Package: guix-patches;
Reported by: Mădălin Ionel Patrașcu <madalinionel.patrascu <at> mdc-berlin.de>
Date: Wed, 1 Mar 2023 07:22:01 UTC
Severity: normal
Tags: patch
Done: Ricardo Wurmus <rekado <at> elephly.net>
Bug is archived. No further changes may be made.
View this message in rfc822 format
From: Mădălin Ionel Patrașcu <madalinionel.patrascu <at> mdc-berlin.de> To: <61891 <at> debbugs.gnu.org> Cc: rekado <at> elephly.net Subject: [bug#61891] Date: Wed, 1 Mar 2023 11:53:39 +0100
Date: Wed, 1 Mar 2023 11:50:40 +0100
Subject: [PATCH] gnu: Test builds for r-maaslin and r-mmuphin.scm
This is my try to make the build of these two package reproducible.
I send this only in the case if the reviewer wants to dig more and maybe he can
solve the non deterministic build.
---
gnu/packages/bioconductor.scm | 138 ++++++++++++++++++++++++++++++++++
1 file changed, 138 insertions(+)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 7de5750e09..15fad711af 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -33,6 +33,7 @@ (define-module (gnu packages bioconductor)
#:use-module ((guix licenses) #:prefix license:)
#:use-module (guix packages)
#:use-module (guix download)
+ #:use-module (guix gexp)
#:use-module (guix git-download)
#:use-module (guix build-system r)
#:use-module (gnu packages)
@@ -6533,6 +6534,80 @@ (define-public r-limma
different technologies, including microarrays, RNA-seq, and quantitative PCR.")
(license license:gpl2+)))
+(define-public r-maaslin2
+ (package
+ (name "r-maaslin2")
+ (version "1.12.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "Maaslin2" version))
+ (sha256
+ (base32 "0ncvsywn9f8766gjb8nxzg82p3w30g8pjs85sy8s0bz9ilanpy89"))))
+ (properties `((upstream-name . "Maaslin2")))
+ (build-system r-build-system)
+ (arguments (list ;;#:tests? #f)) ;test suite is non-deterministic :(
+ #:phases
+ #~(modify-phases %standard-phases
+ ;; During the check there is needed for writable cache directory
+ ;; Fontconfig error: No writable cache directories
+ (add-before 'check 'set-cache
+ (lambda _
+ (setenv "XDG_CACHE_HOME" "/tmp/xdg-cache")))
+ ;; The check phase generates some log and pdf files. This cause that
+ ;; the build to be not reproducible
+ (add-after 'check 'make-reproducible
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let* ((out (string-append (assoc-ref outputs "out") "/site-library/Maaslin2/")))
+ (for-each delete-file-recursively
+ (list ;;(string-append out "Maaslin2-Ex.Rout")
+ ;;(string-append #$output "/Maaslin2-Ex.pdf")
+ ;;(string-append #$output "/Maaslin2-tests/testthat/output")
+ ;;(string-append #$output "/Maaslin2-tests/testthat/output2")
+ ;;(string-append #$output "Maaslin2-tests/testthat.Rout")
+ (string-append out "doc/demo_output/maaslin2.log")
+ (string-append out "doc/demo_output/figures")
+ ;;"doc/demo_output"
+ )))))
+ )))
+ (propagated-inputs
+ (list r-biglm
+ r-car
+ r-chemometrics
+ r-cplm
+ r-data-table
+ r-dplyr
+ r-edger
+ r-ggplot2
+ r-glmmtmb
+ r-hash
+ r-lme4
+ r-lmertest
+ r-logging
+ r-lpsymphony
+ r-mass
+ r-mumin
+ r-metagenomeseq
+ r-optparse
+ r-pbapply
+ r-pcapp
+ r-pheatmap
+ r-pscl
+ r-rmarkdown
+ r-robustbase
+ r-vegan))
+ (native-inputs (list r-knitr))
+ (home-page "http://huttenhower.sph.harvard.edu/maaslin2")
+ (synopsis
+ "Multivariable association discovery in population-scale meta-omics studies")
+ (description
+ "MaAsLin2 is comprehensive R package for efficiently determining multivariable
+association between clinical metadata and microbial meta'omic features. This
+package relies on general linear models to accommodate most modern epidemiological
+study designs, including cross-sectional and longitudinal, and offers a variety
+of data exploration, normalization, and transformation methods.")
+ (license license:expat)))
+
(define-public r-made4
(package
(name "r-made4")
@@ -6760,6 +6835,69 @@ (define-public r-methylkit
TAB-Seq.")
(license license:artistic2.0)))
+(define-public r-mmuphin
+ (package
+ (name "r-mmuphin")
+ (version "1.12.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "MMUPHin" version))
+ (sha256
+ (base32 "0vpap3avmrjy187s3dva6f008al6d935kpdf816xzl5gxl7zvf62"))))
+ (properties `((upstream-name . "MMUPHin")))
+ (build-system r-build-system)
+ (arguments
+ (list ;;#:tests? #f)) ;; non deterministic, also it requieres http access
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'adjusts-paths
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (substitute* "inst/doc/MMUPHin.Rmd"
+ (("../man/figures")
+ (string-append #$output "/site-library/MMUPHin/help/figures")))
+ ;;(substitute* "inst/doc/MMUPHin.R"
+ ;; (("library(ggplot2)") "library(ggplot2)\ngetwd()"))
+ ))
+ (add-after 'install 'add-files
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (install-file "man/figures/structure_types.PNG"
+ (string-append #$output "/site-library/MMUPHin/help/figures"))
+ (install-file "vignettes/references.bib"
+ (string-append #$output "/site-library/MMUPHin/doc"))))
+ (add-before 'check 'set-cache
+ (lambda _
+ (setenv "XDG_CACHE_HOME" "/tmp/xdg-cache")))
+ )))
+ (inputs (list glpk
+ ; ;;pandoc
+ ; ;;r-rmarkdown
+ ))
+ (propagated-inputs
+ (list r-cowplot
+ r-biocstyle
+ r-dplyr
+ r-fpc
+ r-ggplot2
+ r-igraph
+ r-maaslin2
+ r-metafor
+ r-stringr
+ r-tidyr))
+ (native-inputs (list r-knitr))
+ (home-page "https://bioconductor.org/packages/MMUPHin")
+ (synopsis "Meta-analysis with uniform pipeline for heterogeneity in microbiome")
+ (description
+ "MMUPHin is an R package for meta-analysis tasks of microbiome cohorts. It
+has function interfaces for:
+@itemize
+@item covariate-controlled batch- and cohort effect adjustment;
+@item meta-analysis differential abundance testing;
+@item meta-analysis unsupervised discrete structure (clustering) discovery;
+@item meta-analysis unsupervised continuous structure discovery.
+@end itemize")
+ (license license:expat)))
+
(define-public r-motifrg
(package
(name "r-motifrg")
base-commit: efa091f9f4e77068353dff24f0ccd2d0613c3f48
prerequisite-patch-id: 9e08f9ff2621a13d751e3d82c0837144b09494e4
prerequisite-patch-id: 4cfeb51eeb402b18b0d23c6782255a3bc1f1ff43
prerequisite-patch-id: cf4c417ccd15ef1f795ada39f3faee9f59bb3c36
prerequisite-patch-id: d79a8e82e46ec03cf54f25ec101a5b54592fdb1b
prerequisite-patch-id: 81871608ddab1ba624de7432ad473e52221efc08
--
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