[bug#32259] Add R packages from CRAN

[bug#32259] Add R packages from CRAN

[Ricardo Wurmus]

This patch series adds a few more R packages from CRAN.

-- 
Ricardo

[bug#32259] [PATCH 1/4] gnu: Add r-doby.

[Ricardo Wurmus]

* gnu/packages/cran.scm (r-doby): New variable.
---
 gnu/packages/cran.scm | 32 ++++++++++++++++++++++++++++++++
 1 file changed, 32 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index fc4baa5b5..da9b67bff 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -4646,3 +4646,35 @@ matches version and feature constraints.")
 write shebang scripts that gracefully accept positional and optional arguments
 and automatically generate usage notices.")
     (license license:gpl2+)))
+
+(define-public r-doby
+  (package
+    (name "r-doby")
+    (version "4.6-1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "doBy" version))
+       (sha256
+        (base32
+         "1y02awzid23bxz8hx6j8pxd6i7jaq8pdw3k60rag8y6m69incrw5"))))
+    (properties `((upstream-name . "doBy")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-dplyr" ,r-dplyr)
+       ("r-magrittr" ,r-magrittr)
+       ("r-mass" ,r-mass)
+       ("r-matrix" ,r-matrix)
+       ("r-plyr" ,r-plyr)))
+    (home-page "http://people.math.aau.dk/~sorenh/software/doBy/")
+    (synopsis "Groupwise statistics, LSmeans, linear contrasts, and utilities")
+    (description
+     "This package contains:
+
+@itemize
+@item facilities for working with grouped data: @code{do}
+  something to data stratified @code{by} some variables.
+@item implementations of least-squares means, general linear contrasts, and
+@item miscellaneous other utilities.
+@end itemize")
+    (license license:gpl2+)))
-- 
2.18.0

[bug#32259] [PATCH 2/4] gnu: Add r-refgenome.

[Ricardo Wurmus]

* gnu/packages/cran.scm (r-refgenome): New variable.
---
 gnu/packages/cran.scm | 28 ++++++++++++++++++++++++++++
 1 file changed, 28 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index da9b67bff..693a891a0 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -4678,3 +4678,31 @@ and automatically generate usage notices.")
 @item miscellaneous other utilities.
 @end itemize")
     (license license:gpl2+)))
+
+(define-public r-refgenome
+  (package
+    (name "r-refgenome")
+    (version "1.7.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "refGenome" version))
+       (sha256
+        (base32
+         "15p0ra2p1pwhy5ixbhsz1g79c5sc2aap4i4c8kil0m2syg9y45sn"))))
+    (properties `((upstream-name . "refGenome")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-dbi" ,r-dbi)
+       ("r-doby" ,r-doby)
+       ("r-rsqlite" ,r-rsqlite)))
+    (home-page "https://cran.r-project.org/web/packages/refGenome/")
+    (synopsis
+     "Gene and splice site annotation using annotation data from Ensembl and UCSC")
+    (description
+     "This package contains functionality for importing and managing of
+downloaded genome annotation data from the Ensembl genome browser (European
+Bioinformatics Institute) and from the UCSC genome browser (University of
+California, Santa Cruz) and annotation routines for genomic positions and
+splice site positions.")
+    (license license:gpl2)))
-- 
2.18.0

[bug#32259] [PATCH 3/4] gnu: Add r-basix.

[Ricardo Wurmus]

* gnu/packages/cran.scm (r-basix): New variable.
---
 gnu/packages/cran.scm | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 693a891a0..f1511c097 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -4706,3 +4706,23 @@ Bioinformatics Institute) and from the UCSC genome browser (University of
 California, Santa Cruz) and annotation routines for genomic positions and
 splice site positions.")
     (license license:gpl2)))
+
+(define-public r-basix
+  (package
+    (name "r-basix")
+    (version "1.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "BASIX" version))
+       (sha256
+        (base32
+         "18dkvv1iwskfnlpl6xridcgqpalbbpm2616mvc3hfrc0b26v01id"))))
+    (properties `((upstream-name . "BASIX")))
+    (build-system r-build-system)
+    (home-page "https://cran.r-project.org/web/packages/BASIX/")
+    (synopsis "Efficient C/C++ toolset for R")
+    (description
+     "BASIX provides some efficient C/C++ implementations to speed up
+calculations in R.")
+    (license license:gpl2)))
-- 
2.18.0

[bug#32259] [PATCH 3/4] gnu: Add r-basix.

[Ludovic Courtès]

Hi!

Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> skribis:

> +    (home-page "https://cran.r-project.org/web/packages/BASIX/")
> +    (synopsis "Efficient C/C++ toolset for R")
> +    (description
> +     "BASIX provides some efficient C/C++ implementations to speed up
> +calculations in R.")

Perhaps write “implementations of X and Y” to clarify.  Otherwise these
4 patches LGTM, thanks!

Ludo’.

[bug#32259] [PATCH 4/4] gnu: Add r-blockfest.

[Ricardo Wurmus]

* gnu/packages/cran.scm (r-blockfest): New variable.
---
 gnu/packages/cran.scm | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index f1511c097..c04598141 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -4726,3 +4726,27 @@ splice site positions.")
      "BASIX provides some efficient C/C++ implementations to speed up
 calculations in R.")
     (license license:gpl2)))
+
+(define-public r-blockfest
+  (package
+    (name "r-blockfest")
+    (version "1.6")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "BlockFeST" version))
+       (sha256
+        (base32
+         "0hj7a5as7nxbgjac7lbj6qfwffx3g8x8phpf9a55f1c9cdzi73a5"))))
+    (properties `((upstream-name . "BlockFeST")))
+    (build-system r-build-system)
+    (propagated-inputs `(("r-basix" ,r-basix)))
+    (home-page "https://cran.r-project.org/web/packages/BlockFeST/")
+    (synopsis "Bayesian calculation of region-specific fixation index")
+    (description
+     "This package provides an R implementation of an extension of the
+BayeScan software for codominant markers, adding the option to group
+individual SNPs into pre-defined blocks.  A typical application of this new
+approach is the identification of genomic regions, genes, or gene sets
+containing one or more SNPs that evolved under directional selection.")
+    (license license:gpl2)))
-- 
2.18.0

bug#32259: [PATCH 1/4] gnu: Add r-doby.

[Ricardo Wurmus]

I pushed these with minor changes to the description of r-basix.  Thanks
to Ludo for the review!

-- 
Ricardo