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

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2 participants
  • Ricardo Wurmus
  • zimoun
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unassigned
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zimoun
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normal
Z
Z
zimoun wrote on 11 Sep 2020 20:05
(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 packages
using "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 use
the regular ./pre-env-inst guix pull --branch=my-stuff --url=$PWD -p /tmp/new
because of the "new" authentication, another story.)

Last, I have not carefully checked the imported modules, so it could be
possible to perhaps remove 1 or 2 #:use-module (gnu packages <useless>) from
gnu/packages/bioinformatics.scm.


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 2020 20:08
[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.scm
index 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 2020 20:08
[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.scm
index 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.scm
index 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 2020 20:08
[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.scm
index 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.scm
index 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 2020 20:08
[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.scm
index 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.scm
index 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 2020 20:08
[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.scm
index 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.scm
index 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 2020 20:08
[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.scm
index 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.scm
index 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 ?elazny <wzelazny@vurv.cz>
;;; Copyright © 2019 Arne Babenhauserheide <arne_bab@web.de>
+;;; Copyright © 2019, 2020 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2020 Todor Kondi? <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 2020 20:08
[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.scm
index 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.scm
index 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 2020 20:08
[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.scm
index 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.scm
index 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 2020 20:08
[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.scm
index 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.scm
index 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 2020 20:08
[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.scm
index 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.scm
index 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 2020 20:08
[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.scm
index 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.scm
index 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 2020 20:08
[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.scm
index 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.scm
index 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 2020 22:07
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 the
move).

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 you
missed the import of (gnu packages xml) after the move of r-igraph. I
added it. I also updated the commit messages for consistency in
punctuation (sorry for being picky).

Pushed to the “master” branch with commit 8458490bc2.

Thanks again!

--
Ricardo
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