Package: bowtie2 / 2.3.0-2

Metadata

Package Version Patches format
bowtie2 2.3.0-2 3.0 (quilt)

Patch series

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

diff_sample.h | 3 3 + 0 - 0 !
1 file changed, 3 insertions(+)

 suppress "warning: this if clause does not guard...
  [-Wmisleading-indentation]" messages
hardening.patch | (download)

Makefile | 32 17 + 15 - 0 !
1 file changed, 17 insertions(+), 15 deletions(-)

 patch injects hardening c(pp,xx) flags and ldflags
reproducible.patch | (download)

Makefile | 30 15 + 15 - 0 !
bt2_build.cpp | 18 9 + 9 - 0 !
bt2_inspect.cpp | 18 9 + 9 - 0 !
bt2_search.cpp | 18 9 + 9 - 0 !
4 files changed, 42 insertions(+), 42 deletions(-)

 make build reproducible
 This patch removes the embedding of build specific values like
 hostname, time, etc. from the binary. It also ensures a stable
 sorting order for all wildcard expansions in the Makefile.
skip_test_requiring_non free_libmath random perl.patch | (download)

Makefile | 11 5 + 6 - 0 !
example/reads/simulate.pl | 115 0 + 115 - 0 !
2 files changed, 5 insertions(+), 121 deletions(-)

 math::random is in package libmath-random-perl which is
 unfortunately in non-free thus we can not use it for testing while building
 this package.  Thus the occurences of references and the surrounding code
 is removed here.


do not rebuild during test.patch | (download)

scripts/sim/run.sh | 18 9 + 9 - 0 !
scripts/test/simple_tests.sh | 16 8 + 8 - 0 !
2 files changed, 17 insertions(+), 17 deletions(-)

 do not rebuild with default settings during test
 The test suite builds the debug versions of the executables with default
 flags, while is needs to be built with the flags in d/rules.
single cpu for test.patch | (download)

Makefile | 2 1 + 1 - 0 !
scripts/sim/Sim.pm | 10 5 + 5 - 0 !
scripts/sim/run.sh | 2 1 + 1 - 0 !
3 files changed, 7 insertions(+), 7 deletions(-)

 only use single cpu for testing
 This also frees us of the dependency to the non-packaged libsys-info-perl.