Debian Patches

Status for kallisto/0.51.1+dfsg-1

Patch Description Author Forwarded Bugs Origin Last update
use_debian_packaged_htslib.patch Adapt build system to Debian packaged libhts Andreas Tille <tille@debian.org> no 2019-03-21
htslib1.3 Use kseq.h from htslib, not the bundled version Michael R. Crusoe <michael.crusoe@gmail.com> no
gcc11.patch Fix gcc11 FTBFS with including the required library Nilesh Patra <nilesh@debian.org> yes debian 2021-03-04
disable-failing-bustools-test.patch Tests fail with bustools with: terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc
Aborted		 Andrius Merkys <merkys@debian.org> no
fix_bifrost_defines.patch Add default values for MAX_KMER_SIZE and MAX_GMER_SIZE (Any hint how to inject these without patching welcome) Andreas Tille <tille@debian.org> no 2025-10-18
bifrost_typo.patch Seems there is a typo sz_link is a local variable in the constructor, not a class member which leads to

In file included from /build/kallisto-0.51.1+dfsg/ext/bifrost/src/DataManager.hpp:10:
/build/kallisto-0.51.1+dfsg/ext/bifrost/src/DataStorage.tcc: In copy constructor 'DataStorage<Unitig_data_t>::DataStorage(const DataStorage<Unitig_data_t>&)':
/build/kallisto-0.51.1+dfsg/ext/bifrost/src/DataStorage.tcc:81:69: error: 'const class DataStorage<Unitig_data_t>' has no member named 'sz_link' [-Wtemplate-body]
81 | for (size_t i = 0; i != sz_link; ++i) unitig_cs_link[i] = o.sz_link[i].load();
| ^~~~~~~		 Andreas Tille <tille@debian.org> no 2025-10-18
std_gnu17.patch Try hard to get bifrost build with recent gcc Andreas Tille <tille@debian.org> no 2025-10-21
cmake4.patch Fix build using CMake 4 Andreas Tille <tille@debian.org> no debian 2025-10-21
fix_testing.patch Directly kall kallisto in test Andreas Tille <tille@debian.org> no 2025-10-21

All known versions for source package 'kallisto'

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