[Debian-med-packaging] Bug#976551: ngmlr: FTBFS on arm64: ConvexAlignFast.cpp:11:10: fatal error: x86intrin.h: No such file or directory

[Lucas Nussbaum]

Source: ngmlr
Version: 0.2.7+dfsg-2
Severity: important
Justification: FTBFS on arm64
Tags: bullseye sid ftbfs
Usertags: ftbfs-20201205 ftbfs-bullseye

Hi,

During a rebuild of all packages in sid, your package failed to build
on arm64.

Relevant part (hopefully):
> cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src && /usr/bin/c++  -I/usr/include/htslib -I/<<PKGBUILDDIR>>/src/../lib -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ngmlr.dir/ConvexAlignFast.cpp.o -c /<<PKGBUILDDIR>>/src/ConvexAlignFast.cpp
> /<<PKGBUILDDIR>>/src/ConvexAlignFast.cpp:11:10: fatal error: x86intrin.h: No such file or directory
>    11 | #include <x86intrin.h>
>       |          ^~~~~~~~~~~~~
> compilation terminated.
> make[3]: *** [src/CMakeFiles/ngmlr.dir/build.make:163: src/CMakeFiles/ngmlr.dir/ConvexAlignFast.cpp.o] Error 1

The full build log is available from:
   http://qa-logs.debian.net/2020/12/05/ngmlr_0.2.7+dfsg-2_unstable.log

A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!

If you reassign this bug to another package, please marking it as 'affects'-ing
this package. See https://www.debian.org/Bugs/server-control#affects

If you fail to reproduce this, please provide a build log and diff it with me
so that we can identify if something relevant changed in the meantime.

About the archive rebuild: The rebuild was done on EC2 VM instances from
Amazon Web Services, using a clean, minimal and up-to-date chroot. Every
failed build was retried once to eliminate random failures.