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authorRicardo Wurmus <rekado@elephly.net>2021-03-15 23:31:58 +0100
committerRicardo Wurmus <rekado@elephly.net>2021-03-15 23:31:58 +0100
commit8f9fd9b70c7bf166d96a4b1dc8b427f8cdf040b5 (patch)
treed54746fecaf5e55abb102bcc21d101488ab51efa /gnu/packages
parentd99a18252c31fb2c19e3e7ae65bb36e85c3aa1af (diff)
gnu: r-biocparallel: Build reproducibly.
* gnu/packages/bioconductor.scm (r-biocparallel)[arguments]: Add phase "make-reproducible".
Diffstat (limited to 'gnu/packages')
-rw-r--r--gnu/packages/bioconductor.scm28
1 files changed, 28 insertions, 0 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 9212165706..166d30be0f 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1705,6 +1705,34 @@ powerful online queries from gene annotation to database mining.")
(properties
`((upstream-name . "BiocParallel")))
(build-system r-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'make-reproducible
+ (lambda _
+ ;; Remove generated documentation.
+ (for-each delete-file
+ '("inst/doc/BiocParallel_BatchtoolsParam.pdf"
+ "inst/doc/Introduction_To_BiocParallel.pdf"
+ "inst/doc/Errors_Logs_And_Debugging.pdf"
+ "inst/doc/BiocParallel_BatchtoolsParam.R"
+ "inst/doc/Introduction_To_BiocParallel.R"
+ "inst/doc/Errors_Logs_And_Debugging.R"))
+
+ ;; Remove time-dependent macro
+ (substitute* '("inst/doc/BiocParallel_BatchtoolsParam.Rnw"
+ "inst/doc/Introduction_To_BiocParallel.Rnw"
+ "inst/doc/Errors_Logs_And_Debugging.Rnw"
+ "vignettes/BiocParallel_BatchtoolsParam.Rnw"
+ "vignettes/Introduction_To_BiocParallel.Rnw"
+ "vignettes/Errors_Logs_And_Debugging.Rnw")
+ (("\\today") "later"))
+
+ ;; Initialize the random number generator seed when building.
+ (substitute* "R/internal_rng_stream.R"
+ (("\"L'Ecuyer-CMRG\"\\)" m)
+ (string-append
+ m "; if (!is.na(Sys.getenv(\"SOURCE_DATE_EPOCH\"))) {set.seed(100)}\n"))))))))
(propagated-inputs
`(("r-futile-logger" ,r-futile-logger)
("r-snow" ,r-snow)