Package: tigr-glimmer / 3.02b-5

Metadata

Package Version Patches format
tigr-glimmer 3.02b-5 3.0 (quilt)

Patch series

view the series file
Patch File delta Description
10_gcc4.3.patch | (download)

src/Common/delcher.cc | 1 1 + 0 - 0 !
src/Common/fasta.cc | 2 1 + 1 - 0 !
src/Common/gene.cc | 1 1 + 0 - 0 !
src/Glimmer/anomaly.cc | 1 1 + 0 - 0 !
src/Glimmer/glimmer2.cc | 1 1 + 0 - 0 !
src/Glimmer/glimmer3.cc | 3 1 + 2 - 0 !
src/Glimmer/long-orfs.cc | 2 1 + 1 - 0 !
src/ICM/build-fixed.cc | 1 1 + 0 - 0 !
src/ICM/build-icm.cc | 1 1 + 0 - 0 !
src/ICM/icm.cc | 2 2 + 0 - 0 !
src/ICM/score-fixed.cc | 1 1 + 0 - 0 !
src/Util/entropy-score.cc | 2 1 + 1 - 0 !
src/Util/extract.cc | 2 1 + 1 - 0 !
src/Util/multi-extract.cc | 2 1 + 1 - 0 !
src/Util/start-codon-distrib.cc | 1 1 + 0 - 0 !
src/Util/uncovered.cc | 2 1 + 1 - 0 !
16 files changed, 17 insertions(+), 8 deletions(-)

 fix #461691


mayhem.patch | (download)

src/ICM/build-fixed.cc | 18 13 + 5 - 0 !
src/ICM/build-icm.cc | 16 12 + 4 - 0 !
src/ICM/score-fixed.cc | 16 12 + 4 - 0 !
3 files changed, 37 insertions(+), 13 deletions(-)

 fix crashes reported by mayhem
 See http://www.drpaulcarter.com/cs/common-c-errors.php#4.1
 to make fgetc() more safe.  However, the original problem is
 that for empty strings no space at all is allocated.  This is
 now done in advance.


make errs.patch | (download)

src/Makefile | 20 10 + 10 - 0 !
src/c_make.gen | 48 31 + 17 - 0 !
2 files changed, 41 insertions(+), 27 deletions(-)

 reinforce makefile error checking and increase verbosity
 Initial version of the patch only reinforced Makefile error checking, but some
 simili try/catch statement seem to be interfering with proper error
 detection.
 .
 This version increases the verbosity of the build procedure by removing the @
 commands, excepts for the beautifying `echo` statements.  In addition, error
 checking if further reinforced, and the error handling logic of the "if"
 statement has been modified to trigger an exit with the error status of the
 linking command.