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| author | Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> | 2017-04-05 17:57:23 +0200 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2017-04-05 18:06:51 +0200 |
| commit | 1108a920bd09a8a81e5953ede65f3123bc35ad92 (patch) | |
| tree | c400c834f6899dea9e797092fbfaec06429f9866 /gnu | |
| parent | beebe43176b6e63f35932f280f43969c46d951d8 (diff) | |
| download | patches-1108a920bd09a8a81e5953ede65f3123bc35ad92.tar patches-1108a920bd09a8a81e5953ede65f3123bc35ad92.tar.gz | |
gnu: sra-tools: Fix glibc naming conflict.
* gnu/packages/bioinformatics.scm (sra-tools)[arguments]: Add build phase
"patch-away-glibc-conflict" to fix a definition conflict with glibc 2.25.
Diffstat (limited to 'gnu')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 14 |
1 files changed, 13 insertions, 1 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 6a04e69be3..c8219cc2cc 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4832,7 +4832,19 @@ sequence itself can be retrieved from these databases.") (string-append "--with-ngs-sdk-prefix=" (assoc-ref inputs "ngs-sdk")) (string-append "--with-hdf5-prefix=" - (assoc-ref inputs "hdf5"))))))))) + (assoc-ref inputs "hdf5")))))) + ;; This version of sra-tools fails to build with glibc because of a + ;; naming conflict. glibc-2.25/include/bits/mathcalls.h already + ;; contains a definition of "canonicalize", so we rename it. + ;; + ;; See upstream bug report: + ;; https://github.com/ncbi/sra-tools/issues/67 + (add-after 'unpack 'patch-away-glibc-conflict + (lambda _ + (substitute* "tools/bam-loader/bam.c" + (("canonicalize\\(" line) + (string-append "sra_tools_" line))) + #t))))) (native-inputs `(("perl" ,perl))) (inputs `(("ngs-sdk" ,ngs-sdk) |