Debian Patches
Status for sortmerna/7.1.0-1
| Patch | Description | Author | Forwarded | Bugs | Origin | Last update |
|---|---|---|---|---|---|---|
| gcc-13.patch | fix build failure with gcc 13 This patch fixes occurrences of the following error with gcc 13: . /<<PKGBUILDDIR>>/src/sortmerna/kseq_load.cpp:53:12: error: ‘uint64_t’ has not been declared 53 | uint64_t number_total_read, | ^~~~~~~~ |
Étienne Mollier <emollier@debian.org> | no | 2023-09-06 | ||
| rapidarchive.patch | use the system librapidarchive instead of the bundled indexed_bzip2 sortmerna >= 5.0.0 bundles the indexed_bzip2 library (also known as rapidgzip) to provide seekable, block-parallel gzip decompression. The library has since been renamed to librapidarchive and is packaged in Debian. Use the packaged library via find_package(rapidarchive) rather than adding the bundled sources to the build. . The librapidarchive headers include plain names such as <common.hpp>, which collide with the sortmerna headers of the same name. sortmerna includes its own headers with quotes (#include "common.hpp"), so they are provided through -iquote; the librapidarchive headers use angle brackets and keep resolving to the librapidarchive headers. |
Andreas Tille <tille@debian.org> | no | 2026-10-19 | ||
| smr-api-disable.patch | do not build the smr_api self-contained static bundle The smr_api target in src/smr_api merges the object files and the static archives of RocksDB, zlib and parasail into a single self-contained libsmr_api.a. This requires static archives of all three libraries, but Debian's parasail only ships a shared library. The main sortmerna executable does not depend on smr_api, so skip building it. |
Andreas Tille <tille@debian.org> | no | 2026-10-19 |