Package: wise / 2.4.1-17

Metadata

Package Version Patches format
wise 2.4.1-17 3.0 (quilt)

Patch series

view the series file
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.
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.
Bug-Ubuntu: https://bugs.launchpad.net/ubuntu/+source/wise/+bug/832935


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(+)

---
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).