[Debian-med-packaging] Bug#1128956: kallisto builds with -march=native

[Adrian Bunk]

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.