GNU bug report logs -
#77358
[PATCH 1/1] gnu: Remove freebayes.
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bug#77358
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guix-patches
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(Sat, 29 Mar 2025 09:58:03 GMT)
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Andreas Enge <andreas <at> enge.fr>
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Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):
The package does not build since 2023, it fails most of its tests.
Updating to the latest version does not solve the problem.
* gnu/packages/bioinformatics.scm (freebayes): Delete variable.
Change-Id: Ib61e298d639f7c5a86a2fc33cbedf0c764045441
---
gnu/packages/bioinformatics.scm | 82 ---------------------------------
1 file changed, 82 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 0825fbb6ef..96a4c6a2d6 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -22501,88 +22501,6 @@ (define-public vcflib
manipulations on VCF files.")
(license license:expat)))
-(define-public freebayes
- (package
- (name "freebayes")
- (version "1.3.7")
- (source (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/freebayes/freebayes")
- (commit (string-append "v" version))))
- (file-name (git-file-name name version))
- (sha256
- (base32 "163nd1xkq547za80khlys4qkgal64f3sgl6ap3yvik68r0rgyisv"))))
- (build-system meson-build-system)
- (inputs
- (list fastahack htslib smithwaterman tabixpp vcflib))
- (native-inputs
- `(("bash-tap" ,bash-tap)
- ("bc" ,bc)
- ("grep" ,grep) ; Built with perl support.
- ("parallel" ,parallel)
- ("perl" ,perl)
- ("pkg-config" ,pkg-config)
- ("python" ,python)
- ("samtools" ,samtools)
- ("simde" ,simde)
- ;; This submodule is needed to run the tests.
- ("test-simple-bash-src"
- ,(origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/ingydotnet/test-simple-bash/")
- (commit "124673ff204b01c8e96b7fc9f9b32ee35d898acc")))
- (file-name "test-simple-bash-src-checkout")
- (sha256
- (base32 "043plp6z0x9yf7mdpky1fw7zcpwn1p47px95w9mh16603zqqqpga"))))))
- (arguments
- `(#:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'patch-source
- (lambda* (#:key inputs #:allow-other-keys)
- (let ((bash-tap (assoc-ref inputs "bash-tap")))
- (substitute* (find-files "test/t")
- (("BASH_TAP_ROOT=bash-tap")
- (string-append "BASH_TAP_ROOT=" bash-tap "/bin"))
- (("bash-tap/bash-tap-bootstrap")
- (string-append bash-tap "/bin/bash-tap-bootstrap"))
- (("source.*bash-tap-bootstrap")
- (string-append "source " bash-tap "/bin/bash-tap-bootstrap")))
- (substitute* '("src/BedReader.cpp"
- "src/BedReader.h")
- (("../intervaltree/IntervalTree.h") "IntervalTree.h"))
- ;; We don't have Perl support in grep -E.
- (substitute* '("test/t/01_call_variants.t"
- "test/t/01b_call_variants.t")
- (("grep -P") "grep -E")
- (("\\\\t") " "))
- (substitute* "meson.build"
- ;; Our pkg-config file is vcflib.pc
- (("libvcflib") "vcflib")
- (("vcflib_inc,") "")))))
- (add-after 'unpack 'unpack-submodule-sources
- (lambda* (#:key inputs #:allow-other-keys)
- (mkdir-p "test/test-simple-bash")
- (copy-recursively (assoc-ref inputs "test-simple-bash-src")
- "test/test-simple-bash")))
- ;; The slow tests take longer than the specified timeout.
- ,@(if (any (cute string=? <> (%current-system))
- '("armhf-linux" "aarch64-linux"))
- '((replace 'check
- (lambda* (#:key tests? #:allow-other-keys)
- (when tests?
- (invoke "meson" "test" "--timeout-multiplier" "5")))))
- '()))))
- (home-page "https://github.com/freebayes/freebayes")
- (synopsis "Haplotype-based variant detector")
- (description "FreeBayes is a Bayesian genetic variant detector designed to
-find small polymorphisms, specifically SNPs (single-nucleotide polymorphisms),
-indels (insertions and deletions), MNPs (multi-nucleotide polymorphisms), and
-complex events (composite insertion and substitution events) smaller than the
-length of a short-read sequencing alignment.")
- (license license:expat)))
-
(define-public samblaster
(package
(name "samblaster")
--
2.49.0
Reply sent
to
Andreas Enge <andreas <at> enge.fr>
:
You have taken responsibility.
(Sat, 29 Mar 2025 10:01:02 GMT)
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Notification sent
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Andreas Enge <andreas <at> enge.fr>
:
bug acknowledged by developer.
(Sat, 29 Mar 2025 10:01:02 GMT)
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Message #10 received at 77358-done <at> debbugs.gnu.org (full text, mbox):
See the discussion in 77357.
Andreas
This bug report was last modified 6 days ago.
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