printf ' ' | fink --no-use-binary-dist --yes --build-as-nobody rebuild wise2 2>&1 The package 'wise2' will be built without being installed. Reading build dependency for wise2-2.4.1-1... Reading dependency for wise2-2.4.1-1... Reading dependency for wise2-dev-2.4.1-1... Reading build conflict for wise2-2.4.1-1... The package 'glib2-dev' will be installed. Reading dependency for glib2-dev-2.22.4-8... Reading runtime dependency for glib2-dev-2.22.4-8... The package 'pkgconfig' will be installed. Reading dependency for pkgconfig-0.28-1... Reading runtime dependency for pkgconfig-0.28-1... The package 'glib2-shlibs' will be installed. Reading dependency for glib2-shlibs-2.22.4-8... Reading runtime dependency for glib2-shlibs-2.22.4-8... The package 'xdg-base' will be installed. Reading dependency for xdg-base-0.8-2... Reading runtime dependency for xdg-base-0.8-2... The following package will be rebuilt: wise2 The following 4 additional packages will be installed: glib2-dev glib2-shlibs pkgconfig xdg-base Do you want to continue? [Y/n] (assuming default) curl --connect-timeout 30 -f -L -A 'fink/0.37.0' -O http://distfiles.master.finkmirrors.net/distfiles/wise2.4.1.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 0 0 0 0 0 0 0 --:--:-- 0:00:01 --:--:-- 0 0 3119k 0 15683 0 0 11270 0 0:04:43 0:00:01 0:04:42 11266 29 3119k 29 914k 0 0 385k 0 0:00:08 0:00:02 0:00:06 385k 76 3119k 76 2381k 0 0 708k 0 0:00:04 0:00:03 0:00:01 708k 100 3119k 100 3119k 0 0 830k 0 0:00:03 0:00:03 --:--:-- 830k Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/debs/xdg-base_0.8-2_darwin-x86_64.deb Selecting previously deselected package xdg-base. (Reading database ... 4296 files and directories currently installed.) Unpacking xdg-base (from .../xdg-base_0.8-2_darwin-x86_64.deb) ... Setting up xdg-base (0.8-2) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/gnome/glib2-dev_2.22.4-8_darwin-x86_64.deb /sw/fink/debs/glib2-shlibs_2.22.4-8_darwin-x86_64.deb Selecting previously deselected package glib2-dev. (Reading database ... 4298 files and directories currently installed.) Unpacking glib2-dev (from .../glib2-dev_2.22.4-8_darwin-x86_64.deb) ... Selecting previously deselected package glib2-shlibs. Unpacking glib2-shlibs (from .../glib2-shlibs_2.22.4-8_darwin-x86_64.deb) ... Setting up glib2-shlibs (2.22.4-8) ... Setting up glib2-dev (2.22.4-8) ... Clearing dependency_libs of .la files being installed Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/debs/pkgconfig_0.28-1_darwin-x86_64.deb Selecting previously deselected package pkgconfig. (Reading database ... 5041 files and directories currently installed.) Unpacking pkgconfig (from .../pkgconfig_0.28-1_darwin-x86_64.deb) ... Setting up pkgconfig (0.28-1) ... Setting runtime build-lock... dpkg-deb -b /sw/build.build/root-fink-buildlock-wise2-2.4.1-1 /sw/build.build dpkg-deb: building package `fink-buildlock-wise2-2.4.1-1' in `/sw/build.build/fink-buildlock-wise2-2.4.1-1_2014.08.01-17.46.33_darwin-x86_64.deb'. Installing build-lock package... /sw/bin/dpkg-lockwait -i /sw/build.build/fink-buildlock-wise2-2.4.1-1_2014.08.01-17.46.33_darwin-x86_64.deb Selecting previously deselected package fink-buildlock-wise2-2.4.1-1. (Reading database ... 5054 files and directories currently installed.) Unpacking fink-buildlock-wise2-2.4.1-1 (from .../fink-buildlock-wise2-2.4.1-1_2014.08.01-17.46.33_darwin-x86_64.deb) ... Setting up fink-buildlock-wise2-2.4.1-1 (2014.08.01-17.46.33) ... sudo -u fink-bld [ENV] sh -c /tmp/fink.Fl4aP env LANG=C LC_ALL=C /sw/bin/tar --no-same-owner --no-same-permissions -xvf /sw/src/wise2.4.1.tar.gz wise2.4.1/ wise2.4.1/docs/ wise2.4.1/docs/apiend.tex wise2.4.1/docs/appendix.tex wise2.4.1/docs/dynamite.tex wise2.4.1/docs/genewise21.eps wise2.4.1/docs/genewise6.eps wise2.4.1/docs/gettex.pl wise2.4.1/docs/makefile wise2.4.1/docs/papers/ wise2.4.1/docs/papers/alignment.bib wise2.4.1/docs/papers/promoterwise.tex wise2.4.1/docs/README wise2.4.1/docs/wise2.tex wise2.4.1/docs/wise2api.tex wise2.4.1/docs/wise3arch.tex wise2.4.1/INSTALL wise2.4.1/LICENSE wise2.4.1/README wise2.4.1/src/ wise2.4.1/src/api/ wise2.4.1/src/api/examples/ wise2.4.1/src/api/examples/est.dna wise2.4.1/src/api/examples/makefile wise2.4.1/src/api/examples/README wise2.4.1/src/api/examples/revcomp.c wise2.4.1/src/api/examples/roac.pep wise2.4.1/src/api/examples/road.pep wise2.4.1/src/api/examples/sw.c wise2.4.1/src/api/include/ wise2.4.1/src/api/include/basic.h wise2.4.1/src/api/include/dyna.head wise2.4.1/src/api/include/makefile wise2.4.1/src/api/include/models.head wise2.4.1/src/api/include/wisebase_api.h wise2.4.1/src/api/libs/ wise2.4.1/src/api/libs/makefile wise2.4.1/src/api/README wise2.4.1/src/base/ wise2.4.1/src/base/commandline.c wise2.4.1/src/base/commandline.dy wise2.4.1/src/base/commandline.h wise2.4.1/src/base/commandline_api.h wise2.4.1/src/base/commandline_api.t wise2.4.1/src/base/LICENSE wise2.4.1/src/base/linesubs.c wise2.4.1/src/base/linesubs.dy wise2.4.1/src/base/linesubs.h wise2.4.1/src/base/makefile wise2.4.1/src/base/wisebase.h wise2.4.1/src/base/wiseconfig.c wise2.4.1/src/base/wiseconfig.h wise2.4.1/src/base/wiseerror.c wise2.4.1/src/base/wiseerror.dy wise2.4.1/src/base/wiseerror.h wise2.4.1/src/base/wiseerror_api.h wise2.4.1/src/base/wiseerror_api.t wise2.4.1/src/base/wisefile.c wise2.4.1/src/base/wisefile.dy wise2.4.1/src/base/wisefile.h wise2.4.1/src/base/wisefile_api.h wise2.4.1/src/base/wisefile_api.t wise2.4.1/src/base/wisememman.c wise2.4.1/src/base/wisememman.dy wise2.4.1/src/base/wisememman.h wise2.4.1/src/base/wiseoverlay.c wise2.4.1/src/base/wiseoverlay.dy wise2.4.1/src/base/wiseoverlay.h wise2.4.1/src/base/wiserandom.c wise2.4.1/src/base/wiserandom.dy wise2.4.1/src/base/wiserandom.h wise2.4.1/src/base/wisestreaminterface.c wise2.4.1/src/base/wisestreaminterface.dy wise2.4.1/src/base/wisestreaminterface.h wise2.4.1/src/base/wisestring.c wise2.4.1/src/base/wisestring.dy wise2.4.1/src/base/wisestring.h wise2.4.1/src/base/wisetime.c wise2.4.1/src/base/wisetime.dy wise2.4.1/src/base/wisetime.h wise2.4.1/src/contig/ wise2.4.1/src/contig/contig.dy wise2.4.1/src/contig/makefile wise2.4.1/src/contig/overlap.dy wise2.4.1/src/contig/testoverlap.c wise2.4.1/src/corba/ wise2.4.1/src/corba/corba_singleton.c wise2.4.1/src/corba/corba_singleton.h wise2.4.1/src/corba/hspscan_corba.idl wise2.4.1/src/corba/hspscan_corba_wrapper.c wise2.4.1/src/corba/hspscan_corba_wrapper.h wise2.4.1/src/corba/hspscan_server_impl.c wise2.4.1/src/corba/hspscan_server_impl.h wise2.4.1/src/corba/makefile wise2.4.1/src/corba/scanwise_protein_index.c wise2.4.1/src/corba/test_client.c wise2.4.1/src/corba/test_server.c wise2.4.1/src/corba/test_wrapper.c wise2.4.1/src/dnaindex/ wise2.4.1/src/dnaindex/assembly/ wise2.4.1/src/dnaindex/assembly/assemblygraph.dy wise2.4.1/src/dnaindex/assembly/assemblypath.dy wise2.4.1/src/dnaindex/assembly/assemblystats.dy wise2.4.1/src/dnaindex/assembly/badkmer.c wise2.4.1/src/dnaindex/assembly/basegraph.dy wise2.4.1/src/dnaindex/assembly/depthmanager.dy wise2.4.1/src/dnaindex/assembly/grapherror.dy wise2.4.1/src/dnaindex/assembly/graphmanager.dy wise2.4.1/src/dnaindex/assembly/graphtangle.dy wise2.4.1/src/dnaindex/assembly/makefile wise2.4.1/src/dnaindex/assembly/pathwise.c wise2.4.1/src/dnaindex/assembly/supertangle.dy wise2.4.1/src/dnaindex/assembly/test_assemblygraph.c wise2.4.1/src/dnaindex/assembly/test_basegraph.c wise2.4.1/src/dnaindex/assembly/test_graphtangle.c wise2.4.1/src/dnaindex/assembly.c wise2.4.1/src/dnaindex/assembly.dy wise2.4.1/src/dnaindex/assembly.h wise2.4.1/src/dnaindex/assembly_sanger_project.c wise2.4.1/src/dnaindex/assembly_sanger_project.dy wise2.4.1/src/dnaindex/assembly_sanger_project.h wise2.4.1/src/dnaindex/assembly_stream_cons.c wise2.4.1/src/dnaindex/assembly_stream_cons.dy wise2.4.1/src/dnaindex/assembly_stream_cons.h wise2.4.1/src/dnaindex/assembly_stream_fasta.c wise2.4.1/src/dnaindex/assembly_stream_fasta.dy wise2.4.1/src/dnaindex/assembly_stream_fasta.h wise2.4.1/src/dnaindex/assembly_stream_interface.c wise2.4.1/src/dnaindex/assembly_stream_interface.dy wise2.4.1/src/dnaindex/assembly_stream_interface.h wise2.4.1/src/dnaindex/bigseqwise.c wise2.4.1/src/dnaindex/calculate_compara_n50.pl wise2.4.1/src/dnaindex/chhash.c wise2.4.1/src/dnaindex/chhash.h wise2.4.1/src/dnaindex/compara2dotplot.pl wise2.4.1/src/dnaindex/comparapath.c wise2.4.1/src/dnaindex/comparapath.dy wise2.4.1/src/dnaindex/comparapath.h wise2.4.1/src/dnaindex/compressed_protein_index.c wise2.4.1/src/dnaindex/compressed_protein_index.dy wise2.4.1/src/dnaindex/compressed_protein_index.h wise2.4.1/src/dnaindex/dnamapping.c wise2.4.1/src/dnaindex/dnamapping.dy wise2.4.1/src/dnaindex/dnamapping.h wise2.4.1/src/dnaindex/dnanumber.c wise2.4.1/src/dnaindex/dnanumber.dy wise2.4.1/src/dnaindex/dnanumber.h wise2.4.1/src/dnaindex/eulerindex.c wise2.4.1/src/dnaindex/eulerindex.dy wise2.4.1/src/dnaindex/eulerindex.h wise2.4.1/src/dnaindex/findbad_kmer.c wise2.4.1/src/dnaindex/kmer_assembly.c wise2.4.1/src/dnaindex/kmer_assembly.dy wise2.4.1/src/dnaindex/kmer_assembly.h wise2.4.1/src/dnaindex/kmer_assembly_contig.c wise2.4.1/src/dnaindex/kmer_assembly_contig.dy wise2.4.1/src/dnaindex/kmer_assembly_contig.h wise2.4.1/src/dnaindex/kmer_assembly_error.c wise2.4.1/src/dnaindex/kmer_assembly_error.dy wise2.4.1/src/dnaindex/kmer_assembly_error.h wise2.4.1/src/dnaindex/kmer_assembly_untangler.c wise2.4.1/src/dnaindex/kmer_assembly_untangler.dy wise2.4.1/src/dnaindex/kmer_assembly_untangler.h wise2.4.1/src/dnaindex/kmer_count.c wise2.4.1/src/dnaindex/kmer_count.dy wise2.4.1/src/dnaindex/kmer_count.h wise2.4.1/src/dnaindex/kmer_direct.c wise2.4.1/src/dnaindex/kmer_direct.dy wise2.4.1/src/dnaindex/kmer_direct.h wise2.4.1/src/dnaindex/kmer_glib_index.c wise2.4.1/src/dnaindex/kmer_glib_index.dy wise2.4.1/src/dnaindex/kmer_glib_index.h wise2.4.1/src/dnaindex/kmer_hash.c wise2.4.1/src/dnaindex/kmer_hash.dy wise2.4.1/src/dnaindex/kmer_hash.h wise2.4.1/src/dnaindex/kmer_index_interface.c wise2.4.1/src/dnaindex/kmer_index_interface.dy wise2.4.1/src/dnaindex/kmer_index_interface.h wise2.4.1/src/dnaindex/kmer_stat.c wise2.4.1/src/dnaindex/kwise.c wise2.4.1/src/dnaindex/largeseqreader.c wise2.4.1/src/dnaindex/largeseqreader.dy wise2.4.1/src/dnaindex/largeseqreader.h wise2.4.1/src/dnaindex/linkindex.c wise2.4.1/src/dnaindex/linkindex.dy wise2.4.1/src/dnaindex/linkindex.h wise2.4.1/src/dnaindex/make_shotgun.c wise2.4.1/src/dnaindex/make_shotgun.pl wise2.4.1/src/dnaindex/makefile wise2.4.1/src/dnaindex/shotgun.c wise2.4.1/src/dnaindex/shotgun.dy wise2.4.1/src/dnaindex/shotgun.h wise2.4.1/src/dnaindex/singleseqspace.c wise2.4.1/src/dnaindex/singleseqspace.dy wise2.4.1/src/dnaindex/singleseqspace.h wise2.4.1/src/dnaindex/tangle.fa wise2.4.1/src/dnaindex/test_compara.c wise2.4.1/src/dnaindex/test_dnanumber.c wise2.4.1/src/dnaindex/test_euler.c wise2.4.1/src/dnaindex/test_kmer.c wise2.4.1/src/dnaindex/test_linkindex.c wise2.4.1/src/dnaindex/vectorindex.c wise2.4.1/src/dnaindex/vectorindex.dy wise2.4.1/src/dnaindex/vectorindex.h wise2.4.1/src/dyc/ wise2.4.1/src/dyc/api.c wise2.4.1/src/dyc/api.dy wise2.4.1/src/dyc/api.h wise2.4.1/src/dyc/calc.l wise2.4.1/src/dyc/calc.y wise2.4.1/src/dyc/compugen.c wise2.4.1/src/dyc/compugen.h wise2.4.1/src/dyc/dbmpi.c wise2.4.1/src/dyc/dbmpi.dy wise2.4.1/src/dyc/dbmpi.h wise2.4.1/src/dyc/dbthread.c wise2.4.1/src/dyc/dbthread.dy wise2.4.1/src/dyc/dbthread.h wise2.4.1/src/dyc/display.c wise2.4.1/src/dyc/display.dy wise2.4.1/src/dyc/display.h wise2.4.1/src/dyc/docugen.c wise2.4.1/src/dyc/dpimpl.c wise2.4.1/src/dyc/dpimpl.dy wise2.4.1/src/dyc/dpimpl.h wise2.4.1/src/dyc/dy2om.c wise2.4.1/src/dyc/dy2om.dy wise2.4.1/src/dyc/dy2om.h wise2.4.1/src/dyc/dyc.c wise2.4.1/src/dyc/dymain.c wise2.4.1/src/dyc/dymain.dy wise2.4.1/src/dyc/dymain.h wise2.4.1/src/dyc/dyna2.c wise2.4.1/src/dyc/dyna2.dy wise2.4.1/src/dyc/dyna2.h wise2.4.1/src/dyc/dynadb.c wise2.4.1/src/dyc/dynadb.dy wise2.4.1/src/dyc/dynadb.h wise2.4.1/src/dyc/dynadebug.c wise2.4.1/src/dyc/dynadebug.dy wise2.4.1/src/dyc/dynadebug.h wise2.4.1/src/dyc/dynafunc.c wise2.4.1/src/dyc/dynafunc.dy wise2.4.1/src/dyc/dynafunc.h wise2.4.1/src/dyc/dynashadow.c wise2.4.1/src/dyc/dynashadow.dy wise2.4.1/src/dyc/dynashadow.h wise2.4.1/src/dyc/dynfile.c wise2.4.1/src/dyc/dynfile.dy wise2.4.1/src/dyc/dynfile.h wise2.4.1/src/dyc/dyshatter.c wise2.4.1/src/dyc/dyshatter.dy wise2.4.1/src/dyc/dyshatter.h wise2.4.1/src/dyc/exprtree.c wise2.4.1/src/dyc/exprtree.dy wise2.4.1/src/dyc/exprtree.h wise2.4.1/src/dyc/friend.c wise2.4.1/src/dyc/friend.dy wise2.4.1/src/dyc/friend.h wise2.4.1/src/dyc/ftext.c wise2.4.1/src/dyc/ftext.dy wise2.4.1/src/dyc/ftext.h wise2.4.1/src/dyc/funcinfo.c wise2.4.1/src/dyc/funcinfo.dy wise2.4.1/src/dyc/funcinfo.h wise2.4.1/src/dyc/input.c wise2.4.1/src/dyc/input.dy wise2.4.1/src/dyc/input.h wise2.4.1/src/dyc/inputfile.c wise2.4.1/src/dyc/inputfile.dy wise2.4.1/src/dyc/inputfile.h wise2.4.1/src/dyc/kbestsearch.c wise2.4.1/src/dyc/kbestsearch.dy wise2.4.1/src/dyc/kbestsearch.h wise2.4.1/src/dyc/labelmaster.c wise2.4.1/src/dyc/labelmaster.dy wise2.4.1/src/dyc/labelmaster.h wise2.4.1/src/dyc/lex.yy.c wise2.4.1/src/dyc/LICENSE wise2.4.1/src/dyc/linkmap.c wise2.4.1/src/dyc/linkmap.dy wise2.4.1/src/dyc/linkmap.h wise2.4.1/src/dyc/makefile wise2.4.1/src/dyc/method.c wise2.4.1/src/dyc/method.dy wise2.4.1/src/dyc/method.h wise2.4.1/src/dyc/module.c wise2.4.1/src/dyc/module.h wise2.4.1/src/dyc/modulefunc.c wise2.4.1/src/dyc/modulefunc.dy wise2.4.1/src/dyc/modulefunc.h wise2.4.1/src/dyc/moduleinfo.c wise2.4.1/src/dyc/moduleinfo.dy wise2.4.1/src/dyc/moduleinfo.h wise2.4.1/src/dyc/objectinfo.c wise2.4.1/src/dyc/objectinfo.dy wise2.4.1/src/dyc/objectinfo.h wise2.4.1/src/dyc/optimiser.c wise2.4.1/src/dyc/optimiser.dy wise2.4.1/src/dyc/optimiser.h wise2.4.1/src/dyc/probal.c wise2.4.1/src/dyc/probal.dy wise2.4.1/src/dyc/probal.h wise2.4.1/src/dyc/telegraph.c wise2.4.1/src/dyc/telegraph.dy wise2.4.1/src/dyc/telegraph.h wise2.4.1/src/dyc/type.c wise2.4.1/src/dyc/type.dy wise2.4.1/src/dyc/type.h wise2.4.1/src/dyc/variable.c wise2.4.1/src/dyc/variable.dy wise2.4.1/src/dyc/variable.h wise2.4.1/src/dyc/wisec.c wise2.4.1/src/dyc/wisec.dy wise2.4.1/src/dyc/wisec.h wise2.4.1/src/dyc/y.tab.c wise2.4.1/src/dyc/y.tab.h wise2.4.1/src/dynamite_examples/ wise2.4.1/src/dynamite_examples/cdna2genomic.dy wise2.4.1/src/dynamite_examples/dbsearch.c wise2.4.1/src/dynamite_examples/est.dna wise2.4.1/src/dynamite_examples/est2gen.c wise2.4.1/src/dynamite_examples/estgendisplay.c wise2.4.1/src/dynamite_examples/estgendisplay.dy wise2.4.1/src/dynamite_examples/estgendisplay.h wise2.4.1/src/dynamite_examples/genomic.dna wise2.4.1/src/dynamite_examples/makefile wise2.4.1/src/dynamite_examples/proteinsw.dy wise2.4.1/src/dynamite_examples/psw.c wise2.4.1/src/dynamite_examples/README wise2.4.1/src/dynamite_examples/roac.pep wise2.4.1/src/dynamite_examples/road.pep wise2.4.1/src/dynamite_examples/seqaligndisplay.c wise2.4.1/src/dynamite_examples/seqaligndisplay.dy wise2.4.1/src/dynamite_examples/seqaligndisplay.h wise2.4.1/src/dynlibsrc/ wise2.4.1/src/dynlibsrc/aln.c wise2.4.1/src/dynlibsrc/aln.dy wise2.4.1/src/dynlibsrc/aln.h wise2.4.1/src/dynlibsrc/aln.pod wise2.4.1/src/dynlibsrc/aln.tex wise2.4.1/src/dynlibsrc/aln.typemap wise2.4.1/src/dynlibsrc/aln.xs wise2.4.1/src/dynlibsrc/aln_api.h wise2.4.1/src/dynlibsrc/aln_api.t wise2.4.1/src/dynlibsrc/alnconvert.c wise2.4.1/src/dynlibsrc/alnconvert.dy wise2.4.1/src/dynlibsrc/alnconvert.h wise2.4.1/src/dynlibsrc/alnrange.c wise2.4.1/src/dynlibsrc/alnrange.dy wise2.4.1/src/dynlibsrc/alnrange.h wise2.4.1/src/dynlibsrc/alnrange.pod wise2.4.1/src/dynlibsrc/alnrange.tex wise2.4.1/src/dynlibsrc/alnrange.typemap wise2.4.1/src/dynlibsrc/alnrange.xs wise2.4.1/src/dynlibsrc/alnrange_api.h wise2.4.1/src/dynlibsrc/alnrange_api.t wise2.4.1/src/dynlibsrc/arrayseqlookup.c wise2.4.1/src/dynlibsrc/arrayseqlookup.dy wise2.4.1/src/dynlibsrc/arrayseqlookup.h wise2.4.1/src/dynlibsrc/asciibtcanvas.c wise2.4.1/src/dynlibsrc/asciibtcanvas.dy wise2.4.1/src/dynlibsrc/asciibtcanvas.h wise2.4.1/src/dynlibsrc/basematrix.c wise2.4.1/src/dynlibsrc/basematrix.dy wise2.4.1/src/dynlibsrc/basematrix.h wise2.4.1/src/dynlibsrc/basematrix.pod wise2.4.1/src/dynlibsrc/basematrix.tex wise2.4.1/src/dynlibsrc/basematrix.typemap wise2.4.1/src/dynlibsrc/basematrix.xs wise2.4.1/src/dynlibsrc/basematrix_api.h wise2.4.1/src/dynlibsrc/basematrix_api.t wise2.4.1/src/dynlibsrc/btcanvas.c wise2.4.1/src/dynlibsrc/btcanvas.dy wise2.4.1/src/dynlibsrc/btcanvas.h wise2.4.1/src/dynlibsrc/cdna.c wise2.4.1/src/dynlibsrc/cdna.dy wise2.4.1/src/dynlibsrc/cdna.h wise2.4.1/src/dynlibsrc/cdna.pod wise2.4.1/src/dynlibsrc/cdna.tex wise2.4.1/src/dynlibsrc/cdna.typemap wise2.4.1/src/dynlibsrc/cdna.xs wise2.4.1/src/dynlibsrc/cdna_api.h wise2.4.1/src/dynlibsrc/cdna_api.t wise2.4.1/src/dynlibsrc/cdnadb.c wise2.4.1/src/dynlibsrc/cdnadb.dy wise2.4.1/src/dynlibsrc/cdnadb.h wise2.4.1/src/dynlibsrc/cdnadb.pod wise2.4.1/src/dynlibsrc/cdnadb.tex wise2.4.1/src/dynlibsrc/cdnadb.typemap wise2.4.1/src/dynlibsrc/cdnadb.xs wise2.4.1/src/dynlibsrc/cdnadb_api.h wise2.4.1/src/dynlibsrc/cdnadb_api.t wise2.4.1/src/dynlibsrc/codon.c wise2.4.1/src/dynlibsrc/codon.dy wise2.4.1/src/dynlibsrc/codon.h wise2.4.1/src/dynlibsrc/codon.pod wise2.4.1/src/dynlibsrc/codon.tex wise2.4.1/src/dynlibsrc/codon.typemap wise2.4.1/src/dynlibsrc/codon.xs wise2.4.1/src/dynlibsrc/codon_api.h wise2.4.1/src/dynlibsrc/codon_api.t wise2.4.1/src/dynlibsrc/codonmapper.c wise2.4.1/src/dynlibsrc/codonmapper.dy wise2.4.1/src/dynlibsrc/codonmapper.h wise2.4.1/src/dynlibsrc/codonmapper.pod wise2.4.1/src/dynlibsrc/codonmapper.tex wise2.4.1/src/dynlibsrc/codonmapper.typemap wise2.4.1/src/dynlibsrc/codonmapper.xs wise2.4.1/src/dynlibsrc/codonmapper_api.h wise2.4.1/src/dynlibsrc/codonmapper_api.t wise2.4.1/src/dynlibsrc/codonmatrix.c wise2.4.1/src/dynlibsrc/codonmatrix.dy wise2.4.1/src/dynlibsrc/codonmatrix.h wise2.4.1/src/dynlibsrc/complexconsensi.c wise2.4.1/src/dynlibsrc/complexconsensi.dy wise2.4.1/src/dynlibsrc/complexconsensi.h wise2.4.1/src/dynlibsrc/complexevalset.c wise2.4.1/src/dynlibsrc/complexevalset.dy wise2.4.1/src/dynlibsrc/complexevalset.h wise2.4.1/src/dynlibsrc/complexsequence.c wise2.4.1/src/dynlibsrc/complexsequence.dy wise2.4.1/src/dynlibsrc/complexsequence.h wise2.4.1/src/dynlibsrc/complexsequence.pod wise2.4.1/src/dynlibsrc/complexsequence.tex wise2.4.1/src/dynlibsrc/complexsequence.typemap wise2.4.1/src/dynlibsrc/complexsequence.xs wise2.4.1/src/dynlibsrc/complexsequence_api.h wise2.4.1/src/dynlibsrc/complexsequence_api.t wise2.4.1/src/dynlibsrc/compmat.c wise2.4.1/src/dynlibsrc/compmat.dy wise2.4.1/src/dynlibsrc/compmat.h wise2.4.1/src/dynlibsrc/compmat.pod wise2.4.1/src/dynlibsrc/compmat.tex wise2.4.1/src/dynlibsrc/compmat.typemap wise2.4.1/src/dynlibsrc/compmat.xs wise2.4.1/src/dynlibsrc/compmat_api.h wise2.4.1/src/dynlibsrc/compmat_api.t wise2.4.1/src/dynlibsrc/database.h wise2.4.1/src/dynlibsrc/dbsearchimpl.c wise2.4.1/src/dynlibsrc/dbsearchimpl.dy wise2.4.1/src/dynlibsrc/dbsearchimpl.h wise2.4.1/src/dynlibsrc/dbsearchimpl.pod wise2.4.1/src/dynlibsrc/dbsearchimpl.tex wise2.4.1/src/dynlibsrc/dbsearchimpl.typemap wise2.4.1/src/dynlibsrc/dbsearchimpl.xs wise2.4.1/src/dynlibsrc/dbsearchimpl_api.h wise2.4.1/src/dynlibsrc/dbsearchimpl_api.t wise2.4.1/src/dynlibsrc/dna.c wise2.4.1/src/dynlibsrc/dna.dy wise2.4.1/src/dynlibsrc/dna.h wise2.4.1/src/dynlibsrc/dnaindexcons.c wise2.4.1/src/dynlibsrc/dnaindexcons.dy wise2.4.1/src/dynlibsrc/dnaindexcons.h wise2.4.1/src/dynlibsrc/dnamatrix.c wise2.4.1/src/dynlibsrc/dnamatrix.dy wise2.4.1/src/dynlibsrc/dnamatrix.h wise2.4.1/src/dynlibsrc/dnamatrix.pod wise2.4.1/src/dynlibsrc/dnamatrix.tex wise2.4.1/src/dynlibsrc/dnamatrix.typemap wise2.4.1/src/dynlibsrc/dnamatrix.xs wise2.4.1/src/dynlibsrc/dnamatrix_api.h wise2.4.1/src/dynlibsrc/dnamatrix_api.t wise2.4.1/src/dynlibsrc/dpenvelope.c wise2.4.1/src/dynlibsrc/dpenvelope.dy wise2.4.1/src/dynlibsrc/dpenvelope.h wise2.4.1/src/dynlibsrc/dprunimpl.c wise2.4.1/src/dynlibsrc/dprunimpl.dy wise2.4.1/src/dynlibsrc/dprunimpl.h wise2.4.1/src/dynlibsrc/dyna.h wise2.4.1/src/dynlibsrc/dynlibcross.c wise2.4.1/src/dynlibsrc/dynlibcross.dy wise2.4.1/src/dynlibsrc/dynlibcross.h wise2.4.1/src/dynlibsrc/embl.c wise2.4.1/src/dynlibsrc/embl.dy wise2.4.1/src/dynlibsrc/embl.h wise2.4.1/src/dynlibsrc/gene.c wise2.4.1/src/dynlibsrc/gene.dy wise2.4.1/src/dynlibsrc/gene.h wise2.4.1/src/dynlibsrc/gene.pod wise2.4.1/src/dynlibsrc/gene.tex wise2.4.1/src/dynlibsrc/gene.typemap wise2.4.1/src/dynlibsrc/gene.xs wise2.4.1/src/dynlibsrc/gene_api.h wise2.4.1/src/dynlibsrc/gene_api.t wise2.4.1/src/dynlibsrc/genericindexresult.c wise2.4.1/src/dynlibsrc/genericindexresult.dy wise2.4.1/src/dynlibsrc/genericindexresult.h wise2.4.1/src/dynlibsrc/genomic.c wise2.4.1/src/dynlibsrc/genomic.dy wise2.4.1/src/dynlibsrc/genomic.h wise2.4.1/src/dynlibsrc/genomic.pod wise2.4.1/src/dynlibsrc/genomic.tex wise2.4.1/src/dynlibsrc/genomic.typemap wise2.4.1/src/dynlibsrc/genomic.xs wise2.4.1/src/dynlibsrc/genomic_api.h wise2.4.1/src/dynlibsrc/genomic_api.t wise2.4.1/src/dynlibsrc/genomicdb.c wise2.4.1/src/dynlibsrc/genomicdb.dy wise2.4.1/src/dynlibsrc/genomicdb.h wise2.4.1/src/dynlibsrc/genomicdb.pod wise2.4.1/src/dynlibsrc/genomicdb.tex wise2.4.1/src/dynlibsrc/genomicdb.typemap wise2.4.1/src/dynlibsrc/genomicdb.xs wise2.4.1/src/dynlibsrc/genomicdb_api.h wise2.4.1/src/dynlibsrc/genomicdb_api.t wise2.4.1/src/dynlibsrc/genomicregion.c wise2.4.1/src/dynlibsrc/genomicregion.dy wise2.4.1/src/dynlibsrc/genomicregion.h wise2.4.1/src/dynlibsrc/genomicregion.pod wise2.4.1/src/dynlibsrc/genomicregion.tex wise2.4.1/src/dynlibsrc/genomicregion.typemap wise2.4.1/src/dynlibsrc/genomicregion.xs wise2.4.1/src/dynlibsrc/genomicregion_api.h wise2.4.1/src/dynlibsrc/genomicregion_api.t wise2.4.1/src/dynlibsrc/histogram.c wise2.4.1/src/dynlibsrc/histogram.dy wise2.4.1/src/dynlibsrc/histogram.h wise2.4.1/src/dynlibsrc/histogram.pod wise2.4.1/src/dynlibsrc/histogram.tex wise2.4.1/src/dynlibsrc/histogram.typemap wise2.4.1/src/dynlibsrc/histogram.xs 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wise2.4.1/src/dynlibsrc/makefile wise2.4.1/src/dynlibsrc/matrixdebug.c wise2.4.1/src/dynlibsrc/matrixdebug.dy wise2.4.1/src/dynlibsrc/matrixdebug.h wise2.4.1/src/dynlibsrc/packaln.c wise2.4.1/src/dynlibsrc/packaln.dy wise2.4.1/src/dynlibsrc/packaln.h wise2.4.1/src/dynlibsrc/packaln.pod wise2.4.1/src/dynlibsrc/packaln.tex wise2.4.1/src/dynlibsrc/packaln.typemap wise2.4.1/src/dynlibsrc/packaln.xs wise2.4.1/src/dynlibsrc/packaln_api.h wise2.4.1/src/dynlibsrc/packaln_api.t wise2.4.1/src/dynlibsrc/pairbase.c wise2.4.1/src/dynlibsrc/pairbase.dy wise2.4.1/src/dynlibsrc/pairbase.h wise2.4.1/src/dynlibsrc/pairbaseseq.c wise2.4.1/src/dynlibsrc/pairbaseseq.dy wise2.4.1/src/dynlibsrc/pairbaseseq.h wise2.4.1/src/dynlibsrc/probability.c wise2.4.1/src/dynlibsrc/probability.dy wise2.4.1/src/dynlibsrc/probability.h wise2.4.1/src/dynlibsrc/probability.pod wise2.4.1/src/dynlibsrc/probability.tex wise2.4.1/src/dynlibsrc/probability.typemap wise2.4.1/src/dynlibsrc/probability.xs 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wise2.4.1/src/dynlibsrc/proteinstreamedindex.h wise2.4.1/src/dynlibsrc/pthreadpool.c wise2.4.1/src/dynlibsrc/pthreadpool.dy wise2.4.1/src/dynlibsrc/pthreadpool.h wise2.4.1/src/dynlibsrc/randomdb.c wise2.4.1/src/dynlibsrc/randomdb.dy wise2.4.1/src/dynlibsrc/randomdb.h wise2.4.1/src/dynlibsrc/randomdb.pod wise2.4.1/src/dynlibsrc/randomdb.tex wise2.4.1/src/dynlibsrc/randomdb.typemap wise2.4.1/src/dynlibsrc/randomdb.xs wise2.4.1/src/dynlibsrc/randomdb_api.h wise2.4.1/src/dynlibsrc/randomdb_api.t wise2.4.1/src/dynlibsrc/randommodel.c wise2.4.1/src/dynlibsrc/randommodel.dy wise2.4.1/src/dynlibsrc/randommodel.h wise2.4.1/src/dynlibsrc/randommodel.pod wise2.4.1/src/dynlibsrc/randommodel.tex wise2.4.1/src/dynlibsrc/randommodel.typemap wise2.4.1/src/dynlibsrc/randommodel.xs wise2.4.1/src/dynlibsrc/randommodel_api.h wise2.4.1/src/dynlibsrc/randommodel_api.t wise2.4.1/src/dynlibsrc/searchstatinterface.c wise2.4.1/src/dynlibsrc/searchstatinterface.dy wise2.4.1/src/dynlibsrc/searchstatinterface.h wise2.4.1/src/dynlibsrc/searchstatlookup.c wise2.4.1/src/dynlibsrc/searchstatlookup.dy wise2.4.1/src/dynlibsrc/searchstatlookup.h wise2.4.1/src/dynlibsrc/seqalign.c wise2.4.1/src/dynlibsrc/seqalign.dy wise2.4.1/src/dynlibsrc/seqalign.h wise2.4.1/src/dynlibsrc/seqlookup.c wise2.4.1/src/dynlibsrc/seqlookup.dy wise2.4.1/src/dynlibsrc/seqlookup.h wise2.4.1/src/dynlibsrc/sequence.c wise2.4.1/src/dynlibsrc/sequence.dy wise2.4.1/src/dynlibsrc/sequence.h wise2.4.1/src/dynlibsrc/sequence.pod wise2.4.1/src/dynlibsrc/sequence.tex wise2.4.1/src/dynlibsrc/sequence.typemap wise2.4.1/src/dynlibsrc/sequence.xs wise2.4.1/src/dynlibsrc/sequence_api.h wise2.4.1/src/dynlibsrc/sequence_api.t wise2.4.1/src/dynlibsrc/sequence_codon.c wise2.4.1/src/dynlibsrc/sequence_codon.dy wise2.4.1/src/dynlibsrc/sequence_codon.h wise2.4.1/src/dynlibsrc/sequence_codon.pod wise2.4.1/src/dynlibsrc/sequence_codon.tex wise2.4.1/src/dynlibsrc/sequence_codon.typemap wise2.4.1/src/dynlibsrc/sequence_codon.xs wise2.4.1/src/dynlibsrc/sequence_codon_api.h wise2.4.1/src/dynlibsrc/sequence_codon_api.t wise2.4.1/src/dynlibsrc/sequencedb.c wise2.4.1/src/dynlibsrc/sequencedb.dy wise2.4.1/src/dynlibsrc/sequencedb.h wise2.4.1/src/dynlibsrc/sequencedb.pod wise2.4.1/src/dynlibsrc/sequencedb.tex wise2.4.1/src/dynlibsrc/sequencedb.typemap wise2.4.1/src/dynlibsrc/sequencedb.xs wise2.4.1/src/dynlibsrc/sequencedb_api.h wise2.4.1/src/dynlibsrc/sequencedb_api.t wise2.4.1/src/dynlibsrc/sequencestream.c wise2.4.1/src/dynlibsrc/sequencestream.dy wise2.4.1/src/dynlibsrc/sequencestream.h wise2.4.1/src/dynlibsrc/shadowseq.c wise2.4.1/src/dynlibsrc/shadowseq.dy wise2.4.1/src/dynlibsrc/shadowseq.h wise2.4.1/src/dynlibsrc/shadowseqindex.c wise2.4.1/src/dynlibsrc/shadowseqindex.dy wise2.4.1/src/dynlibsrc/shadowseqindex.h wise2.4.1/src/dynlibsrc/shattermatrix.c wise2.4.1/src/dynlibsrc/shattermatrix.dy wise2.4.1/src/dynlibsrc/shattermatrix.h wise2.4.1/src/dynlibsrc/singlenumberspace.c 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wise2.4.1/src/models/seqaligndisplay.tex wise2.4.1/src/models/seqaligndisplay.typemap wise2.4.1/src/models/seqaligndisplay.xs wise2.4.1/src/models/seqaligndisplay_api.h wise2.4.1/src/models/seqaligndisplay_api.t wise2.4.1/src/models/seqerror.c wise2.4.1/src/models/seqerror.dy wise2.4.1/src/models/seqerror.h wise2.4.1/src/models/seqhit.c wise2.4.1/src/models/seqhit.dy wise2.4.1/src/models/seqhit.h wise2.4.1/src/models/seqhit.pod wise2.4.1/src/models/seqhit.tex wise2.4.1/src/models/seqhit.typemap wise2.4.1/src/models/seqhit.xs wise2.4.1/src/models/seqhit_api.h wise2.4.1/src/models/seqhit_api.t wise2.4.1/src/models/seqlist.c wise2.4.1/src/models/slimdba.c wise2.4.1/src/models/slimdba.dy wise2.4.1/src/models/slimdba.h wise2.4.1/src/models/splicesitemodeler.c wise2.4.1/src/models/splicesitemodeler.dy wise2.4.1/src/models/splicesitemodeler.h wise2.4.1/src/models/standardout.c wise2.4.1/src/models/standardout.dy wise2.4.1/src/models/standardout.h wise2.4.1/src/models/statwise.c wise2.4.1/src/models/statwise10.c wise2.4.1/src/models/sw_wrap.c wise2.4.1/src/models/sw_wrap.dy wise2.4.1/src/models/sw_wrap.h wise2.4.1/src/models/sw_wrap.pod wise2.4.1/src/models/sw_wrap.tex wise2.4.1/src/models/sw_wrap.typemap wise2.4.1/src/models/sw_wrap.xs wise2.4.1/src/models/sw_wrap_api.h wise2.4.1/src/models/sw_wrap_api.t wise2.4.1/src/models/syexonmodel.c wise2.4.1/src/models/syexonmodel.dy wise2.4.1/src/models/syexonmodel.h wise2.4.1/src/models/sywise.c wise2.4.1/src/models/sywise20.c wise2.4.1/src/models/sywise20.dy wise2.4.1/src/models/sywise20.h wise2.4.1/src/models/test_aligng.c wise2.4.1/src/models/test_gwhsp.c wise2.4.1/src/models/test_splice.c wise2.4.1/src/models/testdna.c wise2.4.1/src/models/testgenestat.c wise2.4.1/src/models/threestatedb.c wise2.4.1/src/models/threestatedb.dy wise2.4.1/src/models/threestatedb.h wise2.4.1/src/models/threestatedb.pod wise2.4.1/src/models/threestatedb.tex wise2.4.1/src/models/threestatedb.typemap wise2.4.1/src/models/threestatedb.xs wise2.4.1/src/models/threestatedb_api.h wise2.4.1/src/models/threestatedb_api.t wise2.4.1/src/models/threestatedp.c wise2.4.1/src/models/threestatedp.dy wise2.4.1/src/models/threestatedp.h wise2.4.1/src/models/threestateloop.c wise2.4.1/src/models/threestateloop.dy wise2.4.1/src/models/threestateloop.h wise2.4.1/src/models/threestatemodel.c wise2.4.1/src/models/threestatemodel.dy wise2.4.1/src/models/threestatemodel.h wise2.4.1/src/models/threestatemodel.pod wise2.4.1/src/models/threestatemodel.tex wise2.4.1/src/models/threestatemodel.typemap wise2.4.1/src/models/threestatemodel.xs wise2.4.1/src/models/threestatemodel_api.h wise2.4.1/src/models/threestatemodel_api.t wise2.4.1/src/models/transfactor.c wise2.4.1/src/models/transfactor.dy wise2.4.1/src/models/transfactor.h wise2.4.1/src/models/transregion.c wise2.4.1/src/models/transregion.dy wise2.4.1/src/models/transregion.h wise2.4.1/src/models/transregiondp.c wise2.4.1/src/models/transregiondp.dy wise2.4.1/src/models/transregiondp.h wise2.4.1/src/models/version.h wise2.4.1/src/models/wise2xhmmer2.c wise2.4.1/src/models/wise2xhmmer2.dy wise2.4.1/src/models/wise2xhmmer2.h wise2.4.1/src/network/ wise2.4.1/src/network/client_multihspscan.c wise2.4.1/src/network/client_multihspscan.dy wise2.4.1/src/network/client_multihspscan.h wise2.4.1/src/network/makefile wise2.4.1/src/network/net_hspscan.c wise2.4.1/src/network/net_hspscan.dy wise2.4.1/src/network/net_hspscan.h wise2.4.1/src/network/README wise2.4.1/src/network/wise_proteinindex_server.c wise2.4.1/src/other_programs/ wise2.4.1/src/other_programs/makefile wise2.4.1/src/other_programs/orthoset.dy wise2.4.1/src/other_programs/test_ortho.c wise2.4.1/src/perl/ wise2.4.1/src/perl/basic.h wise2.4.1/src/perl/basic.typemap wise2.4.1/src/perl/Makefile wise2.4.1/src/perl/makelib.pl wise2.4.1/src/perl/scripts/ wise2.4.1/src/perl/scripts/blastwise.pl wise2.4.1/src/perl/scripts/estwise.pl wise2.4.1/src/perl/scripts/genewise.pl wise2.4.1/src/perl/scripts/halfwise.pl wise2.4.1/src/perl/scripts/postwise.pl wise2.4.1/src/perl/scripts/protestwise.pl wise2.4.1/src/perl/scripts/README wise2.4.1/src/perl/top.xs wise2.4.1/src/perl/Wise2/ wise2.4.1/src/perl/Wise2/blosum62.bla wise2.4.1/src/perl/Wise2/libs/ wise2.4.1/src/perl/Wise2/libs/README wise2.4.1/src/perl/Wise2/Makefile.PL wise2.4.1/src/perl/Wise2/test.pl wise2.4.1/src/perl/Wise2/Wise2.pm wise2.4.1/src/snp/ wise2.4.1/src/snp/frequency_count.dy wise2.4.1/src/snp/genotype.dy wise2.4.1/src/snp/locus_framework.dy wise2.4.1/src/snp/locus_model_estimators.dy wise2.4.1/src/snp/makefile wise2.4.1/src/snp/person.dy wise2.4.1/src/snp/test_est.c wise2.4.1/src/socket/ wise2.4.1/src/socket/anonobj.c wise2.4.1/src/socket/anonobj.dy wise2.4.1/src/socket/anonobj.h wise2.4.1/src/socket/directsocketwrite.c wise2.4.1/src/socket/directsocketwrite.dy wise2.4.1/src/socket/directsocketwrite.h wise2.4.1/src/socket/functionclient.c wise2.4.1/src/socket/functionclient.dy wise2.4.1/src/socket/functionclient.h wise2.4.1/src/socket/functionserver.c wise2.4.1/src/socket/functionserver.dy wise2.4.1/src/socket/functionserver.h wise2.4.1/src/socket/makefile wise2.4.1/src/socket/simplebufferedserver.c wise2.4.1/src/socket/simplebufferedserver.dy wise2.4.1/src/socket/simplebufferedserver.h wise2.4.1/src/socket/simplesocketclient.c wise2.4.1/src/socket/simplesocketclient.dy wise2.4.1/src/socket/simplesocketclient.h wise2.4.1/src/socket/transferinterface.c wise2.4.1/src/socket/transferinterface.dy wise2.4.1/src/socket/transferinterface.h wise2.4.1/src/SOURCE_ROADMAP wise2.4.1/src/test/ wise2.4.1/src/test/basic_cdna.out wise2.4.1/src/test/basic_dna.out wise2.4.1/src/test/basic_genomic.out wise2.4.1/src/test/dna.db wise2.4.1/src/test/estwise-db.out wise2.4.1/src/test/genewise-db-lite.out wise2.4.1/src/test/genewise-db.out wise2.4.1/src/test/genewisedb-pfam.out wise2.4.1/src/test/go.evi wise2.4.1/src/test/go.out wise2.4.1/src/test/HMM.ascii wise2.4.1/src/test/HMM.binary wise2.4.1/src/test/hmm_cdna.out wise2.4.1/src/test/hmm_genomic.out wise2.4.1/src/test/human.genomic wise2.4.1/src/test/pep.fa wise2.4.1/src/test/promoterwise.out wise2.4.1/src/test/pswdb.out wise2.4.1/src/test/pw.human wise2.4.1/src/test/pw.mouse wise2.4.1/src/test/road.pep wise2.4.1/src/test/rrm.HMM wise2.4.1/src/test/scanwisep.out wise2.4.1/src/test/short.dna wise2.4.1/src/test/short.pep wise2.4.1/src/test/short.test wise2.4.1/src/test/testman.pl wise2.4.1/src/test/wrong.hmm wise2.4.1/src/test/wrong.out wise2.4.1/src/test/wrong_est.out wise2.4.1/src/welcome.csh wise2.4.1/test_data/ wise2.4.1/test_data/alignwise.gen wise2.4.1/test_data/db.hmm wise2.4.1/test_data/dummy_hox.dna wise2.4.1/test_data/epo.genomic wise2.4.1/test_data/epo.pep wise2.4.1/test_data/fugu.gen wise2.4.1/test_data/fugu_human.pep wise2.4.1/test_data/hn_est.fa wise2.4.1/test_data/HOX.HMM wise2.4.1/test_data/human.genomic wise2.4.1/test_data/jason.dna wise2.4.1/test_data/jason.pep wise2.4.1/test_data/keratin_intron.human wise2.4.1/test_data/keratin_intron.mouse wise2.4.1/test_data/pep.fa wise2.4.1/test_data/phased_roa1.pep wise2.4.1/test_data/Q8NAN2.dna wise2.4.1/test_data/Q8NAN2.pep wise2.4.1/test_data/README wise2.4.1/test_data/road.pep wise2.4.1/test_data/rpo_fugu.gen wise2.4.1/test_data/rpo_h_f.anchor wise2.4.1/test_data/rpo_h_m.anchor wise2.4.1/test_data/rpo_h_r.anchor wise2.4.1/test_data/rpo_human.gen wise2.4.1/test_data/rpo_human.intron wise2.4.1/test_data/rpo_human.pep wise2.4.1/test_data/rpo_mouse.gen wise2.4.1/test_data/rpo_rat.gen wise2.4.1/test_data/rrm.HMM wise2.4.1/test_data/rua1.pep wise2.4.1/test_data/vav.dna wise2.4.1/test_data/vav_promoter.human wise2.4.1/test_data/vav_promoter.mouse wise2.4.1/test_data/xeno.cdna wise2.4.1/test_data/xeno.pep wise2.4.1/wisecfg/ wise2.4.1/wisecfg/aa.rnd wise2.4.1/wisecfg/BLOSUM30.bla wise2.4.1/wisecfg/BLOSUM45.bla wise2.4.1/wisecfg/BLOSUM62.bla wise2.4.1/wisecfg/BLOSUM80.bla wise2.4.1/wisecfg/cb.tmf wise2.4.1/wisecfg/codon.martian wise2.4.1/wisecfg/codon.table wise2.4.1/wisecfg/gene.stat wise2.4.1/wisecfg/gon120.bla wise2.4.1/wisecfg/gon160.bla wise2.4.1/wisecfg/gon200.bla wise2.4.1/wisecfg/gon250.bla wise2.4.1/wisecfg/gon350.bla wise2.4.1/wisecfg/human.gf wise2.4.1/wisecfg/human.gp wise2.4.1/wisecfg/human.stats wise2.4.1/wisecfg/idenity.bla wise2.4.1/wisecfg/methods wise2.4.1/wisecfg/pb.gf wise2.4.1/wisecfg/pombe.gf wise2.4.1/wisecfg/tm.pri wise2.4.1/wisecfg/wag55 wise2.4.1/wisecfg/wag65 wise2.4.1/wisecfg/wag75 wise2.4.1/wisecfg/wag85 wise2.4.1/wisecfg/wise.2 wise2.4.1/wisecfg/wise.per wise2.4.1/wisecfg/worm.gf sudo -u fink-bld [ENV] sh -c /tmp/fink.v5pCM perl -pi -e 's|getline|wise2_getline|g' src/HMMer2/sqio.c perl -pi -e 's|glib-config --cflags|pkg-config --cflags glib-2.0|g; s|glib-config --libs|pkg-config --libs glib-2.0|g' `grep -lr glib-config *` sudo -u fink-bld [ENV] sh -c /tmp/fink._kUgY /tmp/fink.sDsco + cd src + export PKG_CONFIG_PATH=/sw/lib/glib-2.0/pkgconfig-strict: + PKG_CONFIG_PATH=/sw/lib/glib-2.0/pkgconfig-strict: + make all (cd base ; /Applications/Xcode.app/Contents/Developer/usr/bin/make CC="cc" CFLAGS="-c -O3 `pkg-config --cflags glib-2.0`" libwisebase.a ) cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include wiseconfig.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include wisestring.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include wiseerror.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include wisememman.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include wisefile.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include wiserandom.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include wisetime.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include wiseoverlay.c wisefile.dy:72:33: warning: format specifies type 'int' but the argument has type 'FILE *' (aka 'struct __sFILE *') [-Wformat] fprintf(stderr,"Closing %d\n",ofp); ~~ ^~~ cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include wisestreaminterface.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include commandline.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include linesubs.c 1 warning generated. ar ru libwisebase.a wiseconfig.o wisestring.o wiseerror.o wisememman.o wisefile.o wiserandom.o wisetime.o wiseoverlay.o wisestreaminterface.o commandline.o linesubs.o ar: creating archive libwisebase.a if test -x /bin/ranlib; then /bin/ranlib libwisebase.a; else exit 0; fi if test -x /usr/bin/ranlib; then /usr/bin/ranlib libwisebase.a; else exit 0; fi (cd HMMer2 ; /Applications/Xcode.app/Contents/Developer/usr/bin/make CC="cc" CFLAGS="-c -O3 `pkg-config --cflags glib-2.0`" libhmmer.a ) cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -c alphabet.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -c core_algorithms.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -c debug.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -c emit.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -c emulation.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -c histogram.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -c hmmio.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -c mathsupport.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -c masks.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -c misc.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -c modelmakers.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -c plan7.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -c plan9.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -c prior.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -c tophits.c prior.c:102:12: warning: implicitly declaring library function 'strcmp' with type 'int (const char *, const char *)' if (strcmp(sptr, "DIRICHLET") == 0) pri->strategy = PRI_DCHLET; ^ prior.c:102:12: note: please include the header or explicitly provide a declaration for 'strcmp' cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -c trace.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -c aligneval.c 1 warning generated. cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -c alignio.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -c cluster.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -c dayhoff.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -c file.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -c getopt.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -c gnuregex.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -c interleaved.c gnuregex.c:1616:17: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -c iupac.c gnuregex.c:1636:17: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -c msf.c gnuregex.c:3758:19: warning: cast to 'fail_stack_elt_t' (aka 'unsigned char *') from smaller integer type 'unsigned int' [-Wint-to-pointer-cast] PUSH_FAILURE_POINT (p1 + mcnt, d, -2); ^ gnuregex.c:2394:5: note: expanded from macro 'PUSH_FAILURE_POINT' PUSH_FAILURE_ITEM (lowest_active_reg); \ ^ gnuregex.c:2315:42: note: expanded from macro 'PUSH_FAILURE_ITEM' fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item ^ gnuregex.c:3758:19: warning: cast to 'fail_stack_elt_t' (aka 'unsigned char *') from smaller integer type 'unsigned int' [-Wint-to-pointer-cast] gnuregex.c:2397:5: note: expanded from macro 'PUSH_FAILURE_POINT' PUSH_FAILURE_ITEM (highest_active_reg); \ ^ gnuregex.c:2315:42: note: expanded from macro 'PUSH_FAILURE_ITEM' fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item ^ gnuregex.c:3905:11: warning: cast to 'fail_stack_elt_t' (aka 'unsigned char *') from smaller integer type 'unsigned int' [-Wint-to-pointer-cast] PUSH_FAILURE_POINT (p + mcnt, NULL, -2); ^ gnuregex.c:2394:5: note: expanded from macro 'PUSH_FAILURE_POINT' PUSH_FAILURE_ITEM (lowest_active_reg); \ ^ gnuregex.c:2315:42: note: expanded from macro 'PUSH_FAILURE_ITEM' fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item ^ gnuregex.c:3905:11: warning: cast to 'fail_stack_elt_t' (aka 'unsigned char *') from smaller integer type 'unsigned int' [-Wint-to-pointer-cast] gnuregex.c:2397:5: note: expanded from macro 'PUSH_FAILURE_POINT' PUSH_FAILURE_ITEM (highest_active_reg); \ ^ gnuregex.c:2315:42: note: expanded from macro 'PUSH_FAILURE_ITEM' fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item ^ gnuregex.c:3958:11: warning: cast to 'fail_stack_elt_t' (aka 'unsigned char *') from smaller integer type 'unsigned int' [-Wint-to-pointer-cast] PUSH_FAILURE_POINT (p + mcnt, d, -2); ^ gnuregex.c:2394:5: note: expanded from macro 'PUSH_FAILURE_POINT' PUSH_FAILURE_ITEM (lowest_active_reg); \ ^ gnuregex.c:2315:42: note: expanded from macro 'PUSH_FAILURE_ITEM' fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item ^ gnuregex.c:3958:11: warning: cast to 'fail_stack_elt_t' (aka 'unsigned char *') from smaller integer type 'unsigned int' [-Wint-to-pointer-cast] gnuregex.c:2397:5: note: expanded from macro 'PUSH_FAILURE_POINT' PUSH_FAILURE_ITEM (highest_active_reg); \ ^ gnuregex.c:2315:42: note: expanded from macro 'PUSH_FAILURE_ITEM' fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item ^ gnuregex.c:4097:11: warning: cast to 'fail_stack_elt_t' (aka 'unsigned char *') from smaller integer type 'unsigned int' [-Wint-to-pointer-cast] PUSH_FAILURE_POINT (0, 0, -2); ^ gnuregex.c:2394:5: note: expanded from macro 'PUSH_FAILURE_POINT' PUSH_FAILURE_ITEM (lowest_active_reg); \ ^ gnuregex.c:2315:42: note: expanded from macro 'PUSH_FAILURE_ITEM' fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item ^ gnuregex.c:4097:11: warning: cast to 'fail_stack_elt_t' (aka 'unsigned char *') from smaller integer type 'unsigned int' [-Wint-to-pointer-cast] gnuregex.c:2397:5: note: expanded from macro 'PUSH_FAILURE_POINT' PUSH_FAILURE_ITEM (highest_active_reg); \ ^ gnuregex.c:2315:42: note: expanded from macro 'PUSH_FAILURE_ITEM' fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item ^ gnuregex.c:4110:11: warning: cast to 'fail_stack_elt_t' (aka 'unsigned char *') from smaller integer type 'unsigned int' [-Wint-to-pointer-cast] PUSH_FAILURE_POINT (0, 0, -2); ^ gnuregex.c:2394:5: note: expanded from macro 'PUSH_FAILURE_POINT' PUSH_FAILURE_ITEM (lowest_active_reg); \ ^ gnuregex.c:2315:42: note: expanded from macro 'PUSH_FAILURE_ITEM' fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item ^ gnuregex.c:4110:11: warning: cast to 'fail_stack_elt_t' (aka 'unsigned char *') from smaller integer type 'unsigned int' [-Wint-to-pointer-cast] gnuregex.c:2397:5: note: expanded from macro 'PUSH_FAILURE_POINT' PUSH_FAILURE_ITEM (highest_active_reg); \ ^ gnuregex.c:2315:42: note: expanded from macro 'PUSH_FAILURE_ITEM' fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item ^ cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -c revcomp.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -c selex.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -c sqerror.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -c sqio.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -c sre_ctype.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -c sre_math.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -c sre_string.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -c stack.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -c translate.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -c types.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -c weight.c 12 warnings generated. ar rcv libhmmer.a alphabet.o core_algorithms.o debug.o emit.o emulation.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o prior.o tophits.o trace.o aligneval.o alignio.o cluster.o dayhoff.o file.o getopt.o gnuregex.o interleaved.o iupac.o msf.o revcomp.o selex.o sqerror.o sqio.o sre_ctype.o sre_math.o sre_string.o stack.o translate.o types.o weight.o a - alphabet.o a - core_algorithms.o a - debug.o a - emit.o a - emulation.o a - histogram.o a - hmmio.o a - mathsupport.o a - masks.o a - misc.o a - modelmakers.o a - plan7.o a - plan9.o a - prior.o a - tophits.o a - trace.o a - aligneval.o a - alignio.o a - cluster.o a - dayhoff.o a - file.o a - getopt.o a - gnuregex.o a - interleaved.o a - iupac.o a - msf.o a - revcomp.o a - selex.o a - sqerror.o a - sqio.o a - sre_ctype.o a - sre_math.o a - sre_string.o a - stack.o a - translate.o a - types.o a - weight.o if test -x /bin/ranlib; then /bin/ranlib libhmmer.a; else exit 0; fi if test -x /usr/bin/ranlib; then /usr/bin/ranlib libhmmer.a; else exit 0; fi if test -x ranlib; then ranlib libhmmer.a; else exit 0; fi chmod 644 libhmmer.a (cd dynlibsrc ; /Applications/Xcode.app/Contents/Developer/usr/bin/make CC="cc" CFLAGS="-c -O3 `pkg-config --cflags glib-2.0`" libdyna.a ) cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ packaln.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ aln.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ dnamatrix.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ probability.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ alnrange.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ alnconvert.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ basematrix.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ shattermatrix.c aln.dy:867:65: warning: data argument not used by format string [-Wformat-extra-args] fprintf(ofp," {%3.2f} ",(double)(*score_to_double)(cuml),cuml); ~~~~~~~~~~~~ ^ cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ matrixdebug.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ dpenvelope.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ dbsearchimpl.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ dprunimpl.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ complexsequence.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ complexevalset.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ complexconsensi.c dpenvelope.dy:68:1: warning: control may reach end of non-void function [-Wreturn-type] } ^ cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ sequence.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ sequencestream.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ seqalign.c 1 warning generated. cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ hitlist.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ hsp.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ hspstream.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ codon.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ compmat.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ codonmatrix.c 1 warning generated. cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ codonmapper.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ sequencedb.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ hscore.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ seqlookup.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ arrayseqlookup.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ genericindexresult.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ linkedlist_lookpos.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ singlenumberspace.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ histogram.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ searchstatinterface.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ searchstatlookup.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ proteindb.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ protein.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ pairbase.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ pairbaseseq.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ genomicdb.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ randommodel.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ randomdb.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ genomic.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ cdna.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ cdnadb.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ dna.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ embl.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ genomicregion.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ gene.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ transcript.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ translation.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ btcanvas.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ asciibtcanvas.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ dynlibcross.c ar ru libdyna.a packaln.o aln.o dnamatrix.o probability.o alnrange.o alnconvert.o basematrix.o shattermatrix.o matrixdebug.o dpenvelope.o dbsearchimpl.o dprunimpl.o complexsequence.o complexevalset.o complexconsensi.o sequence.o sequencestream.o seqalign.o hitlist.o hsp.o hspstream.o codon.o compmat.o codonmatrix.o codonmapper.o sequencedb.o hscore.o seqlookup.o arrayseqlookup.o genericindexresult.o linkedlist_lookpos.o singlenumberspace.o histogram.o searchstatinterface.o searchstatlookup.o proteindb.o protein.o pairbase.o pairbaseseq.o genomicdb.o randommodel.o randomdb.o genomic.o cdna.o cdnadb.o dna.o embl.o genomicregion.o gene.o transcript.o translation.o btcanvas.o asciibtcanvas.o dynlibcross.o ar: creating archive libdyna.a if test -x /bin/ranlib; then /bin/ranlib libdyna.a; else exit 0; fi if test -x /usr/bin/ranlib; then /usr/bin/ranlib libdyna.a; else exit 0; fi (cd dynlibsrc ; /Applications/Xcode.app/Contents/Developer/usr/bin/make CC="cc" CFLAGS="-c -O3 `pkg-config --cflags glib-2.0`" libdyna_glib.a ) cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ subseqhash.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ intallocator.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ proteinstreamedindex.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ shadowseq.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ shadowseqindex.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ hsphandler.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ hspscaninterface.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ hsp2hitscan.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ hsplookupscan.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ hsplookupthreaded.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ hspthreadeddb.c subseqhash.dy:111:29: warning: cast to 'gconstpointer' (aka 'const void *') from smaller integer type 'int' [-Wint-to-void-pointer-cast] if( g_hash_table_lookup(h,(gconstpointer)seq_number) == NULL ) { ^ subseqhash.dy:128:85: warning: cast to 'gconstpointer' (aka 'const void *') from smaller integer type 'int' [-Wint-to-void-pointer-cast] return new_linkedl_SeqLookupResultInterface((SeqLookupPos *)g_hash_table_lookup(h,(gconstpointer)seq_number)); ^ subseqhash.dy:160:54: warning: cast to 'gconstpointer' (aka 'const void *') from smaller integer type 'int' [-Wint-to-void-pointer-cast] if((ret = (SeqLookupPos *) g_hash_table_lookup(h,(gconstpointer)seq_number)) == NULL ) { ^ subseqhash.dy:161:29: warning: cast to 'gpointer' (aka 'void *') from smaller integer type 'int' [-Wint-to-void-pointer-cast] g_hash_table_insert(h,(gpointer)seq_number,p); ^ subseqhash.dy:188:52: warning: cast to 'gconstpointer' (aka 'const void *') from smaller integer type 'int' [-Wint-to-void-pointer-cast] if((ret = (SeqLookupPos *) g_hash_table_lookup(h,(gconstpointer)seq_number)) == NULL ) { ^ subseqhash.dy:189:27: warning: cast to 'gpointer' (aka 'void *') from smaller integer type 'int' [-Wint-to-void-pointer-cast] g_hash_table_insert(h,(gpointer)seq_number,p); ^ hsp2hitscan.dy:210:4: warning: format specifies type 'int' but the argument has type '__darwin_time_t' (aka 'long') [-Wformat] shadowseqindex.dy: use.ru_utime.tv_sec, ^~~~~~~~~~~~~~~~~~~ 285:hsp2hitscan.dy:211:4: warning: format specifies type 'int' but the argument has type 'long' [-Wformat] 59 use.ru_utime.tv_sec/1000, ^~~~~~~~~~~~~~~~~~~~~~~~ :hsp2hitscan.dy:212 warning: :format specifies type 'double' but the argument has type 'unsigned long' [-Wformat] 4: warning fprintf(ofp,"Head memory %d [%.2f Mbytes]\n",total_head,(total_head*sizeof(ShadowArraySeqHead))/100000); ~~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ %.2lu : format specifies type 'int' but the argument has type '__darwin_time_t' (aka 'long') [-Wformat] use.ru_stime.tv_sec, ^~~~~~~~~~~~~~~~~~~ hsp2hitscan.dy:213:4: warning: format specifies type 'int' but the argument has type 'long' [-Wformat] use.ru_stime.tv_sec/1000 ^~~~~~~~~~~~~~~~~~~~~~~~ hsp2hitscan.dy:274:4: warning: format specifies type 'int' but the argument has type '__darwin_time_t' (aka 'long') [-Wformat] use.ru_utime.tv_sec, ^~~~~~~~~~~~~~~~~~~ hsp2hitscan.dy:275:4: warning: format specifies type 'int' but the argument has type 'long' [-Wformat] use.ru_utime.tv_sec/1000, ^~~~~~~~~~~~~~~~~~~~~~~~ hsp2hitscan.dy:276:4: warning: format specifies type 'int' but the argument has type '__darwin_time_t' (aka 'long') [-Wformat] use.ru_stime.tv_sec, ^~~~~~~~~~~~~~~~~~~ hsp2hitscan.dy:277:4: warning: format specifies type 'int' but the argument has type 'long' [-Wformat] use.ru_stime.tv_sec/1000 ^~~~~~~~~~~~~~~~~~~~~~~~ hsp2hitscan.dy:287:4: warning: format specifies type 'int' but the argument has type '__darwin_time_t' (aka 'long') [-Wformat] use.ru_utime.tv_sec, ^~~~~~~~~~~~~~~~~~~ hsp2hitscan.dy:288:4: warning: format specifies type 'int' but the argument has type 'long' [-Wformat] use.ru_utime.tv_sec/1000, ^~~~~~~~~~~~~~~~~~~~~~~~ hsp2hitscan.dy:289:4: warning: format specifies type 'int' but the argument has type '__darwin_time_t' (aka 'long') [-Wformat] use.ru_stime.tv_sec, ^~~~~~~~~~~~~~~~~~~ hsp2hitscan.dy:290:4: warning: format specifies type 'int' but the argument has type 'long' [-Wformat] use.ru_stime.tv_sec/1000 ^~~~~~~~~~~~~~~~~~~~~~~~ hsp2hitscan.dy:303:4: warning: format specifies type 'int' but the argument has type '__darwin_time_t' (aka 'long') [-Wformat] use.ru_utime.tv_sec, ^~~~~~~~~~~~~~~~~~~ hsp2hitscan.dy:304:4: warning: format specifies type 'int' but the argument has type 'long' [-Wformat] use.ru_utime.tv_sec/1000, ^~~~~~~~~~~~~~~~~~~~~~~~ hsp2hitscan.dy:305:4: warning: format specifies type 'int' but the argument has type '__darwin_time_t' (aka 'long') [-Wformat] use.ru_stime.tv_sec, ^~~~~~~~~~~~~~~~~~~ hsp2hitscan.dy:306:4: warning: format specifies type 'int' but the argument has type 'long' [-Wformat] use.ru_stime.tv_sec/1000 ^~~~~~~~~~~~~~~~~~~~~~~~ 6 warnings generated. cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ hspscanruntime.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ hsptwohitscan.c hsplookupthreaded.dy:263:55: warning: format specifies type 'int' but the argument has type 'long' [-Wformat] fprintf(stderr,"retrieved array with %d elements\n",current_oph); ~~ ^~~~~~~~~~~ %ld hsplookupthreaded.dy:567:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ hspthreadeddb.dy:154:73: warning: format specifies type 'int' but the argument has type 'Wise2_HSPDatabaseSegment *' (aka 'struct Wise2_HSPDatabaseSegment *') [-Wformat] fprintf(stderr,"For segment %d, finished query with %d (%d) linear\n",seg,(int)seg->lm,seg->lm->len); ~~ ^~~ 1 warning generated. cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ proteinindexcons.c 16 warnings generated. cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ dnaindexcons.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ staticseq.c 1 warning generated. 2 warnings generated. ar ru libdyna_glib.a subseqhash.o intallocator.o proteinstreamedindex.o shadowseq.o shadowseqindex.o hsphandler.o hspscaninterface.o hsp2hitscan.o hsplookupscan.o hsplookupthreaded.o hspthreadeddb.o hspscanruntime.o hsptwohitscan.o proteinindexcons.o dnaindexcons.o staticseq.o ar: creating archive libdyna_glib.a if test -x /bin/ranlib; then /bin/ranlib libdyna_glib.a; else exit 0; fi if test -x /usr/bin/ranlib; then /usr/bin/ranlib libdyna_glib.a; else exit 0; fi (cd external ; /Applications/Xcode.app/Contents/Developer/usr/bin/make CC="cc" CFLAGS="-c -O3 `pkg-config --cflags glib-2.0`" all ) (cd mott; make CC="cc" CFLAGS="-c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include" all) cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I/sw/include -c -o mott_api.o mott_api.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I/sw/include -c -o gaplib.o gaplib.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../../dynlibsrc -I../../base wise2_mott_bridge.c mott_api.c:64:3: warning: implicit declaration of function 'free' is invalid in C99 [-Wimplicit-function-declaration] free(freq0); ^ mott_api.c:179:16: warning: implicitly declaring library function 'calloc' with type 'void *(unsigned long, unsigned long)' h = (double*)calloc(*hmax-*hmin+1,sizeof(double))-*hmin; ^ mott_api.c:179:16: note: please include the header or explicitly provide a declaration for 'calloc' mott_api.c:207:12: warning: implicit declaration of function 'toupper' is invalid in C99 [-Wimplicit-function-declaration] freq[toupper(seq[n])]++; ^ 3 warnings generated. ar ru libmott.a mott_api.o gaplib.o wise2_mott_bridge.o ar: creating archive libmott.a if test -x /bin/ranlib; then /bin/ranlib libmott.a; else exit 0; fi if test -x /usr/bin/ranlib; then /usr/bin/ranlib libmott.a; else exit 0; fi (cd socket ; /Applications/Xcode.app/Contents/Developer/usr/bin/make CC="cc" CFLAGS="-c -O3 `pkg-config --cflags glib-2.0`" libwisesocket.a ) cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ functionserver.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ functionclient.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ anonobj.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ transferinterface.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ directsocketwrite.c functionclient.dy:193:24: warning: incompatible pointer types passing 'struct sockaddr_in *' to parameter of type 'const struct sockaddr *' [-Wincompatible-pointer-types] connect(out->socket, &server, sizeof(server)); ^~~~~~~ /usr/include/sys/socket.h:558:41: note: passing argument to parameter here int connect(int, const struct sockaddr *, socklen_t) __DARWIN_ALIAS_C( connect); ^ 1 warning generated. ar ru libwisesocket.a functionserver.o functionclient.o anonobj.o transferinterface.o directsocketwrite.o ar: creating archive libwisesocket.a if test -x /bin/ranlib; then /bin/ranlib libwisesocket.a; else exit 0; fi if test -x /usr/bin/ranlib; then /usr/bin/ranlib libwisesocket.a; else exit 0; fi (cd dnaindex ; /Applications/Xcode.app/Contents/Developer/usr/bin/make CC="cc" CFLAGS="-c -O3 `pkg-config --cflags glib-2.0`" all ) cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_assembly.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_index_interface.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_direct.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_hash.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_count.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_glib_index.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models singleseqspace.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models dnamapping.c kmer_hash.dy:318:41: warning: format specifies type 'unsigned long' but the argument has type 'kmer_t' (aka 'long long') [-Wformat] fprintf(stderr, "min_kmer: %016lx\n", khi->min_kmer); ~~~~~~ ^~~~~~~~~~~~~ %016llx kmer_hash.dy:319:41: warning: format specifies type 'unsigned long' but the argument has type 'kmer_t' (aka 'long long') [-Wformat] fprintf(stderr, "max_kmer: %016lx\n", khi->max_kmer); ~~~~~~ ^~~~~~~~~~~~~ %016llx cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models largeseqreader.c kmer_assembly.dy:296:44: warning: format specifies type 'long' but the argument has type 'kmer_t' (aka 'long long') [-Wformat] fprintf(ofp,"Node %ld of sequence %s \n",node->number,buffer); ~~~ ^~~~~~~~~~~~ %lld kmer_assembly.dy:302:104: warning: format specifies type 'long' but the argument has type 'kmer_t' (aka 'long long') [-Wformat] fprintf(ofp," ... prev ... %c, %d to %ld\n",node->prev[i]->base,node->prev[i]->sequence_label_len,node->prev[i]->prev->number); ~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~ %lld kmer_assembly.dy:309:104: warning: format specifies type 'long' but the argument has type 'kmer_t' (aka 'long long') [-Wformat] fprintf(ofp," ... next ... %c, %d to %ld\n",node->next[i]->base,node->next[i]->sequence_label_len,node->next[i]->next->number); ~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~ %lld kmer_assembly.dy:365:88: warning: format specifies type 'long' but the argument has type 'KmerAssemblyLink *' (aka 'struct KmerAssemblyLink *') [-Wformat] fprintf(stderr," ...unable to remove label %ld from link %ld (%d labels)\n",label,kal,kal->sequence_label_len); ~~~ ^~~ kmer_assembly.dy:367:36: warning: more '%' conversions than data arguments [-Wformat] fprintf(stderr," [%ld] is %d label\n",kal->sequence_label[i]); ~^ cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_assembly_untangler.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_assembly_contig.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_assembly_error.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models assembly.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models assembly_stream_interface.c 2 warnings generated. cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models assembly_stream_fasta.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models assembly_sanger_project.c kmer_assembly_untangler.dy:120:80: warning: format specifies type 'long' but the argument has type 'kmer_t' (aka 'long long') [-Wformat] fprintf(stderr,"TANGLE: Node %ld, %s has forward %d and back %d links\n",node->number,buffer,node->next_len,node->prev_len); ~~~ ^~~~~~~~~~~~ %lld kmer_assembly_untangler.dy:141:71: warning: format specifies type 'long' but the argument has type 'kmer_t' (aka 'long long') [-Wformat] fprintf(stderr,"Will attempt untangle starting at %ld to %ld\n",node->prev[i]->prev->number,node->number); ~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~ %lld kmer_assembly_untangler.dy:141:99: warning: format specifies type 'long' but the argument has type 'kmer_t' (aka 'long long') [-Wformat] fprintf(stderr,"Will attempt untangle starting at %ld to %ld\n",node->prev[i]->prev->number,node->number); ~~~ ^~~~~~~~~~~~ %lld kmer_assembly_untangler.dy:157:73: warning: format specifies type 'long' but the argument has type 'kmer_t' (aka 'long long') [-Wformat] fprintf(stderr,"RESOLVED: Node %ld [%s] Fully untangled now...\n",node->number,buffer); ~~~ ^~~~~~~~~~~~ %lld kmer_assembly_untangler.dy:159:69: warning: format specifies type 'long' but the argument has type 'kmer_t' (aka 'long long') [-Wformat] fprintf(stderr,"UNRESOLVED: Node %ld [%s] still tangled...\n",node->number,buffer); ~~~ ^~~~~~~~~~~~ %lld kmer_assembly_untangler.dy:444:89: warning: format specifies type 'long' but the argument has type 'kmer_t' (aka 'long long') [-Wformat] fprintf(stderr,"looking at node %ld with path length %d, next length %d depth %d\n",current->next->number,pathlen,current->next->next_len,current->sequence_label_len); ~~~ ^~~~~~~~~~~~~~~~~~~~~ %lld kmer_assembly_untangler.dy:568:75: warning: incompatible pointer types passing 'long [10000]' to parameter of type 'int *' [-Wincompatible-pointer-types] lift_backward_tangled_tail(kai,newpath->stack[newpath->stack_len-1],path,transferred_label,transferred_pos,transferred_len); ^~~~~~~~~~~~~~~~~ ./kmer_assembly_untangler.h:174:116: note: passing argument to parameter 'start_label' here void Wise2_lift_backward_tangled_tail(KmerAssemblyIndex * kai,KmerAssemblyLink * new,KmerAssemblyPath * tail,int * start_label,SinglePosSequence ** positions,int label_len); ^ kmer_assembly_untangler.dy:746:149: warning: format specifies type 'long' but the argument has type 'kmer_t' (aka 'long long') [-Wformat] fprintf(stderr,"Moving stack position %d, depth %d, transfer %d, between %ld [%s] and %ld [%s]\n",i,kap->stack[i]->sequence_label_len,label_len,kap->stack[i]->prev->number,back,kap->stack[i]->next->number,forw); ~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~ %lld kmer_assembly_untangler.dy:746:182: warning: format specifies type 'long' but the argument has type 'kmer_t' (aka 'long long') [-Wformat] fprintf(stderr,"Moving stack position %d, depth %d, transfer %d, between %ld [%s] and %ld [%s]\n",i,kap->stack[i]->sequence_label_len,label_len,kap->stack[i]->prev->number,back,kap->stack[i]->next->number,forw); ~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~ %lld cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models assembly_stream_cons.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models compressed_protein_index.c 5 warnings generated. kmer_assembly_error.dy:93:66: warning: format specifies type 'long' but the argument has type 'kmer_t' (aka 'long long') [-Wformat] fprintf(stderr,"Marking node (%ld) [%s] as next tangled\n",node->number,buffer); ~~~ ^~~~~~~~~~~~ %lld kmer_assembly_error.dy:105:66: warning: format specifies type 'long' but the argument has type 'kmer_t' (aka 'long long') [-Wformat] fprintf(stderr,"Marking node (%ld) [%s] as prev tangled\n",node->number,buffer); ~~~ ^~~~~~~~~~~~ %lld kmer_assembly_error.dy:351:127: warning: format specifies type 'int' but the argument has type 'int *' [-Wformat] fprintf(stderr,"in considering indel (%d, path %d), real (%c) and error (%c) do not agree at position %d,%d\n",delete_length,current_path,real->base,error->base,real_pos,error_pos); ~~ ^~~~~~~~~~~~ compressed_protein_index.dy:223:10: warning: incompatible pointer to integer conversion returning 'void *' from a function with result type 'boolean' (aka 'int') [-Wint-conversion] return NULL; ^~~~ /usr/include/sys/_types/_null.h:29:15: note: expanded from macro 'NULL' #define NULL __DARWIN_NULL ^~~~~~~~~~~~~ /usr/include/sys/_types.h:91:23: note: expanded from macro '__DARWIN_NULL' #define __DARWIN_NULL ((void *)0) ^~~~~~~~~~~ 3 warnings generated. 1 warning generated. 9 warnings generated. (cd network ; /Applications/Xcode.app/Contents/Developer/usr/bin/make CC="cc" CFLAGS="-c -O3 `pkg-config --cflags glib-2.0`" all ) cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ -I../socket -I../dynlibsrc -I../dnaindex wise_proteinindex_server.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ -I../socket -I../dynlibsrc -I../dnaindex net_hspscan.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ -I../socket -I../dynlibsrc -I../dnaindex client_multihspscan.c client_multihspscan.dy:128:1: warning: control may reach end of non-void function [-Wreturn-type] } ^ 1 warning generated. cc -g -o scanwise_server wise_proteinindex_server.o net_hspscan.o ../dnaindex/compressed_protein_index.o ../dnaindex/kmer_index_interface.o ../dnaindex/singleseqspace.o ../dnaindex/kmer_direct.o -ldyna_glib -ldyna -lwisesocket -lwisebase -g -L../base/ -L../socket -L../dynlibsrc -L../dnaindex -lm `pkg-config --libs glib-2.0` -lpthread (cd models ; /Applications/Xcode.app/Contents/Developer/usr/bin/make CC="cc" CFLAGS="-c -O3 `pkg-config --cflags glib-2.0`" EXTRALIBS="-lm" HMMER_DEFINE="HMMER_INTERNAL" HMMER_INCLUDE="../HMMer2/" HMMER_LIBS="../HMMer2/" all ) cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ -I../dynlibsrc/ dnal.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ -I../dynlibsrc/ dnaalign.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ -I../dynlibsrc/ seqaligndisplay.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ -I../dynlibsrc/ psw.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ -I../dynlibsrc/ proteinsw.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ -I../dynlibsrc/ sw_wrap.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ -I../dynlibsrc/ abc.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ -I../dynlibsrc/ pba.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ -I../dynlibsrc/ pswdb.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ -I../dynlibsrc/ dbac.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ -I../dynlibsrc/ dba.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ -I../dynlibsrc/ slimdba.c dbac.c:413:45: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat] fprintf(stderr,"Got %d with %d vs %d\n",i,strlen(seq),one->len); ~~ ^~~~~~~~~~~ %lu cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ -I../dynlibsrc/ bigdba.c 1 warning generated. cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ -I../dynlibsrc/ dbadisplay.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include estwise.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ -I. cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ -I../dynlibsrc/ geneparser21.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ -I../dynlibsrc/ geneparameter.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ -I../dynlibsrc/ genestats.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ -I../dynlibsrc/ genewisehsp.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ -I../dynlibsrc/ geneutil.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ -I../dynlibsrc/ geneoutput.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ -I../dynlibsrc/ threestatemodel.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ -I../dynlibsrc/ genefrequency.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ -I../dynlibsrc/ splicesitemodeler.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ -I../dynlibsrc/ genewise4.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ -I../dynlibsrc/ genewise6.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ -I../dynlibsrc/ genestretch6.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ -I../dynlibsrc/ genewise21.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ -I../dynlibsrc/ geneloop21.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ -I../dynlibsrc/ geneloop6.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ -I../dynlibsrc/ genephase6.c genephase6.c:873:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ -I../dynlibsrc/ gwlite.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ -I../dynlibsrc/ gwlitemodel.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ -I../dynlibsrc/ gwrap.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ -I../dynlibsrc/ matchsum.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ -I../dynlibsrc/ estwrap.c 1 warning generated. cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ -I../dynlibsrc/ genewisemodel.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ -I../dynlibsrc/ phasemodel.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ -I../dynlibsrc/ cdparser.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ -I../dynlibsrc/ genedisplay.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ -I../dynlibsrc/ estwise3.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ -I../dynlibsrc/ estslim3.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ -I../dynlibsrc/ estloop3.c genedisplay.dy:493:37: warning: data argument not used by format string [-Wformat-extra-args] sprintf(buffer," Intron ??? ",in_number); ~~~~~~~~~~~~~~~~ ^ /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 -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ -I../dynlibsrc/ estfrag3.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ -I../dynlibsrc/ estslimloop.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ -I../dynlibsrc/ gwquickdb.c gwquickdb.dy:46:1: warning: control may reach end of non-void function [-Wreturn-type] } ^ gwquickdb.dy:65:1: warning: control may reach end of non-void function [-Wreturn-type] } ^ 2 warnings generated. cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ -I../dynlibsrc/ threestatedb.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ -I../dynlibsrc/ pfamhmmer1db.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ -I../dynlibsrc/ pwmdna.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../HMMer2/ -DHMMER_INTERNAL -I../base/ -I../dynlibsrc/ wise2xhmmer2.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ -I../dynlibsrc/ genewisemodeldb.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ -I../dynlibsrc/ seqhit.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ -I../dynlibsrc/ standardout.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ -I../dynlibsrc/ geneparser4.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ -I../dynlibsrc/ estquick3.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include genewise.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ -I. cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include genewisedb.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include estwisedb.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ -I../dynlibsrc/ genomewise.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ -I../dynlibsrc/ genomewise9.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ -I../dynlibsrc/ genome_evidence.c genomewise9.c:745:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ genome_evidence.dy:61:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ -I../dynlibsrc/ est_evidence.c 1 warning generated. cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ -I../dynlibsrc/ sywise.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ -I../dynlibsrc/ sywise20.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ -I../dynlibsrc/ syexonmodel.c est_evidence.dy:142:16: warning: incompatible pointer types assigning to 'int (*)(void *)' from 'Wise2_EstEvidence *(Wise2_EstEvidence *)' [-Wincompatible-pointer-types] in->geu_free = free_EstEvidence; ^ ~~~~~~~~~~~~~~~~ sywise20.c:764:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ -I../dynlibsrc/ pseudowise.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ -I../dynlibsrc/ pseudowise7.c 1 warning generated. cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ -I../dynlibsrc/ `pkg-config --cflags glib-2.0` promoterwise.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ -I../dynlibsrc/ localdba.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ -I../dynlibsrc/ `pkg-config --cflags glib-2.0` localcishit.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ -I../dynlibsrc/ localcispara.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ -I../dynlibsrc/ motifmatrix.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ -I../dynlibsrc/ motifmatrixdp.c motifmatrix.c:408:24: warning: incompatible pointer to integer conversion assigning to 'char' from 'void *' [-Wint-conversion] out->mat[i][j] = NULL; ^ ~~~~ 1 warning generated. cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ -I../dynlibsrc/ transfactor.c transfactor.dy:339:1: warning: control may reach end of non-void function [-Wreturn-type] } ^ 1 warning generated. cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ -I../dynlibsrc/ pairwiseshortdna.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ -I../dynlibsrc/ -o scanwisep_wiseserver.o -DSCAN_WISESERVER -I../network -I../socket -I../external/mott scanwisep.c cc -c -O3 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I../base/ -I../dynlibsrc/ `pkg-config --cflags glib-2.0` hsp2aln_sw.c cc -o dnal dnal.o dnaalign.o seqaligndisplay.o -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm hsp2aln_sw.dy:119:71: warning: '&&' within '||' [-Wlogical-op-parentheses] if( tm->current_pos >= tm->input->len || tm->para->no_hitalns > 0 && tm->current_pos > tm->para->no_hitalns || ~~ ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hsp2aln_sw.dy:119:71: note: place parentheses around the '&&' expression to silence this warning if( tm->current_pos >= tm->input->len || tm->para->no_hitalns > 0 && tm->current_pos > tm->para->no_hitalns || ^ ( ) cc -o psw psw.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm cc -o pswdb pswdb.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm 1 warning generated. cc -o dba dbac.o dba.o slimdba.o bigdba.o dbadisplay.o -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm cc -g -o promoterwise promoterwise.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm `pkg-config --libs glib-2.0` -lpthread 1 warning generated. cc -o scanwise scanwisep_wiseserver.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../network/net_hspscan.o ../network/client_multihspscan.o -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -L../external/mott -L../socket -lmott -ldyna_glib -ldyna -lwisesocket -lwisebase -lm -lpthread ar ru libmodel.a geneparser21.o geneparameter.o genestats.o genewisehsp.o geneutil.o geneoutput.o threestatemodel.o genefrequency.o splicesitemodeler.o genewise4.o genewise6.o genestretch6.o genewise21.o geneloop21.o geneloop6.o genephase6.o gwlite.o gwlitemodel.o gwrap.o matchsum.o estwrap.o genewisemodel.o phasemodel.o cdparser.o genedisplay.o estwise3.o estslim3.o estloop3.o estfrag3.o estslimloop.o gwquickdb.o threestatedb.o pfamhmmer1db.o pwmdna.o wise2xhmmer2.o genewisemodeldb.o seqhit.o standardout.o geneparser4.o sw_wrap.o abc.o pba.o seqaligndisplay.o dbadisplay.o proteinsw.o estquick3.o cc -g -o estwise estwise.o geneparser21.o geneparameter.o genestats.o genewisehsp.o geneutil.o geneoutput.o threestatemodel.o genefrequency.o splicesitemodeler.o genewise4.o genewise6.o genestretch6.o genewise21.o geneloop21.o geneloop6.o genephase6.o gwlite.o gwlitemodel.o gwrap.o matchsum.o estwrap.o genewisemodel.o phasemodel.o cdparser.o genedisplay.o estwise3.o estslim3.o estloop3.o estfrag3.o estslimloop.o gwquickdb.o threestatedb.o pfamhmmer1db.o pwmdna.o wise2xhmmer2.o genewisemodeldb.o seqhit.o standardout.o geneparser4.o sw_wrap.o abc.o pba.o seqaligndisplay.o dbadisplay.o proteinsw.o estquick3.o -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -lhmmer -ldyna_glib -ldyna -lwisebase -lm cc -o genewise genewise.o geneparser21.o geneparameter.o genestats.o genewisehsp.o geneutil.o geneoutput.o threestatemodel.o genefrequency.o splicesitemodeler.o genewise4.o genewise6.o genestretch6.o genewise21.o geneloop21.o geneloop6.o genephase6.o gwlite.o gwlitemodel.o gwrap.o matchsum.o estwrap.o genewisemodel.o phasemodel.o cdparser.o genedisplay.o estwise3.o estslim3.o estloop3.o estfrag3.o estslimloop.o gwquickdb.o threestatedb.o pfamhmmer1db.o pwmdna.o wise2xhmmer2.o genewisemodeldb.o seqhit.o standardout.o geneparser4.o sw_wrap.o abc.o pba.o seqaligndisplay.o dbadisplay.o proteinsw.o estquick3.o -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -lhmmer -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase -lm cc -g -o genewisedb genewisedb.o geneparser21.o geneparameter.o genestats.o genewisehsp.o geneutil.o geneoutput.o threestatemodel.o genefrequency.o splicesitemodeler.o genewise4.o genewise6.o genestretch6.o genewise21.o geneloop21.o geneloop6.o genephase6.o gwlite.o gwlitemodel.o gwrap.o matchsum.o estwrap.o genewisemodel.o phasemodel.o cdparser.o genedisplay.o estwise3.o estslim3.o estloop3.o estfrag3.o estslimloop.o gwquickdb.o threestatedb.o pfamhmmer1db.o pwmdna.o wise2xhmmer2.o genewisemodeldb.o seqhit.o standardout.o geneparser4.o sw_wrap.o abc.o pba.o seqaligndisplay.o dbadisplay.o proteinsw.o estquick3.o -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -lhmmer -ldyna_glib -ldyna -lwisebase -lm cc -g -o estwisedb estwisedb.o geneparser21.o geneparameter.o genestats.o genewisehsp.o geneutil.o geneoutput.o threestatemodel.o genefrequency.o splicesitemodeler.o genewise4.o genewise6.o genestretch6.o genewise21.o geneloop21.o geneloop6.o genephase6.o gwlite.o gwlitemodel.o gwrap.o matchsum.o estwrap.o genewisemodel.o phasemodel.o cdparser.o genedisplay.o estwise3.o estslim3.o estloop3.o estfrag3.o estslimloop.o gwquickdb.o threestatedb.o pfamhmmer1db.o pwmdna.o wise2xhmmer2.o genewisemodeldb.o seqhit.o standardout.o geneparser4.o sw_wrap.o abc.o pba.o seqaligndisplay.o dbadisplay.o proteinsw.o estquick3.o -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -lhmmer -ldyna_glib -ldyna -lwisebase -lm cc -g -o genomewise genomewise.o genomewise9.o genome_evidence.o est_evidence.o geneoutput.o geneutil.o -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm cc -g -o pseudowise pseudowise.o pseudowise7.o geneparser21.o geneparameter.o genestats.o genewisehsp.o geneutil.o geneoutput.o threestatemodel.o genefrequency.o splicesitemodeler.o genewise4.o genewise6.o genestretch6.o genewise21.o geneloop21.o geneloop6.o genephase6.o gwlite.o gwlitemodel.o gwrap.o matchsum.o estwrap.o genewisemodel.o phasemodel.o cdparser.o genedisplay.o estwise3.o estslim3.o estloop3.o estfrag3.o estslimloop.o gwquickdb.o threestatedb.o pfamhmmer1db.o pwmdna.o wise2xhmmer2.o genewisemodeldb.o seqhit.o standardout.o geneparser4.o sw_wrap.o abc.o pba.o seqaligndisplay.o dbadisplay.o proteinsw.o estquick3.o -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -lhmmer -ldyna_glib -ldyna -lwisebase -lm ar: creating archive libmodel.a 1 warning generated. cc -g -o sywise sywise.o sywise20.o syexonmodel.o genestats.o pwmdna.o standardout.o geneutil.o -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm /Applications/Xcode.app/Contents/Developer/usr/bin/make bin mkdir bin cp models/pswdb models/psw models/genewisedb models/estwisedb models/estwise models/genewise models/dba models/dnal models/promoterwise network/scanwise_server models/scanwise ./bin csh welcome.csh Welcome to Wise2.4 The executable programs are in the ./bin directory You must set your WISECONFIGDIR to the config directory before using the programs ie, type setenv WISECONFIGDIR /sw/build.build/wise2-2.4.1-1/wise2.4.1/src/../wisecfg/ to try an example, try cd example and then ../bin/genewise road.pep human.genomic to build perl, type make perl and follow the instructions to test the package, type make test + export WISECONFIGDIR=/sw/build.build/wise2-2.4.1-1/wise2.4.1/wisecfg/ + WISECONFIGDIR=/sw/build.build/wise2-2.4.1-1/wise2.4.1/wisecfg/ + make test cd test ; perl testman.pl -cf ../wisecfg < short.test >>> Doing promoterwise promoterwise standard test >>> Calling [../bin/promoterwise -silent pw.human pw.mouse > TEMP-PW] >>> promoterwise ... Passed >>> Doing basic-cdna cdna test case (protein v cdna), all outputs >>> Calling [../bin/estwise short.pep short.dna -indel 1e-5 -subs 1e-5 -pretty -para -sum -alb -pal -silent -alg 333 > TEMP] >>> basic-cdna ... Passed >>> Doing basic-genomic genomic test case (protein v genomic), all outputs >>> Calling [../bin/genewise short.pep short.dna -pretty -para -genes -sum -cdna -trans -ace -gener -alb -pal -quiet -dymem linear > TEMP] >>> basic-genomic ... Passed >>> Doing hmm-binary-cdna cdna test case (protein v cdna), all outputs >>> Calling [../bin/estwise HMM.binary -indel 1e-5 -subs 1e-5 -hmmer short.dna -pretty -para -sum -alb -pal -quiet -alg 333L > TEMP] >>> hmm-binary-cdna ... Passed >>> Doing hmm-wrong-dna HMMs vs DNA sequence when there is no match >>> Calling [../bin/genewise wrong.hmm -hmmer short.dna -alg 623 -pal > TEMP] Information In making HSHNCPA1 a genomic sequence, converted 2 bases (0.5%) to N's from non ATGCN GeneWise6 Matrix calculation: [ 0] Cells 0%[ 1000] Cells 3%[ 2000] Cells 6%[ 3000] Cells 9%[ 4000] Cells 12%[ 5000] Cells 15%[ 6000] Cells 18%[ 7000] Cells 21%[ 8000] Cells 24%[ 9000] Cells 27%[ 10000] Cells 30%[ 11000] Cells 33%[ 12000] Cells 36%[ 13000] Cells 39%[ 14000] Cells 42%[ 15000] Cells 45%[ 16000] Cells 48%[ 17000] Cells 51%[ 18000] Cells 54%[ 19000] Cells 57%[ 20000] Cells 61%[ 21000] Cells 64%[ 22000] Cells 67%[ 23000] Cells 70%[ 24000] Cells 73%[ 25000] Cells 76%[ 26000] Cells 79%[ 27000] Cells 82%[ 28000] Cells 85%[ 29000] Cells 88%[ 30000] Cells 91%[ 31000] Cells 94%[ 32000] Cells 97% >>> hmm-wrong-dna ... Passed >>> Doing hmm-wrong-dna-est HMMs vs DNA sequence when there is no match >>> Calling [../bin/estwise wrong.hmm -hmmer short.dna -alg 333 -pal > TEMP] Information In making HSHNCPA1 a cdna sequence, converted 2 bases (0.5%) to N's from non ATGCN EstWise3 Matrix calculation: [ 0] Cells 0%[ 1000] Cells 3%[ 2000] Cells 6%[ 3000] Cells 9%[ 4000] Cells 12%[ 5000] Cells 15%[ 6000] Cells 18%[ 7000] Cells 21%[ 8000] Cells 24%[ 9000] Cells 27%[ 10000] Cells 30%[ 11000] Cells 33%[ 12000] Cells 36%[ 13000] Cells 39%[ 14000] Cells 42%[ 15000] Cells 45%[ 16000] Cells 48%[ 17000] Cells 51%[ 18000] Cells 54%[ 19000] Cells 57%[ 20000] Cells 61%[ 21000] Cells 64%[ 22000] Cells 67%[ 23000] Cells 70%[ 24000] Cells 73%[ 25000] Cells 76%[ 26000] Cells 79%[ 27000] Cells 82%[ 28000] Cells 85%[ 29000] Cells 88%[ 30000] Cells 91%[ 31000] Cells 94%[ 32000] Cells 97% EstWise3 Matrix calculation: [ 0] Cells 0%[ 1000] Cells 3%[ 2000] Cells 6%[ 3000] Cells 9%[ 4000] Cells 12%[ 5000] Cells 15%[ 6000] Cells 18%[ 7000] Cells 21%[ 8000] Cells 24%[ 9000] Cells 27%[ 10000] Cells 30%[ 11000] Cells 33%[ 12000] Cells 36%[ 13000] Cells 39%[ 14000] Cells 42%[ 15000] Cells 45%[ 16000] Cells 48%[ 17000] Cells 51%[ 18000] Cells 54%[ 19000] Cells 57%[ 20000] Cells 61%[ 21000] Cells 64%[ 22000] Cells 67%[ 23000] Cells 70%[ 24000] Cells 73%[ 25000] Cells 76%[ 26000] Cells 79%[ 27000] Cells 82%[ 28000] Cells 85%[ 29000] Cells 88%[ 30000] Cells 91%[ 31000] Cells 94%[ 32000] Cells 97% >>> hmm-wrong-dna-est ... Passed >>> Doing hmm-ascii-genomic cdna test case (protein v cdna), all outputs >>> Calling [../bin/genewise -init local HMM.ascii -hmmer short.dna -pretty -para -genes -sum -cdna -trans -ace -gener -alb -pal -quiet > TEMP] >>> hmm-ascii-genomic ... Passed >>> Doing genewise-db genewisedb hmm vs DNA sequences. Could take a while >>> Calling [../bin/genewisedb rrm.HMM -hmmer dna.db -pretty -para -gener -genes -cdna -trans -ace -quiet -init global > TEMP] >>> genewise-db ... Passed >>> Doing genewise-db-lite genewisedb hmm vs DNA sequences, using GWLITE. Could take a while >>> Calling [../bin/genewisedb rrm.HMM -hmmer dna.db -pretty -para -gener -genes -cdna -trans -ace -quiet -init global -alg 6LITE > TEMP] >>> genewise-db-lite ... Passed >>> Doing estwise-db estwisedb hmm vs DNA sequences. Could take a while >>> Calling [../bin/estwisedb -init local rrm.HMM -hmmer dna.db -pretty -para -alb -quiet -alg 333 -aalg 333 > TEMP] >>> estwise-db ... Passed >>> Doing pswdb Protein smith waterman db search >>> Calling [../bin/pswdb road.pep pep.fa -quiet > TEMP ] >>> pswdb ... Passed >>> Doing genewisedb-pfam-mode genewisedb designed for Pfam searching >>> Calling [../bin/genewisedb -pfam rrm.HMM -dnas short.dna -pretty -para -alb -quiet -alg 623 -aalg 623L > TEMP] >>> genewisedb-pfam-mode ... Passed Tests passed /bin/rm -rf /sw/build.build/root-wise2-2.4.1-1 /bin/mkdir -p /sw/build.build/root-wise2-2.4.1-1/sw /bin/mkdir -p /sw/build.build/root-wise2-2.4.1-1/DEBIAN /usr/sbin/chown -R fink-bld:fink-bld /sw/build.build/root-wise2-2.4.1-1 sudo -u fink-bld [ENV] sh -c /tmp/fink.GceJQ mkdir -p /sw/build.build/root-wise2-2.4.1-1/sw/bin mv src/bin/* /sw/build.build/root-wise2-2.4.1-1/sw/bin mkdir -p /sw/build.build/root-wise2-2.4.1-1/sw/share/wise2 mv wisecfg test_data /sw/build.build/root-wise2-2.4.1-1/sw/share/wise2/ mkdir -p /sw/build.build/root-wise2-2.4.1-1/sw/lib cp src/base/libwisebase.a /sw/build.build/root-wise2-2.4.1-1/sw/lib cp src/dynlibsrc/libdyna.a /sw/build.build/root-wise2-2.4.1-1/sw/lib cp src/dynlibsrc/libdyna_glib.a /sw/build.build/root-wise2-2.4.1-1/sw/lib cp src/external/mott/libmott.a /sw/build.build/root-wise2-2.4.1-1/sw/lib cp src/models/libmodel.a /sw/build.build/root-wise2-2.4.1-1/sw/lib cp src/socket/libwisesocket.a /sw/build.build/root-wise2-2.4.1-1/sw/lib cp src/HMMer2/libhmmer.a /sw/build.build/root-wise2-2.4.1-1/sw/lib mkdir -p /sw/build.build/root-wise2-2.4.1-1/sw/include mv src/api/include/*.h /sw/build.build/root-wise2-2.4.1-1/sw/include cat src/api/include/dyna.head src/dynlibsrc/*api.t src/dynlibsrc/*api.h > /sw/build.build/root-wise2-2.4.1-1/sw/include/dyna_api.h cat src/api/include/models.head src/models/*api.t src/models/*api.h > /sw/build.build/root-wise2-2.4.1-1/sw/include/model_api.h sudo -u fink-bld [ENV] sh -c /tmp/fink.uUURZ /usr/bin/install -d -m 700 /sw/build.build/root-wise2-2.4.1-1/sw/share/doc/wise2 /bin/cp -r INSTALL /sw/build.build/root-wise2-2.4.1-1/sw/share/doc/wise2/ /bin/cp -r README /sw/build.build/root-wise2-2.4.1-1/sw/share/doc/wise2/ /bin/cp -r LICENSE /sw/build.build/root-wise2-2.4.1-1/sw/share/doc/wise2/ /bin/chmod -R go=u-w /sw/build.build/root-wise2-2.4.1-1/sw/share/doc/wise2 /usr/bin/install -d -m 755 /sw/build.build/root-wise2-2.4.1-1/sw/etc/profile.d echo "setenv WISECONFIGDIR '/sw/share/wise2/wisecfg'" >> /sw/build.build/root-wise2-2.4.1-1/sw/etc/profile.d/wise2.csh.env echo "export WISECONFIGDIR='/sw/share/wise2/wisecfg'" >> /sw/build.build/root-wise2-2.4.1-1/sw/etc/profile.d/wise2.sh.env /usr/bin/touch /sw/build.build/root-wise2-2.4.1-1/sw/etc/profile.d/wise2.csh /usr/bin/touch /sw/build.build/root-wise2-2.4.1-1/sw/etc/profile.d/wise2.sh /bin/cat /sw/build.build/root-wise2-2.4.1-1/sw/etc/profile.d/wise2.csh >> /sw/build.build/root-wise2-2.4.1-1/sw/etc/profile.d/wise2.csh.env /bin/cat /sw/build.build/root-wise2-2.4.1-1/sw/etc/profile.d/wise2.sh >> /sw/build.build/root-wise2-2.4.1-1/sw/etc/profile.d/wise2.sh.env /bin/mv -f /sw/build.build/root-wise2-2.4.1-1/sw/etc/profile.d/wise2.csh.env /sw/build.build/root-wise2-2.4.1-1/sw/etc/profile.d/wise2.csh /bin/mv -f /sw/build.build/root-wise2-2.4.1-1/sw/etc/profile.d/wise2.sh.env /sw/build.build/root-wise2-2.4.1-1/sw/etc/profile.d/wise2.sh /bin/chmod 755 /sw/build.build/root-wise2-2.4.1-1/sw/etc/profile.d/wise2.* /bin/rm -f /sw/build.build/root-wise2-2.4.1-1/sw/info/dir /sw/build.build/root-wise2-2.4.1-1/sw/info/dir.old /sw/build.build/root-wise2-2.4.1-1/sw/share/info/dir /sw/build.build/root-wise2-2.4.1-1/sw/share/info/dir.old /bin/rm -rf /sw/build.build/root-wise2-dev-2.4.1-1 /bin/mkdir -p /sw/build.build/root-wise2-dev-2.4.1-1/sw /bin/mkdir -p /sw/build.build/root-wise2-dev-2.4.1-1/DEBIAN /usr/sbin/chown -R fink-bld:fink-bld /sw/build.build/root-wise2-dev-2.4.1-1 sudo -u fink-bld [ENV] sh -c /tmp/fink.E2TJM /usr/bin/install -d -m 755 /sw/build.build/root-wise2-dev-2.4.1-1/sw/lib /bin/mv /sw/build.build/root-wise2-2.4.1-1/sw/lib/*.a /sw/build.build/root-wise2-dev-2.4.1-1/sw/lib/ /usr/bin/install -d -m 755 /sw/build.build/root-wise2-dev-2.4.1-1/sw /bin/mv /sw/build.build/root-wise2-2.4.1-1/sw/include /sw/build.build/root-wise2-dev-2.4.1-1/sw/ /usr/bin/install -d -m 700 /sw/build.build/root-wise2-dev-2.4.1-1/sw/share/doc/wise2-dev /bin/cp -r INSTALL /sw/build.build/root-wise2-dev-2.4.1-1/sw/share/doc/wise2-dev/ /bin/cp -r README /sw/build.build/root-wise2-dev-2.4.1-1/sw/share/doc/wise2-dev/ /bin/cp -r LICENSE /sw/build.build/root-wise2-dev-2.4.1-1/sw/share/doc/wise2-dev/ /bin/chmod -R go=u-w /sw/build.build/root-wise2-dev-2.4.1-1/sw/share/doc/wise2-dev /bin/rm -f /sw/build.build/root-wise2-dev-2.4.1-1/sw/info/dir /sw/build.build/root-wise2-dev-2.4.1-1/sw/info/dir.old /sw/build.build/root-wise2-dev-2.4.1-1/sw/share/info/dir /sw/build.build/root-wise2-dev-2.4.1-1/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-wise2-2.4.1-1 /sw/fink/10.9/stable/main/binary-darwin-x86_64/sci dpkg-deb: building package `wise2' in `/sw/fink/10.9/stable/main/binary-darwin-x86_64/sci/wise2_2.4.1-1_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-wise2-dev-2.4.1-1 /sw/fink/10.9/stable/main/binary-darwin-x86_64/sci dpkg-deb: building package `wise2-dev' in `/sw/fink/10.9/stable/main/binary-darwin-x86_64/sci/wise2-dev_2.4.1-1_darwin-x86_64.deb'. Removing runtime build-lock... Removing build-lock package... /sw/bin/dpkg-lockwait -r fink-buildlock-wise2-2.4.1-1 (Reading database ... 5055 files and directories currently installed.) Removing fink-buildlock-wise2-2.4.1-1 ...