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
(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)))
