Package: profphd / 1.0.42-3

Metadata

Package Version Patches format
profphd 1.0.42-3 3.0 (quilt)

Patch series

view the series file
Patch File delta Description
1_remove_defined_array.patch | (download)

src/prof/embl/scr/conv_phd2hssp.pl | 5 2 + 3 - 0 !
src/prof/embl/scr/lib-col.pl | 14 7 + 7 - 0 !
src/prof/embl/scr/lib/all5.pl | 2 1 + 1 - 0 !
src/prof/embl/scr/lib/br.pl | 22 11 + 11 - 0 !
src/prof/embl/scr/lib/file.pl | 6 3 + 3 - 0 !
src/prof/embl/scr/lib/formats.pl | 6 3 + 3 - 0 !
src/prof/embl/scr/lib/hssp.pl | 10 5 + 5 - 0 !
src/prof/embl/scr/lib/scr.pl | 12 6 + 6 - 0 !
src/prof/embl/scr/pack/copf.pm | 14 7 + 7 - 0 !
src/prof/embl/scr/pack/hssp_filter.pm | 14 7 + 7 - 0 !
src/prof/scr/conv_prof2hssp.pl | 5 2 + 3 - 0 !
src/prof/scr/lib/dead_code.pl | 3 1 + 2 - 0 !
src/prof/scr/lib/lib-col.pl | 12 6 + 6 - 0 !
src/prof/scr/lib/lib-prof.pl | 42 21 + 21 - 0 !
14 files changed, 82 insertions(+), 85 deletions(-)

 change defined(@array) to @array to use with perl 5.22
2_remove_perlbrew_usage.patch | (download)

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

 remove perlbrew to use latest perl 5.22
3_fix_indexing.patch | (download)

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

 fix error "modification of non-creatable array value attempted, 
 subscript -1 at /usr/share/profphd/prof/scr/lib/lib-prof.pl line 7739"
4_fix_negative_repeat_count.patch | (download)

src/prof/scr/lib/lib-prof.pl | 69 35 + 34 - 0 !
1 file changed, 35 insertions(+), 34 deletions(-)

 fix error "negative repeat count does nothing at" for various 
 lines (including possible places where this error might appear - 
 by semi-autoreplacement)
5_fix_regex_warning.patch | (download)

src/prof/scr/lib/lib-profwrt.pl | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 fixes warning message
 """
 Useless use of greediness modifier '?' in regex; marked by <-- HERE in 
 m/^(.{59}? <-- HERE \S*[\., \-\;\:])/ at 
 /usr/share/profphd/prof/scr/lib/lib-profwrt.pl line 2303.
 """
 which appears when 'prof' is run with 'ascii' parameter, i.e.
   prof /usr/share/profphd/prof/exa/1ppt.hssp fileRdb=1ppt.rdbProfSec sec ascii