Re: [PATCH] Add r-scran 1.2.0 and all its dependencies

[Ra <ilpuccio.febo@gmail.com>]

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Dear Ricardo,
I try to satisfy all the requirements. What do you think ?
In attachment the patches.

Shiny now is in web.scm

I reformat the description and fixed the synopsis. I also re checked the
licenses.
I have created a single patch for each r-package.

--
Raoul



On Tue, Dec 27, 2016 at 6:06 PM Ra <ilpuccio.febo@gmail.com> wrote:

> On Tue, Dec 27, 2016 at 6:00 PM Ricardo Wurmus <rekado@elephly.net> wrote:
>
>
> Ra <ilpuccio.febo@gmail.com> writes:
>
> > guix import cran --archive=bioconductor scater
> >
> > I had to add the missing dependencies by hand, is there a recursive way
> to do so?
>
> Yes, you can just pass “--recursive” or “-r” and the importer will spit
> out package expressions for all unpackaged dependencies.  A current
> limitation is that it doesn’t cross over from Bioconductor to CRAN.
>
> Nice, I will try
>
>
>
> --
> Ricardo
>
> GPG: BCA6 89B6 3655 3801 C3C6  2150 197A 5888 235F ACAC
> http://elephly.net
>
>

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From 4514fa2f0380a146a3b303014c7507b17179fe4f Mon Sep 17 00:00:00 2001
From: Raoul Jean Pierre Bonnal <ilpuccio.febo@gmail.com>
Date: Tue, 27 Dec 2016 20:35:41 +0100
Subject: [PATCH 01/11] gnu: Add r-vipor.

---
 gnu/packages/statistics.scm | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index f868da2..f30e8e9 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -3815,3 +3815,22 @@ with alternating row colors) in LaTeX and HTML formats easily from
 @code{glm}, @code{coxph}, @code{nls}, @code{fitdistr}, @code{mytable} and
 @code{cbind.mytable} objects.")
     (license license:gpl2+)))
+
+(define-public r-vipor
+  (package
+    (name "r-vipor")
+    (version "0.4.4")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "vipor" version))
+              (sha256
+               (base32
+                "0p1z9a3fazl78pj8a1i2n62v8hrs8cinq82j9wpawhmfkn3dggss"))))
+    (build-system r-build-system)
+    (home-page "http://cran.r-project.org/web/packages/vipor")
+    (synopsis "Plot categorical data using quasirandom noise and density estimates")
+    (description
+     "Generate a violin point plot, a combination of a violin/histogram plot
+and a scatter plot by offsetting points within a category based on their
+density using quasirandom noise.")
+    (license license:gpl2+)))
-- 
1.9.1


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From 79fb3da5f9f8a17c43bd47e52bf7f00ff9ca42d3 Mon Sep 17 00:00:00 2001
From: Raoul Jean Pierre Bonnal <ilpuccio.febo@gmail.com>
Date: Tue, 27 Dec 2016 21:52:04 +0100
Subject: [PATCH 04/11] gnu: Add r-ggbeeswarm.

---
 gnu/packages/statistics.scm | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 4440565..fd77ef8 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -3874,3 +3874,26 @@ sourcetools package provides both an R and C++ interface for the
 tokenization of R code, and helpers for interacting with the
 tokenized representation of R code.")
     (license license:expat)))
+
+(define-public r-ggbeeswarm
+  (package
+    (name "r-ggbeeswarm")
+    (version "0.5.3")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "ggbeeswarm" version))
+              (sha256
+               (base32
+                "1jgp55rvmzc4agcrlsjn8m5lk85di9c4wj94xzikqkql4lvq3qpd"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-beeswarm" ,r-beeswarm)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-vipor" ,r-vipor)))
+    (home-page "https://github.com/eclarke/ggbeeswarm")
+    (synopsis "Categorical scatter (violin point) plots")
+    (description
+     "Provides two methods of plotting categorical scatter plots such that
+the arrangement of points within a category reflects the density of data
+at that region, and avoids over-plotting.")
+    (license license:gpl2+)))
-- 
1.9.1


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From 3b309ce67be4aaa2fdbad5d534aaf41ca154b195 Mon Sep 17 00:00:00 2001
From: Raoul Jean Pierre Bonnal <ilpuccio.febo@gmail.com>
Date: Tue, 27 Dec 2016 20:46:47 +0100
Subject: [PATCH 02/11] gnu: Add r-beeswarm.

---
 gnu/packages/statistics.scm | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index f30e8e9..b406e9e 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -3834,3 +3834,21 @@ with alternating row colors) in LaTeX and HTML formats easily from
 and a scatter plot by offsetting points within a category based on their
 density using quasirandom noise.")
     (license license:gpl2+)))
+
+(define-public r-beeswarm
+  (package
+    (name "r-beeswarm")
+    (version "0.2.3")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "beeswarm" version))
+              (sha256
+               (base32
+                "0hy89bwv7jixlg91li1fywa77916am2whqp1m1fx1khd45g44581"))))
+    (build-system r-build-system)
+    (home-page "http://www.cbs.dtu.dk/~eklund/beeswarm/")
+    (synopsis "The beeswarm plot, an alternative to stripchart")
+    (description
+     "The bee swarm plot is a one-dimensional scatter plot like stripchart,
+but with closely-packed, non-overlapping points.")
+    (license license:artistic2.0)))
-- 
1.9.1


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From 60a8c1daff7f20f26ab85993cdc483401b280774 Mon Sep 17 00:00:00 2001
From: Raoul Jean Pierre Bonnal <ilpuccio.febo@gmail.com>
Date: Tue, 27 Dec 2016 21:58:05 +0100
Subject: [PATCH 05/11] gnu: Add r-statmod.

---
 gnu/packages/statistics.scm | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index fd77ef8..36061b1 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -3897,3 +3897,28 @@ tokenized representation of R code.")
 the arrangement of points within a category reflects the density of data
 at that region, and avoids over-plotting.")
     (license license:gpl2+)))
+
+(define-public r-statmod
+  (package
+    (name "r-statmod")
+    (version "1.4.27")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "statmod" version))
+              (sha256
+               (base32
+                "14yilq9d3z20hig4rs8bjqyydw3dfx90mhmzvw9w8p16h0s595sn"))))
+    (build-system r-build-system)
+    (home-page "http://cran.r-project.org/web/packages/statmod")
+    (native-inputs
+     `(("gfortran" ,gfortran)))
+    (synopsis "Statistical modeling")
+    (description
+     "This package provides a collection of algorithms and functions to aid
+statistical modeling.  Includes growth curve comparisons, limiting dilution
+analysis (aka ELDA), mixed linear models, heteroscedastic regression,
+inverse-Gaussian probability calculations, Gauss quadrature and a secure
+convergence algorithm for nonlinear models.  Includes advanced generalized
+linear model functions that implement secure convergence, dispersion modeling
+and Tweedie power-law families.")
+    (license license:gpl3)))
-- 
1.9.1


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From 46c1fffd034616bd12bfff7eb2aad921edff5937 Mon Sep 17 00:00:00 2001
From: Raoul Jean Pierre Bonnal <ilpuccio.febo@gmail.com>
Date: Tue, 27 Dec 2016 22:03:44 +0100
Subject: [PATCH 06/11] gnu: Add r-shiny.

---
 gnu/packages/web.scm | 29 +++++++++++++++++++++++++++++
 1 file changed, 29 insertions(+)

diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm
index 07c4c0d..f048976 100644
--- a/gnu/packages/web.scm
+++ b/gnu/packages/web.scm
@@ -3968,3 +3968,32 @@ useful for users behind restrictive firewalls.  As long as Web traffic is
 allowed, even through a HTTP-only proxy, httptunnel can be combined with other
 tools like SSH (Secure Shell) to reach the outside world.")
     (license l:gpl2+)))
+
+(define-public r-shiny
+  (package
+    (name "r-shiny")
+    (version "0.14.2")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "shiny" version))
+              (sha256
+               (base32
+                "1sx8c490hbj7lsmvwwq5p4a32dcz4fp4wp1zvaaf2pfg713pk593"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-digest" ,r-digest)
+       ("r-htmltools" ,r-htmltools)
+       ("r-httpuv" ,r-httpuv)
+       ("r-jsonlite" ,r-jsonlite)
+       ("r-mime" ,r-mime)
+       ("r-r6" ,r-r6)
+       ("r-sourcetools" ,r-sourcetools)
+       ("r-xtable" ,r-xtable)))
+    (home-page "http://shiny.rstudio.com")
+    (synopsis "Web application framework for R")
+    (description
+     "Makes it incredibly easy to build interactive web applications with R.
+Automatic reactive binding between inputs and outputs and extensive pre-built
+widgets make it possible to build beautiful, responsive, and powerful
+applications with minimal effort.")
+    (license license:gpl3)))
-- 
1.9.1


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From 442d0f0d2c7eceef42670858e7c1f55ce2944143 Mon Sep 17 00:00:00 2001
From: Raoul Jean Pierre Bonnal <ilpuccio.febo@gmail.com>
Date: Tue, 27 Dec 2016 22:11:28 +0100
Subject: [PATCH 08/11] gnu: Add r-tximport.

---
 gnu/packages/bioinformatics.scm | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index d423f08..dbe1b92 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7618,6 +7618,27 @@ for DNA and protein sequences.  This package supports several sequence
 kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.")
     (license license:gpl2+)))
 
+(define-public r-tximport
+  (package
+    (name "r-tximport")
+    (version "1.2.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "tximport" version))
+              (sha256
+               (base32
+                "1k5a7dad6zqg936s17f6cmwgqp11x24z9zhxndsgwbscgpyhpcb0"))))
+    (build-system r-build-system)
+    (home-page "http://bioconductor.org/packages/tximport")
+    (synopsis "Import and summarize transcript-level estimates for gene-level analysis")
+    (description
+     "Imports transcript-level abundance, estimated counts and transcript
+lengths, and summarizes into matrices for use with downstream gene-level
+analysis packages. Average transcript length, weighted by sample-specific
+transcript abundance estimates, is provided as a matrix which can be used
+as an offset for different expression of gene-level counts.")
+    (license license:gpl2)))
+
 (define-public emboss
   (package
     (name "emboss")
-- 
1.9.1


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From 8dbed423c89d9496d0585609fa2abd0589524721 Mon Sep 17 00:00:00 2001
From: Raoul Jean Pierre Bonnal <ilpuccio.febo@gmail.com>
Date: Tue, 27 Dec 2016 22:05:51 +0100
Subject: [PATCH 07/11] gnu: Add r-shinydashboard.

---
 gnu/packages/web.scm | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm
index f048976..d2ca8f6 100644
--- a/gnu/packages/web.scm
+++ b/gnu/packages/web.scm
@@ -3997,3 +3997,24 @@ Automatic reactive binding between inputs and outputs and extensive pre-built
 widgets make it possible to build beautiful, responsive, and powerful
 applications with minimal effort.")
     (license license:gpl3)))
+
+(define-public r-shinydashboard
+  (package
+    (name "r-shinydashboard")
+    (version "0.5.3")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "shinydashboard" version))
+              (sha256
+               (base32
+                "0anw22qxbis69zm0ls6alsc3ann27hvgs5mv1wvr4ppk7q8cg4l2"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-htmltools" ,r-htmltools)
+       ("r-shiny" ,r-shiny)))
+    (home-page "http://rstudio.github.io/shinydashboard/")
+    (synopsis "Create dashboards with shiny")
+    (description
+     "Create dashboards with shiny. This package provides a theme on top of
+Shiny, making it easy to create attractive dashboards.")
+    (license license:gpl2)))
-- 
1.9.1


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From e3d07982bde8c03d6e16f3e93295720a93592e27 Mon Sep 17 00:00:00 2001
From: Raoul Jean Pierre Bonnal <ilpuccio.febo@gmail.com>
Date: Tue, 27 Dec 2016 20:52:20 +0100
Subject: [PATCH 03/11] gnu: Add r-sourcetools.

---
 gnu/packages/statistics.scm | 22 ++++++++++++++++++++++
 1 file changed, 22 insertions(+)

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index b406e9e..4440565 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -3852,3 +3852,25 @@ density using quasirandom noise.")
      "The bee swarm plot is a one-dimensional scatter plot like stripchart,
 but with closely-packed, non-overlapping points.")
     (license license:artistic2.0)))
+
+(define-public r-sourcetools
+  (package
+    (name "r-sourcetools")
+    (version "0.1.5")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "sourcetools" version))
+       (sha256
+        (base32
+         "0jx6kslygfqaic3cmjwag3dy98q1a2dw20cz7z8agsknmmbk6dy2"))))
+    (build-system r-build-system)
+    (home-page "http://cran.r-project.org/web/packages/sourcetools")
+    (synopsis
+     "Tools for reading, tokenizing and parsing R code.")
+    (description
+     "Tools for the reading and tokenization of R code.  The
+sourcetools package provides both an R and C++ interface for the
+tokenization of R code, and helpers for interacting with the
+tokenized representation of R code.")
+    (license license:expat)))
-- 
1.9.1


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From 65736cd4409e136744f0a5b52bece0ba440aec4c Mon Sep 17 00:00:00 2001
From: Raoul Jean Pierre Bonnal <ilpuccio.febo@gmail.com>
Date: Tue, 27 Dec 2016 22:14:28 +0100
Subject: [PATCH 09/11] gnu: Add r-rhdf5.

---
 gnu/packages/bioinformatics.scm | 46 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 46 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index dbe1b92..154f509 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7639,6 +7639,52 @@ transcript abundance estimates, is provided as a matrix which can be used
 as an offset for different expression of gene-level counts.")
     (license license:gpl2)))
 
+(define-public r-rhdf5
+  (package
+    (name "r-rhdf5")
+    (version "2.18.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "rhdf5" version))
+              (sha256
+               (base32
+                "0pb04li55ysag30s7rap7nnivc0rqmgsmpj43kin0rxdabfn1w0k"))))
+    (build-system r-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'unpack-smallhdf5
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* (
+                    (out (assoc-ref %outputs "out"))
+                    (name "src/hdf5source/hdf5small.tgz")
+                    (tar (string-append (assoc-ref %build-inputs "tar") "/bin/tar")))
+               (begin
+                 (system* tar "-xzvf" name "-C" "src/" )
+                 (substitute* "src/Makevars"
+                   (("^.*cd hdf5source &&.*$") "")
+                   (("^.*gunzip -dc hdf5small.tgz.*$") "")
+                   (("^.*rm -rf hdf5.*$") "")
+                   (("^.*mv hdf5source/hdf5 ..*$") ""))
+                 (substitute* "src/hdf5/configure"
+                   (("/bin/mv") "mv")))))))))
+    (propagated-inputs `(("r-zlibbioc" ,r-zlibbioc)))
+    (inputs
+     `(("tar" ,tar)
+       ("perl" ,perl)
+       ("zlib" ,zlib)))
+    (home-page "http://bioconductor.org/packages/rhdf5")
+    (synopsis "HDF5 interface to R")
+    (description
+     "This R/Bioconductor package provides an interface between HDF5 and R.
+HDF5's main features are the ability to store and access very large and/or
+complex datasets and a wide variety of metadata on mass storage (disk) through
+a completely portable file format.  The rhdf5 package is thus suited for the
+exchange of large and/or complex datasets between R and other software package,
+and for letting R applications work on datasets that are larger than the
+available RAM.")
+    (license license:artistic2.0)))
+
 (define-public emboss
   (package
     (name "emboss")
-- 
1.9.1


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From 9832383b32dcafb11b66d8ca398e3258f8adfba9 Mon Sep 17 00:00:00 2001
From: Raoul Jean Pierre Bonnal <ilpuccio.febo@gmail.com>
Date: Tue, 27 Dec 2016 22:18:32 +0100
Subject: [PATCH 11/11] gnu: Add r-scran.

---
 gnu/packages/bioinformatics.scm | 29 +++++++++++++++++++++++++++++
 1 file changed, 29 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 678fae7..5e06664 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7722,6 +7722,35 @@ available RAM.")
 of single-cell RNA-seq gene expression data, with a focus on quality control.")
     (license license:gpl2+)))
 
+(define-public r-scran 
+  (package
+    (name "r-scran")
+    (version "1.2.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "scran" version))
+              (sha256
+               (base32
+                "1wnsmp46x9zgbiacf9hxhpy42gxbvwf8q2x6dchc3r9g4p2s65c5"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biobase" ,r-biobase)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-biocparallel" ,r-biocparallel)
+       ("r-dynamictreecut" ,r-dynamictreecut)
+       ("r-edger" ,r-edger)
+       ("r-scater" ,r-scater)
+       ("r-shiny" ,r-shiny)
+       ("r-statmod" ,r-statmod)
+       ("r-zoo" ,r-zoo)))
+    (home-page "http://bioconductor.org/packages/scran")
+    (synopsis "Methods for single-cell RNA-Seq data analysis")
+    (description
+     "Implements a variety of low-level analyses of single-cell RNA-seq data.
+Methods are provided for normalization of cell-specific biases, assignment of
+cell cycle phase, and detection of highly variable and significantly
+correlated genes.")
+    (license license:gpl3)))
 
 (define-public emboss
   (package
-- 
1.9.1


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From a6468efd3e1e00d97d5581e6282e84321afe468c Mon Sep 17 00:00:00 2001
From: Raoul Jean Pierre Bonnal <ilpuccio.febo@gmail.com>
Date: Tue, 27 Dec 2016 22:16:33 +0100
Subject: [PATCH 10/11] gnu: Add r-scater.

---
 gnu/packages/bioinformatics.scm | 38 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 38 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 154f509..678fae7 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7685,6 +7685,44 @@ and for letting R applications work on datasets that are larger than the
 available RAM.")
     (license license:artistic2.0)))
 
+(define-public r-scater
+  (package
+    (name "r-scater")
+    (version "1.2.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "scater" version))
+              (sha256
+               (base32
+                "0pambafir3aqpgk7kdq5i2pn0278d97bn2qb9712c0jivw363whf"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biobase" ,r-biobase)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-biomart" ,r-biomart)
+       ("r-data-table" ,r-data-table)
+       ("r-dplyr" ,r-dplyr)
+       ("r-edger" ,r-edger)
+       ("r-ggbeeswarm" ,r-ggbeeswarm)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-limma" ,r-limma)
+       ("r-matrixstats" ,r-matrixstats)
+       ("r-plyr" ,r-plyr)
+       ("r-reshape2" ,r-reshape2)
+       ("r-rhdf5" ,r-rhdf5)
+       ("r-rjson" ,r-rjson)
+       ("r-shiny" ,r-shiny)
+       ("r-shinydashboard" ,r-shinydashboard)
+       ("r-tximport" ,r-tximport)
+       ("r-viridis" ,r-viridis)))
+    (home-page "https://github.com/davismcc/scater")
+    (synopsis "Single-cell analysis toolkit for gene expression data in R")
+    (description
+     "This package provides a collection of tools for doing various analyses
+of single-cell RNA-seq gene expression data, with a focus on quality control.")
+    (license license:gpl2+)))
+
+
 (define-public emboss
   (package
     (name "emboss")
-- 
1.9.1