| Patch | Description | Author | Forwarded | Bugs | Origin | Last update |
|---|---|---|---|---|---|---|
| clapack.patch | Use Debian package for BLAS/LAPACK (instead of obsolete clapack) - Use -lblas instead of -lblaswr - Use -ltmglib instead of -ltmg - Do not use f2c, not needed - Introduce prototypes for LAPACK functions used in the package (those are documented in the manpages from the liblapack-doc package) |
Sébastien Villemot <sebastien@debian.org> | yes | 2017-09-10 | ||
| do_not_install_to_opt.patch | Packages should not install anything to /opt | Andreas Tille <tille@debian.org> | no | 2016-05-27 | ||
| use_debian_packaged_libpcre.patch | Use Debian packaged libpcre | Andreas Tille <tille@debian.org> | no | 2016-05-27 | ||
| use_debian_packaged_help2man.patch | Debian packaged help2man creates better results | Andreas Tille <tille@debian.org> | no | 2016-05-27 | ||
| hardening.patch | Propagate hardening options Later edited to add support for CPPFLAGS. This change modifies the build infrastructure for needs that are somewhat Debian specific, hence forwarding not needed. |
Andreas Tille <tille@debian.org> | not-needed | 2025-01-05 | ||
| pcre2.patch | Port from pcre3 to pcre2 | Andreas Tille <tille@debian.org> | yes | debian | 2021-11-19 | |
| gcc-14.patch | fix multiple issues gone fatal with gcc 14. This patch casts a few types to nudge several PCREs to build properly, given a number of mismatches or confusions between pcre2_code and pcre2_compile_context. The most notable change is probably the modified signature of str_re_new, as otherwise the code would have to include a huge amount of type casts for each and every call of str_re_new. . Upstream followed a different path to resolve the problem in upcoming phast versions, so forwarding this patch has become irrelevant. |
Étienne Mollier <emollier@debian.org> | not-needed | debian | 2024-07-31 | |
| make.patch | force sequential access to libphast.a. When building phast using make's parallel capabilities, the build almost always fails because the many subdirectories of src/lib/*/ are trying to add objects to the libphast.a static library at the same time, resulting in corruption and weird error messages like: . gcc -L/<<PKGBUILDDIR>>/src/dless/../../lib -o /<<PKGBUILDDIR>>/src/dless/../../bin/dless dless.o phast_bd_phylo_hmm.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now /usr/bin/ld: /<<PKGBUILDDIR>>/src/dless/../../lib/libphast.a: error adding symbols: malformed archive collect2: error: ld returned 1 exit status . Placing .NOTPARALLEL pseudo targets at strategic locations looks to reliably resolve the problem while preserving otherwise some level of parallelism where the library is not involved. Checkout the GNU Make manual's chapter about [Disabling Parallel Execution] for further details. . [Disabling Parallel Execution]: https://www.gnu.org/software/make/manual/html_node/Parallel-Disable.html |
Étienne Mollier <emollier@debian.org> | yes | debian | 2025-01-05 |