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charset=UTF-8; format=flowed Content-Transfer-Encoding: 7bit Hi, I've spent nearly the day on this and it's driving me crazy. I am trying to package this cyvcf2 [1] I am attaching the packaging I've tried. 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] The .configure file is present in the failed build, so there must be something going on with the setup.py not managing to change directory to htslib in the build_htslib function. If anyone has any guidelines to debug this further it would be much appreciated. Thanks, Alexis [1] https://github.com/brentp/cyvcf2/ [2] https://guix.gnu.org/manual/en/guix.html#Debugging-Build-Failures --------------CxN2Ll0aFXadeBcimTceZLIJ Content-Type: text/x-scheme; charset=UTF-8; name="cyvcf2.scm" Content-Disposition: attachment; filename="cyvcf2.scm" Content-Transfer-Encoding: base64 KGRlZmluZS1tb2R1bGUgKGN5dmNmMikKICAjOnVzZS1tb2R1bGUgKChndWl4IGxpY2Vuc2Vz KSAjOnByZWZpeCBsaWNlbnNlOikKICAjOnVzZS1tb2R1bGUgKGdudSBwYWNrYWdlcykKICAj OnVzZS1tb2R1bGUgKGdudSBwYWNrYWdlcyBiYXNlKQogICM6dXNlLW1vZHVsZSAoZ251IHBh Y2thZ2VzIGF1dG90b29scykKICAjOnVzZS1tb2R1bGUgKGdudSBwYWNrYWdlcyBidWlsZC10 b29scykKICAjOnVzZS1tb2R1bGUgKGdudSBwYWNrYWdlcyBjbWFrZSkKICAjOnVzZS1tb2R1 bGUgKGdudSBwYWNrYWdlcyBjaGVjaykKICAjOnVzZS1tb2R1bGUgKGdudSBwYWNrYWdlcyBw eXRob24pCiAgIzp1c2UtbW9kdWxlIChnbnUgcGFja2FnZXMgcHl0aG9uLWJ1aWxkKQogICM6 dXNlLW1vZHVsZSAoZ251IHBhY2thZ2VzIHB5dGhvbi1jaGVjaykKICAjOnVzZS1tb2R1bGUg KGdudSBwYWNrYWdlcyBweXRob24teHl6KQogICM6dXNlLW1vZHVsZSAoZ251IHBhY2thZ2Vz IHB5dGhvbi1zY2llbmNlKQogICM6dXNlLW1vZHVsZSAoZ251IHBhY2thZ2VzIHB5dGhvbi13 ZWIpCiAgIzp1c2UtbW9kdWxlIChnbnUgcGFja2FnZXMgYmlvaW5mb3JtYXRpY3MpCiAgIzp1 c2UtbW9kdWxlIChnbnUgcGFja2FnZXMgc2VyaWFsaXphdGlvbikKICAjOnVzZS1tb2R1bGUg KGdudSBwYWNrYWdlcyBjb21wcmVzc2lvbikKICAjOnVzZS1tb2R1bGUgKGdudSBwYWNrYWdl cyBjdXJsKQogICM6dXNlLW1vZHVsZSAoZ251IHBhY2thZ2VzIHRscykKICAjOnVzZS1tb2R1 bGUgKGd1aXggcGFja2FnZXMpCiAgIzp1c2UtbW9kdWxlIChndWl4IGRvd25sb2FkKQogICM6 dXNlLW1vZHVsZSAoZ3VpeCB1dGlscykKICAjOnVzZS1tb2R1bGUgKGd1aXggYnVpbGQtc3lz dGVtIHB5dGhvbikKICAjOnVzZS1tb2R1bGUgKGd1aXggYnVpbGQtc3lzdGVtIGNhcmdvKQog ICM6dXNlLW1vZHVsZSAoZ3VpeCBidWlsZC1zeXN0ZW0gY21ha2UpCiAgIzp1c2UtbW9kdWxl IChndWl4IGJ1aWxkLXN5c3RlbSBweXByb2plY3QpKQoKKGRlZmluZS1wdWJsaWMgcHl0aG9u LWN5dmNmMgogIChwYWNrYWdlCiAgICAobmFtZSAicHl0aG9uLWN5dmNmMiIpCiAgICAodmVy c2lvbiAiMC4zMC4yOCIpCiAgICAoc291cmNlCiAgICAgKG9yaWdpbgogICAgICAgKG1ldGhv ZCB1cmwtZmV0Y2gpCiAgICAgICAodXJpIChweXBpLXVyaSAiY3l2Y2YyIiB2ZXJzaW9uKSkK ICAgICAgIChzaGEyNTYKICAgICAgICAoYmFzZTMyICIwM3ljcDdwaHA1bnp2aGdqODlrOGpz OHoyeG0zaThkMWY3Nmpsc2ZkeTQ3MmYwYXBncnl4IikpKSkKICAgIChidWlsZC1zeXN0ZW0g cHl0aG9uLWJ1aWxkLXN5c3RlbSkKICAgIChhcmd1bWVudHMKICAgICBgKCM6dXNlLXNldHVw dG9vbHM/ICNmCiAgICAgICAjOnBoYXNlcwogICAgICAgIChtb2RpZnktcGhhc2VzICVzdGFu ZGFyZC1waGFzZXMKICAgICAgICAgIChhZGQtYmVmb3JlICdidWlsZCAnc2V0ZW52CiAgICAg ICAgICAgICAobGFtYmRhIF8KICAgICAgICAgICAgICAgICAgICAgKHNldGVudiAiQ1lWQ0Yy X0hUU0xJQl9NT0RFIiAiQlVJTFRJTiIpKSkpKSkgOyB1bm5lY2Vzc2FyeQogICAgKHByb3Bh Z2F0ZWQtaW5wdXRzIChsaXN0IHB5dGhvbi1jbGljawogICAgICAgICAgICAgICAgICAgICAg ICAgICAgIHB5dGhvbi1jb2xvcmVkbG9ncwogICAgICAgICAgICAgICAgICAgICAgICAgICAg IHB5dGhvbi1udW1weSkpCiAgICAobmF0aXZlLWlucHV0cyAobGlzdCB6bGliCiAgICAgICAg ICAgICAgICAgICAgICAgICBsaWJkZWZsYXRlCiAgICAgICAgICAgICAgICAgICAgICAgICBj dXJsCiAgICAgICAgICAgICAgICAgICAgICAgICBvcGVuc3NsCiAgICAgICAgICAgICAgICAg ICAgICAgICBhdXRvY29uZgogICAgICAgICAgICAgICAgICAgICAgICAgYXV0b21ha2UKICAg ICAgICAgICAgICAgICAgICAgICAgIDsgaHRzbGliCiAgICAgICAgICAgICAgICAgICAgICAg ICBweXRob24tY3l0aG9uKSkKICAgIChob21lLXBhZ2UgImh0dHBzOi8vZ2l0aHViLmNvbS9i cmVudHAvY3l2Y2YyLyIpCiAgICAoc3lub3BzaXMgImZhc3QgdmNmIHBhcnNpbmcgd2l0aCBj eXRob24gKyBodHNsaWIiKQogICAgKGRlc2NyaXB0aW9uICJmYXN0IHZjZiBwYXJzaW5nIHdp dGggY3l0aG9uICsgaHRzbGliIikKICAgIChsaWNlbnNlIGxpY2Vuc2U6ZXhwYXQpKSkKCg== --------------CxN2Ll0aFXadeBcimTceZLIJ-- From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from mp0.migadu.com ([2001:41d0:303:e16b::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by ms8.migadu.com with LMTPS id oCEqN3gN/WUxeQEAqHPOHw:P1 (envelope-from ) for ; 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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 00:47:39 -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-Flow: FLOW_IN X-Migadu-Country: US X-Migadu-Scanner: mx13.migadu.com X-Migadu-Spam-Score: -4.32 X-Spam-Score: -4.32 X-Migadu-Queue-Id: 7D947434B5 X-TUID: qf+wYX7Y0XTM Message-ID: <20240322010331.rPK74erAtd92x501BqURAIjfbCn7dxgdZQHUneA8pfY@z> This is a multi-part message in MIME format. --------------CxN2Ll0aFXadeBcimTceZLIJ Content-Type: text/plain; charset=UTF-8; format=flowed Content-Transfer-Encoding: 7bit Hi, I've spent nearly the day on this and it's driving me crazy. I am trying to package this cyvcf2 [1] I am attaching the packaging I've tried. 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] The .configure file is present in the failed build, so there must be something going on with the setup.py not managing to change directory to htslib in the build_htslib function. If anyone has any guidelines to debug this further it would be much appreciated. Thanks, Alexis [1] https://github.com/brentp/cyvcf2/ [2] https://guix.gnu.org/manual/en/guix.html#Debugging-Build-Failures --------------CxN2Ll0aFXadeBcimTceZLIJ Content-Type: text/x-scheme; charset=UTF-8; name="cyvcf2.scm" Content-Disposition: attachment; filename="cyvcf2.scm" Content-Transfer-Encoding: base64 KGRlZmluZS1tb2R1bGUgKGN5dmNmMikKICAjOnVzZS1tb2R1bGUgKChndWl4IGxpY2Vuc2Vz KSAjOnByZWZpeCBsaWNlbnNlOikKICAjOnVzZS1tb2R1bGUgKGdudSBwYWNrYWdlcykKICAj OnVzZS1tb2R1bGUgKGdudSBwYWNrYWdlcyBiYXNlKQogICM6dXNlLW1vZHVsZSAoZ251IHBh Y2thZ2VzIGF1dG90b29scykKICAjOnVzZS1tb2R1bGUgKGdudSBwYWNrYWdlcyBidWlsZC10 b29scykKICAjOnVzZS1tb2R1bGUgKGdudSBwYWNrYWdlcyBjbWFrZSkKICAjOnVzZS1tb2R1 bGUgKGdudSBwYWNrYWdlcyBjaGVjaykKICAjOnVzZS1tb2R1bGUgKGdudSBwYWNrYWdlcyBw eXRob24pCiAgIzp1c2UtbW9kdWxlIChnbnUgcGFja2FnZXMgcHl0aG9uLWJ1aWxkKQogICM6 dXNlLW1vZHVsZSAoZ251IHBhY2thZ2VzIHB5dGhvbi1jaGVjaykKICAjOnVzZS1tb2R1bGUg KGdudSBwYWNrYWdlcyBweXRob24teHl6KQogICM6dXNlLW1vZHVsZSAoZ251IHBhY2thZ2Vz IHB5dGhvbi1zY2llbmNlKQogICM6dXNlLW1vZHVsZSAoZ251IHBhY2thZ2VzIHB5dGhvbi13 ZWIpCiAgIzp1c2UtbW9kdWxlIChnbnUgcGFja2FnZXMgYmlvaW5mb3JtYXRpY3MpCiAgIzp1 c2UtbW9kdWxlIChnbnUgcGFja2FnZXMgc2VyaWFsaXphdGlvbikKICAjOnVzZS1tb2R1bGUg KGdudSBwYWNrYWdlcyBjb21wcmVzc2lvbikKICAjOnVzZS1tb2R1bGUgKGdudSBwYWNrYWdl cyBjdXJsKQogICM6dXNlLW1vZHVsZSAoZ251IHBhY2thZ2VzIHRscykKICAjOnVzZS1tb2R1 bGUgKGd1aXggcGFja2FnZXMpCiAgIzp1c2UtbW9kdWxlIChndWl4IGRvd25sb2FkKQogICM6 dXNlLW1vZHVsZSAoZ3VpeCB1dGlscykKICAjOnVzZS1tb2R1bGUgKGd1aXggYnVpbGQtc3lz dGVtIHB5dGhvbikKICAjOnVzZS1tb2R1bGUgKGd1aXggYnVpbGQtc3lzdGVtIGNhcmdvKQog ICM6dXNlLW1vZHVsZSAoZ3VpeCBidWlsZC1zeXN0ZW0gY21ha2UpCiAgIzp1c2UtbW9kdWxl IChndWl4IGJ1aWxkLXN5c3RlbSBweXByb2plY3QpKQoKKGRlZmluZS1wdWJsaWMgcHl0aG9u LWN5dmNmMgogIChwYWNrYWdlCiAgICAobmFtZSAicHl0aG9uLWN5dmNmMiIpCiAgICAodmVy c2lvbiAiMC4zMC4yOCIpCiAgICAoc291cmNlCiAgICAgKG9yaWdpbgogICAgICAgKG1ldGhv ZCB1cmwtZmV0Y2gpCiAgICAgICAodXJpIChweXBpLXVyaSAiY3l2Y2YyIiB2ZXJzaW9uKSkK ICAgICAgIChzaGEyNTYKICAgICAgICAoYmFzZTMyICIwM3ljcDdwaHA1bnp2aGdqODlrOGpz OHoyeG0zaThkMWY3Nmpsc2ZkeTQ3MmYwYXBncnl4IikpKSkKICAgIChidWlsZC1zeXN0ZW0g cHl0aG9uLWJ1aWxkLXN5c3RlbSkKICAgIChhcmd1bWVudHMKICAgICBgKCM6dXNlLXNldHVw dG9vbHM/ICNmCiAgICAgICAjOnBoYXNlcwogICAgICAgIChtb2RpZnktcGhhc2VzICVzdGFu ZGFyZC1waGFzZXMKICAgICAgICAgIChhZGQtYmVmb3JlICdidWlsZCAnc2V0ZW52CiAgICAg ICAgICAgICAobGFtYmRhIF8KICAgICAgICAgICAgICAgICAgICAgKHNldGVudiAiQ1lWQ0Yy X0hUU0xJQl9NT0RFIiAiQlVJTFRJTiIpKSkpKSkgOyB1bm5lY2Vzc2FyeQogICAgKHByb3Bh Z2F0ZWQtaW5wdXRzIChsaXN0IHB5dGhvbi1jbGljawogICAgICAgICAgICAgICAgICAgICAg ICAgICAgIHB5dGhvbi1jb2xvcmVkbG9ncwogICAgICAgICAgICAgICAgICAgICAgICAgICAg IHB5dGhvbi1udW1weSkpCiAgICAobmF0aXZlLWlucHV0cyAobGlzdCB6bGliCiAgICAgICAg ICAgICAgICAgICAgICAgICBsaWJkZWZsYXRlCiAgICAgICAgICAgICAgICAgICAgICAgICBj dXJsCiAgICAgICAgICAgICAgICAgICAgICAgICBvcGVuc3NsCiAgICAgICAgICAgICAgICAg ICAgICAgICBhdXRvY29uZgogICAgICAgICAgICAgICAgICAgICAgICAgYXV0b21ha2UKICAg ICAgICAgICAgICAgICAgICAgICAgIDsgaHRzbGliCiAgICAgICAgICAgICAgICAgICAgICAg ICBweXRob24tY3l0aG9uKSkKICAgIChob21lLXBhZ2UgImh0dHBzOi8vZ2l0aHViLmNvbS9i cmVudHAvY3l2Y2YyLyIpCiAgICAoc3lub3BzaXMgImZhc3QgdmNmIHBhcnNpbmcgd2l0aCBj eXRob24gKyBodHNsaWIiKQogICAgKGRlc2NyaXB0aW9uICJmYXN0IHZjZiBwYXJzaW5nIHdp dGggY3l0aG9uICsgaHRzbGliIikKICAgIChsaWNlbnNlIGxpY2Vuc2U6ZXhwYXQpKSkKCg== --------------CxN2Ll0aFXadeBcimTceZLIJ--