Re: packaging python-cyvcf2

[Simon Tournier]

Hi,

On jeu., 21 mars 2024 at 18:03, Alexis Simon via Guix-Science 
<guix-science@gnu.org> wrote:

> The build is failing with this error:
> running build_ext
> # cyvcf2: htslib mode is BUILTIN
> # cyvcf2: htslib configure options is None
> error: [Errno 2] No such file or directory: './configure'
> error: in phase 'build': uncaught exception:
> %exception #<&invoke-error program: "python" arguments: ("./setup.py" 
> "build") exit-status: 1 term-signal: #f stop-signal: #f>
>
> What is very disturbing is that it builds fine in a debugging 
> environment following the documentation [2]

Indeed!  Well, another undocumented trick. ;-)

        guix build -L . python-cyvcf2 \
             --with-source=python-cyvcf2=/tmp/cyvcf2-0.30.28 

where /tmp/cyvcf2-0.30.28 is the uncompressed output of “guix build -S”
that I tweak.  Adding this:

--8<---------------cut here---------------start------------->8---
diff -u /tmp/guix-build-python-cyvcf2-0.30.28.drv-0/cyvcf2-0.30.28/setup.py 
/tmp/cyvcf2-0.30.28/setup.py
--- /tmp/guix-build-python-cyvcf2-0.30.28.drv-0/cyvcf2-0.30.28/setup.py 
2024-01-30 17:46:32.000000000 +0100
+++ /tmp/cyvcf2-0.30.28/setup.py        2024-03-22 16:15:28.124301350 +0100
@@ -83,7 +83,13 @@
         if htslib_configure_options:
             configure_args.extend(htslib_configure_options.split())
 
-        subprocess.run(configure_args, check=True)
+        print(configure_args,
+              "File exists?", os.path.exists(configure_args[0]),
+              flush=True)
+        try:
+            subprocess.run(configure_args, check=True)
+        except:
+            print("BANG!")
     subprocess.run(["make"], check=True)
 
     os.chdir(current_directory)
--8<---------------cut here---------------end--------------->8---

It leads to this output:

--8<---------------cut here---------------start------------->8---
running build_ext
# cyvcf2: htslib mode is BUILTIN
# cyvcf2: htslib configure options is None
['./configure', 'CFLAGS=-fPIC'] File exists? True
echo '# Default htscodecs.mk generated by Makefile' > htscodecs.mk
echo 'include $(HTSPREFIX)htscodecs_bundled.mk' >> htscodecs.mk
./hts_probe_cc.sh 'gcc' '-g -Wall -O2 -fvisibility=hidden ' 
'-fvisibility=hidden' >> htscodecs.mk
/gnu/store/rib9g2ig1xf3kclyl076w28parmncg4k-bash-minimal-5.1.16/bin/sh: line 1: 
./hts_probe_cc.sh: No such file or directory
Makefile:141: htscodecs.mk: No such file or directory
make: *** [Makefile:124: htscodecs.mk] Error 127
BANG!
Traceback (most recent call last):
[...]
--8<---------------cut here---------------end--------------->8---

Arf, then I have not investigated further.

I think it does not come from ’./configure’ as wrongly reported but from
something triggered by it.

Let me know your progress.  Maybe I could give a closer look next week.

Cheers,
simon