[PATCH 00/12] Move some CRAN packages to (gnu packages cran).

DoneSubmitted by zimoun.
Details
2 participants
  • Ricardo Wurmus
  • zimoun
Owner
unassigned
Severity
normal
Z
Z
zimoun wrote on 11 Sep 20:05 +0200
(address . guix-patches@gnu.org)(name . zimoun)(address . zimon.toutoune@gmail.com)
20200911180527.11253-1-zimon.toutoune@gmail.com
Dear,
Some clean up leading the recent discussion [1]. Now, the only remaining'cran-uri' are from (gnu packages statistics). Modulo maybe some packagesusing "bad" uri, e.g., from r-qtl:
Toggle snippet (4 lines) (uri (string-append "mirror://cran/src/contrib/qtl_" version ".tar.gz"))
To ease the Copyright transfer between files, I used:
git log --grep=<package-name> git log --date=format:"%Y" --format="%ad %an" \ -- gnu/packages/<file>.scm | sort | uniq -c
After each move, I run:
make ./pre-env-inst guix build <package-name> ./pre-env-inst guix build <package-name> --no-grafts --check
to check that everything is fine. And at the end of all the move, I run:
make as-derivation
to verify that "guix pull" is not broken by something. (Well, I failed to usethe regular ./pre-env-inst guix pull --branch=my-stuff --url=$PWD -p /tmp/newbecause of the "new" authentication, another story.)
Last, I have not carefully checked the imported modules, so it could bepossible to perhaps remove 1 or 2 #:use-module (gnu packages <useless>) fromgnu/packages/bioinformatics.scm.
[1] https://lists.gnu.org/archive/html/guix-commits/2020-09/msg00416.html
All the best,simon
zimoun (12): gnu: r-codedepends: Comment why is in bioconductor.scm. gnu: r-adaptivesparsity: Move to (gnu packages cran). gnu: r-diffusionmap: Move to (gnu packages cran). gnu: r-igraph: Move to (gnu packages cran). gnu: r-qtl: Move to (gnu packages cran). gnu: r-qtl2: Move to (gnu packages cran). gnu: r-seqminer: Move to (gnu packages cran). gnu: r-maldiquant: Move to (gnu packages cran). gnu: r-seurat: Move to (gnu packages cran). gnu: r-phangorn: Move to (gnu packages cran). gnu: r-diversitree: Move to (gnu packages cran). gnu: r-absfiltergsea: Move to (gnu packages cran).
gnu/packages/bioconductor.scm | 1 + gnu/packages/bioinformatics.scm | 250 --------------------- gnu/packages/cran.scm | 346 ++++++++++++++++++++++++++++++ gnu/packages/graph.scm | 57 ----- gnu/packages/machine-learning.scm | 35 --- 5 files changed, 347 insertions(+), 342 deletions(-)

base-commit: 24e37fbbc4d7a5a4792c57f97f1f280d3ed36e01-- 2.28.0
Z
Z
zimoun wrote on 11 Sep 20:08 +0200
[PATCH 01/12] gnu: r-codedepends: Comment why is in bioconductor.scm.
(address . 43345@debbugs.gnu.org)(name . zimoun)(address . zimon.toutoune@gmail.com)
20200911180849.12582-1-zimon.toutoune@gmail.com
* gnu/packages/bioconductor.scm (r-codedepends): Add comment.--- gnu/packages/bioconductor.scm | 1 + 1 file changed, 1 insertion(+)
Toggle diff (14 lines)diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scmindex 73d5fe37eb..e3e7fb88bc 100644--- a/gnu/packages/bioconductor.scm+++ b/gnu/packages/bioconductor.scm@@ -1762,6 +1762,7 @@ expressed genes in DNA microarray experiments.") fitting of some classes of graphical Markov models.") (license license:gpl2+))) +;; This is a CRAN package, but it depends on a Bioconductor package. (define-public r-codedepends (package (name "r-codedepends")-- 2.28.0
Z
Z
zimoun wrote on 11 Sep 20:08 +0200
[PATCH 02/12] gnu: r-adaptivesparsity: Move to (gnu packages cran).
(address . 43345@debbugs.gnu.org)(name . zimoun)(address . zimon.toutoune@gmail.com)
20200911180849.12582-2-zimon.toutoune@gmail.com
* gnu/packages/machine-learning.scm (r-adaptivesparsity): Move from here...* gnu/packages/cran.scm (r-adaptivesparsity): ...to here.--- gnu/packages/cran.scm | 36 +++++++++++++++++++++++++++++++ gnu/packages/machine-learning.scm | 35 ------------------------------ 2 files changed, 36 insertions(+), 35 deletions(-)
Toggle diff (92 lines)diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scmindex de4273892d..f701b7fde0 100644--- a/gnu/packages/cran.scm+++ b/gnu/packages/cran.scm@@ -23607,3 +23607,39 @@ environments (e.g. development, test, production). It reads values using a function that determines the current environment and returns the appropriate value.") (license license:gpl3)))++(define-public r-adaptivesparsity+ (package+ (name "r-adaptivesparsity")+ (version "1.6")+ (source (origin+ (method url-fetch)+ (uri (cran-uri "AdaptiveSparsity" version))+ (sha256+ (base32+ "0imr5m8mll9j6n4icsv6z9rl5kbnwsp9wvzrg7n90nnmcxq2cz91"))))+ (properties+ `((upstream-name . "AdaptiveSparsity")))+ (build-system r-build-system)+ (arguments+ `(#:phases+ (modify-phases %standard-phases+ (add-after 'unpack 'link-against-armadillo+ (lambda _+ (substitute* "src/Makevars"+ (("PKG_LIBS=" prefix)+ (string-append prefix "-larmadillo"))))))))+ (propagated-inputs+ `(("r-mass" ,r-mass)+ ("r-matrix" ,r-matrix)+ ("r-rcpp" ,r-rcpp)+ ("r-rcpparmadillo" ,r-rcpparmadillo)))+ (inputs+ `(("armadillo" ,armadillo)))+ (home-page "https://cran.r-project.org/web/packages/AdaptiveSparsity")+ (synopsis "Adaptive sparsity models")+ (description+ "This package implements the Figueiredo machine learning algorithm for+adaptive sparsity and the Wong algorithm for adaptively sparse gaussian+geometric models.")+ (license license:lgpl3+)))diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scmindex 05646dd770..0301b4964a 100644--- a/gnu/packages/machine-learning.scm+++ b/gnu/packages/machine-learning.scm@@ -660,41 +660,6 @@ synchronization, thread-safety, concurrent data structures, and non-blocking I/O.") (license license:asl2.0))) -(define-public r-adaptivesparsity- (package- (name "r-adaptivesparsity")- (version "1.6")- (source (origin- (method url-fetch)- (uri (cran-uri "AdaptiveSparsity" version))- (sha256- (base32- "0imr5m8mll9j6n4icsv6z9rl5kbnwsp9wvzrg7n90nnmcxq2cz91"))))- (properties- `((upstream-name . "AdaptiveSparsity")))- (build-system r-build-system)- (arguments- `(#:phases- (modify-phases %standard-phases- (add-after 'unpack 'link-against-armadillo- (lambda _- (substitute* "src/Makevars"- (("PKG_LIBS=" prefix)- (string-append prefix "-larmadillo"))))))))- (propagated-inputs- `(("r-mass" ,r-mass)- ("r-matrix" ,r-matrix)- ("r-rcpp" ,r-rcpp)- ("r-rcpparmadillo" ,r-rcpparmadillo)))- (inputs- `(("armadillo" ,armadillo)))- (home-page "https://cran.r-project.org/web/packages/AdaptiveSparsity")- (synopsis "Adaptive sparsity models")- (description- "This package implements the Figueiredo machine learning algorithm for-adaptive sparsity and the Wong algorithm for adaptively sparse gaussian-geometric models.")- (license license:lgpl3+))) (define-public gemmlowp-for-tensorflow ;; The commit hash is taken from "tensorflow/workspace.bzl".-- 2.28.0
Z
Z
zimoun wrote on 11 Sep 20:08 +0200
[PATCH 03/12] gnu: r-diffusionmap: Move to (gnu packages cran).
(address . 43345@debbugs.gnu.org)(name . zimoun)(address . zimon.toutoune@gmail.com)
20200911180849.12582-3-zimon.toutoune@gmail.com
* gnu/packages/graph.scm (r-diffusionmap): Move from here ...* gnu/packages/cran.scm (r-diffusionmap): ... to here.--- gnu/packages/cran.scm | 25 +++++++++++++++++++++++++ gnu/packages/graph.scm | 25 ------------------------- 2 files changed, 25 insertions(+), 25 deletions(-)
Toggle diff (71 lines)diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scmindex f701b7fde0..d539dc34a3 100644--- a/gnu/packages/cran.scm+++ b/gnu/packages/cran.scm@@ -23643,3 +23643,28 @@ value.") adaptive sparsity and the Wong algorithm for adaptively sparse gaussian geometric models.") (license license:lgpl3+)))++(define-public r-diffusionmap+ (package+ (name "r-diffusionmap")+ (version "1.2.0")+ (source+ (origin+ (method url-fetch)+ (uri (cran-uri "diffusionMap" version))+ (sha256+ (base32+ "1rvk7069brlm1s9kqj4c31mwwr3mw4hmhay95cjjjfmw5xclff2j"))))+ (properties `((upstream-name . "diffusionMap")))+ (build-system r-build-system)+ (propagated-inputs+ `(("r-igraph" ,r-igraph)+ ("r-matrix" ,r-matrix)+ ("r-scatterplot3d" ,r-scatterplot3d)))+ (home-page "https://www.r-project.org")+ (synopsis "Diffusion map")+ (description "This package implements the diffusion map method of data+parametrization, including creation and visualization of diffusion maps,+clustering with diffusion K-means and regression using the adaptive regression+model.")+ (license license:gpl2)))diff --git a/gnu/packages/graph.scm b/gnu/packages/graph.scmindex 800b567e39..54ced01f6c 100644--- a/gnu/packages/graph.scm+++ b/gnu/packages/graph.scm@@ -153,31 +153,6 @@ random and regular graphs, graph visualization, centrality methods and much more.") (license license:gpl2+))) -(define-public r-diffusionmap- (package- (name "r-diffusionmap")- (version "1.2.0")- (source- (origin- (method url-fetch)- (uri (cran-uri "diffusionMap" version))- (sha256- (base32- "1rvk7069brlm1s9kqj4c31mwwr3mw4hmhay95cjjjfmw5xclff2j"))))- (properties `((upstream-name . "diffusionMap")))- (build-system r-build-system)- (propagated-inputs- `(("r-igraph" ,r-igraph)- ("r-matrix" ,r-matrix)- ("r-scatterplot3d" ,r-scatterplot3d)))- (home-page "https://www.r-project.org")- (synopsis "Diffusion map")- (description "This package implements the diffusion map method of data-parametrization, including creation and visualization of diffusion maps,-clustering with diffusion K-means and regression using the adaptive regression-model.")- (license license:gpl2)))- (define-public r-rgraphviz (package (name "r-rgraphviz")-- 2.28.0
Z
Z
zimoun wrote on 11 Sep 20:08 +0200
[PATCH 04/12] gnu: r-igraph: Move to (gnu packages cran).
(address . 43345@debbugs.gnu.org)(name . zimoun)(address . zimon.toutoune@gmail.com)
20200911180849.12582-4-zimon.toutoune@gmail.com
* gnu/packages/graph.scm (r-igraph): Move from here...* gnu/packages/cran.scm (r-igraph): ...to here.--- gnu/packages/cran.scm | 33 +++++++++++++++++++++++++++++++++ gnu/packages/graph.scm | 32 -------------------------------- 2 files changed, 33 insertions(+), 32 deletions(-)
Toggle diff (93 lines)diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scmindex d539dc34a3..717bd36d4d 100644--- a/gnu/packages/cran.scm+++ b/gnu/packages/cran.scm@@ -91,6 +91,7 @@ #:use-module (gnu packages tcl) #:use-module (gnu packages tls) #:use-module (gnu packages web)+ #:use-module (gnu packages xml) #:use-module (gnu packages xorg)) (define-public r-rticles@@ -23668,3 +23669,35 @@ parametrization, including creation and visualization of diffusion maps, clustering with diffusion K-means and regression using the adaptive regression model.") (license license:gpl2)))++(define-public r-igraph+ (package+ (name "r-igraph")+ (version "1.2.5")+ (source+ (origin+ (method url-fetch)+ (uri (cran-uri "igraph" version))+ (sha256+ (base32+ "126z1ygbmi3g7hk97snf22rnx680dyi30idssm5zacba5rdngp8c"))))+ (build-system r-build-system)+ (native-inputs+ `(("gfortran" ,gfortran)))+ (inputs+ `(("gmp" ,gmp)+ ("glpk" ,glpk)+ ("libxml2" ,libxml2)+ ("zlib" ,zlib)))+ (propagated-inputs+ `(("r-magrittr" ,r-magrittr)+ ("r-matrix" ,r-matrix)+ ("r-pkgconfig" ,r-pkgconfig)))+ (home-page "https://igraph.org")+ (synopsis "Network analysis and visualization")+ (description+ "This package provides routines for simple graphs and network analysis.+It can handle large graphs very well and provides functions for generating+random and regular graphs, graph visualization, centrality methods and much+more.")+ (license license:gpl2+)))diff --git a/gnu/packages/graph.scm b/gnu/packages/graph.scmindex 54ced01f6c..a307fee808 100644--- a/gnu/packages/graph.scm+++ b/gnu/packages/graph.scm@@ -121,38 +121,6 @@ more.") (home-page "https://pypi.org/project/python-igraph/") (synopsis "Python bindings for the igraph network analysis library"))) -(define-public r-igraph- (package- (name "r-igraph")- (version "1.2.5")- (source- (origin- (method url-fetch)- (uri (cran-uri "igraph" version))- (sha256- (base32- "126z1ygbmi3g7hk97snf22rnx680dyi30idssm5zacba5rdngp8c"))))- (build-system r-build-system)- (native-inputs- `(("gfortran" ,gfortran)))- (inputs- `(("gmp" ,gmp)- ("glpk" ,glpk)- ("libxml2" ,libxml2)- ("zlib" ,zlib)))- (propagated-inputs- `(("r-magrittr" ,r-magrittr)- ("r-matrix" ,r-matrix)- ("r-pkgconfig" ,r-pkgconfig)))- (home-page "https://igraph.org")- (synopsis "Network analysis and visualization")- (description- "This package provides routines for simple graphs and network analysis.-It can handle large graphs very well and provides functions for generating-random and regular graphs, graph visualization, centrality methods and much-more.")- (license license:gpl2+)))- (define-public r-rgraphviz (package (name "r-rgraphviz")-- 2.28.0
Z
Z
zimoun wrote on 11 Sep 20:08 +0200
[PATCH 05/12] gnu: r-qtl: Move to (gnu packages cran).
(address . 43345@debbugs.gnu.org)(name . zimoun)(address . zimon.toutoune@gmail.com)
20200911180849.12582-5-zimon.toutoune@gmail.com
* gnu/packages/bioinformatics.scm (r-qtl): Move from here ...* gnu/packages/cran.scm (r-qtl): ... to here.--- gnu/packages/bioinformatics.scm | 25 ------------------------- gnu/packages/cran.scm | 26 ++++++++++++++++++++++++++ 2 files changed, 26 insertions(+), 25 deletions(-)
Toggle diff (79 lines)diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scmindex cab3df222c..ae728f09dc 100644--- a/gnu/packages/bioinformatics.scm+++ b/gnu/packages/bioinformatics.scm@@ -8510,31 +8510,6 @@ Stephens (1990).") throughput genetic sequencing data sets using regression methods.") (license license:artistic2.0))) -(define-public r-qtl- (package- (name "r-qtl")- (version "1.46-2")- (source- (origin- (method url-fetch)- (uri (string-append "mirror://cran/src/contrib/qtl_"- version ".tar.gz"))- (sha256- (base32- "0rbwcnvyy96gq1dsgpxx03pv423qya26h6ws5y0blj3blfdmj83a"))))- (build-system r-build-system)- (home-page "https://rqtl.org/")- (synopsis "R package for analyzing QTL experiments in genetics")- (description "R/qtl is an extension library for the R statistics-system. It is used to analyze experimental crosses for identifying-genes contributing to variation in quantitative traits (so-called-quantitative trait loci, QTLs).--Using a hidden Markov model, R/qtl estimates genetic maps, to-identify genotyping errors, and to perform single-QTL and two-QTL,-two-dimensional genome scans.")- (license license:gpl3)))- (define-public r-qtl2 (package (name "r-qtl2")diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scmindex 717bd36d4d..868f660e41 100644--- a/gnu/packages/cran.scm+++ b/gnu/packages/cran.scm@@ -1,6 +1,7 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net> ;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>+;;; Copyright © 2015, 2016 Pjotr Prins <pjotr.guix@thebird.nl> ;;; Copyright © 2016, 2017 Ben Woodcroft <donttrustben@gmail.com> ;;; Copyright © 2016, 2017, 2018, 2020 Roel Janssen <roel@gnu.org> ;;; Copyright © 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>@@ -23701,3 +23702,28 @@ It can handle large graphs very well and provides functions for generating random and regular graphs, graph visualization, centrality methods and much more.") (license license:gpl2+)))++(define-public r-qtl+ (package+ (name "r-qtl")+ (version "1.46-2")+ (source+ (origin+ (method url-fetch)+ (uri (string-append "mirror://cran/src/contrib/qtl_"+ version ".tar.gz"))+ (sha256+ (base32+ "0rbwcnvyy96gq1dsgpxx03pv423qya26h6ws5y0blj3blfdmj83a"))))+ (build-system r-build-system)+ (home-page "https://rqtl.org/")+ (synopsis "R package for analyzing QTL experiments in genetics")+ (description "R/qtl is an extension library for the R statistics+system. It is used to analyze experimental crosses for identifying+genes contributing to variation in quantitative traits (so-called+quantitative trait loci, QTLs).++Using a hidden Markov model, R/qtl estimates genetic maps, to+identify genotyping errors, and to perform single-QTL and two-QTL,+two-dimensional genome scans.")+ (license license:gpl3)))-- 2.28.0
Z
Z
zimoun wrote on 11 Sep 20:08 +0200
[PATCH 06/12] gnu: r-qtl2: Move to (gnu packages cran).
(address . 43345@debbugs.gnu.org)(name . zimoun)(address . zimon.toutoune@gmail.com)
20200911180849.12582-6-zimon.toutoune@gmail.com
* gnu/packages/bioinformatics.scm (r-qtl2): Move from here ...* gnu/packages/cran.scm (r-qtl2): ... to here.--- gnu/packages/bioinformatics.scm | 26 -------------------------- gnu/packages/cran.scm | 27 +++++++++++++++++++++++++++ 2 files changed, 27 insertions(+), 26 deletions(-)
Toggle diff (81 lines)diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scmindex ae728f09dc..4de52f3aaa 100644--- a/gnu/packages/bioinformatics.scm+++ b/gnu/packages/bioinformatics.scm@@ -8510,32 +8510,6 @@ Stephens (1990).") throughput genetic sequencing data sets using regression methods.") (license license:artistic2.0))) -(define-public r-qtl2- (package- (name "r-qtl2")- (version "0.22-11")- (source (origin- (method url-fetch)- (uri (cran-uri "qtl2" version))- (sha256- (base32 "0dfdzjylqzc92dcszawc8cyinxccjm3p36v9vcq9ma818pqcanmr"))))- (build-system r-build-system)- (propagated-inputs- `(("r-data-table" ,r-data-table)- ("r-jsonlite" ,r-jsonlite)- ("r-rcpp" ,r-rcpp)- ("r-rcppeigen" ,r-rcppeigen)- ("r-rsqlite" ,r-rsqlite)- ("r-yaml" ,r-yaml)))- (home-page "https://kbroman.org/qtl2/")- (synopsis "Quantitative Trait Locus Mapping in Experimental Crosses")- (description- "This package provides a set of tools to perform @dfn{Quantitative Trait-Locus} (QTL) analysis in experimental crosses. It is a reimplementation of the-@code{R/qtl} package to better handle high-dimensional data and complex cross-designs. Broman et al. (2018) <doi:10.1534/genetics.118.301595>.")- (license license:gpl3)))- (define-public r-zlibbioc (package (name "r-zlibbioc")diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scmindex 868f660e41..bd36e1bacb 100644--- a/gnu/packages/cran.scm+++ b/gnu/packages/cran.scm@@ -19,6 +19,7 @@ ;;; Copyright © 2019 Nicolò Balzarotti <anothersms@gmail.com> ;;; Copyright © 2019 Wiktor Żelazny <wzelazny@vurv.cz> ;;; Copyright © 2019 Arne Babenhauserheide <arne_bab@web.de>+;;; Copyright © 2019, 2020 Efraim Flashner <efraim@flashner.co.il> ;;; Copyright © 2020 Todor Kondić <tk.code@protonmail.com> ;;; Copyright © 2020 Danjela Lura <danielaluraa@gmail.com> ;;; Copyright © 2020 Naga Malleswari <nagamalli@riseup.net>@@ -23727,3 +23728,29 @@ Using a hidden Markov model, R/qtl estimates genetic maps, to identify genotyping errors, and to perform single-QTL and two-QTL, two-dimensional genome scans.") (license license:gpl3)))++(define-public r-qtl2+ (package+ (name "r-qtl2")+ (version "0.22-11")+ (source (origin+ (method url-fetch)+ (uri (cran-uri "qtl2" version))+ (sha256+ (base32 "0dfdzjylqzc92dcszawc8cyinxccjm3p36v9vcq9ma818pqcanmr"))))+ (build-system r-build-system)+ (propagated-inputs+ `(("r-data-table" ,r-data-table)+ ("r-jsonlite" ,r-jsonlite)+ ("r-rcpp" ,r-rcpp)+ ("r-rcppeigen" ,r-rcppeigen)+ ("r-rsqlite" ,r-rsqlite)+ ("r-yaml" ,r-yaml)))+ (home-page "https://kbroman.org/qtl2/")+ (synopsis "Quantitative Trait Locus Mapping in Experimental Crosses")+ (description+ "This package provides a set of tools to perform @dfn{Quantitative Trait+Locus} (QTL) analysis in experimental crosses. It is a reimplementation of the+@code{R/qtl} package to better handle high-dimensional data and complex cross+designs. Broman et al. (2018) <doi:10.1534/genetics.118.301595>.")+ (license license:gpl3)))-- 2.28.0
Z
Z
zimoun wrote on 11 Sep 20:08 +0200
[PATCH 07/12] gnu: r-seqminer: Move to (gnu packages cran).
(address . 43345@debbugs.gnu.org)(name . zimoun)(address . zimon.toutoune@gmail.com)
20200911180849.12582-7-zimon.toutoune@gmail.com
* gnu/packages/bioinformatics.scm (r-seqminer): Move from here ...* gnu/packages/cran.scm (r-seqminer): ... to here.--- gnu/packages/bioinformatics.scm | 22 ---------------------- gnu/packages/cran.scm | 22 ++++++++++++++++++++++ 2 files changed, 22 insertions(+), 22 deletions(-)
Toggle diff (65 lines)diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scmindex 4de52f3aaa..40c6363859 100644--- a/gnu/packages/bioinformatics.scm+++ b/gnu/packages/bioinformatics.scm@@ -9393,28 +9393,6 @@ imaging data that can be used in subsequent analyses to adjust for unknown, unmodeled, or latent sources of noise.") (license license:artistic2.0))) -(define-public r-seqminer- (package- (name "r-seqminer")- (version "8.0")- (source- (origin- (method url-fetch)- (uri (cran-uri "seqminer" version))- (sha256- (base32- "00jzj8mwb0zaiwlifd41b26mrq9mzigj18nc29dydi0r42hxg16i"))))- (build-system r-build-system)- (inputs- `(("zlib" ,zlib)))- (home-page "http://seqminer.genomic.codes")- (synopsis "Read nucleotide sequence data (VCF, BCF, and METAL formats)")- (description- "This package provides tools to integrate nucleotide sequencing-data (variant call format, e.g. VCF or BCF) or meta-analysis results in R.")- ;; Any version of the GPL is acceptable- (license (list license:gpl2+ license:gpl3+))))- (define-public r-raremetals2 (package (name "r-raremetals2")diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scmindex bd36e1bacb..5d1e248cc4 100644--- a/gnu/packages/cran.scm+++ b/gnu/packages/cran.scm@@ -23754,3 +23754,25 @@ Locus} (QTL) analysis in experimental crosses. It is a reimplementation of the @code{R/qtl} package to better handle high-dimensional data and complex cross designs. Broman et al. (2018) <doi:10.1534/genetics.118.301595>.") (license license:gpl3)))++(define-public r-seqminer+ (package+ (name "r-seqminer")+ (version "8.0")+ (source+ (origin+ (method url-fetch)+ (uri (cran-uri "seqminer" version))+ (sha256+ (base32+ "00jzj8mwb0zaiwlifd41b26mrq9mzigj18nc29dydi0r42hxg16i"))))+ (build-system r-build-system)+ (inputs+ `(("zlib" ,zlib)))+ (home-page "http://seqminer.genomic.codes")+ (synopsis "Read nucleotide sequence data (VCF, BCF, and METAL formats)")+ (description+ "This package provides tools to integrate nucleotide sequencing+data (variant call format, e.g. VCF or BCF) or meta-analysis results in R.")+ ;; Any version of the GPL is acceptable+ (license (list license:gpl2+ license:gpl3+))))-- 2.28.0
Z
Z
zimoun wrote on 11 Sep 20:08 +0200
[PATCH 08/12] gnu: r-maldiquant: Move to (gnu packages cran).
(address . 43345@debbugs.gnu.org)(name . zimoun)(address . zimon.toutoune@gmail.com)
20200911180849.12582-8-zimon.toutoune@gmail.com
* gnu/packages/bioinformatics.scm (r-maldiquant): Move from here ...* gnu/packages/cran.scm (r-maldiquant): ... to here.--- gnu/packages/bioinformatics.scm | 26 -------------------------- gnu/packages/cran.scm | 26 ++++++++++++++++++++++++++ 2 files changed, 26 insertions(+), 26 deletions(-)
Toggle diff (73 lines)diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scmindex 40c6363859..fecb3c072d 100644--- a/gnu/packages/bioinformatics.scm+++ b/gnu/packages/bioinformatics.scm@@ -9425,32 +9425,6 @@ for analyzing gene-level association tests in meta-analyses for binary trait.") (license license:gpl3))) -(define-public r-maldiquant- (package- (name "r-maldiquant")- (version "1.19.3")- (source- (origin- (method url-fetch)- (uri (cran-uri "MALDIquant" version))- (sha256- (base32- "0b7kdz3x4sdq413h1q09l1qhcvdnnwv6fqsqwllks1cd3xy34c57"))))- (properties `((upstream-name . "MALDIquant")))- (build-system r-build-system)- (home-page "https://cran.r-project.org/web/packages/MALDIquant")- (synopsis "Quantitative analysis of mass spectrometry data")- (description- "This package provides a complete analysis pipeline for matrix-assisted-laser desorption/ionization-time-of-flight (MALDI-TOF) and other-two-dimensional mass spectrometry data. In addition to commonly used plotting-and processing methods it includes distinctive features, namely baseline-subtraction methods such as morphological filters (TopHat) or the-statistics-sensitive non-linear iterative peak-clipping algorithm (SNIP), peak-alignment using warping functions, handling of replicated measurements as well-as allowing spectra with different resolutions.")- (license license:gpl3+)))- (define-public r-protgenerics (package (name "r-protgenerics")diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scmindex 5d1e248cc4..a6c2518978 100644--- a/gnu/packages/cran.scm+++ b/gnu/packages/cran.scm@@ -23776,3 +23776,29 @@ designs. Broman et al. (2018) <doi:10.1534/genetics.118.301595>.") data (variant call format, e.g. VCF or BCF) or meta-analysis results in R.") ;; Any version of the GPL is acceptable (license (list license:gpl2+ license:gpl3+))))++(define-public r-maldiquant+ (package+ (name "r-maldiquant")+ (version "1.19.3")+ (source+ (origin+ (method url-fetch)+ (uri (cran-uri "MALDIquant" version))+ (sha256+ (base32+ "0b7kdz3x4sdq413h1q09l1qhcvdnnwv6fqsqwllks1cd3xy34c57"))))+ (properties `((upstream-name . "MALDIquant")))+ (build-system r-build-system)+ (home-page "https://cran.r-project.org/web/packages/MALDIquant")+ (synopsis "Quantitative analysis of mass spectrometry data")+ (description+ "This package provides a complete analysis pipeline for matrix-assisted+laser desorption/ionization-time-of-flight (MALDI-TOF) and other+two-dimensional mass spectrometry data. In addition to commonly used plotting+and processing methods it includes distinctive features, namely baseline+subtraction methods such as morphological filters (TopHat) or the+statistics-sensitive non-linear iterative peak-clipping algorithm (SNIP), peak+alignment using warping functions, handling of replicated measurements as well+as allowing spectra with different resolutions.")+ (license license:gpl3+)))-- 2.28.0
Z
Z
zimoun wrote on 11 Sep 20:08 +0200
[PATCH 09/12] gnu: r-seurat: Move to (gnu packages cran).
(address . 43345@debbugs.gnu.org)(name . zimoun)(address . zimon.toutoune@gmail.com)
20200911180849.12582-9-zimon.toutoune@gmail.com
* gnu/packages/bioinformatics.scm (r-seurat): Move from here ...* gnu/packages/cran.scm (r-seurat): ... to here.--- gnu/packages/bioinformatics.scm | 65 --------------------------------- gnu/packages/cran.scm | 65 +++++++++++++++++++++++++++++++++ 2 files changed, 65 insertions(+), 65 deletions(-)
Toggle diff (151 lines)diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scmindex fecb3c072d..a6505099fc 100644--- a/gnu/packages/bioinformatics.scm+++ b/gnu/packages/bioinformatics.scm@@ -9735,71 +9735,6 @@ contains a number of utilities to explore the MS/MS results and assess missed and irregular enzymatic cleavages, mass measurement accuracy, etc.") (license license:artistic2.0))) -(define-public r-seurat- (package- (name "r-seurat")- (version "3.2.0")- (source (origin- (method url-fetch)- (uri (cran-uri "Seurat" version))- (sha256- (base32- "1vj3dlsqakgnn4x1jz9fkl2cy0jzc5s65h1c20fnamr7lk45pnf2"))))- (properties `((upstream-name . "Seurat")))- (build-system r-build-system)- (propagated-inputs- `(("r-ape" ,r-ape)- ("r-cluster" ,r-cluster)- ("r-cowplot" ,r-cowplot)- ("r-fitdistrplus" ,r-fitdistrplus)- ("r-future" ,r-future)- ("r-future-apply" ,r-future-apply)- ("r-ggplot2" ,r-ggplot2)- ("r-ggrepel" ,r-ggrepel)- ("r-ggridges" ,r-ggridges)- ("r-httr" ,r-httr)- ("r-ica" ,r-ica)- ("r-igraph" ,r-igraph)- ("r-irlba" ,r-irlba)- ("r-jsonlite" ,r-jsonlite)- ("r-kernsmooth" ,r-kernsmooth)- ("r-leiden" ,r-leiden)- ("r-lmtest" ,r-lmtest)- ("r-mass" ,r-mass)- ("r-matrix" ,r-matrix)- ("r-miniui" ,r-miniui)- ("r-patchwork" ,r-patchwork)- ("r-pbapply" ,r-pbapply)- ("r-plotly" ,r-plotly)- ("r-png" ,r-png)- ("r-rann" ,r-rann)- ("r-rcolorbrewer" ,r-rcolorbrewer)- ("r-rcpp" ,r-rcpp)- ("r-rcppannoy" ,r-rcppannoy)- ("r-rcppeigen" ,r-rcppeigen)- ("r-rcppprogress" ,r-rcppprogress)- ("r-reticulate" ,r-reticulate)- ("r-rlang" ,r-rlang)- ("r-rocr" ,r-rocr)- ("r-rsvd" ,r-rsvd)- ("r-rtsne" ,r-rtsne)- ("r-scales" ,r-scales)- ("r-sctransform" ,r-sctransform)- ("r-shiny" ,r-shiny)- ("r-spatstat" ,r-spatstat)- ("r-tibble" ,r-tibble)- ("r-uwot" ,r-uwot)))- (home-page "http://www.satijalab.org/seurat")- (synopsis "Seurat is an R toolkit for single cell genomics")- (description- "This package is an R package designed for QC, analysis, and-exploration of single cell RNA-seq data. It easily enables widely-used-analytical techniques, including the identification of highly variable genes,-dimensionality reduction; PCA, ICA, t-SNE, standard unsupervised clustering-algorithms; density clustering, hierarchical clustering, k-means, and the-discovery of differentially expressed genes and markers.")- (license license:gpl3)))- (define-public r-aroma-light (package (name "r-aroma-light")diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scmindex a6c2518978..8b2a5fc1dc 100644--- a/gnu/packages/cran.scm+++ b/gnu/packages/cran.scm@@ -23802,3 +23802,68 @@ statistics-sensitive non-linear iterative peak-clipping algorithm (SNIP), peak alignment using warping functions, handling of replicated measurements as well as allowing spectra with different resolutions.") (license license:gpl3+)))++(define-public r-seurat+ (package+ (name "r-seurat")+ (version "3.2.0")+ (source (origin+ (method url-fetch)+ (uri (cran-uri "Seurat" version))+ (sha256+ (base32+ "1vj3dlsqakgnn4x1jz9fkl2cy0jzc5s65h1c20fnamr7lk45pnf2"))))+ (properties `((upstream-name . "Seurat")))+ (build-system r-build-system)+ (propagated-inputs+ `(("r-ape" ,r-ape)+ ("r-cluster" ,r-cluster)+ ("r-cowplot" ,r-cowplot)+ ("r-fitdistrplus" ,r-fitdistrplus)+ ("r-future" ,r-future)+ ("r-future-apply" ,r-future-apply)+ ("r-ggplot2" ,r-ggplot2)+ ("r-ggrepel" ,r-ggrepel)+ ("r-ggridges" ,r-ggridges)+ ("r-httr" ,r-httr)+ ("r-ica" ,r-ica)+ ("r-igraph" ,r-igraph)+ ("r-irlba" ,r-irlba)+ ("r-jsonlite" ,r-jsonlite)+ ("r-kernsmooth" ,r-kernsmooth)+ ("r-leiden" ,r-leiden)+ ("r-lmtest" ,r-lmtest)+ ("r-mass" ,r-mass)+ ("r-matrix" ,r-matrix)+ ("r-miniui" ,r-miniui)+ ("r-patchwork" ,r-patchwork)+ ("r-pbapply" ,r-pbapply)+ ("r-plotly" ,r-plotly)+ ("r-png" ,r-png)+ ("r-rann" ,r-rann)+ ("r-rcolorbrewer" ,r-rcolorbrewer)+ ("r-rcpp" ,r-rcpp)+ ("r-rcppannoy" ,r-rcppannoy)+ ("r-rcppeigen" ,r-rcppeigen)+ ("r-rcppprogress" ,r-rcppprogress)+ ("r-reticulate" ,r-reticulate)+ ("r-rlang" ,r-rlang)+ ("r-rocr" ,r-rocr)+ ("r-rsvd" ,r-rsvd)+ ("r-rtsne" ,r-rtsne)+ ("r-scales" ,r-scales)+ ("r-sctransform" ,r-sctransform)+ ("r-shiny" ,r-shiny)+ ("r-spatstat" ,r-spatstat)+ ("r-tibble" ,r-tibble)+ ("r-uwot" ,r-uwot)))+ (home-page "http://www.satijalab.org/seurat")+ (synopsis "Seurat is an R toolkit for single cell genomics")+ (description+ "This package is an R package designed for QC, analysis, and+exploration of single cell RNA-seq data. It easily enables widely-used+analytical techniques, including the identification of highly variable genes,+dimensionality reduction; PCA, ICA, t-SNE, standard unsupervised clustering+algorithms; density clustering, hierarchical clustering, k-means, and the+discovery of differentially expressed genes and markers.")+ (license license:gpl3)))-- 2.28.0
Z
Z
zimoun wrote on 11 Sep 20:08 +0200
[PATCH 11/12] gnu: r-diversitree: Move to (gnu packages cran).
(address . 43345@debbugs.gnu.org)(name . zimoun)(address . zimon.toutoune@gmail.com)
20200911180849.12582-10-zimon.toutoune@gmail.com
* gnu/packages/bioinformatics.scm (r-diversitree): Move from here ...* gnu/packages/cran.scm (r-diversitree): ... to here.--- gnu/packages/bioinformatics.scm | 31 ------------------------------- gnu/packages/cran.scm | 31 +++++++++++++++++++++++++++++++ 2 files changed, 31 insertions(+), 31 deletions(-)
Toggle diff (83 lines)diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scmindex bec6c1dc4a..6381523009 100644--- a/gnu/packages/bioinformatics.scm+++ b/gnu/packages/bioinformatics.scm@@ -13084,37 +13084,6 @@ analyses in addition to large-scale sequence-level searches.") (supported-systems '("x86_64-linux")) (license license:bsd-3)))) -(define-public r-diversitree- (package- (name "r-diversitree")- (version "0.9-13")- (source- (origin- (method url-fetch)- (uri (cran-uri "diversitree" version))- (sha256- (base32- "00vi4klywi35hd170ksjv3xja3hqqbkcidcnrrlpgv4179k0azix"))))- (build-system r-build-system)- (native-inputs- `(("gfortran" ,gfortran)))- (inputs `(("fftw" ,fftw) ("gsl" ,gsl)))- (propagated-inputs- `(("r-ape" ,r-ape)- ("r-desolve" ,r-desolve)- ("r-rcpp" ,r-rcpp)- ("r-subplex" ,r-subplex)))- (home-page "https://www.zoology.ubc.ca/prog/diversitree")- (synopsis "Comparative 'phylogenetic' analyses of diversification")- (description "This package contains a number of comparative \"phylogenetic\"-methods, mostly focusing on analysing diversification and character evolution.-Contains implementations of \"BiSSE\" (Binary State Speciation and Extinction)-and its unresolved tree extensions, \"MuSSE\" (Multiple State Speciation and-Extinction), \"QuaSSE\", \"GeoSSE\", and \"BiSSE-ness\" Other included methods-include Markov models of discrete and continuous trait evolution and constant-rate speciation and extinction.")- (license license:gpl2+)))- (define-public sjcount ;; There is no tag for version 3.2, nor is there a release archive. (let ((commit "292d3917cadb3f6834c81e509c30e61cd7ead6e5")diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scmindex 140ce11aac..5b65d2a372 100644--- a/gnu/packages/cran.scm+++ b/gnu/packages/cran.scm@@ -23895,3 +23895,34 @@ discovery of differentially expressed genes and markers.") estimation of phylogenetic trees and networks using Maximum Likelihood, Maximum Parsimony, distance methods and Hadamard conjugation.") (license license:gpl2+)))++(define-public r-diversitree+ (package+ (name "r-diversitree")+ (version "0.9-13")+ (source+ (origin+ (method url-fetch)+ (uri (cran-uri "diversitree" version))+ (sha256+ (base32+ "00vi4klywi35hd170ksjv3xja3hqqbkcidcnrrlpgv4179k0azix"))))+ (build-system r-build-system)+ (native-inputs+ `(("gfortran" ,gfortran)))+ (inputs `(("fftw" ,fftw) ("gsl" ,gsl)))+ (propagated-inputs+ `(("r-ape" ,r-ape)+ ("r-desolve" ,r-desolve)+ ("r-rcpp" ,r-rcpp)+ ("r-subplex" ,r-subplex)))+ (home-page "https://www.zoology.ubc.ca/prog/diversitree")+ (synopsis "Comparative 'phylogenetic' analyses of diversification")+ (description "This package contains a number of comparative \"phylogenetic\"+methods, mostly focusing on analysing diversification and character evolution.+Contains implementations of \"BiSSE\" (Binary State Speciation and Extinction)+and its unresolved tree extensions, \"MuSSE\" (Multiple State Speciation and+Extinction), \"QuaSSE\", \"GeoSSE\", and \"BiSSE-ness\" Other included methods+include Markov models of discrete and continuous trait evolution and constant+rate speciation and extinction.")+ (license license:gpl2+)))-- 2.28.0
Z
Z
zimoun wrote on 11 Sep 20:08 +0200
[PATCH 12/12] gnu: r-absfiltergsea: Move to (gnu packages cran).
(address . 43345@debbugs.gnu.org)(name . zimoun)(address . zimon.toutoune@gmail.com)
20200911180849.12582-11-zimon.toutoune@gmail.com
* gnu/packages/bioinformatics.scm (r-absfiltergsea): Move from here ...* gnu/packages/cran.scm (r-absfiltergsea): ... to here.--- gnu/packages/bioinformatics.scm | 27 --------------------------- gnu/packages/cran.scm | 27 +++++++++++++++++++++++++++ 2 files changed, 27 insertions(+), 27 deletions(-)
Toggle diff (75 lines)diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scmindex 6381523009..ffa2618458 100644--- a/gnu/packages/bioinformatics.scm+++ b/gnu/packages/bioinformatics.scm@@ -14083,33 +14083,6 @@ downstream analysis. Poretools operates directly on the native FAST5, a variant of the Hierarchical Data Format (HDF5) standard.") (license license:expat)))) -(define-public r-absfiltergsea- (package- (name "r-absfiltergsea")- (version "1.5.1")- (source- (origin- (method url-fetch)- (uri (cran-uri "AbsFilterGSEA" version))- (sha256- (base32 "15srxkxsvn38kd5frdrwfdf0ad8gskrd0h01wmdf9hglq8fjrp7w"))))- (properties `((upstream-name . "AbsFilterGSEA")))- (build-system r-build-system)- (propagated-inputs- `(("r-biobase" ,r-biobase)- ("r-deseq" ,r-deseq)- ("r-limma" ,r-limma)- ("r-rcpp" ,r-rcpp)- ("r-rcpparmadillo" ,r-rcpparmadillo)))- (home-page "https://cran.r-project.org/web/packages/AbsFilterGSEA/")- (synopsis "Improved false positive control of gene-permuting with absolute filtering")- (description- "This package provides a function that performs gene-permuting of a gene-set-enrichment analysis (GSEA) calculation with or without the absolute filtering.- Without filtering, users can perform (original) two-tailed or one-tailed-absolute GSEA.")- (license license:gpl2)))- (define-public jamm (package (name "jamm")diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scmindex 5b65d2a372..f9b6930f70 100644--- a/gnu/packages/cran.scm+++ b/gnu/packages/cran.scm@@ -23926,3 +23926,30 @@ Extinction), \"QuaSSE\", \"GeoSSE\", and \"BiSSE-ness\" Other included methods include Markov models of discrete and continuous trait evolution and constant rate speciation and extinction.") (license license:gpl2+)))++(define-public r-absfiltergsea+ (package+ (name "r-absfiltergsea")+ (version "1.5.1")+ (source+ (origin+ (method url-fetch)+ (uri (cran-uri "AbsFilterGSEA" version))+ (sha256+ (base32 "15srxkxsvn38kd5frdrwfdf0ad8gskrd0h01wmdf9hglq8fjrp7w"))))+ (properties `((upstream-name . "AbsFilterGSEA")))+ (build-system r-build-system)+ (propagated-inputs+ `(("r-biobase" ,r-biobase)+ ("r-deseq" ,r-deseq)+ ("r-limma" ,r-limma)+ ("r-rcpp" ,r-rcpp)+ ("r-rcpparmadillo" ,r-rcpparmadillo)))+ (home-page "https://cran.r-project.org/web/packages/AbsFilterGSEA/")+ (synopsis "Improved false positive control of gene-permuting with absolute filtering")+ (description+ "This package provides a function that performs gene-permuting of a gene-set+enrichment analysis (GSEA) calculation with or without the absolute filtering.+ Without filtering, users can perform (original) two-tailed or one-tailed+absolute GSEA.")+ (license license:gpl2)))-- 2.28.0
Z
Z
zimoun wrote on 11 Sep 20:08 +0200
[PATCH 10/12] gnu: r-phangorn: Move to (gnu packages cran).
(address . 43345@debbugs.gnu.org)(name . zimoun)(address . zimon.toutoune@gmail.com)
20200911180849.12582-12-zimon.toutoune@gmail.com
* gnu/packages/bioinformatics.scm (r-phangorn): Move from here ...* gnu/packages/cran.scm (r-phangorn): ... to here.--- gnu/packages/bioinformatics.scm | 28 ---------------------------- gnu/packages/cran.scm | 28 ++++++++++++++++++++++++++++ 2 files changed, 28 insertions(+), 28 deletions(-)
Toggle diff (77 lines)diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scmindex a6505099fc..bec6c1dc4a 100644--- a/gnu/packages/bioinformatics.scm+++ b/gnu/packages/bioinformatics.scm@@ -10936,34 +10936,6 @@ are optimized per data type and for subsetted calculations such that both memory usage and processing time is minimized.") (license license:expat))) -(define-public r-phangorn- (package- (name "r-phangorn")- (version "2.5.5")- (source- (origin- (method url-fetch)- (uri (cran-uri "phangorn" version))- (sha256- (base32- "0ihkaykqjmf80d8wrk3saphxvnv58zma6pd13633bd3cwanc33f5"))))- (build-system r-build-system)- (propagated-inputs- `(("r-ape" ,r-ape)- ("r-fastmatch" ,r-fastmatch)- ("r-igraph" ,r-igraph)- ("r-magrittr" ,r-magrittr)- ("r-matrix" ,r-matrix)- ("r-quadprog" ,r-quadprog)- ("r-rcpp" ,r-rcpp)))- (home-page "https://github.com/KlausVigo/phangorn")- (synopsis "Phylogenetic analysis in R")- (description- "Phangorn is a package for phylogenetic analysis in R. It supports-estimation of phylogenetic trees and networks using Maximum Likelihood,-Maximum Parsimony, distance methods and Hadamard conjugation.")- (license license:gpl2+)))- (define-public r-dropbead (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247") (revision "2"))diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scmindex 8b2a5fc1dc..140ce11aac 100644--- a/gnu/packages/cran.scm+++ b/gnu/packages/cran.scm@@ -23867,3 +23867,31 @@ dimensionality reduction; PCA, ICA, t-SNE, standard unsupervised clustering algorithms; density clustering, hierarchical clustering, k-means, and the discovery of differentially expressed genes and markers.") (license license:gpl3)))++(define-public r-phangorn+ (package+ (name "r-phangorn")+ (version "2.5.5")+ (source+ (origin+ (method url-fetch)+ (uri (cran-uri "phangorn" version))+ (sha256+ (base32+ "0ihkaykqjmf80d8wrk3saphxvnv58zma6pd13633bd3cwanc33f5"))))+ (build-system r-build-system)+ (propagated-inputs+ `(("r-ape" ,r-ape)+ ("r-fastmatch" ,r-fastmatch)+ ("r-igraph" ,r-igraph)+ ("r-magrittr" ,r-magrittr)+ ("r-matrix" ,r-matrix)+ ("r-quadprog" ,r-quadprog)+ ("r-rcpp" ,r-rcpp)))+ (home-page "https://github.com/KlausVigo/phangorn")+ (synopsis "Phylogenetic analysis in R")+ (description+ "Phangorn is a package for phylogenetic analysis in R. It supports+estimation of phylogenetic trees and networks using Maximum Likelihood,+Maximum Parsimony, distance methods and Hadamard conjugation.")+ (license license:gpl2+)))-- 2.28.0
R
R
Ricardo Wurmus wrote on 11 Sep 22:07 +0200
Re: [bug#43345] [PATCH 00/12] Move some CRAN packages to (gnu packages cran).
(name . zimoun)(address . zimon.toutoune@gmail.com)(address . 43345-done@debbugs.gnu.org)
87imck13hp.fsf@elephly.net
Hi simon,
thank you for this janitorial work!
Toggle quote (9 lines)> Some clean up leading the recent discussion [1]. Now, the only remaining> 'cran-uri' are from (gnu packages statistics). Modulo maybe some packages> using "bad" uri, e.g., from r-qtl:>> --8<---------------cut here---------------start------------->8---> (uri (string-append "mirror://cran/src/contrib/qtl_"> version ".tar.gz"))> --8<---------------cut here---------------end--------------->8---
I fixed that URL (and a few more things that became obvious during themove).
Toggle quote (12 lines)> To ease the Copyright transfer between files, I used:>> git log --grep=<package-name>> git log --date=format:"%Y" --format="%ad %an" \> -- gnu/packages/<file>.scm | sort | uniq -c>> After each move, I run:>> make> ./pre-env-inst guix build <package-name>> ./pre-env-inst guix build <package-name> --no-grafts --check
Excellent! Thank you for being so dilligent. For some reason youmissed the import of (gnu packages xml) after the move of r-igraph. Iadded it. I also updated the commit messages for consistency inpunctuation (sorry for being picky).
Pushed to the “master” branch with commit 8458490bc2.
Thanks again!
-- Ricardo
Closed
?