From: Alexis Simon <alexis.simon@runbox.com> To: help-guix <help-guix@gnu.org>, guix-science@gnu.org Subject: packaging python-cyvcf2 Date: Thu, 21 Mar 2024 18:03:31 -0700 [thread overview] Message-ID: <d892d5bb-7ec4-478c-8590-82e7966a4758@runbox.com> (raw) [-- Attachment #1: Type: text/plain, Size: 1007 bytes --] 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 [-- Attachment #2: cyvcf2.scm --] [-- Type: text/x-scheme, Size: 2158 bytes --] (define-module (cyvcf2) #:use-module ((guix licenses) #:prefix license:) #:use-module (gnu packages) #:use-module (gnu packages base) #:use-module (gnu packages autotools) #:use-module (gnu packages build-tools) #:use-module (gnu packages cmake) #:use-module (gnu packages check) #:use-module (gnu packages python) #:use-module (gnu packages python-build) #:use-module (gnu packages python-check) #:use-module (gnu packages python-xyz) #:use-module (gnu packages python-science) #:use-module (gnu packages python-web) #:use-module (gnu packages bioinformatics) #:use-module (gnu packages serialization) #:use-module (gnu packages compression) #:use-module (gnu packages curl) #:use-module (gnu packages tls) #:use-module (guix packages) #:use-module (guix download) #:use-module (guix utils) #:use-module (guix build-system python) #:use-module (guix build-system cargo) #:use-module (guix build-system cmake) #:use-module (guix build-system pyproject)) (define-public python-cyvcf2 (package (name "python-cyvcf2") (version "0.30.28") (source (origin (method url-fetch) (uri (pypi-uri "cyvcf2" version)) (sha256 (base32 "03ycp7php5nzvhgj89k8js8z2xm3i8d1f76jlsfdy472f0apgryx")))) (build-system python-build-system) (arguments `(#:use-setuptools? #f #:phases (modify-phases %standard-phases (add-before 'build 'setenv (lambda _ (setenv "CYVCF2_HTSLIB_MODE" "BUILTIN")))))) ; unnecessary (propagated-inputs (list python-click python-coloredlogs python-numpy)) (native-inputs (list zlib libdeflate curl openssl autoconf automake ; htslib python-cython)) (home-page "https://github.com/brentp/cyvcf2/") (synopsis "fast vcf parsing with cython + htslib") (description "fast vcf parsing with cython + htslib") (license license:expat)))
WARNING: multiple messages have this Message-ID (diff)
From: Alexis Simon via Guix-Science <guix-science@gnu.org> To: help-guix <help-guix@gnu.org>, guix-science@gnu.org Subject: packaging python-cyvcf2 Date: Thu, 21 Mar 2024 18:03:31 -0700 [thread overview] Message-ID: <d892d5bb-7ec4-478c-8590-82e7966a4758@runbox.com> (raw) Message-ID: <20240322010331.rPK74erAtd92x501BqURAIjfbCn7dxgdZQHUneA8pfY@z> (raw) [-- Attachment #1: Type: text/plain, Size: 1007 bytes --] 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 [-- Attachment #2: cyvcf2.scm --] [-- Type: text/x-scheme, Size: 2158 bytes --] (define-module (cyvcf2) #:use-module ((guix licenses) #:prefix license:) #:use-module (gnu packages) #:use-module (gnu packages base) #:use-module (gnu packages autotools) #:use-module (gnu packages build-tools) #:use-module (gnu packages cmake) #:use-module (gnu packages check) #:use-module (gnu packages python) #:use-module (gnu packages python-build) #:use-module (gnu packages python-check) #:use-module (gnu packages python-xyz) #:use-module (gnu packages python-science) #:use-module (gnu packages python-web) #:use-module (gnu packages bioinformatics) #:use-module (gnu packages serialization) #:use-module (gnu packages compression) #:use-module (gnu packages curl) #:use-module (gnu packages tls) #:use-module (guix packages) #:use-module (guix download) #:use-module (guix utils) #:use-module (guix build-system python) #:use-module (guix build-system cargo) #:use-module (guix build-system cmake) #:use-module (guix build-system pyproject)) (define-public python-cyvcf2 (package (name "python-cyvcf2") (version "0.30.28") (source (origin (method url-fetch) (uri (pypi-uri "cyvcf2" version)) (sha256 (base32 "03ycp7php5nzvhgj89k8js8z2xm3i8d1f76jlsfdy472f0apgryx")))) (build-system python-build-system) (arguments `(#:use-setuptools? #f #:phases (modify-phases %standard-phases (add-before 'build 'setenv (lambda _ (setenv "CYVCF2_HTSLIB_MODE" "BUILTIN")))))) ; unnecessary (propagated-inputs (list python-click python-coloredlogs python-numpy)) (native-inputs (list zlib libdeflate curl openssl autoconf automake ; htslib python-cython)) (home-page "https://github.com/brentp/cyvcf2/") (synopsis "fast vcf parsing with cython + htslib") (description "fast vcf parsing with cython + htslib") (license license:expat)))
next reply other threads:[~2024-03-22 1:04 UTC|newest] Thread overview: 8+ messages / expand[flat|nested] mbox.gz Atom feed top 2024-03-22 1:03 Alexis Simon [this message] 2024-03-22 1:03 ` packaging python-cyvcf2 Alexis Simon via Guix-Science 2024-03-22 15:25 ` Simon Tournier 2024-03-22 19:38 ` Alexis Simon 2024-03-22 19:38 ` Alexis Simon via Guix-Science 2024-03-26 15:47 ` Simon Tournier 2024-04-18 9:13 ` Ricardo Wurmus 2024-04-21 1:31 ` Alexis Simon via Guix-Science
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