[Debian-med-packaging] Cmake error in diamond-aligner: pthreads - not found

[Ryan Pavlik]

On 3/27/20 9:44 AM, Andrey Rahmatullin wrote:
> On Fri, Mar 27, 2020 at 07:24:38AM -0700, Matthew Fernandez wrote:
>> Hi Andreas,
>>
>> I can’t reproduce this either, but in case your subject was hinting at a
>> suspected cause, I don’t think this is it. The output shows CMake
>> successfully finding Pthreads.
> But the build fails with "/usr/bin/ld.gold: error: cannot find -lpthreads"
> 
>> The line numbers don’t make much sense to
>> me; there is no else statement on line 69, and CMakeLists.txt is only
>> 199 lines long. The final error almost looks like it’s somehow
>> encountered the targets at both line 174 and 179, or its somehow
>> recursively parsing the same CMakeLists.txt again. Maybe there’s
>> something not right in the CMake install on this build machine?
> Have you checked that before or after applying patches?
> https://salsa.debian.org/med-team/diamond-aligner/-/blob/master/debian/patches/multi_arch
> was broken in the "Refresh patches" commit 434c6968.
> 
> 


Looks like two of the patches were actually applied upstream and can be
dropped:

- multi_arch
https://github.com/bbuchfink/diamond/commit/2248fefb362e931ce1cee4d9292efe8d1499f225
- fix_i386_and_s390x
https://github.com/bbuchfink/diamond/commit/aea535c07e09fd41c5ab48ae72b6901d01d8decb

I've done this via gbp pq here:
https://salsa.debian.org/med-team/diamond-aligner/-/merge_requests/2


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