Compilation with GCC 14

[dialvarezs]

Describe the bug
Seqfu doesn't compile under GCC 14

Environment:

• Linux (OpenSUSE Tumbleweed, GCC 14.1.0)
• source
• 1.20.3

Additional context
GCC 14 introduced several changes to make compilation stricter by default (https://gcc.gnu.org/gcc-14/porting_to.html). So, as it is right now, seqfu doesn't compile, trowing errors of "incompatible pointer type":

...
/home/dxh/.cache/nim/sfu_r/@[email protected]@[email protected]@sdocopt.nim.c: In function 'single_match__OOZOnimbleZpkgs50Zdocopt4548O55O4945515655f49ae4955f51b55545048c55564952cf5252a5350d51d5749b56574854e57Zdocopt_u2739':
/home/dxh/.cache/nim/sfu_r/@[email protected]@[email protected]@sdocopt.nim.c:5364:51: error: assignment to 'tyObject_PatterncolonObjectType___A9bHEBNpFTjEgqdXkaIrmFg *' from incompatible pointer type 'tyObject_ArgumentcolonObjectType___Ln77EzbQ9ccyLZm9ceI9c3dMw *' [-Wincompatible-pointer-types]
 5364 |                                         colontmp_ = argument__OOZOnimbleZpkgs50Zdocopt4548O55O4945515655f49ae4955f51b55545048c55564952cf5252a5350d51d5749b56574854e57Zdocopt_u316(colontmpD__2, (*pattern).value);
      |                                                   ^
/home/dxh/.cache/nim/sfu_r/@[email protected]@[email protected]@sdocopt.nim.c: In function 'single_match__OOZOnimbleZpkgs50Zdocopt4548O55O4945515655f49ae4955f51b55545048c55564952cf5252a5350d51d5749b56574854e57Zdocopt_u2751':
/home/dxh/.cache/nim/sfu_r/@[email protected]@[email protected]@sdocopt.nim.c:5570:59: error: assignment to 'tyObject_PatterncolonObjectType___A9bHEBNpFTjEgqdXkaIrmFg *' from incompatible pointer type 'tyObject_CommandcolonObjectType___HvW7Ln9aD64gF1ZsUHj9bz6g *' [-Wincompatible-pointer-types]
 5570 |                                                 colontmp_ = command__OOZOnimbleZpkgs50Zdocopt4548O55O4945515655f49ae4955f51b55545048c55564952cf5252a5350d51d5749b56574854e57Zdocopt_u622(colontmpD__4, colontmpD__5);
      |                                                           ^
CC: ../../../../../../home/dxh/others/spack/opt/spack/linux-opensusetumbleweed2.39-zen3/gcc-14.1.0/nim-2.0.4-gy6owgpzwwf7f3hriyepopcqbo5zosiz/lib/pure/collections/rtarrays.nim
CC: ../../../../../../home/dxh/others/spack/opt/spack/linux-opensusetumbleweed2.39-zen3/gcc-14.1.0/nim-2.0.4-gy6owgpzwwf7f3hriyepopcqbo5zosiz/lib/impure/re.nim
CC: seqfu_utils.nim
CC: ../../../../../../home/dxh/others/spack/opt/spack/linux-opensusetumbleweed2.39-zen3/gcc-14.1.0/nim-2.0.4-gy6owgpzwwf7f3hriyepopcqbo5zosiz/lib/pure/md5.nim
CC: ../../../../../../home/dxh/others/spack/opt/spack/linux-opensusetumbleweed2.39-zen3/gcc-14.1.0/nim-2.0.4-gy6owgpzwwf7f3hriyepopcqbo5zosiz/lib/pure/streams.nim
CC: ../../../../../../home/dxh/others/spack/opt/spack/linux-opensusetumbleweed2.39-zen3/gcc-14.1.0/nim-2.0.4-gy6owgpzwwf7f3hriyepopcqbo5zosiz/lib/pure/json.nim
CC: ../../../../../../home/dxh/others/spack/opt/spack/linux-opensusetumbleweed2.39-zen3/gcc-14.1.0/nim-2.0.4-gy6owgpzwwf7f3hriyepopcqbo5zosiz/lib/pure/encodings.nim
CC: ../.nimble/pkgs2/terminaltables-0.1.1-5fdf88d70cc1d904291204cd4f9e2adf992fb564/terminaltables.nim
CC: stats_utils.nim
Error: execution of an external compiler program 'gcc -c  -w -fmax-errors=3 -pthread -O3 -fno-strict-aliasing -fno-ident -fno-math-errno   -I/home/dxh/others/spack/opt/spack/linux-opensusetumbleweed2.39-zen3/gcc-14.1.0/nim-2.0.4-gy6owgpzwwf7f3hriyepopcqbo5zosiz/lib -I/tmp/dxh/spack-stage/spack-stage-seqfu-1.20.3-qgwbqiyiqcgduapg6nsxv7b7pueabctv/spack-src/src -o /home/dxh/.cache/nim/sfu_r/@[email protected]@[email protected]@sdocopt.nim.c.o /home/dxh/.cache/nim/sfu_r/@[email protected]@[email protected]@sdocopt.nim.c' failed with exit code: 1


make: *** [Makefile:55: bin/seqfu] Error 1
/home/dxh/.cache/nim/sfu_r/@mstats_utils.nim.c: In function 'getFastxStats__stats95utils_u616':
/home/dxh/.cache/nim/sfu_r/@mstats_utils.nim.c:541:31: error: assignment to 'tyObject_kseq_t__JyA8mh6WjaqGke0VEiWn2Q *' from incompatible pointer type 'kseq_t *' [-Wincompatible-pointer-types]
  541 |                         rec_2 = kseq_init(fp);
      |                               ^
/home/dxh/.cache/nim/sfu_r/@mstats_utils.nim.c:552:66: error: passing argument 1 of 'kseq_read' from incompatible pointer type [-Wincompatible-pointer-types]
  552 |                                                 T19_ = kseq_read(rec_2);
      |                                                                  ^~~~~
      |                                                                  |
      |                                                                  tyObject_kseq_t__JyA8mh6WjaqGke0VEiWn2Q *
...

Some of the errors come from docopt, so I guess it is not so easy to solve, so for now I propose to add --passC:"-Wno-error=incompatible-pointer-types" to NIMPARAM in the Makefile. If you are ok with it, I can make a PR.

Disclaimer
I really like seqfu and I would like it to be available in spack. I made a PR for that (spack/spack#44445), and the mantainers asked me if we can solve this in upstream instead of patching it in the package there.

[telatin]

Thanks a million!
Docopt is a tricky part, I would like to plan a major update of Seqfu and I still don't know if docopt is worth the pain :)

Yes please, go ahead with the PR and I'll be happy to merge

EDIT: I will try and check how to fix stats_utils