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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.
This commit is contained in:
Ricardo Wurmus 2017-04-05 17:57:23 +02:00 committed by Ricardo Wurmus
parent beebe43176
commit 1108a920bd
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1 changed files with 13 additions and 1 deletions
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gnu/packages/bioinformatics.scm
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@ -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)