Package: gff2aplot / 2.0-11

Metadata

Package Version Patches format
gff2aplot 2.0-11 3.0 (quilt)

Patch series

view the series file
Patch File delta Description
non_lexical_loop_iterator.patch | (download)

src/gff2aplot.pl | 19 10 + 9 - 0 !
1 file changed, 10 insertions(+), 9 deletions(-)

 make sure that iterator variable is explicitly decalred as
 a lexcical using my keyword. See PBP, page 108.  Add perl shebang.
02 blat2gff.diff | (download)

src/blat2gff.pl | 8 4 + 4 - 0 !
1 file changed, 4 insertions(+), 4 deletions(-)

---
03 parseblast.diff | (download)

src/parseblast.pl | 4 2 + 2 - 0 !
1 file changed, 2 insertions(+), 2 deletions(-)

---
use dpkg buildflags.patch | (download)

src/ali2gff/Makefile | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 use build flags from environment (dpkg-buildflags).
 Necessary for hardening flags.
mayhem.patch | (download)

src/ali2gff/ali2gff.c | 10 7 + 3 - 0 !
1 file changed, 7 insertions(+), 3 deletions(-)

 deal with mayhem issue


fis privacy breach.patch | (download)

examples/mhcregion/index.html | 30 15 + 15 - 0 !
examples/wublast/index.html | 30 15 + 15 - 0 !
2 files changed, 30 insertions(+), 30 deletions(-)

 fix privacy issues by linking to local images, js and css locally
perl_5.28.patch | (download)

src/gff2aplot.pl | 13 9 + 4 - 0 !
1 file changed, 9 insertions(+), 4 deletions(-)

 can't use 'defined(@array)' (maybe you should just omit the defined()?) at /usr/bin/gff2aplot line 1737.


fix_install_ali2gff.patch | (download)

Makefile | 5 3 + 2 - 0 !
1 file changed, 3 insertions(+), 2 deletions(-)

 make sure target dir exists when performing parallel builds
 Somehow CP is resolved to "cp 1" - no idea why, just force proper copy statement


enhance_sprintf_buffer.patch | (download)

src/ali2gff/ali2gff.c | 10 5 + 5 - 0 !
1 file changed, 5 insertions(+), 5 deletions(-)

 enhance print buffer to avoid:
  /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 36 and 3418 bytes into a destination of size 1000
 Finally this patch is not fully working since the enhanced buffers
 make sprint assume that even larger buffers are needed.


fix_README_used_for_test.patch | (download)

examples/splice_sites/README | 3 1 + 2 - 0 !
1 file changed, 1 insertion(+), 2 deletions(-)

 the readme file is used as shell script and one function
 is broken.  It should return basenames of *.ps files.  This is fixed here