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branch master updated: gnu: r-affycompatible: Build reproducibly.
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guix-commits |
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branch master updated: gnu: r-affycompatible: Build reproducibly. |
Date: |
Thu, 14 Jul 2022 18:10:26 -0400 |
This is an automated email from the git hooks/post-receive script.
rekado pushed a commit to branch master
in repository guix.
The following commit(s) were added to refs/heads/master by this push:
new 9238ba5874 gnu: r-affycompatible: Build reproducibly.
9238ba5874 is described below
commit 9238ba58748d99970674e098c9b1b0ed8ca66c14
Author: Ricardo Wurmus <rekado@elephly.net>
AuthorDate: Fri Jul 15 00:06:26 2022 +0200
gnu: r-affycompatible: Build reproducibly.
* gnu/packages/bioconductor.scm (r-affycompatible)[arguments]: Sort XML
elements before generating R code from them.
---
gnu/packages/bioconductor.scm | 19 +++++++++++++++++++
1 file changed, 19 insertions(+)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 38c309caa4..31484799b2 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2940,6 +2940,25 @@ measures for Affymetrix Oligonucleotide Arrays.")
(properties
`((upstream-name . "AffyCompatible")))
(build-system r-build-system)
+ (arguments
+ (list
+ #:phases
+ `(modify-phases %standard-phases
+ (add-after 'unpack 'make-reproducible
+ (lambda _
+ ;; Order DTD elements before generating R code from them.
+ (substitute* "R/methods-AffyCompatible.R"
+ (("dtd <- .*" m)
+ (string-append m "
+elements <- dtd$elements
+ordered <- elements[order(names(elements))]\n"))
+ (("elt in dtd\\$elements")
+ "elt in ordered"))
+ ;; Use a predictable directory name for code generation.
+ (mkdir-p "/tmp/NetAffxResourcePrototype")
+ (substitute* "R/DataClasses.R"
+ (("directory=tempdir\\(\\)")
+ "directory=\"/tmp/NetAffxResourcePrototype\"")))))))
(propagated-inputs
(list r-biostrings r-rcurl r-xml))
(home-page "https://bioconductor.org/packages/AffyCompatible/")
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