| Patch |
File delta |
Description |
| 01_welcome csh.patch | (download) |
src/makefile |
2 1 + 1 - 0 !
src/welcome.csh |
2 1 + 1 - 0 !
2 files changed, 2 insertions(+), 2 deletions(-) |
avoid dependency from csh
|
| 02_isnumber.patch | (download) |
src/models/phasemodel.c |
2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-) |
replace isnumber() (which does not exist on linux) by isdigit().
|
| 03_doc nodycache.patch | (download) |
docs/wise2.tex |
3 2 + 1 - 0 !
1 file changed, 2 insertions(+), 1 deletion(-) |
documentation bugfix.
|
| 04_wise2 pdflatex update.patch | (download) |
docs/wise2.tex |
13 8 + 5 - 0 !
1 file changed, 8 insertions(+), 5 deletions(-) |
make wise2.tex pdflatex compatible.
|
| 05_glib2.patch | (download) |
src/HMMer2/Makefile |
16 8 + 8 - 0 !
src/base/makefile |
6 3 + 3 - 0 !
src/corba/makefile |
14 7 + 7 - 0 !
src/dnaindex/assembly/makefile |
16 8 + 8 - 0 !
src/dnaindex/makefile |
30 15 + 15 - 0 !
src/dynlibsrc/makefile |
36 18 + 18 - 0 !
src/makefile |
6 3 + 3 - 0 !
src/models/makefile |
140 70 + 70 - 0 !
src/network/makefile |
6 3 + 3 - 0 !
src/other_programs/makefile |
4 2 + 2 - 0 !
src/snp/makefile |
6 3 + 3 - 0 !
11 files changed, 140 insertions(+), 140 deletions(-) |
to build wise2 with the glib version 2.0 instead of 1.2.
Forwarded patch to birney@sanger.ac.uk.
|
| 06_getline.patch | (download) |
src/HMMer2/sqio.c |
68 34 + 34 - 0 !
1 file changed, 34 insertions(+), 34 deletions(-) |
fixed conflicting definitions of getline().
|
| 07_ld as needed.patch | (download) |
src/models/makefile |
12 6 + 6 - 0 !
1 file changed, 6 insertions(+), 6 deletions(-) |
fix ftbfs with ld --as-needed.
|
| 08_mayhem.patch | (download) |
src/models/dbac.c |
8 6 + 2 - 0 !
src/models/estwise.c |
11 7 + 4 - 0 !
src/models/estwisedb.c |
7 5 + 2 - 0 !
src/models/genewise.c |
6 4 + 2 - 0 !
src/models/promoterwise.c |
8 6 + 2 - 0 !
5 files changed, 28 insertions(+), 12 deletions(-) |
fix run time errors detected by mayhem
|
| 09_dnal add return statement.patch | (download) |
src/models/dnal.c |
2 2 + 0 - 0 !
1 file changed, 2 insertions(+) |
make sure dnal has a valid return value
This affects a bug reported against python-biopython.
|
| 10_fix_path_to_data_files.patch | (download) |
src/models/estwise.c |
4 2 + 2 - 0 !
src/models/estwisedb.c |
6 3 + 3 - 0 !
src/models/genestats.c |
4 2 + 2 - 0 !
src/models/genestats.dy |
4 2 + 2 - 0 !
src/models/genewise.c |
8 4 + 4 - 0 !
src/models/genewisedb.c |
8 4 + 4 - 0 !
src/models/psw.c |
4 2 + 2 - 0 !
src/models/pswdb.c |
6 3 + 3 - 0 !
src/models/scanwisep.c |
4 2 + 2 - 0 !
src/models/testgenestat.c |
2 1 + 1 - 0 !
src/test/basic_cdna.out |
4 2 + 2 - 0 !
src/test/basic_genomic.out |
6 3 + 3 - 0 !
src/test/estwise-db.out |
2 1 + 1 - 0 !
src/test/genewise-db-lite.out |
4 2 + 2 - 0 !
src/test/genewise-db.out |
4 2 + 2 - 0 !
src/test/genewisedb-pfam.out |
4 2 + 2 - 0 !
src/test/hmm_cdna.out |
2 1 + 1 - 0 !
src/test/hmm_genomic.out |
4 2 + 2 - 0 !
src/test/pswdb.out |
2 1 + 1 - 0 !
19 files changed, 41 insertions(+), 41 deletions(-) |
brute force patch to fix the path to the data files to make the
tools finding the needed data for the test suite
.
In principle the PATH should be configurable and the test suite script even
contains a parameter (-cf) for this - but this seems to be ignored.
.
The correct way to deal with this would be a configuration option but I had
no intend to spend to much time into some software that was declared to be
orphaned (superseded by exonerate). So this primitive patch works to run
the test suite successfully (which is not the case without the patch).
|
| 11_consistent_manual_dates.patch | (download) |
docs/dynamite.tex |
2 2 + 0 - 0 !
docs/wise2.tex |
2 2 + 0 - 0 !
docs/wise2api.tex |
2 2 + 0 - 0 !
3 files changed, 6 insertions(+) |
use fixed dates for manuals.
These make the build reproducible. I have picked the file modificatin dates of
the corresponding source .tex files.
|
| spelling.patch | (download) |
LICENSE |
2 1 + 1 - 0 !
docs/dynamite.tex |
4 2 + 2 - 0 !
docs/wise2.tex |
32 16 + 16 - 0 !
docs/wise3arch.tex |
2 1 + 1 - 0 !
src/base/wisefile.c |
10 5 + 5 - 0 !
src/base/wisefile.dy |
10 5 + 5 - 0 !
src/base/wisefile.h |
2 1 + 1 - 0 !
src/corba/scanwise_protein_index.c |
2 1 + 1 - 0 !
src/dnaindex/assembly/badkmer.c |
2 1 + 1 - 0 !
src/dnaindex/assembly/pathwise.c |
2 1 + 1 - 0 !
src/dnaindex/bigseqwise.c |
2 1 + 1 - 0 !
src/dnaindex/findbad_kmer.c |
2 1 + 1 - 0 !
src/dnaindex/kwise.c |
2 1 + 1 - 0 !
src/dyc/api.c |
2 1 + 1 - 0 !
src/dyc/api.dy |
2 1 + 1 - 0 !
src/dyc/dbthread.c |
2 1 + 1 - 0 !
src/dyc/dbthread.dy |
2 1 + 1 - 0 !
src/dyc/dynafunc.c |
6 3 + 3 - 0 !
src/dyc/dynafunc.dy |
6 3 + 3 - 0 !
src/dyc/dynashadow.c |
2 1 + 1 - 0 !
src/dyc/dynashadow.dy |
2 1 + 1 - 0 !
src/dyc/funcinfo.c |
2 1 + 1 - 0 !
src/dyc/funcinfo.dy |
2 1 + 1 - 0 !
src/dyc/method.c |
4 2 + 2 - 0 !
src/dyc/method.dy |
4 2 + 2 - 0 !
src/dyc/method.h |
2 1 + 1 - 0 !
src/dyc/type.c |
2 1 + 1 - 0 !
src/dyc/type.dy |
2 1 + 1 - 0 !
src/dynlibsrc/aln.c |
2 1 + 1 - 0 !
src/dynlibsrc/aln.dy |
2 1 + 1 - 0 !
src/dynlibsrc/aln.h |
2 1 + 1 - 0 !
src/dynlibsrc/basematrix.h |
2 1 + 1 - 0 !
src/dynlibsrc/cdna.c |
4 2 + 2 - 0 !
src/dynlibsrc/cdna.dy |
4 2 + 2 - 0 !
src/dynlibsrc/cdna.h |
4 2 + 2 - 0 !
src/dynlibsrc/cdna.pod |
2 1 + 1 - 0 !
src/dynlibsrc/cdna.tex |
2 1 + 1 - 0 !
src/dynlibsrc/cdna_api.h |
2 1 + 1 - 0 !
src/dynlibsrc/codon.c |
2 1 + 1 - 0 !
src/dynlibsrc/codon.dy |
2 1 + 1 - 0 !
src/dynlibsrc/codon.h |
2 1 + 1 - 0 !
src/dynlibsrc/codon.pod |
2 1 + 1 - 0 !
src/dynlibsrc/codon.tex |
2 1 + 1 - 0 !
src/dynlibsrc/codon_api.h |
2 1 + 1 - 0 !
src/dynlibsrc/codonmapper.c |
2 1 + 1 - 0 !
src/dynlibsrc/codonmapper.dy |
2 1 + 1 - 0 !
src/dynlibsrc/codonmapper.h |
2 1 + 1 - 0 !
src/dynlibsrc/codonmapper.pod |
2 1 + 1 - 0 !
src/dynlibsrc/codonmapper.tex |
2 1 + 1 - 0 !
src/dynlibsrc/codonmapper_api.h |
2 1 + 1 - 0 !
src/dynlibsrc/codonmatrix.c |
2 1 + 1 - 0 !
src/dynlibsrc/codonmatrix.dy |
2 1 + 1 - 0 !
src/dynlibsrc/codonmatrix.h |
2 1 + 1 - 0 !
src/dynlibsrc/dna.c |
4 2 + 2 - 0 !
src/dynlibsrc/dna.dy |
4 2 + 2 - 0 !
src/dynlibsrc/dna.h |
4 2 + 2 - 0 !
src/dynlibsrc/dynlibcross.c |
2 1 + 1 - 0 !
src/dynlibsrc/dynlibcross.dy |
2 1 + 1 - 0 !
src/dynlibsrc/dynlibcross.h |
2 1 + 1 - 0 !
src/dynlibsrc/genomic.c |
6 3 + 3 - 0 !
src/dynlibsrc/genomic.dy |
6 3 + 3 - 0 !
src/dynlibsrc/genomic.h |
6 3 + 3 - 0 !
src/dynlibsrc/genomic.pod |
6 3 + 3 - 0 !
src/dynlibsrc/genomic.tex |
6 3 + 3 - 0 !
src/dynlibsrc/genomic_api.h |
6 3 + 3 - 0 !
src/dynlibsrc/genomicdb.c |
6 3 + 3 - 0 !
src/dynlibsrc/genomicdb.dy |
6 3 + 3 - 0 !
src/dynlibsrc/genomicregion.c |
4 2 + 2 - 0 !
src/dynlibsrc/genomicregion.dy |
4 2 + 2 - 0 !
src/dynlibsrc/genomicregion.h |
4 2 + 2 - 0 !
src/dynlibsrc/genomicregion.pod |
4 2 + 2 - 0 !
src/dynlibsrc/genomicregion.tex |
4 2 + 2 - 0 !
src/dynlibsrc/genomicregion_api.h |
4 2 + 2 - 0 !
src/dynlibsrc/hscore.c |
2 1 + 1 - 0 !
src/dynlibsrc/hscore.dy |
2 1 + 1 - 0 !
src/dynlibsrc/hspscaninterface.c |
2 1 + 1 - 0 !
src/dynlibsrc/hspscaninterface.dy |
2 1 + 1 - 0 !
src/dynlibsrc/hspstream.c |
4 2 + 2 - 0 !
src/dynlibsrc/hspstream.dy |
4 2 + 2 - 0 !
src/dynlibsrc/hspstream.h |
2 1 + 1 - 0 !
src/dynlibsrc/pairbase.c |
2 1 + 1 - 0 !
src/dynlibsrc/pairbase.dy |
2 1 + 1 - 0 !
src/dynlibsrc/pairbase.h |
2 1 + 1 - 0 !
src/dynlibsrc/protein.c |
4 2 + 2 - 0 !
src/dynlibsrc/protein.dy |
4 2 + 2 - 0 !
src/dynlibsrc/protein.h |
4 2 + 2 - 0 !
src/dynlibsrc/proteinindexcons.c |
4 2 + 2 - 0 !
src/dynlibsrc/proteinindexcons.dy |
4 2 + 2 - 0 !
src/dynlibsrc/proteinstreamedindex.c |
2 1 + 1 - 0 !
src/dynlibsrc/proteinstreamedindex.dy |
2 1 + 1 - 0 !
src/dynlibsrc/sequence.c |
10 5 + 5 - 0 !
src/dynlibsrc/sequence.h |
6 3 + 3 - 0 !
src/dynlibsrc/sequence.pod |
4 2 + 2 - 0 !
src/dynlibsrc/sequence.tex |
4 2 + 2 - 0 !
src/dynlibsrc/sequence_api.h |
4 2 + 2 - 0 !
src/dynlibsrc/sequence_codon.c |
2 1 + 1 - 0 !
src/dynlibsrc/sequence_codon.dy |
2 1 + 1 - 0 !
src/dynlibsrc/sequence_codon.h |
2 1 + 1 - 0 !
src/dynlibsrc/sequence_codon.pod |
2 1 + 1 - 0 !
src/dynlibsrc/sequence_codon.tex |
2 1 + 1 - 0 !
src/dynlibsrc/sequence_codon_api.h |
2 1 + 1 - 0 !
src/dynlibsrc/translation.c |
2 1 + 1 - 0 !
src/dynlibsrc/translation.dy |
2 1 + 1 - 0 !
src/models/abc.c |
4 2 + 2 - 0 !
src/models/alignwise.c |
2 1 + 1 - 0 !
src/models/alignwisedp.c |
2 1 + 1 - 0 !
src/models/amplimer_resolver.c |
2 1 + 1 - 0 !
src/models/bigdba.c |
2 1 + 1 - 0 !
src/models/cdnawise.c |
2 1 + 1 - 0 !
src/models/cdnawise10.c |
4 2 + 2 - 0 !
src/models/clonewise.c |
2 1 + 1 - 0 !
src/models/clonewisedp.c |
2 1 + 1 - 0 !
src/models/dba.c |
2 1 + 1 - 0 !
src/models/dbac.c |
2 1 + 1 - 0 !
src/models/dnaalign.c |
2 1 + 1 - 0 !
src/models/dnal.c |
2 1 + 1 - 0 !
src/models/dnaprofiledp.c |
2 1 + 1 - 0 !
src/models/dnawise.c |
2 1 + 1 - 0 !
src/models/editdist.c |
2 1 + 1 - 0 !
src/models/editdistdp.c |
2 1 + 1 - 0 !
src/models/estfrag3.c |
2 1 + 1 - 0 !
src/models/estloop3.c |
4 2 + 2 - 0 !
src/models/estquick3.c |
4 2 + 2 - 0 !
src/models/estslim3.c |
4 2 + 2 - 0 !
src/models/estslimloop.c |
4 2 + 2 - 0 !
src/models/estwise.c |
2 1 + 1 - 0 !
src/models/estwise3.c |
4 2 + 2 - 0 !
src/models/estwisedb.c |
6 3 + 3 - 0 !
src/models/evopairwise.c |
2 1 + 1 - 0 !
src/models/fivestar.c |
2 1 + 1 - 0 !
src/models/fivestarscan.c |
2 1 + 1 - 0 !
src/models/fivestarsearch.c |
2 1 + 1 - 0 !
src/models/fivestate.c |
2 1 + 1 - 0 !
src/models/genefrequency.c |
8 4 + 4 - 0 !
src/models/genefrequency.dy |
8 4 + 4 - 0 !
src/models/genefrequency.h |
4 2 + 2 - 0 !
src/models/geneloop21.c |
4 2 + 2 - 0 !
src/models/geneloop6.c |
4 2 + 2 - 0 !
src/models/genephase6.c |
2 1 + 1 - 0 !
src/models/genestats.c |
2 1 + 1 - 0 !
src/models/genestats.dy |
2 1 + 1 - 0 !
src/models/genestats.h |
2 1 + 1 - 0 !
src/models/genestretch6.c |
4 2 + 2 - 0 !
src/models/genewise.c |
2 1 + 1 - 0 !
src/models/genewise21.c |
4 2 + 2 - 0 !
src/models/genewise4.c |
4 2 + 2 - 0 !
src/models/genewise6.c |
4 2 + 2 - 0 !
src/models/genewisedb.c |
4 2 + 2 - 0 !
src/models/genewisemodel.c |
4 2 + 2 - 0 !
src/models/genewisemodel.dy |
4 2 + 2 - 0 !
src/models/genewisemodel.h |
2 1 + 1 - 0 !
src/models/genewisemodeldb.c |
2 1 + 1 - 0 !
src/models/genewisemodeldb.dy |
2 1 + 1 - 0 !
src/models/genewisemodeldb.h |
2 1 + 1 - 0 !
src/models/genomewise.c |
2 1 + 1 - 0 !
src/models/genomewise9.c |
2 1 + 1 - 0 !
src/models/gwlite.c |
4 2 + 2 - 0 !
src/models/largeblockdp.c |
2 1 + 1 - 0 !
src/models/lba.c |
2 1 + 1 - 0 !
src/models/localclonewisedp.c |
2 1 + 1 - 0 !
src/models/localdba.c |
2 1 + 1 - 0 !
src/models/motifcluster.c |
2 1 + 1 - 0 !
src/models/motifdiff.c |
2 1 + 1 - 0 !
src/models/motifmatrix.c |
2 1 + 1 - 0 !
src/models/motifmatrix.dy |
2 1 + 1 - 0 !
src/models/motifmatrixdp.c |
2 1 + 1 - 0 !
src/models/motifwise.c |
2 1 + 1 - 0 !
src/models/oldpostwise.c |
2 1 + 1 - 0 !
src/models/pba.c |
4 2 + 2 - 0 !
src/models/phasemodel.c |
2 1 + 1 - 0 !
src/models/phasemodel.dy |
2 1 + 1 - 0 !
src/models/promotercluster.c |
2 1 + 1 - 0 !
src/models/promoterwise.c |
2 1 + 1 - 0 !
src/models/proteinsw.c |
4 2 + 2 - 0 !
src/models/pseudowise.c |
2 1 + 1 - 0 !
src/models/pseudowise7.c |
4 2 + 2 - 0 !
src/models/psw.c |
2 1 + 1 - 0 !
src/models/pswdb.c |
4 2 + 2 - 0 !
src/models/scanwisep.c |
2 1 + 1 - 0 !
src/models/seqerror.dy |
2 1 + 1 - 0 !
src/models/seqerror.h |
2 1 + 1 - 0 !
src/models/slimdba.c |
2 1 + 1 - 0 !
src/models/standardout.c |
2 1 + 1 - 0 !
src/models/standardout.dy |
2 1 + 1 - 0 !
src/models/statwise.c |
2 1 + 1 - 0 !
src/models/statwise10.c |
2 1 + 1 - 0 !
src/models/sw_wrap.c |
8 4 + 4 - 0 !
src/models/sw_wrap.dy |
8 4 + 4 - 0 !
src/models/sw_wrap.h |
2 1 + 1 - 0 !
src/models/sw_wrap.pod |
2 1 + 1 - 0 !
src/models/sw_wrap.tex |
2 1 + 1 - 0 !
src/models/sw_wrap_api.h |
2 1 + 1 - 0 !
src/models/sywise.c |
2 1 + 1 - 0 !
src/models/sywise20.c |
2 1 + 1 - 0 !
src/models/threestatedp.c |
2 1 + 1 - 0 !
src/models/threestateloop.c |
2 1 + 1 - 0 !
src/models/threestatemodel.c |
4 2 + 2 - 0 !
src/models/threestatemodel.dy |
8 4 + 4 - 0 !
src/models/threestatemodel.h |
8 4 + 4 - 0 !
src/models/threestatemodel.pod |
4 2 + 2 - 0 !
src/models/threestatemodel.tex |
4 2 + 2 - 0 !
src/models/threestatemodel_api.h |
4 2 + 2 - 0 !
src/models/transregiondp.c |
2 1 + 1 - 0 !
src/network/wise_proteinindex_server.c |
2 1 + 1 - 0 !
src/perl/scripts/blastwise.pl |
2 1 + 1 - 0 !
src/perl/scripts/halfwise.pl |
2 1 + 1 - 0 !
src/test/estwise-db.out |
2 1 + 1 - 0 !
src/test/genewise-db-lite.out |
2 1 + 1 - 0 !
src/test/genewise-db.out |
2 1 + 1 - 0 !
src/test/genewisedb-pfam.out |
2 1 + 1 - 0 !
src/test/pswdb.out |
2 1 + 1 - 0 !
211 files changed, 331 insertions(+), 331 deletions(-) |
fix spelling issues
|
| cross.patch | (download) |
src/corba/makefile |
11 6 + 5 - 0 !
src/dnaindex/assembly/makefile |
5 3 + 2 - 0 !
src/dnaindex/makefile |
11 6 + 5 - 0 !
src/dynlibsrc/makefile |
13 7 + 6 - 0 !
src/makefile |
7 4 + 3 - 0 !
src/models/makefile |
25 13 + 12 - 0 !
src/network/makefile |
5 3 + 2 - 0 !
src/other_programs/makefile |
5 3 + 2 - 0 !
src/snp/makefile |
5 3 + 2 - 0 !
9 files changed, 48 insertions(+), 39 deletions(-) |
do not hard code the build architecture pkg-config
|
| implicit function declaration.patch | (download) |
src/HMMer2/prior.c |
1 1 + 0 - 0 !
src/external/mott/mott_api.c |
2 2 + 0 - 0 !
2 files changed, 3 insertions(+) |
fix implicit-function-declaration build errors
|
| executable is script.patch | (download) |
src/test/testman.pl |
2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-) |
fix perl binary location for
executable-not-elf-or-script lintian warning
|
| gcc 14.patch | (download) |
src/dnaindex/compressed_protein_index.dy |
2 1 + 1 - 0 !
src/dnaindex/kmer_assembly_untangler.dy |
9 8 + 1 - 0 !
src/dyc/dynafunc.dy |
1 1 + 0 - 0 !
src/dyc/dynafunc.h |
1 1 + 0 - 0 !
src/dyc/inputfile.c |
2 1 + 1 - 0 !
src/dyc/lex.yy.c |
12 0 + 12 - 0 !
src/models/est_evidence.dy |
2 1 + 1 - 0 !
src/socket/functionclient.dy |
2 1 + 1 - 0 !
8 files changed, 14 insertions(+), 17 deletions(-) |
fix multiple issues gone fatal with gcc 14.
|
| fix_blhc.patch | (download) |
src/dyc/makefile |
4 2 + 2 - 0 !
1 file changed, 2 insertions(+), 2 deletions(-) |
pass missing flags to fix blhc
|
| fix_ftbfs_with_gcc 15.patch | (download) |
src/HMMer2/gnuregex.c |
29 16 + 13 - 0 !
src/dnaindex/kmer_assembly_error.dy |
14 7 + 7 - 0 !
src/models/genewisehsp.dy |
14 7 + 7 - 0 !
src/models/genewisehsp.h |
2 1 + 1 - 0 !
4 files changed, 31 insertions(+), 28 deletions(-) |
fix ftbfs with gcc-15
|
| side effects.patch | (download) |
src/dnaindex/compressed_protein_index.c |
2 1 + 1 - 0 !
src/dnaindex/kmer_assembly_error.c |
14 7 + 7 - 0 !
src/dnaindex/kmer_assembly_untangler.c |
17 12 + 5 - 0 !
src/models/est_evidence.c |
2 1 + 1 - 0 !
src/models/genewisehsp.c |
14 7 + 7 - 0 !
src/socket/functionclient.c |
2 1 + 1 - 0 !
6 files changed, 29 insertions(+), 22 deletions(-) |
apply changes to generated files
|
