Package: mapsembler2 / 2.2.4+dfsg1-3

Metadata

Package Version Patches format
mapsembler2 2.2.4+dfsg1-3 3.0 (quilt)

Patch series

view the series file
Patch File delta Description
use_debian_libs | (download)

mapsembler2_extremities/thirdparty/gatb-core/CMakeLists.txt | 2 1 + 1 - 0 !
mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/math/LargeInt.hpp | 2 1 + 1 - 0 !
mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/math/NativeInt128.hpp | 2 1 + 1 - 0 !
mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/math/NativeInt16.hpp | 2 1 + 1 - 0 !
mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/math/NativeInt64.hpp | 2 1 + 1 - 0 !
mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/math/NativeInt8.hpp | 2 1 + 1 - 0 !
mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/api/Abundance.hpp | 2 1 + 1 - 0 !
mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/api/IHistogram.hpp | 2 1 + 1 - 0 !
mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5.hpp | 2 1 + 1 - 0 !
mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp | 2 1 + 1 - 0 !
mapsembler2_extremities/thirdparty/gatb-core/thirdparty/CMakeLists.txt | 42 0 + 42 - 0 !
11 files changed, 10 insertions(+), 52 deletions(-)

 use debian libs instead of embedded one
run_pipeline | (download)

run_mapsembler2_pipeline.sh | 20 10 + 10 - 0 !
1 file changed, 10 insertions(+), 10 deletions(-)

 use tools in path instead of local dirs as upstream
Last-Updated: 2014-08-20
add_hardening | (download)

kissreads/Makefile | 4 4 + 0 - 0 !
kissreads_graph/makefile | 5 4 + 1 - 0 !
mapsembler2_extend/makefile | 7 6 + 1 - 0 !
mapsembler2_extremities/CMakeLists.txt | 1 1 + 0 - 0 !
4 files changed, 15 insertions(+), 2 deletions(-)

 add hardening
skip_mphe | (download)

mapsembler2_extremities/thirdparty/gatb-core/CMakeLists.txt | 1 1 + 0 - 0 !
1 file changed, 1 insertion(+)

 mphe uses sse which is not available on all archs
 Disable in makefile the use of this lib as not mandatory
gcc 5.patch | (download)

mapsembler2_extend/mapsembler_extend.cpp | 4 2 + 2 - 0 !
1 file changed, 2 insertions(+), 2 deletions(-)

 fix type of prefix_trashable since gcc-5 is picky about it


libgomp.patch | (download)

kissreads/Makefile | 4 2 + 2 - 0 !
1 file changed, 2 insertions(+), 2 deletions(-)

 add missing -lgomp


spelling.patch | (download)

kissreads_graph/KissReadsGraph.cpp | 2 1 + 1 - 0 !
mapsembler2_extend/IterativeExtensions.cpp | 4 2 + 2 - 0 !
2 files changed, 3 insertions(+), 3 deletions(-)

 fix spelling
no_std_hash_redefinition.patch | (download)

mapsembler2_extend/GraphOutput.h | 12 0 + 12 - 0 !
1 file changed, 12 deletions(-)

 remove redefinition of ‘struct std::hash<__int128 unsigned>’
 This definition is not needed anymore with recent compiler versions apparently
 on _LP64 systems.  I'm not sure yet of The proper approach to address it in a
 more architecture independent way.
gcc10.patch | (download)

kissreads/include/commons.h | 40 20 + 20 - 0 !
kissreads/include/fragment_index.h | 8 4 + 4 - 0 !
2 files changed, 24 insertions(+), 24 deletions(-)

 fix common gcc10 ftbfs issue
 After fixing #957519 with no_std_hash_redefinition.patch, a few more issues
 common to Gcc 10 cropped up.  This patch addresses them.
check_memory.patch | (download)

minia/OAHash.cpp | 11 11 + 0 - 0 !
1 file changed, 11 insertions(+)

 check memory of oahash construction
 This has been written to try debugging why autopkgtest failures occurred on
 32bit architectures.  While the package ended up being removed out of 32 bits
 architectures repositories, this sort of control may remain useful to users of
 mapsembler2 to diagnose issues; this is more useful message than "Segmentation
 fault".
cross.patch | (download)

kissreads_graph/makefile | 8 4 + 4 - 0 !
mapsembler2_extend/makefile | 12 6 + 6 - 0 !
2 files changed, 10 insertions(+), 10 deletions(-)

 mapsembler2 ftcbfs: multiple reasons
 mapsembler2 fails to cross build from source, because it builds for the
 build architecture. It does not pass any cross flags to cmake nor any
 cross tools to make. In general, these kind of issues can often be
 solved using dh_auto_*. In this case, that mostly does the trick except
 for one aspect. Some makefiles use CC to store a C++ compiler. During
 cross compilation, dh_auto_build passes a C compiler via CC and that
 doesn't go well. I recommend changing the variable name to CXX, which is
 what everyone uses.