ncbi/network/apple/README ncbi/network/blast3/ ncbi/network/blast3/client/ ncbi/network/blast3/client/blastpat.h ncbi/network/blast3/client/blstspc.asn 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ncbi/object/objscoremat.c ncbi/object/objscoremat.h ncbi/object/objseq.c ncbi/object/objseq.h ncbi/object/objsset.c ncbi/object/objsset.h ncbi/object/objsub.c ncbi/object/objsub.h ncbi/object/objtable.c ncbi/object/objtable.h ncbi/object/objtseq.c ncbi/object/objtseq.h ncbi/object/scoremat.h ncbi/platform/ ncbi/platform/alphaOSF1.ncbi.mk ncbi/platform/beos.ncbi.mk ncbi/platform/darwin-univ.ncbi.mk ncbi/platform/darwin.ncbi.mk ncbi/platform/freebsd.ncbi.mk ncbi/platform/hppalinux.ncbi.mk ncbi/platform/hpux.ncbi.mk ncbi/platform/hpux_ia64.ncbi.mk ncbi/platform/ibm_auto.ncbi.mk ncbi/platform/ibm_auto64.ncbi.mk ncbi/platform/linux-alpha.ncbi.mk ncbi/platform/linux-power.ncbi.mk ncbi/platform/linux-x86.ncbi.mk ncbi/platform/linux.ncbi.mk ncbi/platform/linux64.ncbi.mk ncbi/platform/linux_ecc.ncbi.mk ncbi/platform/linux_icc.ncbi.mk ncbi/platform/linux_icc9.ncbi.mk ncbi/platform/netbsd.ncbi.mk ncbi/platform/ppclinux.ncbi.mk ncbi/platform/qnx.ncbi.mk ncbi/platform/sgi-mips4.ncbi.mk 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ncbi/tools/impatool.c ncbi/tools/kappa.c ncbi/tools/list.h ncbi/tools/lnfac.h ncbi/tools/lookup.c ncbi/tools/lookup.h ncbi/tools/mbalign.c ncbi/tools/mbalign.h ncbi/tools/mblast.c ncbi/tools/mblast.h ncbi/tools/motif.c ncbi/tools/motif.h ncbi/tools/ncbisam.c ncbi/tools/ncbisam.h ncbi/tools/ncbisami.h ncbi/tools/ncbisort.c ncbi/tools/ncbisort.h ncbi/tools/ncbisrti.h ncbi/tools/pattern1.c ncbi/tools/pobutil.c ncbi/tools/pobutil.h ncbi/tools/posit.c ncbi/tools/posit.h ncbi/tools/posit2.c ncbi/tools/profiles.h ncbi/tools/pseed3.c ncbi/tools/readdb.c ncbi/tools/readdb.h ncbi/tools/rpsutil.c ncbi/tools/rpsutil.h ncbi/tools/salign.c ncbi/tools/salign.h ncbi/tools/salmedia.h ncbi/tools/salptool.c ncbi/tools/salptool.h ncbi/tools/sec.c ncbi/tools/sec.h ncbi/tools/seed.h ncbi/tools/seg.c ncbi/tools/seg.h ncbi/tools/sim2.c ncbi/tools/sim3.c ncbi/tools/sim4.c ncbi/tools/simutil.c ncbi/tools/simutil.h ncbi/tools/slist.c ncbi/tools/spidey.c ncbi/tools/spidey.h ncbi/tools/splutil.c ncbi/tools/splutil.h ncbi/tools/stsutil.c ncbi/tools/stsutil.h ncbi/tools/suggadj.c ncbi/tools/suggest.c ncbi/tools/suggest.h ncbi/tools/suggslp.c ncbi/tools/suggslp.h ncbi/tools/taxblast.c ncbi/tools/taxblast.h ncbi/tools/terr.h ncbi/tools/tfuns.c ncbi/tools/tfuns.h ncbi/tools/toasn3.c ncbi/tools/toasn3.h ncbi/tools/toporg.c ncbi/tools/toporg.h ncbi/tools/urkbias.c ncbi/tools/urkbias.h ncbi/tools/urkcnsrt.c ncbi/tools/urkcnsrt.h ncbi/tools/urkdust.c ncbi/tools/urkdust.h ncbi/tools/urkepi.c ncbi/tools/urkepi.h ncbi/tools/urkfltr.c ncbi/tools/urkfltr.h ncbi/tools/urkgraph.c ncbi/tools/urkgraph.h ncbi/tools/urkpcc.c ncbi/tools/urkpcc.h ncbi/tools/urkptpf.c ncbi/tools/urkptpf.h ncbi/tools/urksigu.c ncbi/tools/urksigu.h ncbi/tools/urktree.c ncbi/tools/urktree.h ncbi/tools/urkutil.c ncbi/tools/urkutil.h ncbi/tools/vecscrn.c ncbi/tools/vecscrn.h ncbi/tools/xmlblast.c ncbi/tools/xmlblast.h ncbi/util/ ncbi/util/creaders/ ncbi/util/creaders/alnread.c ncbi/util/creaders/alnread.h 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ncbi/vibrant/viewerp.h ncbi/webdesign/ ncbi/webdesign/designs/ ncbi/webdesign/designs/cubby/ ncbi/webdesign/designs/cubby/filters/ ncbi/webdesign/designs/cubby/filters/ClinicalTrials_files/ ncbi/webdesign/designs/cubby/filters/ClinicalTrials_files/GoUp1.gif ncbi/webdesign/designs/cubby/filters/ClinicalTrials_files/GoUp2.gif ncbi/webdesign/designs/cubby/filters/ClinicalTrials_files/bkgd.gif ncbi/webdesign/designs/cubby/filters/ClinicalTrials_files/cubby.jfif ncbi/webdesign/designs/cubby/filters/ClinicalTrials_files/filters.css ncbi/webdesign/designs/cubby/filters/ClinicalTrials_files/left.GIF ncbi/webdesign/designs/cubby/filters/ClinicalTrials_files/ncbi_test.css ncbi/webdesign/designs/cubby/filters/ClinicalTrials_files/new.gif ncbi/webdesign/designs/cubby/filters/ClinicalTrials_files/query.js ncbi/webdesign/designs/cubby/filters/ClinicalTrials_files/transparent.gif ncbi/webdesign/designs/cubby/filters/ClinicalTrials.html ncbi/webdesign/designs/cubby/storedsearch/ ncbi/webdesign/designs/cubby/storedsearch/Templates/ ncbi/webdesign/designs/cubby/storedsearch/Templates/Blueprint.html ncbi/webdesign/designs/cubby/storedsearch/Templates/Blueprint.jpg ncbi/webdesign/designs/cubby/storedsearch/Templates/DeleteSearch.gif ncbi/webdesign/designs/cubby/storedsearch/Templates/DeleteSelected.gif ncbi/webdesign/designs/cubby/storedsearch/Templates/EditSearch.html ncbi/webdesign/designs/cubby/storedsearch/Templates/EditSearchWithSchedule.html ncbi/webdesign/designs/cubby/storedsearch/Templates/EditSub.gif ncbi/webdesign/designs/cubby/storedsearch/Templates/Makefile ncbi/webdesign/designs/cubby/storedsearch/Templates/MySearches.html ncbi/webdesign/designs/cubby/storedsearch/Templates/PubMed.html ncbi/webdesign/designs/cubby/storedsearch/Templates/RunSearch.gif ncbi/webdesign/designs/cubby/storedsearch/Templates/SaveSearch.html ncbi/webdesign/designs/cubby/storedsearch/Templates/SaveSearchWithSchedule.html ncbi/webdesign/designs/cubby/storedsearch/Templates/SelectSearch.gif ncbi/webdesign/designs/cubby/storedsearch/Templates/Untitled.gif ncbi/webdesign/designs/cubby/storedsearch/Templates/WhatsNew.html ncbi/webdesign/designs/cubby/storedsearch/Templates/WhatsNewForSelected.gif ncbi/webdesign/designs/cubby/storedsearch/Templates/WhatsNewSearch.gif ncbi/webdesign/designs/cubby/storedsearch/Templates/WhatsNewSummary.html ncbi/webdesign/designs/cubby/storedsearch/Templates/calendar.gif ncbi/webdesign/designs/cubby/storedsearch/Templates/cancel.gif ncbi/webdesign/designs/cubby/storedsearch/Templates/cubby.css ncbi/webdesign/designs/cubby/storedsearch/Templates/delete.gif ncbi/webdesign/designs/cubby/storedsearch/Templates/done.gif ncbi/webdesign/designs/cubby/storedsearch/Templates/done.jpg ncbi/webdesign/designs/cubby/storedsearch/Templates/edit.gif ncbi/webdesign/designs/cubby/storedsearch/Templates/headers.gif ncbi/webdesign/designs/cubby/storedsearch/Templates/help.gif ncbi/webdesign/designs/cubby/storedsearch/Templates/mail.gif ncbi/webdesign/designs/cubby/storedsearch/Templates/plus.gif ncbi/webdesign/designs/cubby/storedsearch/Templates/run.gif ncbi/webdesign/designs/cubby/storedsearch/Templates/save.gif ncbi/webdesign/designs/cubby/storedsearch/Templates/whatsnew.gif ncbi/webdesign/designs/cubby/storedsearch/Templates/x.gif ncbi/webdesign/designs/cubby/storedsearch/Blueprint.graffle ncbi/webdesign/designs/cubby/storedsearch/EditSearch.graffle ncbi/webdesign/designs/cubby/storedsearch/EditSearchSimple.graffle ncbi/webdesign/designs/cubby/storedsearch/PubMed.graffle ncbi/webdesign/designs/cubby/storedsearch/SavedSearches.graffle ncbi/webdesign/designs/pmc/ ncbi/webdesign/designs/pmc/jbacter.html ncbi/webdesign/designs/pmc/jbacterx.html ncbi/webdesign/designs/pmc/layout.css ncbi/webdesign/designs/pmc/printstyle.css ncbi/webdesign/designs/pmc/style.css ncbi/.cvsignore ncbi/asnstat/ ncbi/asnstat/asngen.h ncbi/asnstat/asnsset.h ncbi/asnstat/asnfeat.h ncbi/asnstat/asntable.h ncbi/asnstat/asnalign.h ncbi/asnstat/asnloc.h ncbi/asnstat/asnres.h ncbi/asnstat/asnmedli.h ncbi/asnstat/asnbibli.h ncbi/asnstat/asnseq.h ncbi/asnstat/asnpub.h ncbi/asnstat/asnacces.h ncbi/asnstat/allpub.h ncbi/asnstat/all.h ncbi/asnstat/cdrom.h ncbi/asnstat/asnsubmt.h ncbi/asnstat/asncode.h ncbi/asnstat/asnblock.h ncbi/asnstat/asnfdef.h ncbi/asnstat/asnneten.h ncbi/asnstat/asnmla.h ncbi/asnstat/asntaxon.h ncbi/asnstat/asnid0.h ncbi/asnstat/spell.h ncbi/asnstat/asnprt.h ncbi/asnstat/mmdb1.h ncbi/asnstat/mmdb2.h ncbi/asnstat/mmdb3.h ncbi/asnstat/cn3d.h ncbi/asnstat/blstspc.h ncbi/asnstat/sugmap.h ncbi/asnstat/taxon1.h ncbi/asnstat/asnmime.h ncbi/asnstat/asnpubme.h ncbi/asnstat/asnmdrs.h ncbi/asnstat/asnproj.h ncbi/asnstat/asnent2.h ncbi/asnstat/asnmim.h ncbi/asnstat/asntax3.h ncbi/asnstat/asnentgene.h ncbi/asnstat/asnmla2.h ncbi/asnstat/asngbseq.h ncbi/asnstat/asninsdseq.h ncbi/asnstat/asntseq.h ncbi/asnstat/asnmacro.h ncbi/lib/ ncbi/include/ ncbi/build/ ncbi/bin/ sudo -u fink-bld [ENV] sh -c /tmp/fink.G9q90 cp /sw/src/vector.Z . sudo -u fink-bld [ENV] sh -c /tmp/fink.IdBvf [ -r /sw/fink/dists/stable/main/finkinfo/sci/ncbitools.patch ] sudo -u fink-bld [ENV] sh -c /tmp/fink.iQyUc [ -r /sw/fink/dists/stable/main/finkinfo/sci/ncbitools-x86_64.patch ] sudo -u fink-bld [ENV] sh -c /tmp/fink.q5wgd patch -p1 < /sw/fink/dists/stable/main/finkinfo/sci/ncbitools.patch patching file LICENSE patching file demo.fasta patching file ncbi/api/salsap.h patching file ncbi/api/salutil.h patching file ncbi/platform/darwin.ncbi.mk if [[ "x86_64" == "x86_64" ]]; then patch -p1 < /sw/fink/dists/stable/main/finkinfo/sci/ncbitools-x86_64.patch; fi patching file ncbi/corelib/ncbienv.c patching file ncbi/corelib/ncbiwin.h Hunk #1 succeeded at 168 with fuzz 1. patching file ncbi/make/makedis.csh perl -pi -e 's|\/Developer\/Tools\/Rez|`xcode-select -print-path`/Tools/Rez|g' ncbi/make/makedis.csh ncbi/make/makenet.unx sudo -u fink-bld [ENV] sh -c /tmp/fink.YCKAI ncbi/make/makedis.csh platform is darwin Darwin aurora 13.3.0 Darwin Kernel Version 13.3.0: Tue Jun 3 21:27:35 PDT 2014; root:xnu-2422.110.17~1/RELEASE_X86_64 x86_64 Disabling assert(). BLAST version is 2.2.18 make CFLAGS1="-DNDEBUG -O2 -c -no-cpp-precomp " LDFLAGS1="-framework CoreServices -O2" OTHERLIBS="-lc" SHELL="/bin/sh" LCL="dwn" RAN="ranlib" AR="ar" CC="cc -pipe" all chmod -R ug+rw,o+r . ../include ./ln-if-absent ../corelib/tsprintf.h ../include ./ln-if-absent ../corelib/gifgen.h ../include ./ln-if-absent ../corelib/ncbi*.h ../include ./ln-if-absent ../corelib/tree*.h ../include ./ln-if-absent ../corelib/regex.h ../include ./ln-if-absent ../corelib/matrix.h ../include ./ln-if-absent ../corelib/binary.h ../include ./ln-if-absent ../corelib/morefile/*.h ../include ./ln-if-absent ../corelib/morefile/*.c . ./ln-if-absent ../link/macmet/MoreCarbonAccessors.h ../include ./ln-if-absent ../corelib/ncbilcl.dwn ../include/ncbilcl.h ./ln-if-absent ../corelib/*.c . ./ln-if-absent ../corelib/core*.h . ./ln-if-absent ../asnlib/*.h . mv asn.h ../include ./ln-if-absent ../asnlib/*.c . ./ln-if-absent ../connect/*.c . ./ln-if-absent ../connect/ncbi_ansi_ext.h . ./ln-if-absent ../connect/ncbi_assert.h . ./ln-if-absent ../connect/ncbi_priv.h . ./ln-if-absent ../connect/ncbi_comm.h . ./ln-if-absent ../connect/ncbi_config.h . ./ln-if-absent ../connect/ncbi_lbsm.h . make: [copy] Error 1 (ignored) ./ln-if-absent ../connect/ncbi_lbsm_ipc.h . make: [copy] Error 1 (ignored) ./ln-if-absent ../connect/ncbi_host_infop.h . ./ln-if-absent ../connect/ncbi_server_infop.h . ./ln-if-absent ../connect/ncbi_servicep.h . ./ln-if-absent ../connect/ncbi_dispd.h . ./ln-if-absent ../connect/ncbi_lbsmd.h . ./ln-if-absent ../connect/ncbi_local.h . ./ln-if-absent ../connect/ncbi_lb.h . ./ln-if-absent ../connect/*.h ../include mkdir ../include/connect chmod ug+rw,o+r ../include/connect rm ../include/ncbi_*.h ../include/connect_export.h cp -fp ../connect/ncbi_*.h ../connect/connect_export.h ../include/connect ./ln-if-absent ../util/tables/*.c . mkdir -p ../include/util/tables cp -fp ../util/tables/*.h ../include/util/tables ./ln-if-absent ../util/creaders/*.c . mkdir -p ../include/util/creaders cp -fp ../util/creaders/*.h ../include/util/creaders ./ln-if-absent ../ctools/*.c . ./ln-if-absent ../ctools/*.h . mkdir ../include/ctools chmod ug+rw,o+r ../include/ctools cp -fp ../ctools/*.h ../include/ctools ./ln-if-absent ../object/*.c . ./ln-if-absent ../object/*.h ../include ./ln-if-absent ../access/*.c . ./ln-if-absent ../access/*.h ../include ./ln-if-absent ../asnstat/*.h ../include ./ln-if-absent ../api/*.h ../include ./ln-if-absent ../api/*.c . ./ln-if-absent ../cdromlib/*.h ../include ./ln-if-absent ../cdromlib/*.c . ./ln-if-absent ../vibrant/*.h ../include ./ln-if-absent ../vibrant/*.c . ./ln-if-absent ../desktop/*.h ../include ./ln-if-absent ../desktop/*.c . ./ln-if-absent ../biostruc/*.h ../include ./ln-if-absent ../biostruc/*.c . ./ln-if-absent ../biostruc/cdd/*.h ../include ./ln-if-absent ../biostruc/cdd/*.c . ./ln-if-absent ../biostruc/cn3d/*.h ../include ./ln-if-absent ../biostruc/cn3d/*.c . ./ln-if-absent ../tools/*.h ../include ./ln-if-absent ../tools/*.c . ./ln-if-absent ../cn3d/*.h ../include ./ln-if-absent ../cn3d/*.c . ./ln-if-absent ../gif/*.c . ./ln-if-absent ../gif/*.h ../include ./ln-if-absent ../ddv/*.h ../include ./ln-if-absent ../ddv/*.c . ./ln-if-absent ../regexp/*.c . ./ln-if-absent ../regexp/*.h ../include ./ln-if-absent ../internal/compr/*.c . set: No match. make: [copy] Error 1 (ignored) ./ln-if-absent ../internal/compr/*.h ../include set: No match. make: [copy] Error 1 (ignored) ./ln-if-absent ../internal/libindx/*.c . set: No match. make: [copy] Error 1 (ignored) ./ln-if-absent ../internal/libindx/*.h ../include set: No match. make: [copy] Error 1 (ignored) ./ln-if-absent ../internal/libpars/*.c . set: No match. make: [copy] Error 1 (ignored) ./ln-if-absent ../internal/libpars/*.h ../include set: No match. make: [copy] Error 1 (ignored) ./ln-if-absent ../internal/ideogram/*.c . set: No match. make: [copy] Error 1 (ignored) ./ln-if-absent ../internal/ideogram/*.dat . set: No match. make: [copy] Error 1 (ignored) ./ln-if-absent ../internal/ideogram/ideochr*.h ../include set: No match. make: [copy] Error 1 (ignored) ./ln-if-absent ../internal/ideogram/ideoorgs.h . make: [copy] Error 1 (ignored) ./ln-if-absent ../internal/ccap/*.c . set: No match. make: [copy] Error 1 (ignored) ./ln-if-absent ../internal/ccap/*.dat . set: No match. make: [copy] Error 1 (ignored) ./ln-if-absent ../internal/ccap/*.h ../include set: No match. make: [copy] Error 1 (ignored) ./ln-if-absent ncbidraw.c ncbidrwg.c ./ln-if-absent ncbithr.c ncbithrs.c ./ln-if-absent ../network/nsclilib/*.h ../include ./ln-if-absent ../network/blast3/client/*.h ../include ./ln-if-absent ../network/id1arch/*.h ../include ./ln-if-absent ../network/id2arch/*.h ../include mkdir -p ../include/algo/blast/core ./ln-if-absent ../algo/blast/core/*.c . ./ln-if-absent ../algo/blast/core/*.h . cp -fp ../algo/blast/core/*.h ../include/algo/blast/core mkdir -p ../include/algo/blast/composition_adjustment ./ln-if-absent ../algo/blast/composition_adjustment/*.c . ./ln-if-absent ../algo/blast/composition_adjustment/*.h ../include cp -fp ../algo/blast/composition_adjustment/*.h \ ../include/algo/blast/composition_adjustment mkdir -p ../include/algo/blast/api ./ln-if-absent ../algo/blast/api/*.c . cp -fp ../algo/blast/api/*.h ../include/algo/blast/api chmod -R ug+rw,o+r . echo Waiting...go Waiting...go cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include ncbithr.c cp -p ncbithr.o ../lib cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include ncbimain.c ncbimain.c:81:1: warning: type specifier missing, defaults to 'int' [-Wimplicit-int] main(int argc, char *argv[]) ^~~~ 1 warning generated. cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include ncbibs.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include wwwutils.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include ncbierr.c ncbierr.c:419:11: warning: comparison of unsigned enum expression < 0 is always false [-Wtautological-compare] if (sev < 0 || SEV_MAX < sev) ~~~ ^ ~ ncbierr.c:952:31: warning: the value of the size argument in 'strncat' is too large, might lead to a buffer overflow [-Wstrncat-size] strncat(path,file,sizeof(path)); ^~~~~~~~~~~~ ncbierr.c:952:31: note: change the argument to be the free space in the destination buffer minus the terminating null byte strncat(path,file,sizeof(path)); ^~~~~~~~~~~~ sizeof(path) - strlen(path) - 1 2 warnings generated. cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include ncbienv.c ncbienv.c:2008:11: warning: 'FSPathMakeRef' is deprecated: first deprecated in OS X 10.8 [-Wdeprecated-declarations] err = FSPathMakeRef ((unsigned char *) aPath, &contentsFRef, &isDirectory); ^ /System/Library/Frameworks/CoreServices.framework/Frameworks/CarbonCore.framework/Headers/Files.h:4115:18: note: 'FSPathMakeRef' declared here extern OSStatus FSPathMakeRef(const UInt8 *path, FSRef *ref, Boolean *isDirectory) __OSX_AVAILABLE_BUT_DEPRECATED(__MAC_10_0, __MAC_10_8, __IPHONE_NA, __IPHONE_NA); ^ ncbienv.c:2495:8: warning: 'Gestalt' is deprecated: first deprecated in OS X 10.8 [-Wdeprecated-declarations] if ( Gestalt (gestaltSystemVersion, &sysVer) == noErr) { ^ /System/Library/Frameworks/CoreServices.framework/Frameworks/CarbonCore.framework/Headers/Gestalt.h:123:1: note: 'Gestalt' declared here Gestalt( ^ 2 warnings generated. cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include ncbifile.c ncbifile.c:1374:16: warning: 'tempnam' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of tempnam(3), it is highly recommended that you use mkstemp(3) instead. [-Wdeprecated-declarations] filename = tempnam("/tmp", "ncbi."); ^ /usr/include/stdio.h:389:7: note: 'tempnam' declared here char *tempnam(const char *, const char *) __DARWIN_ALIAS(tempnam); ^ 1 warning generated. cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include ncbiprop.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include ncbimath.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include ncbimem.c ncbimem.c:551:24: warning: 'NewHandle' is deprecated: first deprecated in OS X 10.8 [-Wdeprecated-declarations] hnd = (Nlm_Handle) NewHandle (size); ^ /System/Library/Frameworks/CoreServices.framework/Frameworks/CarbonCore.framework/Headers/MacMemory.h:451:1: note: 'NewHandle' declared here NewHandle(Size byteCount) __OSX_AVAILABLE_BUT_DEPRECATED(__MAC_10_0, __MAC_10_8, __IPHONE_NA, __IPHONE_NA); ^ ncbimem.c:623:5: warning: 'SetHandleSize' is deprecated: first deprecated in OS X 10.8 [-Wdeprecated-declarations] SetHandleSize ((Handle)hnd, (Size)size); ^ /System/Library/Frameworks/CoreServices.framework/Frameworks/CarbonCore.framework/Headers/MacMemory.h:1321:1: note: 'SetHandleSize' declared here SetHandleSize( ^ ncbimem.c:625:9: warning: 'MemError' is deprecated: first deprecated in OS X 10.8 [-Wdeprecated-declarations] if (MemError() != noErr) ^ /System/Library/Frameworks/CoreServices.framework/Frameworks/CarbonCore.framework/Headers/MacMemory.h:330:1: note: 'MemError' declared here MemError(void) __OSX_AVAILABLE_BUT_DEPRECATED(__MAC_10_0, __MAC_10_8, __IPHONE_NA, __IPHONE_NA); ^ ncbimem.c:663:9: warning: 'DisposeHandle' is deprecated: first deprecated in OS X 10.8 [-Wdeprecated-declarations] DisposeHandle ((Handle) hnd); ^ /System/Library/Frameworks/CoreServices.framework/Frameworks/CarbonCore.framework/Headers/MacMemory.h:1278:1: note: 'DisposeHandle' declared here DisposeHandle(Handle h) __OSX_AVAILABLE_BUT_DEPRECATED(__MAC_10_0, __MAC_10_8, __IPHONE_NA, __IPHONE_NA); ^ ncbimem.c:704:5: warning: 'HLock' is deprecated: first deprecated in OS X 10.8 [-Wdeprecated-declarations] HLock ((Handle) hnd); ^ /System/Library/Frameworks/CoreServices.framework/Frameworks/CarbonCore.framework/Headers/MacMemory.h:725:1: note: 'HLock' declared here HLock(Handle h) __OSX_AVAILABLE_BUT_DEPRECATED(__MAC_10_0, __MAC_10_8, __IPHONE_NA, __IPHONE_NA); ^ ncbimem.c:739:9: warning: 'HUnlock' is deprecated: first deprecated in OS X 10.8 [-Wdeprecated-declarations] HUnlock ((Handle) hnd); ^ /System/Library/Frameworks/CoreServices.framework/Frameworks/CarbonCore.framework/Headers/MacMemory.h:791:1: note: 'HUnlock' declared here HUnlock(Handle h) __OSX_AVAILABLE_BUT_DEPRECATED(__MAC_10_0, __MAC_10_8, __IPHONE_NA, __IPHONE_NA); ^ 6 warnings generated. cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include ncbimisc.c ncbimisc.c:1942:27: warning: 'memset' call operates on objects of type 'struct md5context_' while the size is based on a different type 'Nlm_MD5ContextPtr' (aka 'struct md5context_ *') [-Wsizeof-pointer-memaccess] memset(ctx, 0, sizeof(ctx)); /* In case it's sensitive */ ~~~ ^~~ ncbimisc.c:1942:27: note: did you mean to dereference the argument to 'sizeof' (and multiply it by the number of elements)? memset(ctx, 0, sizeof(ctx)); /* In case it's sensitive */ ^~~ 1 warning generated. cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include ncbimsg.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include ncbistr.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include ncbisgml.c ncbisgml.c:191:30: warning: the value of the size argument in 'strncat' is too large, might lead to a buffer overflow [-Wstrncat-size] strncat(buf,"sgmlbb.ent",sizeof buf); ^~~~~~~~~~ ncbisgml.c:191:30: note: change the argument to be the free space in the destination buffer minus the terminating null byte strncat(buf,"sgmlbb.ent",sizeof buf); ^~~~~~~~~~ sizeof(buf) - strlen(buf) - 1 1 warning generated. cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include ncbitime.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include ncbilang.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include asnbufo.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include asndebin.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include asnenbin.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include asngen.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include asnio.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include asnlex.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include asnlext.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include asnout.c asnout.c:160:15: warning: format string is not a string literal (potentially insecure) [-Wformat-security] fprintf(fp, headerlines[i]); ^~~~~~~~~~~~~~ 1 warning generated. cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include asnprint.c asnprint.c:198:7: warning: expression result unused [-Wunused-value] for (currmod; currmod != NULL; currmod = currmod->next) ^~~~~~~ 1 warning generated. cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include asntypes.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include asngenob.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include gifgen.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include togif.c cc -pipe -DNCBI_NOTHREADS_AVAIL -DNDEBUG -O2 -c -no-cpp-precomp -I../include ncbithrs.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include -DHAVE_STRING_H -DREGEX_MALLOC regex.c regex.c:1661:17: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ regex.c:1681:17: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ regex.c:3764:19: warning: cast to 'fail_stack_elt_t' (aka 'const unsigned char *') from smaller integer type 'unsigned int' [-Wint-to-pointer-cast] PUSH_FAILURE_POINT (p1 + mcnt, d, -2); ^ regex.c:2417:5: note: expanded from macro 'PUSH_FAILURE_POINT' PUSH_FAILURE_ITEM (lowest_active_reg); \ ^ regex.c:2338:42: note: expanded from macro 'PUSH_FAILURE_ITEM' fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item ^ regex.c:3764:19: warning: cast to 'fail_stack_elt_t' (aka 'const unsigned char *') from smaller integer type 'unsigned int' [-Wint-to-pointer-cast] regex.c:2420:5: note: expanded from macro 'PUSH_FAILURE_POINT' PUSH_FAILURE_ITEM (highest_active_reg); \ ^ regex.c:2338:42: note: expanded from macro 'PUSH_FAILURE_ITEM' fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item ^ regex.c:3911:11: warning: cast to 'fail_stack_elt_t' (aka 'const unsigned char *') from smaller integer type 'unsigned int' [-Wint-to-pointer-cast] PUSH_FAILURE_POINT (p + mcnt, NULL, -2); ^ regex.c:2417:5: note: expanded from macro 'PUSH_FAILURE_POINT' PUSH_FAILURE_ITEM (lowest_active_reg); \ ^ regex.c:2338:42: note: expanded from macro 'PUSH_FAILURE_ITEM' fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item ^ regex.c:3911:11: warning: cast to 'fail_stack_elt_t' (aka 'const unsigned char *') from smaller integer type 'unsigned int' [-Wint-to-pointer-cast] regex.c:2420:5: note: expanded from macro 'PUSH_FAILURE_POINT' PUSH_FAILURE_ITEM (highest_active_reg); \ ^ regex.c:2338:42: note: expanded from macro 'PUSH_FAILURE_ITEM' fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item ^ regex.c:3964:11: warning: cast to 'fail_stack_elt_t' (aka 'const unsigned char *') from smaller integer type 'unsigned int' [-Wint-to-pointer-cast] PUSH_FAILURE_POINT (p + mcnt, d, -2); ^ regex.c:2417:5: note: expanded from macro 'PUSH_FAILURE_POINT' PUSH_FAILURE_ITEM (lowest_active_reg); \ ^ regex.c:2338:42: note: expanded from macro 'PUSH_FAILURE_ITEM' fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item ^ regex.c:3964:11: warning: cast to 'fail_stack_elt_t' (aka 'const unsigned char *') from smaller integer type 'unsigned int' [-Wint-to-pointer-cast] regex.c:2420:5: note: expanded from macro 'PUSH_FAILURE_POINT' PUSH_FAILURE_ITEM (highest_active_reg); \ ^ regex.c:2338:42: note: expanded from macro 'PUSH_FAILURE_ITEM' fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item ^ regex.c:4103:11: warning: cast to 'fail_stack_elt_t' (aka 'const unsigned char *') from smaller integer type 'unsigned int' [-Wint-to-pointer-cast] PUSH_FAILURE_POINT (0, 0, -2); ^ regex.c:2417:5: note: expanded from macro 'PUSH_FAILURE_POINT' PUSH_FAILURE_ITEM (lowest_active_reg); \ ^ regex.c:2338:42: note: expanded from macro 'PUSH_FAILURE_ITEM' fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item ^ regex.c:4103:11: warning: cast to 'fail_stack_elt_t' (aka 'const unsigned char *') from smaller integer type 'unsigned int' [-Wint-to-pointer-cast] regex.c:2420:5: note: expanded from macro 'PUSH_FAILURE_POINT' PUSH_FAILURE_ITEM (highest_active_reg); \ ^ regex.c:2338:42: note: expanded from macro 'PUSH_FAILURE_ITEM' fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item ^ regex.c:4116:11: warning: cast to 'fail_stack_elt_t' (aka 'const unsigned char *') from smaller integer type 'unsigned int' [-Wint-to-pointer-cast] PUSH_FAILURE_POINT (0, 0, -2); ^ regex.c:2417:5: note: expanded from macro 'PUSH_FAILURE_POINT' PUSH_FAILURE_ITEM (lowest_active_reg); \ ^ regex.c:2338:42: note: expanded from macro 'PUSH_FAILURE_ITEM' fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item ^ regex.c:4116:11: warning: cast to 'fail_stack_elt_t' (aka 'const unsigned char *') from smaller integer type 'unsigned int' [-Wint-to-pointer-cast] regex.c:2420:5: note: expanded from macro 'PUSH_FAILURE_POINT' PUSH_FAILURE_ITEM (highest_active_reg); \ ^ regex.c:2338:42: note: expanded from macro 'PUSH_FAILURE_ITEM' fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item ^ 12 warnings generated. cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include tsprintf.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include ncbiargs.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include tree.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include matrix.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include ncbi_socket.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include ncbi_buffer.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include ncbi_types.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include ncbi_core.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include ncbi_core_c.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include ncbi_util.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include ncbi_priv.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include ncbi_ansi_ext.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include ncbi_connection.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include ncbi_connector.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include ncbi_connutil.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include ncbi_file_connector.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include ncbi_heapmgr.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include ncbi_http_connector.c ncbi_http_connector.c:1056:48: warning: adding 'int' to a string does not append to the string [-Wstring-plus-int] if (strncasecmp(s++, "\nReferer: " + first, 10 - first) == 0) ~~~~~~~~~~~~~~^~~~~~~ ncbi_http_connector.c:1056:48: note: use array indexing to silence this warning if (strncasecmp(s++, "\nReferer: " + first, 10 - first) == 0) ^ & [ ] 1 warning generated. cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include ncbi_memory_connector.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include ncbi_lbsmd_stub.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include ncbi_host_info.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include ncbi_server_info.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include ncbi_service.c ncbi_service.c:629:22: warning: format specifies type 'unsigned short' but the argument has type 'int' [-Wformat] SERV_CLIENT_REVISION_MAJOR, SERV_CLIENT_REVISION_MINOR); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/connect/ncbi_service.h:41:37: note: expanded from macro 'SERV_CLIENT_REVISION_MAJOR' #define SERV_CLIENT_REVISION_MAJOR 6 ^ /usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf' __builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__) ^ ncbi_service.c:619:61: note: format string is defined here static const char client_revision[] = "Client-Revision: %hu.%hu\r\n"; ^~~ %d ncbi_service.c:629:50: warning: format specifies type 'unsigned short' but the argument has type 'int' [-Wformat] SERV_CLIENT_REVISION_MAJOR, SERV_CLIENT_REVISION_MINOR); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/connect/ncbi_service.h:42:37: note: expanded from macro 'SERV_CLIENT_REVISION_MINOR' #define SERV_CLIENT_REVISION_MINOR 240 ^~~ /usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf' __builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__) ^ ncbi_service.c:619:65: note: format string is defined here static const char client_revision[] = "Client-Revision: %hu.%hu\r\n"; ^~~ %d 2 warnings generated. cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include ncbi_service_connector.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include ncbi_ftp_connector.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include ncbi_dispd.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include ncbi_lb.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include ncbi_local.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include ncbi_socket_connector.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include urlquery.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include binary.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include ncbi_sendmail.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include asn_connection.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include raw_scoremat.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include drwnflpt.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include drwnfspc.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include drwnmfls.c rm -f libncbi.a ar cru libncbi.a ncbimain.o ncbibs.o wwwutils.o ncbierr.o ncbienv.o ncbifile.o ncbiprop.o ncbimath.o ncbimem.o ncbimisc.o ncbimsg.o ncbistr.o ncbisgml.o ncbitime.o ncbilang.o asnbufo.o asndebin.o asnenbin.o asngen.o asnio.o asnlex.o asnlext.o asnout.o asnprint.o asntypes.o asngenob.o gifgen.o togif.o ncbithrs.o regex.o tsprintf.o ncbiargs.o tree.o matrix.o ncbi_socket.o ncbi_buffer.o ncbi_types.o ncbi_core.o ncbi_core_c.o ncbi_util.o ncbi_priv.o ncbi_ansi_ext.o ncbi_connection.o ncbi_connector.o ncbi_connutil.o ncbi_file_connector.o ncbi_heapmgr.o ncbi_http_connector.o ncbi_memory_connector.o ncbi_lbsmd_stub.o ncbi_host_info.o ncbi_server_info.o ncbi_service.o ncbi_service_connector.o ncbi_ftp_connector.o ncbi_dispd.o ncbi_lb.o ncbi_local.o ncbi_socket_connector.o urlquery.o binary.o ncbi_sendmail.o asn_connection.o raw_scoremat.o drwnflpt.o drwnfspc.o drwnmfls.o /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: libncbi.a(drwnflpt.o) has no symbols /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: libncbi.a(drwnfspc.o) has no symbols /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: libncbi.a(drwnmfls.o) has no symbols cp -p libncbi.a ../lib ranlib ../lib/libncbi.a /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: ../lib/libncbi.a(drwnflpt.o) has no symbols /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: ../lib/libncbi.a(drwnfspc.o) has no symbols /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: ../lib/libncbi.a(drwnmfls.o) has no symbols cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include objacces.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include objalign.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include objall.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include objbibli.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include objfeat.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include objgen.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include objloc.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include objmedli.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include objpub.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include objres.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include objscoremat.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include objseq.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include objblock.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include objcode.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include objsset.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include objsub.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include objprt.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include objfdef.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include objalignloc.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include objtable.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include objpubme.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include objmdrs.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include objproj.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include objgbseq.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include objtseq.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include objinsdseq.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include objmacro.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include objent2.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include ent2api.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include pmfapi.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include objtax3.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include tax3api.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include objegkludge.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include objentgene.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include objmla2.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include mla2api.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include qblastapi.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include vecscnapi.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include objmim.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include mimapi.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include cddapi.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include seqport.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include sequtil.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include prtutil.c prtutil.c:1270:36: warning: equality comparison with extraneous parentheses [-Wparentheses-equality] for (wrd = str, space = 0; (*wrd == ' '); wrd++) ~~~~~^~~~~~ prtutil.c:1270:36: note: remove extraneous parentheses around the comparison to silence this warning for (wrd = str, space = 0; (*wrd == ' '); wrd++) ~ ^ ~ prtutil.c:1270:36: note: use '=' to turn this equality comparison into an assignment for (wrd = str, space = 0; (*wrd == ' '); wrd++) ^~ = 1 warning generated. cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include simple.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include tofasta.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include tofile.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include tomedlin.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include valid.c valid.c:12557:38: warning: '&&' within '||' [-Wlogical-op-parentheses] if (bvsp->is_mrna || cdscount == 1 && genecount < 2) { ~~ ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ valid.c:12557:38: note: place parentheses around the '&&' expression to silence this warning if (bvsp->is_mrna || cdscount == 1 && genecount < 2) { ^ ( ) 1 warning generated. cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include alignmgr.c alignmgr.c:1589:19: warning: cast to 'Nlm_VoidPtr' (aka 'void *') from smaller integer type 'Nlm_Boolean' (aka 'unsigned char') [-Wint-to-void-pointer-cast] sap->saip = (Pointer)AMAlignIndexFree(amaip); ^ 1 warning generated. cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include aliparse.c aliparse.c:929:37: warning: '&&' within '||' [-Wlogical-op-parentheses] (s_configInfo.useMaybes == FALSE) && ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ aliparse.c:929:37: note: place parentheses around the '&&' expression to silence this warning (s_configInfo.useMaybes == FALSE) && ^ aliparse.c:1193:36: warning: '&&' within '||' [-Wlogical-op-parentheses] (seqLinePtr->maybe == TRUE) && (s_configInfo.useMaybes == TRUE)) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aliparse.c:1193:36: note: place parentheses around the '&&' expression to silence this warning (seqLinePtr->maybe == TRUE) && (s_configInfo.useMaybes == TRUE)) ^ ( ) aliparse.c:1603:36: warning: '&&' within '||' [-Wlogical-op-parentheses] (seqLinePtr->maybe == TRUE) && (s_configInfo.useMaybes == TRUE)) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aliparse.c:1603:36: note: place parentheses around the '&&' expression to silence this warning (seqLinePtr->maybe == TRUE) && (s_configInfo.useMaybes == TRUE)) ^ ( ) aliparse.c:2092:8: warning: type specifier missing, defaults to 'int' [-Wimplicit-int] static s_IsExistingId (AlignFileDataPtr fileInfoPtr, ~~~~~~ ^ aliparse.c:2150:33: warning: '&&' within '||' [-Wlogical-op-parentheses] (seqLinePtr->maybe == TRUE) && ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ aliparse.c:2150:33: note: place parentheses around the '&&' expression to silence this warning (seqLinePtr->maybe == TRUE) && ^ aliparse.c:3161:15: warning: expression result unused [-Wunused-value] for (d; dsubtype == omp->subtype && ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ sqnutil1.c:4828:48: note: place parentheses around the '&&' expression to silence this warning } else if (last->subtype == omp->subtype && ^ 1 warning generated. cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include sqnutil2.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include sqnutil3.c sqnutil3.c:6232:16: warning: 'extern' variable has an initializer [-Wextern-initializer] extern CharPtr discReportInconsistentLocusTagPrefixFmt = "%d features have locus tag prefix %s."; ^ sqnutil3.c:6233:16: warning: 'extern' variable has an initializer [-Wextern-initializer] extern CharPtr discReportInconsistentProteinIDPrefixFmt = "%d sequences have protein ID prefix %s."; ^ sqnutil3.c:6234:16: warning: 'extern' variable has an initializer [-Wextern-initializer] extern CharPtr discReportBadProteinIdFmt = "%d proteins have invalid IDs."; ^ sqnutil3.c:6517:16: warning: 'extern' variable has an initializer [-Wextern-initializer] extern CharPtr discReportDuplicateLocusTagFmt = "%d genes have duplicate locus tags."; ^ sqnutil3.c:6518:16: warning: 'extern' variable has an initializer [-Wextern-initializer] extern CharPtr discReportOneDuplicateLocusTagFmt = "%d genes have locus tag %s."; ^ sqnutil3.c:6519:16: warning: 'extern' variable has an initializer [-Wextern-initializer] extern CharPtr discReportMissingLocusTags = "%d genes have no locus tags."; ^ sqnutil3.c:9657:16: warning: 'extern' variable has an initializer [-Wextern-initializer] extern CharPtr discReportDuplicateProteinIDFmt = "%d coding regions have non-unique protein IDs"; ^ sqnutil3.c:9658:16: warning: 'extern' variable has an initializer [-Wextern-initializer] extern CharPtr discReportOneDuplicateProteinIDFmt = "%d coding regions have protein ID %s"; ^ sqnutil3.c:9659:16: warning: 'extern' variable has an initializer [-Wextern-initializer] extern CharPtr discReportMissingProteinIDFmt = "%d coding regions have missing protein IDs"; ^ sqnutil3.c:9660:16: warning: 'extern' variable has an initializer [-Wextern-initializer] extern CharPtr discReportDuplicateTranscriptIdFmt = "%d mRNAs have non-unique transcript IDs"; ^ sqnutil3.c:9661:16: warning: 'extern' variable has an initializer [-Wextern-initializer] extern CharPtr discReportOneDuplicateTranscriptIdFmt = "%d mRNAs have non-unique transcript ID %s"; ^ sqnutil3.c:9662:16: warning: 'extern' variable has an initializer [-Wextern-initializer] extern CharPtr discReportMissingTranscriptIDFmt = "%d mRNAs have missing transcript IDs"; ^ sqnutil3.c:10461:20: warning: format string is not a string literal (potentially insecure) [-Wformat-security] fprintf (fp, row_text); ^~~~~~~~ 13 warnings generated. cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include sqnutil4.c sqnutil4.c:5664:29: warning: format string is not a string literal (potentially insecure) [-Wformat-security] sprintf (description, gene_name); ^~~~~~~~~ /usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf' __builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__) ^ 1 warning generated. cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include subutil.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include edutil.c edutil.c:5161:7: warning: '&&' within '||' [-Wlogical-op-parentheses] && sfp->data.choice == SEQFEAT_CDREGION) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ edutil.c:5161:7: note: place parentheses around the '&&' expression to silence this warning && sfp->data.choice == SEQFEAT_CDREGION) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ edutil.c:6346:11: warning: '&&' within '||' [-Wlogical-op-parentheses] && sfp->data.choice == SEQFEAT_CDREGION) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ edutil.c:6346:11: note: place parentheses around the '&&' expression to silence this warning && sfp->data.choice == SEQFEAT_CDREGION) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ edutil.c:6409:11: warning: '&&' within '||' [-Wlogical-op-parentheses] && sfp->data.choice == SEQFEAT_CDREGION) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ edutil.c:6409:11: note: place parentheses around the '&&' expression to silence this warning && sfp->data.choice == SEQFEAT_CDREGION) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ edutil.c:6557:1: warning: '/*' within block comment [-Wcomment] /* This section of code deals with editing the sequence by inserting and removing characters. ^ 4 warnings generated. cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include asn2ff1.c asn2ff1.c:2403:24: warning: '&&' within '||' [-Wlogical-op-parentheses] if (ajp->genome_view && gbp->map == FALSE || ajp->contig_view) { ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ ~~ asn2ff1.c:2403:24: note: place parentheses around the '&&' expression to silence this warning if (ajp->genome_view && gbp->map == FALSE || ajp->contig_view) { ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ 1 warning generated. cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include asn2ff2.c asn2ff2.c:1350:8: warning: type specifier missing, defaults to 'int' [-Wimplicit-int] static ChoicePID(SeqIdPtr sid) ~~~~~~ ^ 1 warning generated. cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include asn2ff3.c asn2ff3.c:3728:24: warning: format specifies type 'long' but the argument has type 'Nlm_Int4' (aka 'int') [-Wformat] sprintf(buf, "%ld", sip->data.intvalue); ~~~ ^~~~~~~~~~~~~~~~~~ %d /usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf' __builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__) ^ asn2ff3.c:3771:25: warning: format specifies type 'long' but the argument has type 'Nlm_Int4' (aka 'int') [-Wformat] sprintf(buf, "%ld", sip->data.intvalue); ~~~ ^~~~~~~~~~~~~~~~~~ %d /usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf' __builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__) ^ 2 warnings generated. cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include asn2ff4.c asn2ff4.c:1126:5: warning: add explicit braces to avoid dangling else [-Wdangling-else] }else{ ^ asn2ff4.c:1347:8: warning: type specifier missing, defaults to 'int' [-Wimplicit-int] static CmpImpFeat (ImpFeatPtr f1, ImpFeatPtr f2) ~~~~~~ ^ 2 warnings generated. cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include asn2ff5.c asn2ff5.c:1023:36: warning: '&&' within '||' [-Wlogical-op-parentheses] format == EMBLPEPT_FMT && afp->choice == 1) ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ asn2ff5.c:1023:36: note: place parentheses around the '&&' expression to silence this warning format == EMBLPEPT_FMT && afp->choice == 1) ^ ( ) asn2ff5.c:1683:5: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ asn2ff5.c:2124:12: warning: expression result unused [-Wunused-value] temp++; *ptr_in++; ^~~~~~~~~ 3 warnings generated. cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include asn2ff6.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include asn2gnb1.c asn2gnb1.c:4215:22: warning: format string is not a string literal (potentially insecure) [-Wformat-security] fprintf (fp, ffhead); ^~~~~~ asn2gnb1.c:4266:22: warning: format string is not a string literal (potentially insecure) [-Wformat-security] fprintf (fp, fftail); ^~~~~~ 2 warnings generated. cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include asn2gnb2.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include asn2gnb3.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include asn2gnb4.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include asn2gnb5.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include asn2gnb6.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include ftusrstr.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include gbfeat.c gbfeat.c:1529:33: warning: '&&' within '||' [-Wlogical-op-parentheses] for (str = bptr; *str != '\0' && IS_ALPHA(*str) || IS_DIGIT(*str) ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ ~~ gbfeat.c:1529:33: note: place parentheses around the '&&' expression to silence this warning for (str = bptr; *str != '\0' && IS_ALPHA(*str) || IS_DIGIT(*str) ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1 warning generated. cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include gbftglob.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include gbparint.c gbparint.c:2064:52: warning: for loop has empty body [-Wempty-body] for (; IS_DIGIT(*current_col); current_col++) ; ^ gbparint.c:2064:52: note: put the semicolon on a separate line to silence this warning gbparint.c:2129:7: warning: add explicit braces to avoid dangling else [-Wdangling-else] }else{ ^ gbparint.c:2450:52: warning: for loop has empty body [-Wempty-body] for (; IS_DIGIT(*current_col); current_col++) ; ^ gbparint.c:2450:52: note: put the semicolon on a separate line to silence this warning gbparint.c:2515:7: warning: add explicit braces to avoid dangling else [-Wdangling-else] }else{ ^ 4 warnings generated. cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include utilpars.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include utilpub.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include ffprint.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include wprint.c wprint.c:781:17: warning: format specifies type 'long' but the argument has type 'Nlm_Int4' (aka 'int') [-Wformat] link_ff, (Int4) gi, itemID, entityID); ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf' __builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__) ^ wprint.c:825:24: warning: format specifies type 'long' but the argument has type 'Nlm_Int4' (aka 'int') [-Wformat] link_muid, (Int4) muid); ~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf' __builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__) ^ 2 warnings generated. cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include satutil.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include seqmgr.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include objmgr.c objmgr.c:1195:16: warning: comparison of constant 4294967295 with expression of type 'Nlm_Uint2' (aka 'unsigned short') is always true [-Wtautological-constant-out-of-range-compare] if (omp->hold < OBJMGR_MAX) ~~~~~~~~~ ^ ~~~~~~~~~~ objmgr.c:3184:4: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long' [-Wformat] (unsigned long)(omdp->touch)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2 warnings generated. cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include gather.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include accmmdbs.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include acccn3ds.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include lsqfetch.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include findrepl.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include codon.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include jzcoll.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include jzmisc.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include maputil.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include mconsist.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include macroapi.c macroapi.c:8158:25: warning: format specifies type 'char *' but the argument has type 'Nlm_Int4' (aka 'int') [-Wformat] sprintf (buf, "%s", dbtag->tag->id); ~~ ^~~~~~~~~~~~~~ %d /usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf' __builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__) ^ 1 warning generated. cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include salpedit.c salpedit.c:126:19: warning: implicit declaration of function 'is_salp_in_sap' is invalid in C99 [-Wimplicit-function-declaration] salp = is_salp_in_sap (bsp->annot, 2); ^ salpedit.c:126:17: warning: incompatible integer to pointer conversion assigning to 'SeqAlignPtr' (aka 'struct seqalign *') from 'int' [-Wint-conversion] salp = is_salp_in_sap (bsp->annot, 2); ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ salpedit.c:136:17: warning: incompatible integer to pointer conversion assigning to 'SeqAlignPtr' (aka 'struct seqalign *') from 'int' [-Wint-conversion] salp = is_salp_in_sap (bssp->annot, 2); ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 3 warnings generated. cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include salpstat.c salpstat.c:310:10: warning: '&&' within '||' [-Wlogical-op-parentheses] if(dsp && (((mmatches || mmismatches) && bsp_1 && bsp_2)) || !(mmatches || mmismatches)) { ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~ salpstat.c:310:10: note: place parentheses around the '&&' expression to silence this warning if(dsp && (((mmatches || mmismatches) && bsp_1 && bsp_2)) || !(mmatches || mmismatches)) { ^ ( ) salpstat.c:1945:17: warning: equality comparison with extraneous parentheses [-Wparentheses-equality] if((bsp1->mol == Seq_mol_aa)) ~~~~~~~~~~^~~~~~~~~~~~~ salpstat.c:1945:17: note: remove extraneous parentheses around the comparison to silence this warning if((bsp1->mol == Seq_mol_aa)) ~ ^ ~ salpstat.c:1945:17: note: use '=' to turn this equality comparison into an assignment if((bsp1->mol == Seq_mol_aa)) ^~ = salpstat.c:1949:17: warning: equality comparison with extraneous parentheses [-Wparentheses-equality] if((bsp2->mol == Seq_mol_aa)) ~~~~~~~~~~^~~~~~~~~~~~~ salpstat.c:1949:17: note: remove extraneous parentheses around the comparison to silence this warning if((bsp2->mol == Seq_mol_aa)) ~ ^ ~ salpstat.c:1949:17: note: use '=' to turn this equality comparison into an assignment if((bsp2->mol == Seq_mol_aa)) ^~ = 3 warnings generated. cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include salpacc.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include salprop.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include salsap.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include salstruc.c salstruc.c:1854:21: warning: format string is not a string literal (potentially insecure) [-Wformat-security] fprintf (fout, label); ^~~~~ salstruc.c:1998:19: warning: implicit declaration of function 'is_salp_in_sap' is invalid in C99 [-Wimplicit-function-declaration] salp = is_salp_in_sap (bsp->annot, 2); ^ salstruc.c:1998:17: warning: incompatible integer to pointer conversion assigning to 'SeqAlignPtr' (aka 'struct seqalign *') from 'int' [-Wint-conversion] salp = is_salp_in_sap (bsp->annot, 2); ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ salstruc.c:2015:17: warning: incompatible integer to pointer conversion assigning to 'SeqAlignPtr' (aka 'struct seqalign *') from 'int' [-Wint-conversion] salp = is_salp_in_sap (bssp->annot, 2); ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 4 warnings generated. cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include salutil.c salutil.c:2398:12: warning: add explicit braces to avoid dangling else [-Wdangling-else] else if (!with_prot && feat->data == NULL) ^ 1 warning generated. cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include udvseq.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include blocks.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include pgppop.c pgppop.c:2997:16: warning: format string is not a string literal (potentially insecure) [-Wformat-security] fprintf(fp,szSeq); ^~~~~ 1 warning generated. cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include samutil.c samutil.c:1794:13: warning: multiple unsequenced modifications to 'Index' [-Wunsequenced] Index = ++Index % DDE_STACK_SIZE; ~ ^ 1 warning generated. cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include ddvcolor.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include viewmgr.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include ddvcreate.c ddvcreate.c:493:22: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] while (more = AlnMgrGetNextAlnBit(mpplp->sap, amp)) ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ddvcreate.c:493:22: note: place parentheses around the assignment to silence this warning while (more = AlnMgrGetNextAlnBit(mpplp->sap, amp)) ^ ( ) ddvcreate.c:493:22: note: use '==' to turn this assignment into an equality comparison while (more = AlnMgrGetNextAlnBit(mpplp->sap, amp)) ^ == ddvcreate.c:779:22: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] while (more = AlnMgrGetNextAlnBit(mpplp->sap, amp)) ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ddvcreate.c:779:22: note: place parentheses around the assignment to silence this warning while (more = AlnMgrGetNextAlnBit(mpplp->sap, amp)) ^ ( ) ddvcreate.c:779:22: note: use '==' to turn this assignment into an equality comparison while (more = AlnMgrGetNextAlnBit(mpplp->sap, amp)) ^ == 2 warnings generated. cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include jsavlt.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include needleman.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include txalign.c txalign.c:1769:179: warning: format specifies type 'long' but the argument has type 'Nlm_Int4' (aka 'int') [-Wformat] sprintf(checkboxBuf, "", sip->data.intvalue, query_number_glb); ~~~ ^~~~~~~~~~~~~~~~~~ %d /usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf' __builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__) ^ txalign.c:1769:199: warning: format specifies type 'long' but the argument has type 'int' [-Wformat] sprintf(checkboxBuf, "", sip->data.intvalue, query_number_glb); ~~~ ^~~~~~~~~~~~~~~~ %d /usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf' __builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__) ^ txalign.c:1770:27: warning: format string is not a string literal (potentially insecure) [-Wformat-security] sprintf(docbuf+pos,checkboxBuf); ^~~~~~~~~~~ /usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf' __builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__) ^ txalign.c:1776:26: warning: format string is not a string literal (potentially insecure) [-Wformat-security] sprintf(docbuf+pos, HTML_buffer); ^~~~~~~~~~~ /usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf' __builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__) ^ txalign.c:1793:65: warning: format string is not a string literal (potentially insecure) [-Wformat-security] sprintf(docbuf+pos, HTML_buffer); ^~~~~~~~~~~ /usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf' __builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__) ^ txalign.c:1802:65: warning: format string is not a string literal (potentially insecure) [-Wformat-security] sprintf(docbuf+pos, HTML_buffer); ^~~~~~~~~~~ /usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf' __builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__) ^ txalign.c:1818:152: warning: format specifies type 'long' but the argument has type 'int' [-Wformat] sprintf(checkboxBuf, "", query_number_glb); ~~~ ^~~~~~~~~~~~~~~~ %d /usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf' __builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__) ^ txalign.c:1819:26: warning: format string is not a string literal (potentially insecure) [-Wformat-security] sprintf(docbuf+pos,checkboxBuf); ^~~~~~~~~~~ /usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf' __builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__) ^ txalign.c:2743:21: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] if (bsp = BioseqLockById(SeqLocId(ssp->loc->next))) { ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ txalign.c:2743:21: note: place parentheses around the assignment to silence this warning if (bsp = BioseqLockById(SeqLocId(ssp->loc->next))) { ^ ( ) txalign.c:2743:21: note: use '==' to turn this assignment into an equality comparison if (bsp = BioseqLockById(SeqLocId(ssp->loc->next))) { ^ == txalign.c:5007:39: warning: '&&' within '||' [-Wlogical-op-parentheses] } else if (bestid != NULL && !(options & TXALIGN_NO_DUMPGNL) || (options & TXALIGN_NO_ENTREZ)) ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~ txalign.c:5007:39: note: place parentheses around the '&&' expression to silence this warning } else if (bestid != NULL && !(options & TXALIGN_NO_DUMPGNL) || (options & TXALIGN_NO_ENTREZ)) ^ ( ) txalign.c:5011:37: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] if (bsp = BioseqLockById(bestid)) { ~~~~^~~~~~~~~~~~~~~~~~~~~~~~ txalign.c:5011:37: note: place parentheses around the assignment to silence this warning if (bsp = BioseqLockById(bestid)) { ^ ( ) txalign.c:5011:37: note: use '==' to turn this assignment into an equality comparison if (bsp = BioseqLockById(bestid)) { ^ == 11 warnings generated. cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include fdlobj.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include alignmgr2.c alignmgr2.c:872:18: warning: expression result unused [-Wunused-value] for (j; jnumseg && next == -1; j++) ^ alignmgr2.c:2964:18: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] if (ldelta = ABS(s->beg - beg)) { ~~~~~~~^~~~~~~~~~~~~~~~~~~ alignmgr2.c:2964:18: note: place parentheses around the assignment to silence this warning if (ldelta = ABS(s->beg - beg)) { ^ ( ) alignmgr2.c:2964:18: note: use '==' to turn this assignment into an equality comparison if (ldelta = ABS(s->beg - beg)) { ^ == alignmgr2.c:3201:12: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] while (a = AlnMgr2GetNextSeqPiece(a)) { ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ alignmgr2.c:3201:12: note: place parentheses around the assignment to silence this warning while (a = AlnMgr2GetNextSeqPiece(a)) { ^ ( ) alignmgr2.c:3201:12: note: use '==' to turn this assignment into an equality comparison while (a = AlnMgr2GetNextSeqPiece(a)) { ^ == alignmgr2.c:3203:14: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] while (b = AlnMgr2GetNextLimitedSeqPiece(b, a)) { ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ alignmgr2.c:3203:14: note: place parentheses around the assignment to silence this warning while (b = AlnMgr2GetNextLimitedSeqPiece(b, a)) { ^ ( ) alignmgr2.c:3203:14: note: use '==' to turn this assignment into an equality comparison while (b = AlnMgr2GetNextLimitedSeqPiece(b, a)) { ^ == alignmgr2.c:3213:12: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] while (A = AlnMgr2GetNextSeqPiece(A)) { ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ alignmgr2.c:3213:12: note: place parentheses around the assignment to silence this warning while (A = AlnMgr2GetNextSeqPiece(A)) { ^ ( ) alignmgr2.c:3213:12: note: use '==' to turn this assignment into an equality comparison while (A = AlnMgr2GetNextSeqPiece(A)) { ^ == alignmgr2.c:3217:16: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] while (B = AlnMgr2GetNextLimitedSeqPiece(B, A)) {}; ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ alignmgr2.c:3217:16: note: place parentheses around the assignment to silence this warning while (B = AlnMgr2GetNextLimitedSeqPiece(B, A)) {}; ^ ( ) alignmgr2.c:3217:16: note: use '==' to turn this assignment into an equality comparison while (B = AlnMgr2GetNextLimitedSeqPiece(B, A)) {}; ^ == alignmgr2.c:5603:22: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] while (more = AlnMgr2GetNextAlnBit(sap, amp)) ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ alignmgr2.c:5603:22: note: place parentheses around the assignment to silence this warning while (more = AlnMgr2GetNextAlnBit(sap, amp)) ^ ( ) alignmgr2.c:5603:22: note: use '==' to turn this assignment into an equality comparison while (more = AlnMgr2GetNextAlnBit(sap, amp)) ^ == alignmgr2.c:5616:29: warning: format string is not a string literal (potentially insecure) [-Wformat-security] fprintf(ofp, buf); ^~~ alignmgr2.c:6311:12: warning: expression result unused [-Wunused-value] for (i; isegnum; i++) ^ 9 warnings generated. cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include alnread.c alnread.c:717:36: warning: format string is not a string literal (potentially insecure) [-Wformat-security] sprintf (eip->message, msg); ^~~ /usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf' __builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__) ^ 1 warning generated. rm -f libncbiobj.a ar cru libncbiobj.a objacces.o objalign.o objall.o objbibli.o objfeat.o objgen.o objloc.o objmedli.o objpub.o objres.o objscoremat.o objseq.o objblock.o objcode.o objsset.o objsub.o objprt.o objfdef.o objalignloc.o objtable.o objpubme.o objmdrs.o objproj.o objgbseq.o objtseq.o objinsdseq.o objmacro.o objent2.o ent2api.o pmfapi.o objtax3.o tax3api.o objegkludge.o objentgene.o objmla2.o mla2api.o qblastapi.o vecscnapi.o objmim.o mimapi.o cddapi.o seqport.o sequtil.o prtutil.o simple.o tofasta.o tofile.o tomedlin.o valid.o alignmgr.o aliparse.o aliread.o alignval.o sqnutil1.o sqnutil2.o sqnutil3.o sqnutil4.o subutil.o edutil.o asn2ff1.o asn2ff2.o asn2ff3.o asn2ff4.o asn2ff5.o asn2ff6.o asn2gnb1.o asn2gnb2.o asn2gnb3.o asn2gnb4.o asn2gnb5.o asn2gnb6.o ftusrstr.o gbfeat.o gbftglob.o gbparint.o utilpars.o utilpub.o ffprint.o wprint.o satutil.o seqmgr.o objmgr.o gather.o accmmdbs.o acccn3ds.o lsqfetch.o findrepl.o codon.o jzcoll.o jzmisc.o maputil.o mconsist.o macroapi.o salpedit.o salpstat.o salpacc.o salprop.o salsap.o salstruc.o salutil.o udvseq.o blocks.o pgppop.o samutil.o ddvcolor.o viewmgr.o ddvcreate.o jsavlt.o needleman.o txalign.o fdlobj.o alignmgr2.o alnread.o cp -p libncbiobj.a ../lib ranlib ../lib/libncbiobj.a cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include cdentrez.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include cdromlib.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include cdnewlib.c cdnewlib.c:1342:12: warning: cast to 'AsnIo *' (aka 'struct asnio *') from smaller integer type 'int' [-Wint-to-pointer-cast] return (AsnIo*) CatastrophicFailure(1); ^ cdnewlib.c:1937:10: warning: cast to 'long *' from smaller integer type 'int' [-Wint-to-pointer-cast] return (long*)CatastrophicFailure(1); ^ cdnewlib.c:1945:10: warning: cast to 'long *' from smaller integer type 'int' [-Wint-to-pointer-cast] return (long*)CatastrophicFailure(1); ^ cdnewlib.c:2679:48: warning: the value of the size argument in 'strncat' is too large, might lead to a buffer overflow [-Wstrncat-size] strncat(volname,cddev->volume->volume_name,sizeof volname); ^~~~~~~~~~~~~~ cdnewlib.c:2679:48: note: change the argument to be the free space in the destination buffer minus the terminating null byte strncat(volname,cddev->volume->volume_name,sizeof volname); ^~~~~~~~~~~~~~ sizeof(volname) - strlen(volname) - 1 cdnewlib.c:2751:33: warning: the value of the size argument in 'strncat' is too large, might lead to a buffer overflow [-Wstrncat-size] strncat(fpath,cddev->inf.root,sizeof fpath); ^~~~~~~~~~~~ cdnewlib.c:2751:33: note: change the argument to be the free space in the destination buffer minus the terminating null byte strncat(fpath,cddev->inf.root,sizeof fpath); ^~~~~~~~~~~~ sizeof(fpath) - strlen(fpath) - 1 cdnewlib.c:2769:36: warning: the value of the size argument in 'strncat' is too large, might lead to a buffer overflow [-Wstrncat-size] strncat(fpath,cddev->inf.root,sizeof fpath); ^~~~~~~~~~~~ cdnewlib.c:2769:36: note: change the argument to be the free space in the destination buffer minus the terminating null byte strncat(fpath,cddev->inf.root,sizeof fpath); ^~~~~~~~~~~~ sizeof(fpath) - strlen(fpath) - 1 6 warnings generated. cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include casn.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include cdconfig.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include objentr.c rm -f libncbicdr.a ar cru libncbicdr.a cdentrez.o cdromlib.o cdnewlib.o casn.o cdconfig.o objentr.o /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: libncbicdr.a(cdromlib.o) has no symbols cp -p libncbicdr.a ../lib ranlib ../lib/libncbicdr.a /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: ../lib/libncbicdr.a(cdromlib.o) has no symbols cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include accentr.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include accutils.c rm -f libncbiacc.a ar cru libncbiacc.a accentr.o accutils.o cp -p libncbiacc.a ../lib ranlib ../lib/libncbiacc.a cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include corematx.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include dvncode.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include objmmdb1.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include objmmdb2.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include objmmdb3.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include objcn3d.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include mmdbapi.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include mmdbapi1.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include mmdbapi2.c mmdbapi2.c:1477:6: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ mmdbapi2.c:1497:17: warning: if statement has empty body [-Wempty-body] if (iCoord) ; /* later eh */ ^ mmdbapi2.c:1497:17: note: put the semicolon on a separate line to silence this warning 2 warnings generated. cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include mmdbapi3.c mmdbapi3.c:843:9: warning: add explicit braces to avoid dangling else [-Wdangling-else] else if (org->taxname) sprintf(orgstring, "ORGANISM_SCIENTIFIC: %s", ^ 1 warning generated. cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include mmdbapi4.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include mmdbentr.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include vastsubs.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include prunebsc.c prunebsc.c:559:13: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] if (vnp = ValNodeFindNext(currentbp->descr, NULL, BiomolDescr_name)) ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ prunebsc.c:559:13: note: place parentheses around the assignment to silence this warning if (vnp = ValNodeFindNext(currentbp->descr, NULL, BiomolDescr_name)) ^ ( ) prunebsc.c:559:13: note: use '==' to turn this assignment into an equality comparison if (vnp = ValNodeFindNext(currentbp->descr, NULL, BiomolDescr_name)) ^ == prunebsc.c:574:13: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] if (vnp = ValNodeFindNext(het->descr, NULL, BiomolDescr_name)) ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ prunebsc.c:574:13: note: place parentheses around the assignment to silence this warning if (vnp = ValNodeFindNext(het->descr, NULL, BiomolDescr_name)) ^ ( ) prunebsc.c:574:13: note: use '==' to turn this assignment into an equality comparison if (vnp = ValNodeFindNext(het->descr, NULL, BiomolDescr_name)) ^ == prunebsc.c:663:13: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] if (vnp = ValNodeFindNext(bsfsp->descr, NULL, BiostrucFeatureSetDescr_name)) ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ prunebsc.c:663:13: note: place parentheses around the assignment to silence this warning if (vnp = ValNodeFindNext(bsfsp->descr, NULL, BiostrucFeatureSetDescr_name)) ^ ( ) prunebsc.c:663:13: note: use '==' to turn this assignment into an equality comparison if (vnp = ValNodeFindNext(bsfsp->descr, NULL, BiostrucFeatureSetDescr_name)) ^ == 3 warnings generated. cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include objcdd.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include cddutil.c cddutil.c:6267:1: warning: '/*' within block comment [-Wcomment] /*---------------------------------------------------------------------------*/ ^ 1 warning generated. cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include cddposutil.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include objmime.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include strucapi.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include thrdalgs.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include thrdatd.c thrdatd.c:1804:40: warning: data argument not used by format string [-Wformat-extra-args] fprintf(pFile, "for each thread:\n", ttb->n); ~~~~~~~~~~~~~~~~~~~~ ^ 1 warning generated. cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include thrdbwfi.c thrdbwfi.c:114:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ 1 warning generated. cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include thrdcpal.c thrdcpal.c:210:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ 1 warning generated. cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include thrdcpll.c thrdcpll.c:229:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ 1 warning generated. cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include thrdcprl.c thrdcprl.c:261:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ 1 warning generated. cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include thrdcxei.c thrdcxei.c:205:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ 1 warning generated. cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include thrddgri.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include thrdrsmp.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include thrdsal0.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include thrdsalr.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include thrdsalu.c thrdsalu.c:83:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ 1 warning generated. cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include thrdsgoi.c thrdsgoi.c:123:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ 1 warning generated. cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include thrdslo0.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include thrdslor.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include thrdslou.c thrdslou.c:114:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ 1 warning generated. cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include thrdspci.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include thrdspea.c thrdspea.c:189:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ 1 warning generated. cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include thrdspel.c thrdspel.c:188:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ 1 warning generated. cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include thrdspni.c thrdspni.c:238:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ 1 warning generated. cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include thrdttb0.c thrdttb0.c:75:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ 1 warning generated. cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include thrdttbi.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include thrdzsc.c thrdzsc.c:369:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ 1 warning generated. rm -f libncbimmdb.a ar cru libncbimmdb.a corematx.o dvncode.o objmmdb1.o objmmdb2.o objmmdb3.o objcn3d.o mmdbapi.o mmdbapi1.o mmdbapi2.o mmdbapi3.o mmdbapi4.o mmdbentr.o vastsubs.o prunebsc.o objcdd.o cddutil.o cddposutil.o objmime.o strucapi.o thrdalgs.o thrdatd.o thrdbwfi.o thrdcpal.o thrdcpll.o thrdcprl.o thrdcxei.o thrddgri.o thrdrsmp.o thrdsal0.o thrdsalr.o thrdsalu.o thrdsgoi.o thrdslo0.o thrdslor.o thrdslou.o thrdspci.o thrdspea.o thrdspel.o thrdspni.o thrdttb0.o thrdttbi.o thrdzsc.o cp -p libncbimmdb.a ../lib ranlib ../lib/libncbimmdb.a cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include csim.c csim.c:893:38: warning: '&&' within '||' [-Wlogical-op-parentheses] if (c > midc || CC[j] != DD[j] && RR[j] == SS[j]) ~~ ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ csim.c:893:38: note: place parentheses around the '&&' expression to silence this warning if (c > midc || CC[j] != DD[j] && RR[j] == SS[j]) ^ ( ) csim.c:1061:31: warning: '&&' within '||' [-Wlogical-op-parentheses] if ( ! rflag && ( ci > rl && cj > cl || di > rl && dj > cl ~~~~~~~~^~~~~~~~~~ ~~ csim.c:1061:31: note: place parentheses around the '&&' expression to silence this warning if ( ! rflag && ( ci > rl && cj > cl || di > rl && dj > cl ^ ( ) csim.c:1061:53: warning: '&&' within '||' [-Wlogical-op-parentheses] if ( ! rflag && ( ci > rl && cj > cl || di > rl && dj > cl ~~ ~~~~~~~~^~~~~~~~~~ csim.c:1061:53: note: place parentheses around the '&&' expression to silence this warning if ( ! rflag && ( ci > rl && cj > cl || di > rl && dj > cl ^ ( ) csim.c:1062:44: warning: '&&' within '||' [-Wlogical-op-parentheses] || fi > rl && fj > cl ) ) ~~ ~~~~~~~~^~~~~~~~~~ csim.c:1062:44: note: place parentheses around the '&&' expression to silence this warning || fi > rl && fj > cl ) ) ^ ( ) csim.c:1071:34: warning: '&&' within '||' [-Wlogical-op-parentheses] if ( ! cflag && ( ci > rl && cj > cl || di > rl && dj > cl ~~~~~~~~^~~~~~~~~~ ~~ csim.c:1071:34: note: place parentheses around the '&&' expression to silence this warning if ( ! cflag && ( ci > rl && cj > cl || di > rl && dj > cl ^ ( ) csim.c:1071:56: warning: '&&' within '||' [-Wlogical-op-parentheses] if ( ! cflag && ( ci > rl && cj > cl || di > rl && dj > cl ~~ ~~~~~~~~^~~~~~~~~~ csim.c:1071:56: note: place parentheses around the '&&' expression to silence this warning if ( ! cflag && ( ci > rl && cj > cl || di > rl && dj > cl ^ ( ) csim.c:1072:20: warning: '&&' within '||' [-Wlogical-op-parentheses] || fi > rl && fj > cl ) ) ~~ ~~~~~~~~^~~~~~~~~~ csim.c:1072:20: note: place parentheses around the '&&' expression to silence this warning || fi > rl && fj > cl ) ) ^ ( ) csim.c:1128:38: warning: '&&' within '||' [-Wlogical-op-parentheses] if ( ! cflag && ( ci > rl && cj > cl || di > rl && dj > cl ~~~~~~~~^~~~~~~~~~ ~~ csim.c:1128:38: note: place parentheses around the '&&' expression to silence this warning if ( ! cflag && ( ci > rl && cj > cl || di > rl && dj > cl ^ ( ) csim.c:1128:60: warning: '&&' within '||' [-Wlogical-op-parentheses] if ( ! cflag && ( ci > rl && cj > cl || di > rl && dj > cl ~~ ~~~~~~~~^~~~~~~~~~ csim.c:1128:60: note: place parentheses around the '&&' expression to silence this warning if ( ! cflag && ( ci > rl && cj > cl || di > rl && dj > cl ^ ( ) csim.c:1129:29: warning: '&&' within '||' [-Wlogical-op-parentheses] || fi > rl && fj > cl ) ) ~~ ~~~~~~~~^~~~~~~~~~ csim.c:1129:29: note: place parentheses around the '&&' expression to silence this warning || fi > rl && fj > cl ) ) ^ ( ) csim.c:1138:34: warning: '&&' within '||' [-Wlogical-op-parentheses] if ( ! rflag && ( ci > rl && cj > cl || di > rl && dj > cl ~~~~~~~~^~~~~~~~~~ ~~ csim.c:1138:34: note: place parentheses around the '&&' expression to silence this warning if ( ! rflag && ( ci > rl && cj > cl || di > rl && dj > cl ^ ( ) csim.c:1138:56: warning: '&&' within '||' [-Wlogical-op-parentheses] if ( ! rflag && ( ci > rl && cj > cl || di > rl && dj > cl ~~ ~~~~~~~~^~~~~~~~~~ csim.c:1138:56: note: place parentheses around the '&&' expression to silence this warning if ( ! rflag && ( ci > rl && cj > cl || di > rl && dj > cl ^ ( ) csim.c:1139:47: warning: '&&' within '||' [-Wlogical-op-parentheses] || fi > rl && fj > cl ) ) ~~ ~~~~~~~~^~~~~~~~~~ csim.c:1139:47: note: place parentheses around the '&&' expression to silence this warning || fi > rl && fj > cl ) ) ^ ( ) csim.c:1144:29: warning: '&&' within '||' [-Wlogical-op-parentheses] if ( (plist->m1) == 1 && (plist->n1) == 1 || no_cross(flag, plist, &rl, &cl) ) ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ ~~ csim.c:1144:29: note: place parentheses around the '&&' expression to silence this warning if ( (plist->m1) == 1 && (plist->n1) == 1 || no_cross(flag, plist, &rl, &cl) ) ^ ( ) csim.c:1363:3: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ 15 warnings generated. cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include db_slist.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include dust.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include blast_dust.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include falign.c falign.c:668:10: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] if (df = cdiag_prev[l]) { ~~~^~~~~~~~~~~~~~~ falign.c:668:10: note: place parentheses around the assignment to silence this warning if (df = cdiag_prev[l]) { ^ ( ) falign.c:668:10: note: use '==' to turn this assignment into an equality comparison if (df = cdiag_prev[l]) { ^ == falign.c:710:10: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] if (df = diag_prev[len1+len2-1-pos]) { ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ falign.c:710:10: note: place parentheses around the assignment to silence this warning if (df = diag_prev[len1+len2-1-pos]) { ^ ( ) falign.c:710:10: note: use '==' to turn this assignment into an equality comparison if (df = diag_prev[len1+len2-1-pos]) { ^ == falign.c:719:9: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] if (df=diag_prev[l]) { ~~^~~~~~~~~~~~~ falign.c:719:9: note: place parentheses around the assignment to silence this warning if (df=diag_prev[l]) { ^ ( ) falign.c:719:9: note: use '==' to turn this assignment into an equality comparison if (df=diag_prev[l]) { ^ == falign.c:881:10: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] if (df = diag_prev[len1+se2-pos]) { ~~~^~~~~~~~~~~~~~~~~~~~~~~~~ falign.c:881:10: note: place parentheses around the assignment to silence this warning if (df = diag_prev[len1+se2-pos]) { ^ ( ) falign.c:881:10: note: use '==' to turn this assignment into an equality comparison if (df = diag_prev[len1+se2-pos]) { ^ == falign.c:889:10: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] if (df = diag_prev[len1+se2-pos]) { ~~~^~~~~~~~~~~~~~~~~~~~~~~~~ falign.c:889:10: note: place parentheses around the assignment to silence this warning if (df = diag_prev[len1+se2-pos]) { ^ ( ) falign.c:889:10: note: use '==' to turn this assignment into an equality comparison if (df = diag_prev[len1+se2-pos]) { ^ == falign.c:1547:9: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] if (pf = diag_prev[ocur_diag]) { ~~~^~~~~~~~~~~~~~~~~~~~~~ falign.c:1547:9: note: place parentheses around the assignment to silence this warning if (pf = diag_prev[ocur_diag]) { ^ ( ) falign.c:1547:9: note: use '==' to turn this assignment into an equality comparison if (pf = diag_prev[ocur_diag]) { ^ == falign.c:1897:8: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] if (s = findS(f->bgf)) { ~~^~~~~~~~~~~~~~~ falign.c:1897:8: note: place parentheses around the assignment to silence this warning if (s = findS(f->bgf)) { ^ ( ) falign.c:1897:8: note: use '==' to turn this assignment into an equality comparison if (s = findS(f->bgf)) { ^ == falign.c:1958:9: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] if (pf = diag_prev[cur_diag]) { ~~~^~~~~~~~~~~~~~~~~~~~~ falign.c:1958:9: note: place parentheses around the assignment to silence this warning if (pf = diag_prev[cur_diag]) { ^ ( ) falign.c:1958:9: note: use '==' to turn this assignment into an equality comparison if (pf = diag_prev[cur_diag]) { ^ == falign.c:1999:9: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] if (pf = cdiag_prev[cur_diag]) { ~~~^~~~~~~~~~~~~~~~~~~~~~ falign.c:1999:9: note: place parentheses around the assignment to silence this warning if (pf = cdiag_prev[cur_diag]) { ^ ( ) falign.c:1999:9: note: use '==' to turn this assignment into an equality comparison if (pf = cdiag_prev[cur_diag]) { ^ == falign.c:2054:9: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] if (pf = cdiag_prev[cur_diag]) { ~~~^~~~~~~~~~~~~~~~~~~~~~ falign.c:2054:9: note: place parentheses around the assignment to silence this warning if (pf = cdiag_prev[cur_diag]) { ^ ( ) falign.c:2054:9: note: use '==' to turn this assignment into an equality comparison if (pf = cdiag_prev[cur_diag]) { ^ == falign.c:2109:9: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] if (pf = cdiag_prev[cur_diag]) { ~~~^~~~~~~~~~~~~~~~~~~~~~ falign.c:2109:9: note: place parentheses around the assignment to silence this warning if (pf = cdiag_prev[cur_diag]) { ^ ( ) falign.c:2109:9: note: use '==' to turn this assignment into an equality comparison if (pf = cdiag_prev[cur_diag]) { ^ == 11 warnings generated. cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include g_any.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include sim2.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include sim3.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include sim4.c sim4.c:630:12: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] while(i1 = sgp->Blist[i].next) { ~~~^~~~~~~~~~~~~~~~~~~~ sim4.c:630:12: note: place parentheses around the assignment to silence this warning while(i1 = sgp->Blist[i].next) { ^ ( ) sim4.c:630:12: note: use '==' to turn this assignment into an equality comparison while(i1 = sgp->Blist[i].next) { ^ == sim4.c:1792:16: warning: add explicit braces to avoid dangling else [-Wdangling-else] } else goto fin; ^ sim4.c:1836:27: warning: add explicit braces to avoid dangling else [-Wdangling-else] } else goto fin; ^ sim4.c:1881:27: warning: add explicit braces to avoid dangling else [-Wdangling-else] } else goto fin; ^ sim4.c:1989:22: warning: add explicit braces to avoid dangling else [-Wdangling-else] } else goto fin; ^ sim4.c:2035:22: warning: add explicit braces to avoid dangling else [-Wdangling-else] } else goto fin; ^ sim4.c:2080:22: warning: add explicit braces to avoid dangling else [-Wdangling-else] } else goto fin; ^ sim4.c:2625:35: warning: '&&' within '||' [-Wlogical-op-parentheses] if (a >= ALINE+50 || i >= M && j >= N) ~~ ~~~~~~~^~~~~~~~~ sim4.c:2625:35: note: place parentheses around the '&&' expression to silence this warning if (a >= ALINE+50 || i >= M && j >= N) ^ ( ) 8 warnings generated. cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include simutil.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include slist.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include sec.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include tfuns.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include toasn3.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include toporg.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include pobutil.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include stsutil.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include suggadj.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include suggest.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include suggslp.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include blast.c blast.c:3179:29: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] if (virtual_oidlist = rdfp_chain->oidlist) { ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ blast.c:3179:29: note: place parentheses around the assignment to silence this warning if (virtual_oidlist = rdfp_chain->oidlist) { ^ ( ) blast.c:3179:29: note: use '==' to turn this assignment into an equality comparison if (virtual_oidlist = rdfp_chain->oidlist) { ^ == blast.c:3210:29: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] if (virtual_oidlist = BlastGetVirtualOIDList(rdfp)) { ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ blast.c:3210:29: note: place parentheses around the assignment to silence this warning if (virtual_oidlist = BlastGetVirtualOIDList(rdfp)) { ^ ( ) blast.c:3210:29: note: use '==' to turn this assignment into an equality comparison if (virtual_oidlist = BlastGetVirtualOIDList(rdfp)) { ^ == blast.c:10121:25: warning: add explicit braces to avoid dangling else [-Wdangling-else] else if( del_index < new_index ) ^ 3 warnings generated. cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include blastutl.c blastutl.c:7542:12: warning: expression result unused [-Wunused-value] stop_timer("after repeat filtering"); ^~~~~~~~~~~~~~~~~~~~~~~~ blastutl.c:10270:12: warning: expression result unused [-Wunused-value] stop_timer("after BlastGappedScoreInternal"); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2 warnings generated. cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include blastool.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include blastconcat.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include splutil.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include gapxdrop.c gapxdrop.c:866:4: warning: add explicit braces to avoid dangling else [-Wdangling-else] else if ((t/10)%3 == 2) k = 3; ^ gapxdrop.c:869:4: warning: add explicit braces to avoid dangling else [-Wdangling-else] else if ((t/30) == 2) k = 3; ^ 2 warnings generated. cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include bandalg0.c bandalg0.c:277:4: warning: add explicit braces to avoid dangling else [-Wdangling-else] } else { ^ 1 warning generated. cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include bandalg1.c bandalg1.c:210:7: warning: add explicit braces to avoid dangling else [-Wdangling-else] else data->CD[leftd - 1].DD = e; ^ 1 warning generated. cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include bandalg2.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include bandalg3.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include bandalg4.c bandalg4.c:828:7: warning: add explicit braces to avoid dangling else [-Wdangling-else] else if ((t/10)%3 == 2) k = 3; ^ bandalg4.c:831:7: warning: add explicit braces to avoid dangling else [-Wdangling-else] else if ((t/30) == 2) k = 3; ^ 2 warnings generated. cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include bandalg5.c bandalg5.c:294:7: warning: add explicit braces to avoid dangling else [-Wdangling-else] else if ((t/10)%3 == 2) k = 3; ^ bandalg5.c:297:7: warning: add explicit braces to avoid dangling else [-Wdangling-else] else if ((t/30) == 2) k = 3; ^ 2 warnings generated. cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include bandalgn.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include blastkar.c blastkar.c:4936:10: warning: implicit conversion from 'double' to 'Nlm_Int2' (aka 'short') changes value from 0.5 to 0 [-Wliteral-conversion] return 0.5; ~~~~~~ ^~~ 1 warning generated. cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include actutils.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include posit.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include lookup.c lookup.c:1047:35: warning: '&' within '|' [-Wbitwise-op-parentheses] GET_EXTRA_CODE_18_OPT(seq)) & no_bit0; ^~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/lookup.h:299:61: note: expanded from macro 'GET_EXTRA_CODE_18_OPT' #define GET_EXTRA_CODE_18_OPT(s) (((*(s+1))<<2) | (*(s+2))) & MASK_EXTRA_OPT ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ lookup.c:1047:35: note: place parentheses around the '&' expression to silence this warning GET_EXTRA_CODE_18_OPT(seq)) & no_bit0; ^~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/lookup.h:299:61: note: expanded from macro 'GET_EXTRA_CODE_18_OPT' #define GET_EXTRA_CODE_18_OPT(s) (((*(s+1))<<2) | (*(s+2))) & MASK_EXTRA_OPT ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ lookup.c:1051:35: warning: '&' within '|' [-Wbitwise-op-parentheses] GET_EXTRA_CODE_18_OPT(seq)) & no_bit0; ^~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/lookup.h:299:61: note: expanded from macro 'GET_EXTRA_CODE_18_OPT' #define GET_EXTRA_CODE_18_OPT(s) (((*(s+1))<<2) | (*(s+2))) & MASK_EXTRA_OPT ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ lookup.c:1051:35: note: place parentheses around the '&' expression to silence this warning GET_EXTRA_CODE_18_OPT(seq)) & no_bit0; ^~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/lookup.h:299:61: note: expanded from macro 'GET_EXTRA_CODE_18_OPT' #define GET_EXTRA_CODE_18_OPT(s) (((*(s+1))<<2) | (*(s+2))) & MASK_EXTRA_OPT ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ lookup.c:1078:31: warning: '&' within '|' [-Wbitwise-op-parentheses] GET_EXTRA_CODE_18_OPT(seq) | bit0; ^~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/lookup.h:299:61: note: expanded from macro 'GET_EXTRA_CODE_18_OPT' #define GET_EXTRA_CODE_18_OPT(s) (((*(s+1))<<2) | (*(s+2))) & MASK_EXTRA_OPT ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ lookup.c:1078:31: note: place parentheses around the '&' expression to silence this warning GET_EXTRA_CODE_18_OPT(seq) | bit0; ^~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/lookup.h:299:61: note: expanded from macro 'GET_EXTRA_CODE_18_OPT' #define GET_EXTRA_CODE_18_OPT(s) (((*(s+1))<<2) | (*(s+2))) & MASK_EXTRA_OPT ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ lookup.c:1082:31: warning: '&' within '|' [-Wbitwise-op-parentheses] GET_EXTRA_CODE_18_OPT(seq) | bit0; ^~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/lookup.h:299:61: note: expanded from macro 'GET_EXTRA_CODE_18_OPT' #define GET_EXTRA_CODE_18_OPT(s) (((*(s+1))<<2) | (*(s+2))) & MASK_EXTRA_OPT ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ lookup.c:1082:31: note: place parentheses around the '&' expression to silence this warning GET_EXTRA_CODE_18_OPT(seq) | bit0; ^~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/lookup.h:299:61: note: expanded from macro 'GET_EXTRA_CODE_18_OPT' #define GET_EXTRA_CODE_18_OPT(s) (((*(s+1))<<2) | (*(s+2))) & MASK_EXTRA_OPT ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ lookup.c:1198:56: warning: for loop has empty body [-Wempty-body] index>0; index=mb_lt->next_pos[index], pcount++); ^ lookup.c:1198:56: note: put the semicolon on a separate line to silence this warning 5 warnings generated. cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include readdb.c readdb.c:2462:13: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ readdb.c:3079:37: warning: format specifies type 'long long *' but the argument has type 'Nlm_Int8 *' (aka 'long *') [-Wformat] sscanf(ptr, "%lld", &(rdbap->len)); ~~~~ ^~~~~~~~~~~~~ %ld readdb.c:4177:42: warning: comparison of unsigned expression >= 0 is always true [-Wtautological-compare] if (rdfp_list->aliasnseq >= 0 ~~~~~~~~~~~~~~~~~~~~ ^ ~ readdb.c:6205:34: warning: 'memset' call operates on objects of type 'char' while the size is based on a different type 'Nlm_CharPtr' (aka 'char *') [-Wsizeof-pointer-memaccess] MemSet(defline, '\0', sizeof(defline)); ~~~~~~~ ^~~~~~~ readdb.c:6205:34: note: did you mean to provide an explicit length? MemSet(defline, '\0', sizeof(defline)); ^~~~~~~ readdb.c:7806:19: warning: comparison of unsigned enum expression >= 0 is always true [-Wtautological-compare] if (clean_opt >= 0 && clean_opt < eCleanOptMax) ~~~~~~~~~ ^ ~ readdb.c:7956:60: warning: format specifies type 'long' but the argument has type 'int' [-Wformat] sprintf(opts_tmp.base_name, "%s.%02ld", base_name, volume); ~~~~~ ^~~~~~ %02d /usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf' __builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__) ^ readdb.c:11517:64: warning: format specifies type 'char *' but the argument has type 'int' [-Wformat] "(read %d fields instead of the expected %d)", total+1, ^~~~~~~ readdb.c:11518:17: warning: format specifies type 'int' but the argument has type 'Nlm_CharPtr' (aka 'char *') [-Wformat] difilename, readstat, kNumFieldsDiFile); ^~~~~~~~~~ 8 warnings generated. cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include ncbisam.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include ncbisort.c ncbisort.c:692:12: warning: type specifier missing, defaults to 'int' [-Wimplicit-int] register tmpa = UCHAR(*a), tmpb = UCHAR(*b); ~~~~~~~~ ^ ncbisort.c:692:30: warning: type specifier missing, defaults to 'int' [-Wimplicit-int] register tmpa = UCHAR(*a), tmpb = UCHAR(*b); ~~~~~~~~ ^ 2 warnings generated. cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include salign.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include salptool.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include urkutil.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include urkpcc.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include urkptpf.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include urkepi.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include urkfltr.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include urkdust.c urkdust.c:196:42: warning: '&&' within '||' [-Wlogical-op-parentheses] (dcvp->curlevel <= newlevel) && dcvp->curend == loop+1) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ urkdust.c:196:42: note: place parentheses around the '&&' expression to silence this warning (dcvp->curlevel <= newlevel) && dcvp->curend == loop+1) ^ ( ) 1 warning generated. cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include urksigu.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include seg.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include urkbias.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include urkcnsrt.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include urktree.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include pseed3.c pseed3.c:504:20: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] while (pattern = get_a_pat(patfp, &pname, occurArray, hitArray, &numPatOccur, &effectiveOccurrences, program_flag, unfilter_query, query, search->sbp->query_length, is_dna, patternSearch, seedSearch, showDiagnostics, &(search->error_return), info_vnp, hitArraySz)) { ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pseed3.c:504:20: note: place parentheses around the assignment to silence this warning while (pattern = get_a_pat(patfp, &pname, occurArray, hitArray, &numPatOccur, &effectiveOccurrences, program_flag, unfilter_query, query, search->sbp->query_length, is_dna, patternSearch, seedSearch, showDiagnostics, &(search->error_return), info_vnp, hitArraySz)) { ^ ( ) pseed3.c:504:20: note: use '==' to turn this assignment into an equality comparison while (pattern = get_a_pat(patfp, &pname, occurArray, hitArray, &numPatOccur, &effectiveOccurrences, program_flag, unfilter_query, query, search->sbp->query_length, is_dna, patternSearch, seedSearch, showDiagnostics, &(search->error_return), info_vnp, hitArraySz)) { ^ == 1 warning generated. cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include pattern1.c pattern1.c:534:13: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] if (tmp = (prefixMatchedBitPattern & patternSearch->DNAwhichPrefixPosPtr[seq[i]])) { ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pattern1.c:534:13: note: place parentheses around the assignment to silence this warning if (tmp = (prefixMatchedBitPattern & patternSearch->DNAwhichPrefixPosPtr[seq[i]])) { ^ ( ) pattern1.c:534:13: note: use '==' to turn this assignment into an equality comparison if (tmp = (prefixMatchedBitPattern & patternSearch->DNAwhichPrefixPosPtr[seq[i]])) { ^ == pattern1.c:547:11: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] if (tmp = (prefixMatchedBitPattern & patternSearch->DNAwhichPrefixPosPtr[seq[i]])) { ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pattern1.c:547:11: note: place parentheses around the assignment to silence this warning if (tmp = (prefixMatchedBitPattern & patternSearch->DNAwhichPrefixPosPtr[seq[i]])) { ^ ( ) pattern1.c:547:11: note: use '==' to turn this assignment into an equality comparison if (tmp = (prefixMatchedBitPattern & patternSearch->DNAwhichPrefixPosPtr[seq[i]])) { ^ == pattern1.c:744:8: warning: type specifier missing, defaults to 'int' [-Wimplicit-int] static and(Int4 *result, Int4 *a, Int4 *b, patternSearchItems *patternSearch) ~~~~~~ ^ pattern1.c:750:21: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] if (result[i] = (a[i] & b[i])) ~~~~~~~~~~^~~~~~~~~~~~~~~ pattern1.c:750:21: note: place parentheses around the assignment to silence this warning if (result[i] = (a[i] & b[i])) ^ ( ) pattern1.c:750:21: note: use '==' to turn this assignment into an equality comparison if (result[i] = (a[i] & b[i])) ^ == pattern1.c:1107:6: warning: add explicit braces to avoid dangling else [-Wdangling-else] else { ^ 5 warnings generated. cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include impatool.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include posit2.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include mbalign.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include vecscrn.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include mblast.c mblast.c:961:13: warning: expression result unused [-Wunused-value] stop_timer("BioseqBlastEngineCore: before do_the_blast_run()"); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mblast.c:987:13: warning: expression result unused [-Wunused-value] stop_timer("MegaBlastEngineCore: after do_the_blast_run()"); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2 warnings generated. cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include rpsutil.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include kappa.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include xmlblast.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include bxmlobj.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include dotseq.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include spidey.c spidey.c:2091:37: warning: format string is not a string literal (potentially insecure) [-Wformat-security] fprintf(ofp2, buf); ^~~ spidey.c:2420:39: warning: format string is not a string literal (potentially insecure) [-Wformat-security] fprintf(ofp2, buf); ^~~ 2 warnings generated. cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include motif.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include blfmtutl.c rm -f libncbitool.a ar cru libncbitool.a csim.o db_slist.o dust.o blast_dust.o falign.o g_any.o sim2.o sim3.o sim4.o simutil.o slist.o sec.o tfuns.o toasn3.o toporg.o pobutil.o stsutil.o suggadj.o suggest.o suggslp.o blast.o blastutl.o blastool.o blastconcat.o splutil.o gapxdrop.o bandalg0.o bandalg1.o bandalg2.o bandalg3.o bandalg4.o bandalg5.o bandalgn.o blastkar.o actutils.o posit.o lookup.o readdb.o ncbisam.o ncbisort.o salign.o salptool.o urkutil.o urkpcc.o urkptpf.o urkepi.o urkfltr.o urkdust.o urksigu.o seg.o urkbias.o urkcnsrt.o urktree.o pseed3.o pattern1.o impatool.o posit2.o mbalign.o vecscrn.o mblast.o rpsutil.o kappa.o xmlblast.o bxmlobj.o dotseq.o spidey.o motif.o blfmtutl.o cp -p libncbitool.a ../lib ranlib ../lib/libncbitool.a cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include matrix_frequency_data.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include compo_mode_condition.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include composition_adjustment.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include nlm_linear_algebra.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include optimize_target_freq.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include compo_heap.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include smith_waterman.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include redo_alignment.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include unified_pvalues.c rm -f libblastcompadj.a ar cru libblastcompadj.a matrix_frequency_data.o compo_mode_condition.o composition_adjustment.o nlm_linear_algebra.o optimize_target_freq.o compo_heap.o smith_waterman.o redo_alignment.o unified_pvalues.o cp -p libblastcompadj.a ../lib ranlib ../lib/libblastcompadj.a cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include chartables.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include get.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include maketables.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include pcre.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include pcreposix.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include study.c rm -f libregexp.a ar cru libregexp.a chartables.o get.o maketables.o pcre.o pcreposix.o study.o /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: libregexp.a(chartables.o) has no symbols cp -p libregexp.a ../lib ranlib ../lib/libregexp.a /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: ../lib/libregexp.a(chartables.o) has no symbols cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include aa_ungapped.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include blast_diagnostics.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include blast_engine.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include blast_extend.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include blast_filter.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include blast_gapalign.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include blast_hits.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include blast_itree.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include blast_lookup.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include blast_message.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include blast_options.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include blast_seg.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include blast_seqsrc.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include blast_sw.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include blast_setup.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include blast_stat.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include blast_traceback.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include blast_util.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include gapinfo.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include greedy_align.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include hspstream_collector.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include link_hsps.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include lookup_wrap.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include na_ungapped.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include ncbi_math.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include ncbi_std.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include pattern.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include phi_extend.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include phi_lookup.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include lookup_util.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include blast_encoding.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include blast_psi.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include blast_psi_priv.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include blast_kappa.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include matrix_freq_ratios.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include blast_hspstream.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include blast_parameters.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include blast_posit.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include phi_gapalign.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include blast_program.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include blast_query_info.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include blast_tune.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include blast_aalookup.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include blast_nalookup.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include blast_aascan.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include blast_nascan.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include blast_dynarray.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include split_query.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include gencode_singleton.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include index_ungapped.c rm -f libblast.a ar cru libblast.a aa_ungapped.o blast_diagnostics.o blast_engine.o blast_extend.o blast_filter.o blast_gapalign.o blast_hits.o blast_itree.o blast_lookup.o blast_message.o blast_options.o blast_seg.o blast_seqsrc.o blast_sw.o blast_setup.o blast_stat.o blast_traceback.o blast_util.o gapinfo.o greedy_align.o hspstream_collector.o link_hsps.o lookup_wrap.o na_ungapped.o ncbi_math.o ncbi_std.o pattern.o phi_extend.o phi_lookup.o lookup_util.o blast_encoding.o blast_psi.o blast_psi_priv.o blast_kappa.o matrix_freq_ratios.o blast_hspstream.o blast_parameters.o blast_posit.o phi_gapalign.o blast_program.o blast_query_info.o blast_tune.o blast_aalookup.o blast_nalookup.o blast_aascan.o blast_nascan.o blast_dynarray.o split_query.o gencode_singleton.o index_ungapped.o cp -p libblast.a ../lib ranlib ../lib/libblast.a cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include blast_api.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include blast_input.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include blast_format.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include blast_mtlock.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include blast_options_api.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include blast_prelim.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include blast_returns.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include blast_seq.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include blast_seqalign.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include blast_tabular.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include hspstream_queue.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include repeats_filter.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include seqsrc_multiseq.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include seqsrc_readdb.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include twoseq_api.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include dust_filter.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include blast_message_api.c rm -f libblastapi.a ar cru libblastapi.a blast_api.o blast_input.o blast_format.o blast_mtlock.o blast_options_api.o blast_prelim.o blast_returns.o blast_seq.o blast_seqalign.o blast_tabular.o hspstream_queue.o repeats_filter.o seqsrc_multiseq.o seqsrc_readdb.o twoseq_api.o dust_filter.o blast_message_api.o cp -p libblastapi.a ../lib ranlib ../lib/libblastapi.a cc -pipe -o asntool -framework CoreServices -O2 -I../include -L../lib asntool.c asncode.c ../lib/libncbi.a -lc asncode.c:2371:9: warning: data argument not used by format string [-Wformat-extra-args] iter->stack->slot_name); ^ /usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf' __builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__) ^ asncode.c:2750:4: warning: data argument not used by format string [-Wformat-extra-args] right_outer->slot_name); ^ /usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf' __builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__) ^ asncode.c:2765:4: warning: data argument not used by format string [-Wformat-extra-args] right_outer->slot_name); ^ /usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf' __builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__) ^ asncode.c:3287:9: warning: add explicit braces to avoid dangling else [-Wdangling-else] } else if (now_atp->type->isa == CHOICE_TYPE) { ^ asncode.c:3472:59: warning: format specifies type 'unsigned int' but the argument has type 'AsnCodeSpooledPtr' (aka 'struct struct_spooled *') [-Wformat] fprintf ((iter->acip -> bug_fp), "Dumping:%x<%s>\n", routine, TESTNIL (line->line)); ~~ ^~~~~~~ asncode.c:3509:69: warning: format specifies type 'unsigned int' but the argument has type 'AsnCodeSpooledPtr' (aka 'struct struct_spooled *') [-Wformat] fprintf ((iter->acip -> bug_fp), "Buf (%d):%x<%s>\n", lineno, iter->cur_routine, TESTNIL (iter->buf)); ~~ ^~~~~~~~~~~~~~~~~ asncode.c:4366:9: warning: add explicit braces to avoid dangling else [-Wdangling-else] } else { ^ asncode.c:4639:88: warning: data argument not used by format string [-Wformat-extra-args] sprintf (iter->buf, "\treturn (Pointer) %sAsnRead (aip, atp);\n}\n\n", objnamemc, objnamemc); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf' __builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__) ^ 8 warnings generated. cp -p asntool ../bin make -f makedemo.unx CFLAGS1="-DNDEBUG -O2 -c -no-cpp-precomp" LDFLAGS1="-framework CoreServices -O2" SHELL="/bin/sh" LCL="dwn" RAN="ranlib" AR="ar" CC="cc -pipe" ./ln-if-absent ../demo/*.* . ./ln-if-absent ../regexp/test/*.* . ./ln-if-absent ../regexp/demo/*.* . ./ln-if-absent ../internal/*.* . set: No match. make: [copy] Error 1 (ignored) chmod -R ug+rw,o+r . echo Waiting...go Waiting...go cc -pipe -o testcore -framework CoreServices -O2 -I../include -L../lib testcore.c -lncbi -lm testcore.c:326:34: warning: format specifies type 'long' but the argument has type 'Nlm_Int4' (aka 'int') [-Wformat] sprintf(tbuf, "%ld", value); ~~~ ^~~~~ %d /usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf' __builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__) ^ 1 warning generated. cc -pipe -o makeset -framework CoreServices -O2 -I../include -L../lib makeset.c -lncbiobj -lncbi -lm cc -pipe -o getmesh -framework CoreServices -O2 -I../include -L../lib getmesh.c -lncbiobj -lncbi -lm cc -pipe -o indexpub -framework CoreServices -O2 -I../include -L../lib indexpub.c -lncbiobj -lncbi -lm indexpub.c:60:29: warning: format specifies type 'long' but the argument has type 'Nlm_Int4' (aka 'int') [-Wformat] fprintf(fp, "%ld %ld\n", uid, seekptr); ~~~ ^~~ %d indexpub.c:60:34: warning: format specifies type 'long' but the argument has type 'Nlm_Int4' (aka 'int') [-Wformat] fprintf(fp, "%ld %ld\n", uid, seekptr); ~~~ ^~~~~~~ %d 2 warnings generated. cc -pipe -o getpub -framework CoreServices -O2 -I../include -L../lib getpub.c -lncbiobj -lncbi -lm getpub.c:64:34: warning: format specifies type 'long *' but the argument has type 'Nlm_Int4 *' (aka 'int *') [-Wformat] retval = fscanf(fp, "%ld %ld", &uid, &seekptr); ~~~ ^~~~ %d getpub.c:64:40: warning: format specifies type 'long *' but the argument has type 'Nlm_Int4 *' (aka 'int *') [-Wformat] retval = fscanf(fp, "%ld %ld", &uid, &seekptr); ~~~ ^~~~~~~~ %d 2 warnings generated. cc -pipe -o testobj -framework CoreServices -O2 -I../include -L../lib testobj.c -lncbiobj -lncbi -lm cc -pipe -o seqtest -framework CoreServices -O2 -I../include -L../lib seqtest.c -lncbiobj -lncbi -lm seqtest.c:98:46: warning: format specifies type 'long' but the argument has type 'Nlm_Int4' (aka 'int') [-Wformat] fprintf(fp, "len=%ld gaps=%ld segs=%ld\n", BioseqGetLen(seqlist[i]), ~~~ ^~~~~~~~~~~~~~~~~~~~~~~~ %d seqtest.c:99:3: warning: format specifies type 'long' but the argument has type 'Nlm_Int4' (aka 'int') [-Wformat] BioseqGetGaps(seqlist[i]), numseg); ^~~~~~~~~~~~~~~~~~~~~~~~~ seqtest.c:99:30: warning: format specifies type 'long' but the argument has type 'Nlm_Int4' (aka 'int') [-Wformat] BioseqGetGaps(seqlist[i]), numseg); ^~~~~~ seqtest.c:103:34: warning: format specifies type 'long' but the argument has type 'Nlm_Int4' (aka 'int') [-Wformat] fprintf(fp, " len = %ld\n", lens[j]); ~~~ ^~~~~~~ %d 4 warnings generated. cc -pipe -o dosimple -framework CoreServices -O2 -I../include -L../lib dosimple.c -lncbiobj -lncbi -lm cc -pipe -o asn2ff -framework CoreServices -O2 -I../include -L../lib asn2ff.c -lncbiobj -lncbi -lm cc -pipe -o checksub -framework CoreServices -O2 -I../include -L../lib checksub.c -lncbiobj -lncbi -lm cc -pipe -o asndhuff -framework CoreServices -O2 -I../include -L../lib asndhuff.c -lncbiacc -lncbicdr -lncbiobj -lncbi -lm asndhuff.c:182:21: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] for (count=0; entry=CASN_NextMedlineEntry(casnh); ++count) ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ asndhuff.c:182:21: note: place parentheses around the assignment to silence this warning for (count=0; entry=CASN_NextMedlineEntry(casnh); ++count) ^ ( ) asndhuff.c:182:21: note: use '==' to turn this assignment into an equality comparison for (count=0; entry=CASN_NextMedlineEntry(casnh); ++count) ^ == asndhuff.c:221:21: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] for (count=0; entry=CASN_NextSeqEntry(casnh); ++count) ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ asndhuff.c:221:21: note: place parentheses around the assignment to silence this warning for (count=0; entry=CASN_NextSeqEntry(casnh); ++count) ^ ( ) asndhuff.c:221:21: note: use '==' to turn this assignment into an equality comparison for (count=0; entry=CASN_NextSeqEntry(casnh); ++count) ^ == 2 warnings generated. cc -pipe -o entrcmd -framework CoreServices -O2 -I../include -L../lib entrcmd.c -lncbiacc -lncbicdr -lncbiobj -lncbi -lm entrcmd.c:722:53: warning: format specifies type 'long' but the argument has type 'Nlm_Int4' (aka 'int') [-Wformat] fprintf(exportFilePtr, "%ld\n", lsp->uids[i]); ~~~ ^~~~~~~~~~~~ %d entrcmd.c:730:50: warning: format specifies type 'long' but the argument has type 'Nlm_Int4' (aka 'int') [-Wformat] fprintf (master_fp, "%ld\n", lsp->uids[i]); ~~~ ^~~~~~~~~~~~ %d entrcmd.c:773:70: warning: format specifies type 'int' but the argument has type 'long' [-Wformat] fprintf (master_fp, "out of %d total entries.

\n", totalCount); ~~ ^~~~~~~~~~ %ld entrcmd.c:887:53: warning: format specifies type 'long' but the argument has type 'Nlm_Int4' (aka 'int') [-Wformat] fprintf(exportFilePtr, "%ld\n", lsp->uids[i]); ~~~ ^~~~~~~~~~~~ %d entrcmd.c:895:50: warning: format specifies type 'long' but the argument has type 'Nlm_Int4' (aka 'int') [-Wformat] fprintf (master_fp, "%ld\n", lsp->uids[i]); ~~~ ^~~~~~~~~~~~ %d entrcmd.c:915:70: warning: format specifies type 'int' but the argument has type 'long' [-Wformat] fprintf (master_fp, "out of %d total entries.

\n", totalCount); ~~ ^~~~~~~~~~ %ld 6 warnings generated. cc -pipe -o errhdr -framework CoreServices -O2 -I../include -L../lib errhdr.c -lncbiobj -lncbi -lm errhdr.c:44:24: warning: the value of the size argument in 'strncat' is too large, might lead to a buffer overflow [-Wstrncat-size] strncat(mod,argv[i],sizeof mod); ^~~~~~~~~~ errhdr.c:44:24: note: change the argument to be the free space in the destination buffer minus the terminating null byte strncat(mod,argv[i],sizeof mod); ^~~~~~~~~~ sizeof(mod) - strlen(mod) - 1 1 warning generated. cc -pipe -o cdscan -framework CoreServices -O2 -I../include -L../lib cdscan.c -lncbiacc -lncbicdr -lncbiobj -lncbi -lm cc -pipe -o findspl -framework CoreServices -O2 -I../include -L../lib findspl.c -lncbiacc -lncbicdr -lncbiobj -lncbi -lm cc -pipe -o ncbisort -framework CoreServices -O2 -I../include -L../lib sortcmd.c -lncbitool -lblastcompadj \ -lncbi -lm cc -pipe -o fa2htgs -framework CoreServices -O2 -I../include -L../lib fa2htgs.c -lncbiobj -lncbi -lm cc -pipe -o fastacmd -framework CoreServices -O2 -I../include -L../lib fastacmd.c -lncbitool -lblastcompadj \ -lncbiobj -lncbi -lm cc -pipe -o formatdb -framework CoreServices -O2 -I../include -L../lib formatdb.c -lncbitool -lblastcompadj \ -lncbiobj -lncbi -lm cc -pipe -o formatrpsdb -framework CoreServices -O2 -I../include -L../lib formatrpsdb.c -lblastapi -lncbitool \ -lblastcompadj -lblast -lncbiobj -lncbi -lm cc -pipe -o blast -framework CoreServices -O2 -I../include -L../lib blast_driver.c -lblastapi \ -lblast -lncbitool -lblastcompadj -lncbiobj -lncbi -lm \ cc -pipe -o blastall -framework CoreServices -O2 -I../include -L../lib blastall.c -lblastapi \ -lblast -lncbitool -lblastcompadj -lncbiobj -lncbi \ -lm cc -pipe -o blastall_old -framework CoreServices -O2 -I../include -L../lib -DBLASTALL_TOOLS_ONLY blastall.c \ -lncbitool -lblastcompadj -lncbiobj -lncbi \ -lm cc -pipe -o blastpgp -framework CoreServices -O2 -I../include -L../lib blastpgp.c -lncbitool \ -lblastcompadj -lncbiobj -lncbi -lm cc -pipe -o testval -framework CoreServices -O2 -I../include -L../lib testval.c -lncbiobj -lncbi -lm cc -pipe -o seedtop -framework CoreServices -O2 -I../include -L../lib seedtop.c -lncbitool \ -lblastcompadj -lncbiobj -lncbi -lm seedtop.c:358:17: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] while (pattern = get_a_pat(patfp, &pname, occurArray, hitArray, ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ seedtop.c:358:17: note: place parentheses around the assignment to silence this warning while (pattern = get_a_pat(patfp, &pname, occurArray, hitArray, ^ seedtop.c:358:17: note: use '==' to turn this assignment into an equality comparison while (pattern = get_a_pat(patfp, &pname, occurArray, hitArray, ^ == 1 warning generated. cc -pipe -o makemat -framework CoreServices -O2 -I../include -L../lib makemat.c -lncbitool \ -lblastcompadj -lncbiobj -lncbi -lm cc -pipe -o copymat -framework CoreServices -O2 -I../include -L../lib copymat.c -lblast -lncbitool \ -lblastcompadj -lncbiobj -lncbi -lm cc -pipe -o impala -framework CoreServices -O2 -I../include -L../lib profiles.c -lncbitool \ -lblastcompadj -lncbiobj -lncbi -lm cc -pipe -o megablast -framework CoreServices -O2 -I../include -L../lib megablast.c -lblastapi \ -lblast -lncbitool -lblastcompadj -lncbiobj -lncbi -lm \ cc -pipe -o vecscreen -framework CoreServices -O2 -I../include -L../lib vecscreen.c -lncbitool \ -lblastcompadj -lncbiobj -lncbi -lm cc -pipe -o gil2bin -framework CoreServices -O2 -I../include -L../lib gil2bin.c -lncbitool -lblastcompadj \ -lncbiobj -lncbi -lm gil2bin.c:73:33: warning: format specifies type 'long' but the argument has type 'Nlm_Int4' (aka 'int') [-Wformat] fprintf(outfp, "%ld\n", gilist[i].gi); ~~~ ^~~~~~~~~~~~ %d 1 warning generated. cc -pipe -o blastclust -framework CoreServices -O2 -I../include -L../lib blastclust.c -lncbitool \ -lblastcompadj -lncbiobj -lncbi -lm blastclust.c:430:44: warning: format specifies type 'long' but the argument has type 'Nlm_Int4' (aka 'int') [-Wformat] fprintf(global_fp, "%ld ", cluster[index]->elements[i]->gi); ~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ %d blastclust.c:1064:19: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] if (tmpdir = getenv("TMPDIR")) { ~~~~~~~^~~~~~~~~~~~~~~~~~ blastclust.c:1064:19: note: place parentheses around the assignment to silence this warning if (tmpdir = getenv("TMPDIR")) { ^ ( ) blastclust.c:1064:19: note: use '==' to turn this assignment into an equality comparison if (tmpdir = getenv("TMPDIR")) { ^ == blastclust.c:1230:47: warning: format specifies type 'long' but the argument has type 'int' [-Wformat] sprintf(id_list[i], "%ld", gi_list[i]); ~~~ ^~~~~~~~~~ %d /usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf' __builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__) ^ blastclust.c:1268:30: warning: format specifies type 'long' but the argument has type 'Nlm_Int4' (aka 'int') [-Wformat] timestr, num_queries, first_seq); ^~~~~~~~~~~ blastclust.c:1268:43: warning: format specifies type 'long' but the argument has type 'Nlm_Int4' (aka 'int') [-Wformat] timestr, num_queries, first_seq); ^~~~~~~~~ blastclust.c:1271:30: warning: format specifies type 'long' but the argument has type 'Nlm_Int4' (aka 'int') [-Wformat] timestr, num_queries); ^~~~~~~~~~~ blastclust.c:1331:31: warning: format specifies type 'long' but the argument has type 'int' [-Wformat] timestr, index+1); ^~~~~~~ 7 warnings generated. cc -pipe -o rpsblast -framework CoreServices -O2 -I../include -L../lib rpsblast.c -lblastapi \ -lblast -lncbitool -lblastcompadj -lncbiobj -lncbi -lm \ cc -pipe -o asn2xml -framework CoreServices -O2 -I../include -L../lib asn2xml.c -lncbiobj -lncbi -lm cc -pipe -o debruijn -framework CoreServices -O2 -I../include -L../lib debruijn.c -lblast -lncbi -lm debruijn.c:72:12: warning: assigning to 'Nlm_Uint1 *' (aka 'unsigned char *') from 'Nlm_CharPtr' (aka 'char *') converts between pointers to integer types with different sign [-Wpointer-sign] alphabet = myargs[1].strvalue; ^ ~~~~~~~~~~~~~~~~~~ debruijn.c:80:14: warning: passing 'Nlm_Uint1 *' (aka 'unsigned char *') to parameter of type 'const char *' converts between pointers to integer types with different sign [-Wpointer-sign] k = strlen(alphabet); ^~~~~~~~ /usr/include/string.h:82:28: note: passing argument to parameter here size_t strlen(const char *); ^ debruijn.c:89:10: warning: assigning to 'Nlm_Uint1 *' (aka 'unsigned char *') from 'char *' converts between pointers to integer types with different sign [-Wpointer-sign] output = (char *) malloc(outputsize + 1); ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ debruijn.c:106:8: warning: passing 'Nlm_Uint1 *' (aka 'unsigned char *') to parameter of type 'const char *' converts between pointers to integer types with different sign [-Wpointer-sign] puts(output); ^~~~~~ /usr/include/stdio.h:260:23: note: passing argument to parameter here int puts(const char *); ^ debruijn.c:109:1: warning: control may reach end of non-void function [-Wreturn-type] } ^ 5 warnings generated. cc -pipe -o asn2idx -framework CoreServices -O2 -I../include -L../lib asn2idx.c -lncbitool -lblastcompadj -lncbiobj \ -lncbi -lm cc -pipe -o sortbyquote -framework CoreServices -O2 -I../include -L../lib sortbyquote.c -lncbiobj -lncbi -lm cc -pipe -o test_regexp -framework CoreServices -O2 -I../include -L../lib pcretest.c -lregexp pcretest.c:497:5: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat] size_offsets_max * sizeof(int)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pcretest.c:779:9: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat] size, gotten_store); ^~~~ pcretest.c:779:15: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat] size, gotten_store); ^~~~~~~~~~~~ pcretest.c:1021:15: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat] size_offsets_max * sizeof(int)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 4 warnings generated. cc -pipe -o demo_regexp -framework CoreServices -O2 -I../include -L../lib pcredemo.c -lregexp cc -pipe -o demo_regexp_grep -framework CoreServices -O2 -I../include -L../lib pcregrep.c -lregexp make -f makedemo.unx CFLAGS1="-DNDEBUG -O2 -c -no-cpp-precomp" LDFLAGS1="-framework CoreServices -O2" SHELL="/bin/sh" LCL="dwn" RAN="ranlib" AR="ar" CC="cc -pipe" THREAD_OBJ=ncbithr.o THREAD_OTHERLIBS="" blast blastall blastall_old blastpgp seedtop megablast rpsblast blastclust ./ln-if-absent ../demo/*.* . ./ln-if-absent ../regexp/test/*.* . ./ln-if-absent ../regexp/demo/*.* . ./ln-if-absent ../internal/*.* . set: No match. make: [copy] Error 1 (ignored) chmod -R ug+rw,o+r . cc -pipe -o blast -framework CoreServices -O2 -I../include -L../lib blast_driver.c ncbithr.o -lblastapi \ -lblast -lncbitool -lblastcompadj -lncbiobj -lncbi -lm \ cc -pipe -o blastall -framework CoreServices -O2 -I../include -L../lib blastall.c ncbithr.o -lblastapi \ -lblast -lncbitool -lblastcompadj -lncbiobj -lncbi \ -lm cc -pipe -o blastall_old -framework CoreServices -O2 -I../include -L../lib -DBLASTALL_TOOLS_ONLY blastall.c \ ncbithr.o -lncbitool -lblastcompadj -lncbiobj -lncbi \ -lm cc -pipe -o blastpgp -framework CoreServices -O2 -I../include -L../lib blastpgp.c ncbithr.o -lncbitool \ -lblastcompadj -lncbiobj -lncbi -lm cc -pipe -o seedtop -framework CoreServices -O2 -I../include -L../lib seedtop.c ncbithr.o -lncbitool \ -lblastcompadj -lncbiobj -lncbi -lm seedtop.c:358:17: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] while (pattern = get_a_pat(patfp, &pname, occurArray, hitArray, ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ seedtop.c:358:17: note: place parentheses around the assignment to silence this warning while (pattern = get_a_pat(patfp, &pname, occurArray, hitArray, ^ seedtop.c:358:17: note: use '==' to turn this assignment into an equality comparison while (pattern = get_a_pat(patfp, &pname, occurArray, hitArray, ^ == 1 warning generated. cc -pipe -o megablast -framework CoreServices -O2 -I../include -L../lib megablast.c ncbithr.o -lblastapi \ -lblast -lncbitool -lblastcompadj -lncbiobj -lncbi -lm \ cc -pipe -o rpsblast -framework CoreServices -O2 -I../include -L../lib rpsblast.c ncbithr.o -lblastapi \ -lblast -lncbitool -lblastcompadj -lncbiobj -lncbi -lm \ cc -pipe -o blastclust -framework CoreServices -O2 -I../include -L../lib blastclust.c ncbithr.o -lncbitool \ -lblastcompadj -lncbiobj -lncbi -lm blastclust.c:430:44: warning: format specifies type 'long' but the argument has type 'Nlm_Int4' (aka 'int') [-Wformat] fprintf(global_fp, "%ld ", cluster[index]->elements[i]->gi); ~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ %d blastclust.c:1064:19: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] if (tmpdir = getenv("TMPDIR")) { ~~~~~~~^~~~~~~~~~~~~~~~~~ blastclust.c:1064:19: note: place parentheses around the assignment to silence this warning if (tmpdir = getenv("TMPDIR")) { ^ ( ) blastclust.c:1064:19: note: use '==' to turn this assignment into an equality comparison if (tmpdir = getenv("TMPDIR")) { ^ == blastclust.c:1230:47: warning: format specifies type 'long' but the argument has type 'int' [-Wformat] sprintf(id_list[i], "%ld", gi_list[i]); ~~~ ^~~~~~~~~~ %d /usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf' __builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__) ^ blastclust.c:1268:30: warning: format specifies type 'long' but the argument has type 'Nlm_Int4' (aka 'int') [-Wformat] timestr, num_queries, first_seq); ^~~~~~~~~~~ blastclust.c:1268:43: warning: format specifies type 'long' but the argument has type 'Nlm_Int4' (aka 'int') [-Wformat] timestr, num_queries, first_seq); ^~~~~~~~~ blastclust.c:1271:30: warning: format specifies type 'long' but the argument has type 'Nlm_Int4' (aka 'int') [-Wformat] timestr, num_queries); ^~~~~~~~~~~ blastclust.c:1331:31: warning: format specifies type 'long' but the argument has type 'int' [-Wformat] timestr, index+1); ^~~~~~~ 7 warnings generated. make -f makenet.unx CFLAGS1="-DNDEBUG -O2 -c -no-cpp-precomp " LDFLAGS1="-framework CoreServices -O2" SHELL="/bin/sh" AR="ar" CC="cc -pipe" RAN="ranlib" OTHERLIBS="-lc" THREAD_OBJ=ncbithr.o THREAD_OTHERLIBS="" NETENTREZVERSION="2.02c2ASN1SPEC6 " VIB="blastcl3 idfetch bl2seq asn2gb tbl2asn gene2xml nph-viewgif.cgi wblast2.REAL wblast2_cs.REAL bl2bag.cgi " ./ln-if-absent ../connect/test/*.c . ./ln-if-absent ../network/entrez/client/*.h ../include ./ln-if-absent ../network/entrez/client/*.c . ./ln-if-absent ../network/medarch/client/*.h ../include ./ln-if-absent ../network/medarch/client/*.c . ./ln-if-absent ../network/taxonomy/client/*.h ../include set: No match. make: [copy] Error 1 (ignored) ./ln-if-absent ../network/taxonomy/client/*.c . set: No match. make: [copy] Error 1 (ignored) ./ln-if-absent ../network/taxon1/common/*.h ../include ./ln-if-absent ../network/taxon1/common/*.c . ./ln-if-absent ../network/taxon1/taxon2/*.h ../include ./ln-if-absent ../network/taxon1/taxon2/*.c . ./ln-if-absent ../network/id0arch/client/*.h ../include set: No match. make: [copy] Error 1 (ignored) ./ln-if-absent ../network/id0arch/client/*.c . set: No match. make: [copy] Error 1 (ignored) ./ln-if-absent ../network/id1arch/*.h ../include ./ln-if-absent ../network/id1arch/*.c . ./ln-if-absent ../network/id2arch/*.h ../include ./ln-if-absent ../network/id2arch/*.c . ./ln-if-absent ../network/spell/client/*.h ../include ./ln-if-absent ../network/spell/client/*.c . ./ln-if-absent ../network/suggest/client/*.h ../include ./ln-if-absent ../network/suggest/client/*.c . ./ln-if-absent ../network/blast3/client/*.h ../include ./ln-if-absent ../network/blast3/client/*.c . ./ln-if-absent ../tools/taxblast.h ../include ./ln-if-absent ../tools/taxblast.c . ./ln-if-absent /*.c . set: No match. make: [copy] Error 1 (ignored) ./ln-if-absent ../internal/misc/*.c . set: No match. make: [copy] Error 1 (ignored) ./ln-if-absent ../internal/misc/*.h ../include set: No match. make: [copy] Error 1 (ignored) ./ln-if-absent ../internal/ssparse/*.c . set: No match. make: [copy] Error 1 (ignored) ./ln-if-absent ../internal/ssparse/*.h ../include set: No match. make: [copy] Error 1 (ignored) ./ln-if-absent ../internal/libparsn/*.c . set: No match. make: [copy] Error 1 (ignored) ./ln-if-absent ../internal/libparsn/*.h ../include set: No match. make: [copy] Error 1 (ignored) ./ln-if-absent ../internal/smart/smartnet/*.c . set: No match. make: [copy] Error 1 (ignored) ./ln-if-absent ../internal/smart/smartnet/*.h ../include set: No match. make: [copy] Error 1 (ignored) ./ln-if-absent ../internal/www/*.c . set: No match. make: [copy] Error 1 (ignored) ./ln-if-absent ../internal/www/*.h ../include set: No match. make: [copy] Error 1 (ignored) ./ln-if-absent ../internal/query/*.c . set: No match. make: [copy] Error 1 (ignored) ./ln-if-absent ../internal/query/*.h ../include set: No match. make: [copy] Error 1 (ignored) ./ln-if-absent ../network/sybutils/ctlib/*.c . set: No match. make: [copy] Error 1 (ignored) ./ln-if-absent ../network/sybutils/ctlib/*.h ../include set: No match. make: [copy] Error 1 (ignored) ./ln-if-absent ../network/sybutils/oslib/*.c . set: No match. make: [copy] Error 1 (ignored) ./ln-if-absent ../network/sybutils/oslib/*.h ../include set: No match. make: [copy] Error 1 (ignored) ./ln-if-absent ../network/sybutils/idloadlib/*.c . set: No match. make: [copy] Error 1 (ignored) ./ln-if-absent ../network/sybutils/idloadlib/*.h ../include set: No match. make: [copy] Error 1 (ignored) ./ln-if-absent ../network/nsclilib/*.h ../include ./ln-if-absent ../network/nsclilib/*.c . ./ln-if-absent ../network/vibnet/*.c . ./ln-if-absent ../network/vibnet/*.h ../include ./ln-if-absent ../cdromlib/*.h ../include ./ln-if-absent ../network/wwwblast/Src/*.c . ./ln-if-absent ../network/wwwblast/Src/*.h ../include ./ln-if-absent ../cdromlib/accentr.c . ./ln-if-absent ../cdromlib/accutils.c . ./ln-if-absent ../sequin/*.* . ./ln-if-absent ../demo/entrez.c . ./ln-if-absent ../demo/seqget.c . ./ln-if-absent ../demo/entrcmd.c . ./ln-if-absent ../demo/batch.c . ./ln-if-absent ../demo/qbatch.c . ./ln-if-absent ../demo/elecpcr.c . ./ln-if-absent ../demo/asn2fast.c . ./ln-if-absent ../demo/asn2asn.c . ./ln-if-absent ../demo/cleanasn.c . ./ln-if-absent ../demo/cspeedtest.c . ./ln-if-absent ../demo/fetchent.c . ./ln-if-absent ../demo/udvmain.c . ./ln-if-absent ../demo/rtestval.c . ./ln-if-absent ../demo/asn2ff.c . ./ln-if-absent ../demo/asn2gb.c . ./ln-if-absent ../demo/asn2fsa.c . ./ln-if-absent ../demo/asn2all.c . ./ln-if-absent ../demo/gene2xml.c . ./ln-if-absent ../demo/asnval.c . ./ln-if-absent ../demo/asndisc.c . ./ln-if-absent ../demo/asnmacro.c . ./ln-if-absent ../demo/asnstrip.c . ./ln-if-absent ../demo/tbl2asn.c . ./ln-if-absent ../demo/raw2delt.c . ./ln-if-absent ../demo/flint.c . ./ln-if-absent ../demo/gbseqget.c . ./ln-if-absent ../demo/insdseqget.c . ./ln-if-absent ../demo/nps2gps.c . ./ln-if-absent ../demo/testent2.c . ./ln-if-absent ../demo/trna2sap.c . ./ln-if-absent ../demo/trna2tbl.c . ./ln-if-absent ../demo/entrez2.c . ./ln-if-absent ../demo/condense.c . ./ln-if-absent ../demo/spideymain.c . ./ln-if-absent ../demo/dotmain.c . ./ln-if-absent ../demo/ingenmain.c . ./ln-if-absent ../demo/bl2seq.c . ./ln-if-absent ../demo/blastall.c . ./ln-if-absent ../demo/blast_driver.c . ./ln-if-absent ../demo/srchnt.c ../demo/srchaa.c ../demo/mts.c ../demo/sigme.c ../demo/dst.c ../demo/ccp.c ../demo/epi.c ../demo/twop.c ../demo/cnsrt.c ../demo/cnsgn.c ../demo/ccpv.c ../demo/dustv.c ../demo/epiv.c ../demo/sigmev.c ../demo/twopv.c ../demo/cnsrtv.c ../demo/cnsgnv.c ../demo/searchv.c . ./ln-if-absent ../network/entrez/server/*.* . set: No match. make: [copy] Error 1 (ignored) ./ln-if-absent ../network/suggest/server/*.* . chmod -R ug+rw,o+r . echo Waiting...go Waiting...go cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" ni_lib_.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" ni_debug.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" ni_service.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" ni_error.c rm -f libnetcli.a ar cru libnetcli.a ni_lib_.o ni_debug.o ni_service.o ni_error.o cp -p libnetcli.a ../lib ranlib ../lib/libnetcli.a cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" netentr.c netentr.c:798:5: warning: '/*' within block comment [-Wcomment] /*MsgSetReadTimeout(Entrez_ni, 60);*/ ^ 1 warning generated. cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" netlib.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" objneten.c rm -f libnetentr.a ar cru libnetentr.a netentr.o netlib.o objneten.o cp -p libnetentr.a ../lib ranlib ../lib/libnetentr.a ./ln-if-absent accentr.c Naccentr.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" -D_NETENT_ Naccentr.c rm -f libncbiNacc.a ar cru libncbiNacc.a Naccentr.o accutils.o cp -p libncbiNacc.a ../lib ranlib ../lib/libncbiNacc.a ./ln-if-absent accentr.c Caccentr.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" -D_NET_AND_CD_ Caccentr.c rm -f libncbiCacc.a ar cru libncbiCacc.a Caccentr.o accutils.o cp -p libncbiCacc.a ../lib ranlib ../lib/libncbiCacc.a cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" objblst3.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" netblap3.c rm -f libnetblast.a ar cru libnetblast.a objblst3.o netblap3.o cp -p libnetblast.a ../lib ranlib ../lib/libnetblast.a cc -pipe -g -o blastcl3 -framework CoreServices -O2 -I../include -L../lib -DBLAST_CS_API blastall.c \ -lblastapi -lblast -lnetblast -lncbitool -lblastcompadj \ -lnetcli -lncbiobj -lncbi -lc cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" id1gen.c cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" id1arch.c id1arch.c:563:47: warning: incomplete format specifier [-Wformat] fprintf(fp,"%-20d%-20s%",old_gi,repl_date); ^ 1 warning generated. cc -pipe -DNDEBUG -O2 -c -no-cpp-precomp -I../include -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" accid1.c rm -f libncbiid1.a ar cru libncbiid1.a id1gen.o id1arch.o accid1.o cp -p libncbiid1.a ../lib ranlib ../lib/libncbiid1.a cc -pipe -g -o idfetch -framework CoreServices -O2 -I../include -L../lib idfetch.c -lncbiid1 -lnetcli -lncbiobj -lncbi -lc idfetch.c:1439:38: warning: format specifies type 'short' but the argument has type 'Nlm_Int4' (aka 'int') [-Wformat] sprintf( pFormat, "%%s%%0%hdhd", DigitsStart); ~~~ ^~~~~~~~~~~ %d /usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf' __builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__) ^ 1 warning generated. cc -pipe -o bl2seq -framework CoreServices -O2 -I../include -L../lib bl2seq.c -lblastapi -lblast -lncbitool \ -lblastcompadj -lncbiid1 -lnetcli -lncbiobj -lncbi \ -lc cc -pipe -g -o asn2gb -framework CoreServices -O2 -I../include -L../lib asn2gb.c -lncbiid1 -lnetcli \ -lncbitool -lblastcompadj -lncbiobj -lncbi -lc cc -pipe -o tbl2asn -framework CoreServices -O2 -I../include -L../lib tbl2asn.c -lncbitool -lblastcompadj \ -lncbiobj -lnetcli -lncbi -lc cc -pipe -g -o gene2xml -framework CoreServices -O2 -I../include -L../lib gene2xml.c -lnetcli -lncbiobj -lncbi -lc cc -pipe -o nph-viewgif.cgi -framework CoreServices -O2 -I../include -L../lib viewgif.c viewgif.c:85:9: warning: implicit declaration of function 'write' is invalid in C99 [-Wimplicit-function-declaration] write(1, tmp_buff, strlen(tmp_buff)); ^ 1 warning generated. cc -pipe -o wblast2.REAL -framework CoreServices -O2 -I../include -L../lib -DBL2SEQ_STANDALONE wblast2.c \ -lblastapi -lncbitool -lblastcompadj -lncbiobj -lblast -lncbi -lc wblast2.c:759:76: warning: format specifies type 'int' but the argument has type 'Nlm_FloatHi' (aka 'double') [-Wformat] printf("\n", options->gap_x_dropoff); ~~ ^~~~~~~~~~~~~~~~~~~~~~ %f wblast2.c:1052:16: warning: incompatible pointer types assigning to 'Nlm_ByteStorePtr' (aka 'struct bytestore *') from 'SeqDataPtr' (aka 'struct SeqData *') [-Wincompatible-pointer-types] seq_data = q_bsp->seq_data; ^ ~~~~~~~~~~~~~~~ wblast2.c:1057:26: warning: incompatible pointer types assigning to 'SeqDataPtr' (aka 'struct SeqData *') from 'Nlm_ByteStorePtr' (aka 'struct bytestore *') [-Wincompatible-pointer-types] q_bsp->seq_data = seq_data; ^ ~~~~~~~~ wblast2.c:1070:23: warning: incompatible pointer types assigning to 'SeqDataPtr' (aka 'struct SeqData *') from 'Nlm_ByteStorePtr' (aka 'struct bytestore *') [-Wincompatible-pointer-types] q_bsp->seq_data = seq_data; ^ ~~~~~~~~ wblast2.c:1080:126: warning: format specifies type 'long' but the argument has type 'Nlm_Int2' (aka 'short') [-Wformat] printf("Identities = %ld/%ld (%ld%%), Positives = %ld/%ld (%ld%%)", (long) asp->identical, (long) asp->totlen, percent_identical, ~~~ ^~~~~~~~~~~~~~~~~ %hd wblast2.c:1082:35: warning: format specifies type 'long' but the argument has type 'int' [-Wformat] asp->totlen, (percent_identical+percent_positive)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ wblast2.c:1084:97: warning: format specifies type 'long' but the argument has type 'Nlm_Int2' (aka 'short') [-Wformat] printf("Identities = %ld/%ld (%ld%%)", (long) asp->identical, (long) asp->totlen, percent_identical); ~~~ ^~~~~~~~~~~~~~~~~ %hd wblast2.c:1647:83: warning: format specifies type 'int' but the argument has type 'Nlm_FloatHi' (aka 'double') [-Wformat] printf("x_dropoff: \n", options->gap_x_dropoff); ~~ ^~~~~~~~~~~~~~~~~~~~~~ %f wblast2.c:1724:96: warning: format specifies type 'long' but the argument has type 'Nlm_Int4' (aka 'int') [-Wformat] printf("gi|%ld|%s", gi, gi, buf); ~~~ ^~ %d wblast2.c:1724:100: warning: format specifies type 'long' but the argument has type 'Nlm_Int4' (aka 'int') [-Wformat] printf("gi|%ld|%s", gi, gi, buf); ~~~ ^~ %d wblast2.c:1741:30: warning: format specifies type 'long' but the argument has type 'Nlm_Int4' (aka 'int') [-Wformat] printf("Length = %ld\n", len1); ~~~ ^~~~ %d wblast2.c:1743:34: warning: format specifies type 'long' but the argument has type 'Nlm_Int4' (aka 'int') [-Wformat] printf("(%ld .. %ld)\n", from, to); ~~~ ^~~~ %d wblast2.c:1743:40: warning: format specifies type 'long' but the argument has type 'Nlm_Int4' (aka 'int') [-Wformat] printf("(%ld .. %ld)\n", from, to); ~~~ ^~ %d wblast2.c:1749:96: warning: format specifies type 'long' but the argument has type 'Nlm_Int4' (aka 'int') [-Wformat] printf("gi|%ld|%s", gi, gi, buf); ~~~ ^~ %d wblast2.c:1749:100: warning: format specifies type 'long' but the argument has type 'Nlm_Int4' (aka 'int') [-Wformat] printf("gi|%ld|%s", gi, gi, buf); ~~~ ^~ %d wblast2.c:1765:30: warning: format specifies type 'long' but the argument has type 'Nlm_Int4' (aka 'int') [-Wformat] printf("Length = %ld\n", len2); ~~~ ^~~~ %d wblast2.c:1767:34: warning: format specifies type 'long' but the argument has type 'Nlm_Int4' (aka 'int') [-Wformat] printf("(%ld .. %ld)\n", ffrom, tto); ~~~ ^~~~~ %d wblast2.c:1767:41: warning: format specifies type 'long' but the argument has type 'Nlm_Int4' (aka 'int') [-Wformat] printf("(%ld .. %ld)\n", ffrom, tto); ~~~ ^~~ %d wblast2.c:3121:9: warning: implicit declaration of function 'BlastProgram2Number' is invalid in C99 [-Wimplicit-function-declaration] BlastProgram2Number(progname, &program_number); ^ 19 warnings generated. cc -pipe -o wblast2_cs.REAL -framework CoreServices -O2 -I../include -L../lib -DNCBI_ENTREZ_CLIENT -DBL2SEQ_STANDALONE \ wblast2.c -lncbiid1 -lnetcli -lblastapi -lncbitool -lblastcompadj \ -lncbiobj -lblast -lncbi \ -lc wblast2.c:759:76: warning: format specifies type 'int' but the argument has type 'Nlm_FloatHi' (aka 'double') [-Wformat] printf("\n", options->gap_x_dropoff); ~~ ^~~~~~~~~~~~~~~~~~~~~~ %f wblast2.c:1052:16: warning: incompatible pointer types assigning to 'Nlm_ByteStorePtr' (aka 'struct bytestore *') from 'SeqDataPtr' (aka 'struct SeqData *') [-Wincompatible-pointer-types] seq_data = q_bsp->seq_data; ^ ~~~~~~~~~~~~~~~ wblast2.c:1057:26: warning: incompatible pointer types assigning to 'SeqDataPtr' (aka 'struct SeqData *') from 'Nlm_ByteStorePtr' (aka 'struct bytestore *') [-Wincompatible-pointer-types] q_bsp->seq_data = seq_data; ^ ~~~~~~~~ wblast2.c:1070:23: warning: incompatible pointer types assigning to 'SeqDataPtr' (aka 'struct SeqData *') from 'Nlm_ByteStorePtr' (aka 'struct bytestore *') [-Wincompatible-pointer-types] q_bsp->seq_data = seq_data; ^ ~~~~~~~~ wblast2.c:1080:126: warning: format specifies type 'long' but the argument has type 'Nlm_Int2' (aka 'short') [-Wformat] printf("Identities = %ld/%ld (%ld%%), Positives = %ld/%ld (%ld%%)", (long) asp->identical, (long) asp->totlen, percent_identical, ~~~ ^~~~~~~~~~~~~~~~~ %hd wblast2.c:1082:35: warning: format specifies type 'long' but the argument has type 'int' [-Wformat] asp->totlen, (percent_identical+percent_positive)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ wblast2.c:1084:97: warning: format specifies type 'long' but the argument has type 'Nlm_Int2' (aka 'short') [-Wformat] printf("Identities = %ld/%ld (%ld%%)", (long) asp->identical, (long) asp->totlen, percent_identical); ~~~ ^~~~~~~~~~~~~~~~~ %hd wblast2.c:1459:4: warning: implicit declaration of function 'ID1BioseqFetchEnable' is invalid in C99 [-Wimplicit-function-declaration] ID1BioseqFetchEnable ("wblast2", TRUE); ^ wblast2.c:1482:12: warning: implicit declaration of function 'ID1FindSeqId' is invalid in C99 [-Wimplicit-function-declaration] gi = ID1FindSeqId (sip); ^ wblast2.c:1535:11: warning: implicit declaration of function 'ID1BioseqFetchDisable' is invalid in C99 [-Wimplicit-function-declaration] ID1BioseqFetchDisable(); ^ wblast2.c:1573:17: warning: incompatible pointer types assigning to 'Nlm_ByteStorePtr' (aka 'struct bytestore *') from 'SeqDataPtr' (aka 'struct SeqData *') [-Wincompatible-pointer-types] old_seq_data = bsp->seq_data; ^ ~~~~~~~~~~~~~ wblast2.c:1574:18: warning: incompatible pointer types assigning to 'SeqDataPtr' (aka 'struct SeqData *') from 'Nlm_ByteStorePtr' (aka 'struct bytestore *') [-Wincompatible-pointer-types] bsp->seq_data = BSNew(bsp->length); ^ ~~~~~~~~~~~~~~~~~~ wblast2.c:1582:15: warning: incompatible pointer types passing 'SeqDataPtr' (aka 'struct SeqData *') to parameter of type 'Nlm_ByteStorePtr' (aka 'struct bytestore *') [-Wincompatible-pointer-types] BSWrite(bsp->seq_data, buf, retval); ^~~~~~~~~~~~~ ../include/ncbibs.h:115:65: note: passing argument to parameter 'bsp' here NLM_EXTERN Nlm_Int4 LIBCALL Nlm_BSWrite PROTO((Nlm_ByteStorePtr bsp, Nlm_VoidPtr ptr, Nlm_Int4 len)); ^ ../include/ncbilcl.h:169:18: note: expanded from macro 'PROTO' #define PROTO(x) x /* Prototypes are acceptable */ ^ wblast2.c:1647:83: warning: format specifies type 'int' but the argument has type 'Nlm_FloatHi' (aka 'double') [-Wformat] printf("x_dropoff: \n", options->gap_x_dropoff); ~~ ^~~~~~~~~~~~~~~~~~~~~~ %f wblast2.c:1724:96: warning: format specifies type 'long' but the argument has type 'Nlm_Int4' (aka 'int') [-Wformat] printf("gi|%ld|%s", gi, gi, buf); ~~~ ^~ %d wblast2.c:1724:100: warning: format specifies type 'long' but the argument has type 'Nlm_Int4' (aka 'int') [-Wformat] printf("gi|%ld|%s", gi, gi, buf); ~~~ ^~ %d wblast2.c:1741:30: warning: format specifies type 'long' but the argument has type 'Nlm_Int4' (aka 'int') [-Wformat] printf("Length = %ld\n", len1); ~~~ ^~~~ %d wblast2.c:1743:34: warning: format specifies type 'long' but the argument has type 'Nlm_Int4' (aka 'int') [-Wformat] printf("(%ld .. %ld)\n", from, to); ~~~ ^~~~ %d wblast2.c:1743:40: warning: format specifies type 'long' but the argument has type 'Nlm_Int4' (aka 'int') [-Wformat] printf("(%ld .. %ld)\n", from, to); ~~~ ^~ %d wblast2.c:1749:96: warning: format specifies type 'long' but the argument has type 'Nlm_Int4' (aka 'int') [-Wformat] printf("gi|%ld|%s", gi, gi, buf); ~~~ ^~ %d wblast2.c:1749:100: warning: format specifies type 'long' but the argument has type 'Nlm_Int4' (aka 'int') [-Wformat] printf("gi|%ld|%s", gi, gi, buf); ~~~ ^~ %d wblast2.c:1765:30: warning: format specifies type 'long' but the argument has type 'Nlm_Int4' (aka 'int') [-Wformat] printf("Length = %ld\n", len2); ~~~ ^~~~ %d wblast2.c:1767:34: warning: format specifies type 'long' but the argument has type 'Nlm_Int4' (aka 'int') [-Wformat] printf("(%ld .. %ld)\n", ffrom, tto); ~~~ ^~~~~ %d wblast2.c:1767:41: warning: format specifies type 'long' but the argument has type 'Nlm_Int4' (aka 'int') [-Wformat] printf("(%ld .. %ld)\n", ffrom, tto); ~~~ ^~~ %d wblast2.c:3121:9: warning: implicit declaration of function 'BlastProgram2Number' is invalid in C99 [-Wimplicit-function-declaration] BlastProgram2Number(progname, &program_number); ^ 25 warnings generated. cc -pipe -o bl2bag.cgi -framework CoreServices -O2 -I../include -L../lib bl2bag.c -lncbi -lc Put the date stamp to the file ../VERSION ********************************************************* *The new binaries are located in ./ncbi/build/ directory* ********************************************************* /bin/rm -rf /sw/build.build/root-ncbitools-20080302-1 /bin/mkdir -p /sw/build.build/root-ncbitools-20080302-1/sw /bin/mkdir -p /sw/build.build/root-ncbitools-20080302-1/DEBIAN /usr/sbin/chown -R fink-bld:fink-bld /sw/build.build/root-ncbitools-20080302-1 sudo -u fink-bld [ENV] sh -c /tmp/fink.IRO69 /tmp/fink.DNZBZ #!/bin/sh -ev ### install programs install -d -m 755 /sw/build.build/root-ncbitools-20080302-1/sw/bin ## list generated from '/bin/ls -1 ncbi/build'. export binaries="asn2ff asn2gb asn2idx asn2xml asndhuff asntool bl2bag.cgi bl2seq blast blastall blastall_old blastcl3 blastclust blastpgp cdscan checksub copymat debruijn demo_regexp demo_regexp_grep dosimple entrcmd errhdr fa2htgs fastacmd findspl formatdb formatrpsdb gene2xml getmesh getpub gil2bin idfetch impala indexpub makemat makeset megablast ncbisort nph-viewgif.cgi rpsblast seedtop seqtest tbl2asn test_regexp testcore testobj testval vecscreen wblast2.REAL wblast2_cs.REAL" ## these are only built on 32bit installs export binaries_32bit="blast.REAL blast_cs.REAL ddv entrez2 Psequin psiblast.REAL psiblast_cs.REAL sbtedit udv" if [[ "x86_64" != "x86_64" ]]; then export binaries="$binaries $binaries_32bit"; fi for file in $binaries; do install -c -p -m 755 ncbi/build/$file /sw/build.build/root-ncbitools-20080302-1/sw/bin; done ### install manfiles install -d -m 755 /sw/build.build/root-ncbitools-20080302-1/sw/share/man/man1 export manfiles="asn2all.1 asn2asn.1 asn2ff.1 asn2fsa.1 asn2gb.1 asn2idx.1 asn2xml.1 asndhuff.1 asntool.1 asnval.1 bl2seq.1 blast.1 blastall.1 blastall_old.1 blastcl3.1 blastclust.1 blastpgp.1 cdscan.1 checksub.1 cleanasn.1 copymat.1 debruijn.1 errhdr.1 fa2htgs.1 fastacmd.1 findspl.1 fmerge.1 formatdb.1 formatrpsdb.1 gbseqget.1 gene2xml.1 getmesh.1 getpub.1 gil2bin.1 idfetch.1 impala.1 indexpub.1 insdseqget.1 makemat.1 makeset.1 megablast.1 nps2gps.1 rpsblast.1 seedtop.1 sortbyquote.1 spidey.1 tbl2asn.1 trna2sap.1 trna2tbl.1 vecscreen.1" export manfiles_32bit="ddv.1 entrez2.1 Psequin.1 sbtedit.1 udv.1" if [[ "x86_64" != "x86_64" ]]; then export manfiles="$manfiles $manfiles_32bit"; fi for file in $manfiles; do install -c -p -m 644 ncbi/doc/man/$file /sw/build.build/root-ncbitools-20080302-1/sw/share/man/man1; done install -d -m 755 /sw/build.build/root-ncbitools-20080302-1/sw/include/ncbitools-20080302/connect install -c -p -m 644 ncbi/include/*.h /sw/build.build/root-ncbitools-20080302-1/sw/include/ncbitools-20080302 install -c -p -m 644 ncbi/include/connect/*.h /sw/build.build/root-ncbitools-20080302-1/sw/include/ncbitools-20080302/connect ln -s ncbitools-20080302 /sw/build.build/root-ncbitools-20080302-1/sw/include/ncbitools ### install static libraries install -d -m 755 /sw/build.build/root-ncbitools-20080302-1/sw/lib export libraries="blast blastapi blastcompadj ncbi ncbiCacc ncbiNacc ncbiacc ncbicdr ncbiid1 ncbimmdb ncbiobj ncbitool netblast netcli netentr regexp" export libraries_32bit="ddvlib ncbicn3d ncbidesk ncbimla ncbitxc2 vibgif vibnet vibrant" if [[ "x86_64" != "x86_64" ]]; then export libraries="$libraries $libraries_32bit"; fi for file in $libraries; do install -c -p -m 644 ncbi/lib/lib$file.a /sw/build.build/root-ncbitools-20080302-1/sw/lib/lib$file-20080302.a; ln -s lib$file-20080302.a /sw/build.build/root-ncbitools-20080302-1/sw/lib/lib$file.a; done for file in ncbithr; do install -c -p -m 644 ncbi/lib/$file.o /sw/build.build/root-ncbitools-20080302-1/sw/lib/$file-20080302.o; ln -s $file-20080302.o /sw/build.build/root-ncbitools-20080302-1/sw/lib/$file.o; done ### copy the doc directory install -d -m 755 /sw/build.build/root-ncbitools-20080302-1/sw/share/doc/ncbitools cp -r ncbi/doc/* /sw/build.build/root-ncbitools-20080302-1/sw/share/doc/ncbitools cp -p ncbi/platform/darwin.ncbi.mk ncbi/platform/darwin.ncbi.mk.dist cat ncbi/platform/darwin.ncbi.mk.dist | sed 's,/home/coremake/ncbi/bin,/sw/bin,g' | sed 's,/home/coremake/ncbi/include,/sw/include/ncbitools,g' | sed 's,/home/coremake/ncbi/lib,/sw/lib,g' | sed 's,/home/coremake/ncbi/altlib,/sw/altlib,g' > ncbi/platform/darwin.ncbi.mk install -d -m 755 /sw/build.build/root-ncbitools-20080302-1/sw/lib/ncbitools/20080302 install -c -p -m 644 ncbi/platform/darwin.ncbi.mk /sw/build.build/root-ncbitools-20080302-1/sw/lib/ncbitools/20080302 install -d -m 755 /sw/build.build/root-ncbitools-20080302-1/sw/share/ncbitools ln -s /sw/lib/ncbitools/20080302/darwin.ncbi.mk /sw/build.build/root-ncbitools-20080302-1/sw/share/ncbitools/ncbi.mk install -d -m 755 /sw/build.build/root-ncbitools-20080302-1/sw/share/ncbitools/data install -c -p -m 644 ncbi/data/* /sw/build.build/root-ncbitools-20080302-1/sw/share/ncbitools/data install -d -m 755 /sw/build.build/root-ncbitools-20080302-1/sw/share/ncbitools/demo uncompress -cf vector.Z > /sw/build.build/root-ncbitools-20080302-1/sw/share/ncbitools/demo/vector install -c -p -m 644 demo.fasta /sw/build.build/root-ncbitools-20080302-1/sw/share/ncbitools/demo /sw/build.build/root-ncbitools-20080302-1/sw/bin/formatdb -i /sw/build.build/root-ncbitools-20080302-1/sw/share/ncbitools/demo/vector -p F echo "#!/bin/sh" > /sw/build.build/root-ncbitools-20080302-1/sw/share/ncbitools/demo/blastall.sh echo "blastall -p blastn -d /sw/share/ncbitools/demo/vector -i /sw/share/ncbitools/demo/demo.fasta" >> /sw/build.build/root-ncbitools-20080302-1/sw/share/ncbitools/demo/blastall.sh chmod 755 /sw/build.build/root-ncbitools-20080302-1/sw/share/ncbitools/demo/blastall.sh sudo -u fink-bld [ENV] sh -c /tmp/fink.SINps /usr/bin/install -d -m 700 /sw/build.build/root-ncbitools-20080302-1/sw/share/doc/ncbitools /bin/cp -r LICENSE /sw/build.build/root-ncbitools-20080302-1/sw/share/doc/ncbitools/ /bin/cp -r ncbi/README /sw/build.build/root-ncbitools-20080302-1/sw/share/doc/ncbitools/ /bin/cp -r ncbi/README.htm /sw/build.build/root-ncbitools-20080302-1/sw/share/doc/ncbitools/ /bin/chmod -R go=u-w /sw/build.build/root-ncbitools-20080302-1/sw/share/doc/ncbitools /usr/bin/install -d -m 755 /sw/build.build/root-ncbitools-20080302-1/sw/etc/profile.d echo "setenv BLASTMAT '/sw/share/ncbitools/data'" >> /sw/build.build/root-ncbitools-20080302-1/sw/etc/profile.d/ncbitools.csh.env echo "export BLASTMAT='/sw/share/ncbitools/data'" >> /sw/build.build/root-ncbitools-20080302-1/sw/etc/profile.d/ncbitools.sh.env echo "setenv BLASTDB '/data/blastdb'" >> /sw/build.build/root-ncbitools-20080302-1/sw/etc/profile.d/ncbitools.csh.env echo "export BLASTDB='/data/blastdb'" >> /sw/build.build/root-ncbitools-20080302-1/sw/etc/profile.d/ncbitools.sh.env /usr/bin/touch /sw/build.build/root-ncbitools-20080302-1/sw/etc/profile.d/ncbitools.csh /usr/bin/touch /sw/build.build/root-ncbitools-20080302-1/sw/etc/profile.d/ncbitools.sh /bin/cat /sw/build.build/root-ncbitools-20080302-1/sw/etc/profile.d/ncbitools.csh >> /sw/build.build/root-ncbitools-20080302-1/sw/etc/profile.d/ncbitools.csh.env /bin/cat /sw/build.build/root-ncbitools-20080302-1/sw/etc/profile.d/ncbitools.sh >> /sw/build.build/root-ncbitools-20080302-1/sw/etc/profile.d/ncbitools.sh.env /bin/mv -f /sw/build.build/root-ncbitools-20080302-1/sw/etc/profile.d/ncbitools.csh.env /sw/build.build/root-ncbitools-20080302-1/sw/etc/profile.d/ncbitools.csh /bin/mv -f /sw/build.build/root-ncbitools-20080302-1/sw/etc/profile.d/ncbitools.sh.env /sw/build.build/root-ncbitools-20080302-1/sw/etc/profile.d/ncbitools.sh /bin/chmod 755 /sw/build.build/root-ncbitools-20080302-1/sw/etc/profile.d/ncbitools.* /bin/rm -f /sw/build.build/root-ncbitools-20080302-1/sw/info/dir /sw/build.build/root-ncbitools-20080302-1/sw/info/dir.old /sw/build.build/root-ncbitools-20080302-1/sw/share/info/dir /sw/build.build/root-ncbitools-20080302-1/sw/share/info/dir.old /bin/rm -rf /sw/build.build/root-ncbitools-dev-20080302-1 /bin/mkdir -p /sw/build.build/root-ncbitools-dev-20080302-1/sw /bin/mkdir -p /sw/build.build/root-ncbitools-dev-20080302-1/DEBIAN /usr/sbin/chown -R fink-bld:fink-bld /sw/build.build/root-ncbitools-dev-20080302-1 sudo -u fink-bld [ENV] sh -c /tmp/fink.b81eF /usr/bin/install -d -m 755 /sw/build.build/root-ncbitools-dev-20080302-1/sw /bin/mv /sw/build.build/root-ncbitools-20080302-1/sw/include /sw/build.build/root-ncbitools-dev-20080302-1/sw/ /usr/bin/install -d -m 755 /sw/build.build/root-ncbitools-dev-20080302-1/sw/lib /bin/mv /sw/build.build/root-ncbitools-20080302-1/sw/lib/*.a /sw/build.build/root-ncbitools-dev-20080302-1/sw/lib/ /bin/mv /sw/build.build/root-ncbitools-20080302-1/sw/lib/*.o /sw/build.build/root-ncbitools-dev-20080302-1/sw/lib/ /usr/bin/install -d -m 755 /sw/build.build/root-ncbitools-dev-20080302-1/sw/share/ncbitools /bin/mv /sw/build.build/root-ncbitools-20080302-1/sw/share/ncbitools/ncbi.mk /sw/build.build/root-ncbitools-dev-20080302-1/sw/share/ncbitools/ /usr/bin/install -d -m 755 /sw/build.build/root-ncbitools-dev-20080302-1/sw/lib/ncbitools/20080302 /bin/mv /sw/build.build/root-ncbitools-20080302-1/sw/lib/ncbitools/20080302/darwin.ncbi.mk /sw/build.build/root-ncbitools-dev-20080302-1/sw/lib/ncbitools/20080302/ /usr/bin/install -d -m 700 /sw/build.build/root-ncbitools-dev-20080302-1/sw/share/doc/ncbitools-dev /bin/cp -r LICENSE /sw/build.build/root-ncbitools-dev-20080302-1/sw/share/doc/ncbitools-dev/ /bin/cp -r ncbi/README /sw/build.build/root-ncbitools-dev-20080302-1/sw/share/doc/ncbitools-dev/ /bin/chmod -R go=u-w /sw/build.build/root-ncbitools-dev-20080302-1/sw/share/doc/ncbitools-dev /bin/rm -f /sw/build.build/root-ncbitools-dev-20080302-1/sw/info/dir /sw/build.build/root-ncbitools-dev-20080302-1/sw/info/dir.old /sw/build.build/root-ncbitools-dev-20080302-1/sw/share/info/dir /sw/build.build/root-ncbitools-dev-20080302-1/sw/share/info/dir.old Reverting ownership of install dir to root Writing control file... Writing md5sums file... env LANG=C LC_ALL=C dpkg-deb -b root-ncbitools-20080302-1 /sw/fink/10.9/stable/main/binary-darwin-x86_64/sci dpkg-deb: building package `ncbitools' in `/sw/fink/10.9/stable/main/binary-darwin-x86_64/sci/ncbitools_20080302-1_darwin-x86_64.deb'. Reverting ownership of install dir to root Writing control file... Writing md5sums file... env LANG=C LC_ALL=C dpkg-deb -b root-ncbitools-dev-20080302-1 /sw/fink/10.9/stable/main/binary-darwin-x86_64/sci dpkg-deb: building package `ncbitools-dev' in `/sw/fink/10.9/stable/main/binary-darwin-x86_64/sci/ncbitools-dev_20080302-1_darwin-x86_64.deb'. Removing runtime build-lock... Removing build-lock package... /sw/bin/dpkg-lockwait -r fink-buildlock-ncbitools-20080302-1 (Reading database ... 4297 files and directories currently installed.) Removing fink-buildlock-ncbitools-20080302-1 ...