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

[Matthew Fernandez]

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. 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?

Thanks,
Matt

> On Mar 27, 2020, at 03:32, Andreas Tille <andreas at an3as.eu> wrote:
> 
> Hi folks,
> 
> I have problems to upgrade diamond-aligner[1] to its latest upstream
> version and upstream can't reproduce the issue.  Sorry, currently I'm
> swamped with COVID-19 issues so I'd like to ask here simply for a patch
> which is probably not that hard.  In pbuilder I get:
> 
> ...
> -- Looking for pthread.h
> -- Looking for pthread.h - found
> -- Performing Test CMAKE_HAVE_LIBC_PTHREAD
> -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
> -- Looking for pthread_create in pthreads
> -- Looking for pthread_create in pthreads - not found
> -- Looking for pthread_create in pthread
> -- Looking for pthread_create in pthread - found
> -- Found Threads: TRUE..
> CMake Error at CMakeLists.txt:69 (else):
>  else An ELSE command was found outside of a proper IF ENDIF structure.  Or
>  its arguments did not match the opening IF command.
> 
> 
> CMake Error at CMakeLists.txt:166 (endif):
>  endif An ENDIF command was found outside of a proper IF ENDIF structure.
>  Or its arguments did not match the opening IF command.
> 
> 
> CMake Error at CMakeLists.txt:271 (add_executable):
>  add_executable cannot create target "diamond" because another target with
>  the same name already exists.  The existing target is an executable created
>  in source directory "/build/diamond-aligner-0.9.31".  See documentation for
>  policy CMP0002 for more details.
> 
> 
> -- Configuring incomplete, errors occurred!
> See also "/build/diamond-aligner-0.9.31/obj-x86_64-linux-gnu/CMakeFiles/CMakeOutput.log".
> See also "/build/diamond-aligner-0.9.31/obj-x86_64-linux-gnu/CMakeFiles/CMakeError.log".
> ...
> 
> 
> Any patch would be really welcome.
> 
> Thanks a lot
> 
>      Andreas.
> 
> 
> [1] https://salsa.debian.org/med-team/diamond-aligner
> 
> 
> -- 
> http://fam-tille.de
>