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[194.254.61.42]) by smtp.gmail.com with ESMTPSA id v15-20020a05600c444f00b004146a884bffsm3314912wmn.18.2024.03.22.08.25.25 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 22 Mar 2024 08:25:25 -0700 (PDT) From: Simon Tournier To: Alexis Simon , help-guix , guix-science@gnu.org Subject: Re: packaging python-cyvcf2 In-Reply-To: References: Date: Fri, 22 Mar 2024 16:25:20 +0100 Message-ID: <87il1eb867.fsf@gmail.com> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Received-SPF: pass client-ip=2a00:1450:4864:20::32d; envelope-from=zimon.toutoune@gmail.com; helo=mail-wm1-x32d.google.com X-Spam_score_int: -20 X-Spam_score: -2.1 X-Spam_bar: -- X-Spam_report: (-2.1 / 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_NONE=-0.0001, SPF_HELO_NONE=0.001, SPF_PASS=-0.001 autolearn=ham autolearn_force=no X-Spam_action: no action 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: , Errors-To: guix-science-bounces+larch=yhetil.org@gnu.org Sender: guix-science-bounces+larch=yhetil.org@gnu.org X-Migadu-Flow: FLOW_IN X-Migadu-Country: US X-Migadu-Queue-Id: ABA3646415 X-Spam-Score: -9.61 X-Migadu-Spam-Score: -9.61 X-Migadu-Scanner: mx11.migadu.com X-TUID: 2NQwjY2Eesu/ 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"=20 > "build") exit-status: 1 term-signal: #f stop-signal: #f> > > What is very disturbing is that it builds fine in a debugging=20 > environment following the documentation [2] Indeed! Well, another undocumented trick. ;-) guix build -L . python-cyvcf2 \ --with-source=3Dpython-cyvcf2=3D/tmp/cyvcf2-0.30.28=20 where /tmp/cyvcf2-0.30.28 is the uncompressed output of =E2=80=9Cguix build= -S=E2=80=9D 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 202= 4-01-30 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()) =20 - subprocess.run(configure_args, check=3DTrue) + print(configure_args, + "File exists?", os.path.exists(configure_args[0]), + flush=3DTrue) + try: + subprocess.run(configure_args, check=3DTrue) + except: + print("BANG!") subprocess.run(["make"], check=3DTrue) =20 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=3D-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=3Dhidden ' '-fvisibility= =3Dhidden' >> htscodecs.mk /gnu/store/rib9g2ig1xf3kclyl076w28parmncg4k-bash-minimal-5.1.16/bin/sh: lin= e 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 =E2=80=99./configure=E2=80=99 as wrongly repo= rted but from something triggered by it. Let me know your progress. Maybe I could give a closer look next week. Cheers, simon