Debian Patches
Status for ampliconnoise/1.29-17
| Patch | Description | Author | Forwarded | Bugs | Origin | Last update |
|---|---|---|---|---|---|---|
| fix-path-for-data.patch | Description: The upstream software is built so as to run from the build environment and look for data in ../Data. In Debian the binaries belong in /usr/bin and the data belongs in /usr/share. With this patch the binaries will run from any directory. A better fix would be to allow setting of the Data directory via an environment variable or a variable passed to MAKE at build time. This could be contributed back to upstream. . The package is orphaned upstream, hence not forwarded. |
Tim Booth <tbooth@ceh.ac.uk> | no | 2011-04-28 | ||
| fix-segfault-on-non-fasta-input.patch | Some apps segfault when non-FASTA data is inputted, and this is flagged as a security concern. I suspect there are still ways to segfault this app, but at least this fixes an obvious crash. Also fixes https://code.google.com/p/ampliconnoise/issues/detail?id=10 . The package is orphaned upstream, hence not forwarded. |
Tim Booth | no | 2013-06-27 | ||
| hardening.patch | Propagate hardening options The package is orphaned upstream, hence the patch is not forwarded. | Andreas Tille <tille@debian.org> | no | 2024-08-07 | ||
| clang-ftbfs.patch | Fix FTBFS with clang instead of gcc The package is orphaned upstream, hence not forwarded. | Arthur Marble <arthur@info9.net> | no | debian | 2014-02-24 | |
| mayhem.patch | Fix Mayhem issues by making reading fasta files more robust The package is orphaned upstream, hence not forwarded. | Andreas Tille <tille@debian.org> | no | debian | 2015-12-18 | |
| fix_sequence_of_function_definitions.patch | fix sequence of function definitions Fix the sequence of function definitions to make sure UpdateMinCacheForRow() is known before its first usage. . This package is orphaned upstream, hence the patch not being forwarded. |
Andreas Tille <tille@debian.org> | no | debian | 2024-04-11 | |
| fix_missing_header.patch | Add missing header file The package is orphaned upstream, hence not forwarded. | Andreas Tille <tille@debian.org> | no | debian | 2024-04-11 | |
| gcc-14.patch | declare void functions implicitly typed int. This fixes the following error, now fatal, with gcc-14: . FCluster.c:223:1: error: return type defaults to ‘int’ [-Wimplicit-int] 223 | UpdateMinCacheForRow(struct t_Min* asMin,int i,float** aafDistMatrix) | ^~~~~~~~~~~~~~~~~~~~ FCluster.c:244:1: error: return type defaults to ‘int’ [-Wimplicit-int] 244 | UpdateMinCacheForMarkedRows(struct t_Min* asMin,float** aafDistMatrix,int nN) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ |
Étienne Mollier <emollier@emlwks999.eu> | no | debian | 2024-08-07 | |
| gcc-15.patch | Fix FTBFS with GCC 15 | Adrian Bunk <bunk@debian.org> | no | debian | ||
| cross.patch | Fix cross building with openmpi. ampliconnoise fails to cross build from source as it misses mpi compiler flags. In theory, it uses mpicc, but cross builds override CC with a non-mpi cross compiler and that's where flags go missing. Fundamentally, mpicc and cross building are incompatible. For openmpi, the solution is to use pkgconf, but mpich does not provide mpi-c anymore. I'm proposing a compromise here: Attempt to use pkgconf to add the flags, but do not fail when pkgconf doesn't work (e.g. on 32bit archs that use mpich). Then native building will continue to work everywhere (as it continues to use mpicc) while cross building will work for 64bit targets (where openmpi is used). Cross builds to 32bit architectures remain broken for now. |
Helmut Grohne <helmut@subdivi.de> | no | debian | 2025-06-07 |