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Received: from [10.9.9.73] (helo=submission02.runbox) by mailtransmit02.runbox with esmtp (Exim 4.86_2) (envelope-from ) id 1rnkj9-0004dU-R5; Fri, 22 Mar 2024 20:38:55 +0100 Received: by submission02.runbox with esmtpsa [Authenticated ID (1174703)] (TLS1.2:ECDHE_SECP256R1__RSA_PSS_RSAE_SHA256__AES_256_GCM:256) (Exim 4.93) id 1rnkj0-00EeGz-1n; Fri, 22 Mar 2024 20:38:46 +0100 Content-Type: multipart/mixed; boundary="------------9Vkflbvrs3eZRnULLW90cmbH" Message-ID: <7b845ef7-f15e-45b9-9a31-e645ce736ec4@runbox.com> Date: Fri, 22 Mar 2024 12:38:41 -0700 MIME-Version: 1.0 User-Agent: Mozilla Thunderbird Subject: Re: packaging python-cyvcf2 To: Simon Tournier , help-guix , guix-science@gnu.org References: <87il1eb867.fsf@gmail.com> Content-Language: en-US In-Reply-To: <87il1eb867.fsf@gmail.com> Received-SPF: pass client-ip=2a0c:5a00:149::26; envelope-from=alexis.simon@runbox.com; helo=mailtransmit05.runbox.com X-Spam_score_int: -27 X-Spam_score: -2.8 X-Spam_bar: -- X-Spam_report: (-2.8 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, DKIM_VALID_EF=-0.1, FREEMAIL_FROM=0.001, RCVD_IN_DNSWL_LOW=-0.7, SPF_HELO_PASS=-0.001, SPF_PASS=-0.001 autolearn=ham autolearn_force=no X-Spam_action: no action X-Mailman-Approved-At: Fri, 22 Mar 2024 17:31:47 -0400 X-BeenThere: guix-science@gnu.org X-Mailman-Version: 2.1.29 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , From: Alexis Simon via Guix-Science Reply-To: Alexis Simon Errors-To: guix-science-bounces+larch=yhetil.org@gnu.org Sender: guix-science-bounces+larch=yhetil.org@gnu.org X-Migadu-Country: US X-Migadu-Flow: FLOW_IN X-Spam-Score: -5.82 X-Migadu-Queue-Id: 7256A558DA X-Migadu-Scanner: mx13.migadu.com X-Migadu-Spam-Score: -5.82 X-TUID: 9UvlKL7Yg/E8 Message-ID: <20240322193841.K_DHUqx-tDHS_JZDmw705Tp9TdflgjdeYxSM0cWdrI8@z> This is a multi-part message in MIME format. --------------9Vkflbvrs3eZRnULLW90cmbH Content-Type: text/plain; charset=UTF-8; format=flowed Content-Transfer-Encoding: 8bit On 22/03/2024 08:25, Simon Tournier wrote: > Hi, > > On jeu., 21 mars 2024 at 18:03, Alexis Simon via Guix-Science 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. Thanks a lot for the trick, I was able to finish compiling it, but going another route (i.e. unbundling htslib). I've abandoned running the tests though, I'm hitting a module not found error. pytest doesn't manage to load the just built module, probably an issue with the paths. I'm attaching the new version for reference. 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