guix_mirror_bot pushed a commit to branch master
in repository guix.
commit e371d6bbf16e18e069486be026bba6e0ae34ca29
Author: Andreas Enge <[email protected]>
AuthorDate: Mon Nov 24 11:10:38 2025 +0100
gnu: Remove blasr-libcpp.
* gnu/packages/bioinformatics.scm (blasr-libcpp): Delete variable.
Change-Id: I93cbb12041bd544d381851e44b17d3bd1596e4cf
---
gnu/packages/bioinformatics.scm | 58 -----------------------------------------
1 file changed, 58 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 5f03f11e97..5f5dc2c2bc 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2046,64 +2046,6 @@ formats when enabled. Parallel decompression is
somewhat faster, but the true
speedup comes during compression.")
(license license:expat))))
-(define-public blasr-libcpp
- (package
- (name "blasr-libcpp")
- (version "5.3.5")
- (source (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/PacificBiosciences/blasr_libcpp";)
- (commit version)))
- (file-name (git-file-name name version))
- (sha256
- (base32
- "07cdfnfl29zf2j7fpaaqaxghq3p0wnc109razs0icwm2q6l3gycb"))))
- (build-system meson-build-system)
- (arguments
- `(#:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'link-with-hdf5
- (lambda* (#:key inputs #:allow-other-keys)
- (let ((hdf5 (assoc-ref inputs "hdf5")))
- (substitute* "meson.build"
- (("libblasr_deps = \\[" m)
- (string-append
- m
- (format #f "cpp.find_library('hdf5', dirs : '~a'), \
-cpp.find_library('hdf5_cpp', dirs : '~a'), "
- hdf5 hdf5)))))))
- (add-after 'unpack 'find-googletest
- (lambda* (#:key inputs #:allow-other-keys)
- ;; It doesn't find gtest_main because there's no pkg-config file
- ;; for it. Find it another way.
- (substitute* "unittest/meson.build"
- (("libblasr_gtest_dep = dependency\\('gtest_main'.*")
- (format #f "cpp = meson.get_compiler('cpp')
-libblasr_gtest_dep = cpp.find_library('gtest_main', dirs : '~a')\n"
- (assoc-ref inputs "googletest")))))))
- ;; TODO: unittest/libblasr_unittest cannot be linked
- ;; ld: ;;
unittest/df08227@@libblasr_unittest@exe/alignment_utils_FileUtils_gtest.cpp.o:
- ;; undefined reference to symbol
- ;; '_ZN7testing8internal9DeathTest6CreateEPKcPKNS0_2REES3_iPPS1_'
- ;; ld: /gnu/store/...-googletest-1.8.0/lib/libgtest.so:
- ;; error adding symbols: DSO missing from command line
- #:tests? #f
- #:configure-flags '("-Dtests=false")))
- (inputs
- (list boost hdf5 htslib pbbam zlib))
- (native-inputs
- (list googletest pkg-config))
- (home-page
- (string-append "https://web.archive.org/web/20201106122415/";
- "https://github.com/PacificBiosciences/blasr_libcpp";))
- (synopsis "Library for analyzing PacBio genomic sequences")
- (description
- "This package provides three libraries used by applications for analyzing
-PacBio genomic sequences. This library contains three sub-libraries: pbdata,
-hdf and alignment.")
- (license license:bsd-3)))
-
(define-public randfold
(package
(name "randfold")
