Your message dated Sat, 23 May 2026 13:04:01 +0000
with message-id <[email protected]>
and subject line Bug#1128956: fixed in kallisto 0.51.1+dfsg-2
has caused the Debian Bug report #1128956,
regarding kallisto builds with -march=native
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
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misconfiguration somewhere. Please contact [email protected]
immediately.)
--
1128956: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1128956
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: kallisto
Version: 0.51.1+dfsg-1
Severity: serious
https://buildd.debian.org/status/fetch.php?pkg=kallisto&arch=ppc64el&ver=0.51.1%2Bdfsg-1&stamp=1771777712&raw=0
...
cd /build/reproducible-path/kallisto-0.51.1+dfsg/ext/bifrost/build/src &&
/usr/bin/c++ -DMAX_GMER_SIZE=63 -DMAX_KMER_SIZE=31
-I/build/reproducible-path/kallisto-0.51.1+dfsg/ext/bifrost/src
-Wno-subobject-linkage -Wno-return-type -Wno-deprecated-declarations -std=c++11
-march=native -O3 -DNDEBUG -O3 -MD -MT
src/CMakeFiles/bifrost_static.dir/Bifrost.cpp.o -MF
CMakeFiles/bifrost_static.dir/Bifrost.cpp.o.d -o
CMakeFiles/bifrost_static.dir/Bifrost.cpp.o -c
/build/reproducible-path/kallisto-0.51.1+dfsg/ext/bifrost/src/Bifrost.cpp
c++: error: unrecognized command-line option ‘-march=native’; did you mean
‘-mcpu=native’?
make[6]: *** [src/CMakeFiles/bifrost_static.dir/build.make:79:
src/CMakeFiles/bifrost_static.dir/Bifrost.cpp.o] Error 1
-march=native is a baseline violation on architectures where
it is supported, and causes a FTBFS on architectures where
it is not supported.
It also changes the set of machines where the package might run
based on the capabilities of the buildd, e.g. on amd64 code built
on an AMD buildd might not run on Intel hardware and code built
on an Intel buildd might not run on AMD hardware.
The shortest fix would be:
--- kallisto-0.51.1+dfsg.orig/ext/bifrost/CMakeLists.txt
+++ kallisto-0.51.1+dfsg/ext/bifrost/CMakeLists.txt
@@ -8,7 +8,7 @@ find_package(Threads REQUIRED)
SET(MAX_KMER_SIZE "31" CACHE STRING "MAX_KMER_SIZE")
SET(MAX_GMER_SIZE "63" CACHE STRING "MAX_GMER_SIZE")
# Enable architecture optimizations
-SET(COMPILATION_ARCH "native" CACHE STRING "COMPILATION_ARCH")
+SET(COMPILATION_ARCH "OFF" CACHE STRING "COMPILATION_ARCH")
# Enable AVX2 instructions
SET(ENABLE_AVX2 "ON" CACHE STRING "ENABLE_AVX2")
The proper fix would be that the vendored bifrost is not
supposed to be used, but something seems to be incomplete
in the patches to use the system bifrost.
--- End Message ---
--- Begin Message ---
Source: kallisto
Source-Version: 0.51.1+dfsg-2
Done: Andreas Tille <[email protected]>
We believe that the bug you reported is fixed in the latest version of
kallisto, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <[email protected]> (supplier of updated kallisto package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Sat, 23 May 2026 14:39:43 +0200
Source: kallisto
Architecture: source
Version: 0.51.1+dfsg-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Andreas Tille <[email protected]>
Closes: 1128956
Changes:
kallisto (0.51.1+dfsg-2) unstable; urgency=medium
.
[ Adrian Bunk ]
* Do not build with -march=native
Closes: #1128956
.
[ Andreas Tille ]
* Update standards version to 4.7.4, no changes needed.
* d/rules: Remove core dump from failed test to not make it into the
resulting package. The proper fix would certainly be to fix the test!)
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