Debian Patches
Status for arb/7.0+ds-1
| Patch | Description | Author | Forwarded | Bugs | Origin | Last update |
|---|---|---|---|---|---|---|
| 50_private_nameservers | change nameservers to be per-user By default, ARB shares one "name server" database across an installation. This is historical and no longer a useful default for "unadministered" use of ARB. The patch changes the config to create separate name databases for each user, avoiding the necessity for a directory writeable by all ARB users. |
Elmar Pruesse <elmar@oruesse.net> | no | other | ||
| 60_use_packaged_phyml | use phyml package instead of version source distributed with ARB | Elmar Pruesse <elmar@pruesse.net> | no | other | ||
| 70_skip_compler_version_check.patch | Skip compiler version check at all | Andreas Tille <tille@debian.org> | no | debian | 2026-10-23 | |
| 80_enable_new_dtags.patch | Apparently back in 1995 the ELF standard was tweaked to handle some crufty behaviour of RPATH - see http://blog.tremily.us/posts/rpath/ but Debian never adopted it. But for this package we do want it, so add the extra linker flag. |
From: Tim Booth <avarus@fastmail.fm> | no | 2026-10-23 | ||
| 90_do_not_create_MAFFT_symlinks.patch | do not create MAFFT symlinks | Fabian Klötzl <fabian@kloetzl.info> | no | 2017-09-12 | ||
| 100_use_tirpc.patch | Append relevant flags to cxxflags and lfags to build with tirpc Also accept C++ standards newer than C++14 in cxxforward.h. GCC 16 uses C++23 by default for the no-standard compatibility build. |
Nilesh Patra <nilesh@debian.org> | no | 2026-10-23 | ||
| 110_narrowing.patch | Fix types for arm64, others To avoid "error: narrowing conversion of '-2' from 'int' to 'char' [-Wnarrowing]" |
Michael R. Crusoe <crusoe@debian.org> | no | |||
| 111_fgets.patch | never use gets(3). This patch changes gets(3) calls for fgets(3) invocations instead. | Étienne Mollier <emollier@debian.org> | no | 2024-08-24 | ||
| gcc-16+ | Fix compilation with gcc 16 =================================================================== |
no | ||||
| 120_disable_vectorize_check.patch | Disable vectorization checks for Debian builds GCC 16 fails some LOOP_VECTORIZED checks (e.g. in CORE/arb_strarray.cxx), which causes a FTBFS. The vectorization itself is unaffected; only the compile-time verification is turned off. |
Andreas Tille <tille@debian.org> | no | 2026-10-23 | ||
| 130_bundled_raxml_build_c17.patch | Build bundled RAxML/SATIVA sources as C17 GCC 16 defaults to C23, where 'bool' is a keyword and the bundled RAxML8 and SATIVA sources fail to compile ('typedef int bool', implicit function declarations). Build the bundled copies as C17 to keep them compiling. |
Andreas Tille <tille@debian.org> | no | 2026-10-23 | ||
| 140_compile_compat_strip_c_std.patch | Strip C standard from no-standard compatibility build debian/rules adds -std=gnu17 to CFLAGS to build the old C sources as C17 (GCC 16 defaults to C23). ARB passes CFLAGS to C++ compilations as well, so the 'nostd' compatibility target has to remove that option to really build without an explicit C++ standard. |
Andreas Tille <tille@debian.org> | no | 2026-10-23 | ||
| 145_use_system_libeigen.patch | Build RNACMA against system libeigen3 instead of bundled Eigen The bundled Eigen user copy in HEADERLIBS is Eigen 2.0.16, whose Altivec code (Eigen/src/Core/arch/AltiVec/PacketMath.h) uses intrinsics (__builtin_vec_ld on float/int vectors) that GCC 14+ rejects on little-endian PowerPC, so arb FTBFSes on ppc64el. Use the system library libeigen3-dev (Eigen 3.4.0) instead and stop unpacking the bundled copy at build time. RNACMA's Cma.cxx needs one Eigen 3 API adjustment (a DiagonalWrapper expression can no longer be subtracted from a matrix; it has to be materialised first) and the legacy lowercase include path has to point at the Debian layout (/usr/include/eigen3). The bundled HEADERLIBS/eigen copy is left in the source tree for now and only the build no longer depends on it. |
Andreas Tille <tille@debian.org> | no | debian | 2026-10-23 |