* [PATCH] Add r-scran 1.2.0 and all its dependencies
@ 2016-12-27 9:14 Ra
2016-12-27 16:02 ` Ricardo Wurmus
0 siblings, 1 reply; 9+ messages in thread
From: Ra @ 2016-12-27 9:14 UTC (permalink / raw)
To: guix-devel
[-- Attachment #1.1: Type: text/plain, Size: 691 bytes --]
Hi devs,
in attachment a patch for the inclusion of an R/Bioconductor library named
"scran" https://bioconductor.org/packages/release/bioc/html/scran.html ,
scran has a lot of dependencies and I placed those related to
bioinformatics/bioconductor into bioinformatics.scm and those related just
to R insto statistics.scm.
There are a total of 11 new R libraries in this patch and the most
complicated is the r-rhdf5 where I had to modify a bit the original
installation because it contains a sub_tar_archive ( I had a brief
discussion with Rekado on irc - I saw your message/replay today- ).
Let me know if this big-patch is acceptable or how do I need to submit it.
Thanks a lot.
Raoul
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[-- Attachment #2: 0001-Add-r-scran-1.2.0-and-all-its-dependencies.patch --]
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From b64c564c0d7719732e672116269690c4d00d3422 Mon Sep 17 00:00:00 2001
From: Raoul Jean Pierre Bonnal <ilpuccio.febo@gmail.com>
Date: Tue, 27 Dec 2016 09:32:42 +0100
Subject: [PATCH] Add r-scran 1.2.0 and all its dependencies
---
gnu/packages/bioinformatics.scm | 132 ++++++++++++++++++++++++++++++++++
gnu/packages/statistics.scm | 156 ++++++++++++++++++++++++++++++++++++++++
2 files changed, 288 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 912941e..d20da9a 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7876,3 +7876,135 @@ replacement for strverscmp.")
samples into a single report. It contains modules for a large number of
common bioinformatics tools.")
(license license:gpl3)))
+
+(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 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 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 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)))
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index f868da2..20be97e 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -3815,3 +3815,159 @@ 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-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)))
+
+(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")
+ (inputs
+ `(;; We need not only cairo here, but pango to ensure that tests for the
+ ;; "cairo" bitmapType plotting backend succeed.
+ ("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)))
+
+(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+)))
+
+(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)))
+
+(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)))
+
+(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 Bee Swarm 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)))
+
+(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
[-- Attachment #3: r-scran.svg --]
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^ permalink raw reply related [flat|nested] 9+ messages in thread
* Re: [PATCH] Add r-scran 1.2.0 and all its dependencies
2016-12-27 9:14 [PATCH] Add r-scran 1.2.0 and all its dependencies Ra
@ 2016-12-27 16:02 ` Ricardo Wurmus
2016-12-27 16:34 ` Ra
0 siblings, 1 reply; 9+ messages in thread
From: Ricardo Wurmus @ 2016-12-27 16:02 UTC (permalink / raw)
To: Ra; +Cc: guix-devel
Hi Raoul,
> in attachment a patch for the inclusion of an R/Bioconductor library named
> "scran" https://bioconductor.org/packages/release/bioc/html/scran.html ,
> scran has a lot of dependencies and I placed those related to
> bioinformatics/bioconductor into bioinformatics.scm and those related just
> to R insto statistics.scm.
Nice! Thank you for your efforts!
> Let me know if this big-patch is acceptable or how do I need to submit it.
We have a policy of one commit per package. Each commit has a commit
summary in a standard format (you’ll see when running git log).
Going through the big patch I noticed a couple of things:
* the indentation is rather uneven. If you’re using Emacs it’s very
simple to correct this by using TAB and/or hitting C-M-q on the
expression. (Also make sure parentheses are not all by themselves on
an otherwise empty line.)
* line length (especially in descriptions) exceeds the limits.
* Please edit the descriptions. Package descriptions for Guix have to
use full sentences.
Judging from the indentation this doesn’t look like it was created by
the *recursive* importer. Were there any problems using the recursive
CRAN/Bioconductor importer?
The package for “r-shiny” needs a closer look. AFAIR it contains
minified Javascript, which does not count as actual source code. If
that’s in fact the case we would need to fiddle with the package a
little to replace minified Javascript blobs with Javascript source files
(which may be minified as part of the build process). I’d prefer if
“r-shiny” were added to “web.scm”.
In the “r-statmod” package expression the comment above the gfortran
input (which should be a native input) doesn’t seem to apply.
Please also double-check that the licenses are correct. The importer
may not necessary get things right.
Finally, please use lower-case words in the synopsis. In R packages
this is often capitalised.
Could you please send an updated patch set?
--
Ricardo
GPG: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC
http://elephly.net
^ permalink raw reply [flat|nested] 9+ messages in thread
* Re: [PATCH] Add r-scran 1.2.0 and all its dependencies
2016-12-27 16:02 ` Ricardo Wurmus
@ 2016-12-27 16:34 ` Ra
2016-12-27 16:59 ` Ricardo Wurmus
0 siblings, 1 reply; 9+ messages in thread
From: Ra @ 2016-12-27 16:34 UTC (permalink / raw)
To: Ricardo Wurmus; +Cc: guix-devel
[-- Attachment #1: Type: text/plain, Size: 2856 bytes --]
Hi Ricardo,
On Tue, Dec 27, 2016 at 5:02 PM Ricardo Wurmus <rekado@elephly.net> wrote:
Hi Raoul,
> in attachment a patch for the inclusion of an R/Bioconductor library
named
> "scran" https://bioconductor.org/packages/release/bioc/html/scran.html ,
> scran has a lot of dependencies and I placed those related to
> bioinformatics/bioconductor into bioinformatics.scm and those related just
> to R insto statistics.scm.
Nice! Thank you for your efforts!
Thanks, the result worth the effort.
> Let me know if this big-patch is acceptable or how do I need to submit it.
We have a policy of one commit per package. Each commit has a commit
summary in a standard format (you’ll see when running git log).
Ok, when I was adding r-scran I was just trying the make it the work. I'll
go back and create a patch for each dependency.
Going through the big patch I noticed a couple of things:
* the indentation is rather uneven. If you’re using Emacs it’s very
simple to correct this by using TAB and/or hitting C-M-q on the
expression. (Also make sure parentheses are not all by themselves on
an otherwise empty line.)
I was using Vim, I will try with Emacs and also I was practicing a bit.
* line length (especially in descriptions) exceeds the limits.
* Please edit the descriptions. Package descriptions for Guix have to
use full sentences.
Judging from the indentation this doesn’t look like it was created by
the *recursive* importer. Were there any problems using the recursive
CRAN/Bioconductor importer?
with guix 0.12.0 I was able to use guix import, I had some problem in the
past due to certificates and x509.
I used:
guix import cran --archive=bioconductor scater
I had to add the missing dependencies by hand, is there a recursive way to
do so?
The package for “r-shiny” needs a closer look. AFAIR it contains
minified Javascript, which does not count as actual source code. If
that’s in fact the case we would need to fiddle with the package a
little to replace minified Javascript blobs with Javascript source files
(which may be minified as part of the build process). I’d prefer if
“r-shiny” were added to “web.scm”.
Ok for web.scm.
In the “r-statmod” package expression the comment above the gfortran
input (which should be a native input) doesn’t seem to apply.
Ok, bad comment placed there during tests.
Please also double-check that the licenses are correct. The importer
may not necessary get things right.
Actually I noticed that and I fixed them, I will check again.
Finally, please use lower-case words in the synopsis. In R packages
this is often capitalised.
Ok.
Could you please send an updated patch set?
Sure, in a couple of days, I think.
--
Raoul
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^ permalink raw reply [flat|nested] 9+ messages in thread
* Re: [PATCH] Add r-scran 1.2.0 and all its dependencies
2016-12-27 16:34 ` Ra
@ 2016-12-27 16:59 ` Ricardo Wurmus
2016-12-27 17:06 ` Ra
0 siblings, 1 reply; 9+ messages in thread
From: Ricardo Wurmus @ 2016-12-27 16:59 UTC (permalink / raw)
To: Ra; +Cc: guix-devel
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.
--
Ricardo
GPG: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC
http://elephly.net
^ permalink raw reply [flat|nested] 9+ messages in thread
* Re: [PATCH] Add r-scran 1.2.0 and all its dependencies
2016-12-27 16:59 ` Ricardo Wurmus
@ 2016-12-27 17:06 ` Ra
2016-12-27 21:25 ` Ra
0 siblings, 1 reply; 9+ messages in thread
From: Ra @ 2016-12-27 17:06 UTC (permalink / raw)
To: Ricardo Wurmus; +Cc: guix-devel
[-- Attachment #1: Type: text/plain, Size: 636 bytes --]
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
>
>
[-- Attachment #2: Type: text/html, Size: 1530 bytes --]
^ permalink raw reply [flat|nested] 9+ messages in thread
* Re: [PATCH] Add r-scran 1.2.0 and all its dependencies
2016-12-27 17:06 ` Ra
@ 2016-12-27 21:25 ` Ra
2016-12-28 9:26 ` Ra
0 siblings, 1 reply; 9+ messages in thread
From: Ra @ 2016-12-27 21:25 UTC (permalink / raw)
To: Ricardo Wurmus; +Cc: guix-devel
[-- Attachment #1.1: Type: text/plain, Size: 1001 bytes --]
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
>
>
[-- Attachment #1.2: Type: text/html, Size: 2562 bytes --]
[-- Attachment #2: 0001-gnu-Add-r-vipor.patch --]
[-- Type: application/octet-stream, Size: 1441 bytes --]
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
[-- Attachment #3: 0004-gnu-Add-r-ggbeeswarm.patch --]
[-- Type: application/octet-stream, Size: 1552 bytes --]
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
[-- Attachment #4: 0002-gnu-Add-r-beeswarm.patch --]
[-- Type: application/octet-stream, Size: 1376 bytes --]
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
[-- Attachment #5: 0005-gnu-Add-r-statmod.patch --]
[-- Type: application/octet-stream, Size: 1746 bytes --]
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
[-- Attachment #6: 0006-gnu-Add-r-shiny.patch --]
[-- Type: application/octet-stream, Size: 1753 bytes --]
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
[-- Attachment #7: 0008-gnu-Add-r-tximport.patch --]
[-- Type: application/octet-stream, Size: 1689 bytes --]
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
[-- Attachment #8: 0007-gnu-Add-r-shinydashboard.patch --]
[-- Type: application/octet-stream, Size: 1449 bytes --]
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
[-- Attachment #9: 0003-gnu-Add-r-sourcetools.patch --]
[-- Type: application/octet-stream, Size: 1469 bytes --]
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
[-- Attachment #10: 0009-gnu-Add-r-rhdf5.patch --]
[-- Type: application/octet-stream, Size: 2736 bytes --]
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
[-- Attachment #11: 0011-gnu-Add-r-scran.patch --]
[-- Type: application/octet-stream, Size: 1811 bytes --]
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
[-- Attachment #12: 0010-gnu-Add-r-scater.patch --]
[-- Type: application/octet-stream, Size: 2064 bytes --]
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
^ permalink raw reply related [flat|nested] 9+ messages in thread
* Re: [PATCH] Add r-scran 1.2.0 and all its dependencies
2016-12-27 21:25 ` Ra
@ 2016-12-28 9:26 ` Ra
2016-12-29 21:52 ` Ricardo Wurmus
0 siblings, 1 reply; 9+ messages in thread
From: Ra @ 2016-12-28 9:26 UTC (permalink / raw)
To: Ricardo Wurmus; +Cc: guix-devel
[-- Attachment #1.1: Type: text/plain, Size: 1222 bytes --]
Hi Ricardo,
there was an issue with the r-shiny patch, the license was wrong. So this
is the new set of patches.
On Tue, Dec 27, 2016 at 10:25 PM Ra <ilpuccio.febo@gmail.com> wrote:
> 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
>
>
[-- Attachment #1.2: Type: text/html, Size: 3500 bytes --]
[-- Attachment #2: 0006-gnu-Add-r-shiny.patch --]
[-- Type: application/octet-stream, Size: 1747 bytes --]
From bb3c01e940be4c4357591aa066b9ffc65371615c Mon Sep 17 00:00:00 2001
From: Raoul Jean Pierre Bonnal <ilpuccio.febo@gmail.com>
Date: Wed, 28 Dec 2016 10:11:45 +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..cec659e 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 l:gpl3)))
--
1.9.1
[-- Attachment #3: 0005-gnu-Add-r-statmod.patch --]
[-- Type: application/octet-stream, Size: 1746 bytes --]
From a9b2d5a94ea4c2560611e46b523f57d091abab3c 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
[-- Attachment #4: 0010-gnu-Add-r-scater.patch --]
[-- Type: application/octet-stream, Size: 2064 bytes --]
From 14222e8cdbfc49093172d9f1a3bcc7999e72bcb5 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
[-- Attachment #5: 0008-gnu-Add-r-tximport.patch --]
[-- Type: application/octet-stream, Size: 1689 bytes --]
From e6855970c278627a0ebbbe557c054bac653c513c 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
[-- Attachment #6: 0003-gnu-Add-r-sourcetools.patch --]
[-- Type: application/octet-stream, Size: 1469 bytes --]
From 6821f41f9bf79b853724eb1fd5f01d7acba5fe5a 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
[-- Attachment #7: 0001-gnu-Add-r-vipor.patch --]
[-- Type: application/octet-stream, Size: 1441 bytes --]
From 40318a6d2d4f6ca1c5539dfe21c63b503ca00aea 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
[-- Attachment #8: 0002-gnu-Add-r-beeswarm.patch --]
[-- Type: application/octet-stream, Size: 1376 bytes --]
From b5b9ae7e2386c8ddb8f86f8b9edad0d000f34928 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
[-- Attachment #9: 0007-gnu-Add-r-shinydashboard.patch --]
[-- Type: application/octet-stream, Size: 1437 bytes --]
From 7b4704fcc4bdf455522c045002e88d875e050e16 Mon Sep 17 00:00:00 2001
From: Raoul Jean Pierre Bonnal <ilpuccio.febo@gmail.com>
Date: Wed, 28 Dec 2016 10:15:48 +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 cec659e..724abd1 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 l: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 l:gpl2)))
--
1.9.1
[-- Attachment #10: 0004-gnu-Add-r-ggbeeswarm.patch --]
[-- Type: application/octet-stream, Size: 1552 bytes --]
From e96e737470adbd7cf39c7308b2125b6724c3d3ea 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
[-- Attachment #11: 0009-gnu-Add-r-rhdf5.patch --]
[-- Type: application/octet-stream, Size: 2736 bytes --]
From 922c7db2c1e4e9f9f8e1a9795686ada137d2fc7f 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
[-- Attachment #12: 0011-gnu-Add-r-scran.patch --]
[-- Type: application/octet-stream, Size: 1811 bytes --]
From 187f678cdc529b7c6d1cf11931866394a427dfd3 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
^ permalink raw reply related [flat|nested] 9+ messages in thread
* Re: [PATCH] Add r-scran 1.2.0 and all its dependencies
2016-12-28 9:26 ` Ra
@ 2016-12-29 21:52 ` Ricardo Wurmus
2017-01-31 21:47 ` Ricardo Wurmus
0 siblings, 1 reply; 9+ messages in thread
From: Ricardo Wurmus @ 2016-12-29 21:52 UTC (permalink / raw)
To: Ra; +Cc: guix-devel
Ra <ilpuccio.febo@gmail.com> writes:
> Hi Ricardo,
> there was an issue with the r-shiny patch, the license was wrong. So this
> is the new set of patches.
Thank you. I updated and pushed all patches up to r-shiny. The changes
are:
* Changed the descriptions, so that they are made up of full sentences.
* Added a proper commit message.
Please take a look at those changes for future reference.
I didn’t push r-shiny, because it contains a lot of minified Javascript
files without corresponding source files.
Here is an edited list:
shiny/inst/www/shared/babel-polyfill.min.js
shiny/inst/www/shared/highlight/highlight.pack.js
shiny/inst/www/shared/json2-min.js
shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.nb.min.js
shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.th.min.js
shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.pt.min.js
shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.az.min.js
shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.en-AU.min.js
shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.ms.min.js
shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.id.min.js
shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.me.min.js
shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.hr.min.js
shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.bs.min.js
shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.lv.min.js
shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.ka.min.js
shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.ja.min.js
shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.sk.min.js
shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.nl.min.js
shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.is.min.js
shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.fr.min.js
shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.mk.min.js
shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.fr-CH.min.js
shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.sq.min.js
shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.pt-BR.min.js
shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.vi.min.js
shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.ru.min.js
shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.fo.min.js
shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.ko.min.js
shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.it-CH.min.js
shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.cs.min.js
shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.ca.min.js
shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.mn.min.js
shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.kk.min.js
shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.fa.min.js
shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.nl-BE.min.js
shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.sl.min.js
shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.zh-CN.min.js
shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.rs-latin.min.js
shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.tr.min.js
shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.zh-TW.min.js
shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.cy.min.js
shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.pl.min.js
shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.lt.min.js
shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.el.min.js
shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.no.min.js
shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.da.min.js
shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.gl.min.js
shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.uk.min.js
shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.eu.min.js
shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.hy.min.js
shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.ro.min.js
shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.et.min.js
shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.kh.min.js
shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.eo.min.js
shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.he.min.js
shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.it.min.js
shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.es.min.js
shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.bg.min.js
shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.ar.min.js
shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.sw.min.js
shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.sv.min.js
shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.rs.min.js
shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.en-GB.min.js
shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.kr.min.js
shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.de.min.js
shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.fi.min.js
shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.sr-latin.min.js
shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.sr.min.js
shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.hu.min.js
shiny/inst/www/shared/bootstrap/shim/respond.min.js
shiny/inst/www/shared/bootstrap/shim/html5shiv.min.js
shiny/inst/www/shared/selectize/js/es5-shim.min.js
shiny/inst/www/shared/selectize/js/selectize.min.js
shiny/inst/www/shared/datatables/js/jquery.dataTables.min.js
shiny/inst/www/shared/strftime/strftime-min.js
shiny/inst/www/shared/ionrangeslider/js/ion.rangeSlider.min.js
I removed those Javascript files from the list that seem to have
matching source files (so we’d only need to minify them in a build
phase).
We cannot accept the patch for r-shiny when it contains these minified
JavaScript files, as they are not source code. Unfortunately, replacing
them won’t be easy, because things like babel-polyfill require an npm
build system.
If you want to use the r-shiny package you can add it to a module file
in a directory that’s listed on your GUIX_PACKAGE_PATH. That’s how
we’re using r-shiny at my institute as well.
--
Ricardo
GPG: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC
http://elephly.net
^ permalink raw reply [flat|nested] 9+ messages in thread
* Re: [PATCH] Add r-scran 1.2.0 and all its dependencies
2016-12-29 21:52 ` Ricardo Wurmus
@ 2017-01-31 21:47 ` Ricardo Wurmus
0 siblings, 0 replies; 9+ messages in thread
From: Ricardo Wurmus @ 2017-01-31 21:47 UTC (permalink / raw)
To: Ra; +Cc: guix-devel
Ricardo Wurmus <rekado@elephly.net> writes:
> Ra <ilpuccio.febo@gmail.com> writes:
>
>> Hi Ricardo,
>> there was an issue with the r-shiny patch, the license was wrong. So this
>> is the new set of patches.
>
> Thank you. I updated and pushed all patches up to r-shiny. The changes
> are:
>
> * Changed the descriptions, so that they are made up of full sentences.
> * Added a proper commit message.
>
> Please take a look at those changes for future reference.
I also pushed two more, the last two patches in the series that are not
affected by the lack of r-shiny.
> I didn’t push r-shiny, because it contains a lot of minified Javascript
> files without corresponding source files.
>
> Here is an edited list:
>
> shiny/inst/www/shared/babel-polyfill.min.js
> shiny/inst/www/shared/highlight/highlight.pack.js
> shiny/inst/www/shared/json2-min.js
> shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.nb.min.js
> shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.th.min.js
> shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.pt.min.js
> shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.az.min.js
> shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.en-AU.min.js
> shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.ms.min.js
> shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.id.min.js
> shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.me.min.js
> shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.hr.min.js
> shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.bs.min.js
> shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.lv.min.js
> shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.ka.min.js
> shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.ja.min.js
> shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.sk.min.js
> shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.nl.min.js
> shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.is.min.js
> shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.fr.min.js
> shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.mk.min.js
> shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.fr-CH.min.js
> shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.sq.min.js
> shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.pt-BR.min.js
> shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.vi.min.js
> shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.ru.min.js
> shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.fo.min.js
> shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.ko.min.js
> shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.it-CH.min.js
> shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.cs.min.js
> shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.ca.min.js
> shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.mn.min.js
> shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.kk.min.js
> shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.fa.min.js
> shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.nl-BE.min.js
> shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.sl.min.js
> shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.zh-CN.min.js
> shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.rs-latin.min.js
> shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.tr.min.js
> shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.zh-TW.min.js
> shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.cy.min.js
> shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.pl.min.js
> shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.lt.min.js
> shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.el.min.js
> shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.no.min.js
> shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.da.min.js
> shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.gl.min.js
> shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.uk.min.js
> shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.eu.min.js
> shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.hy.min.js
> shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.ro.min.js
> shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.et.min.js
> shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.kh.min.js
> shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.eo.min.js
> shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.he.min.js
> shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.it.min.js
> shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.es.min.js
> shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.bg.min.js
> shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.ar.min.js
> shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.sw.min.js
> shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.sv.min.js
> shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.rs.min.js
> shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.en-GB.min.js
> shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.kr.min.js
> shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.de.min.js
> shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.fi.min.js
> shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.sr-latin.min.js
> shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.sr.min.js
> shiny/inst/www/shared/datepicker/js/locales/bootstrap-datepicker.hu.min.js
> shiny/inst/www/shared/bootstrap/shim/respond.min.js
> shiny/inst/www/shared/bootstrap/shim/html5shiv.min.js
> shiny/inst/www/shared/selectize/js/es5-shim.min.js
> shiny/inst/www/shared/selectize/js/selectize.min.js
> shiny/inst/www/shared/datatables/js/jquery.dataTables.min.js
> shiny/inst/www/shared/strftime/strftime-min.js
> shiny/inst/www/shared/ionrangeslider/js/ion.rangeSlider.min.js
>
> I removed those Javascript files from the list that seem to have
> matching source files (so we’d only need to minify them in a build
> phase).
>
> We cannot accept the patch for r-shiny when it contains these minified
> JavaScript files, as they are not source code. Unfortunately, replacing
> them won’t be easy, because things like babel-polyfill require an npm
> build system.
I’d really like to have Shiny in Guix proper. If we could at least get
the unminified variants of these Javascript files we could bundle them
as they are. Do you think it’s possible to get these files without
having to go down the npm rabbit hole?
--
Ricardo
GPG: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC
https://elephly.net
^ permalink raw reply [flat|nested] 9+ messages in thread
end of thread, other threads:[~2017-01-31 21:47 UTC | newest]
Thread overview: 9+ messages (download: mbox.gz / follow: Atom feed)
-- links below jump to the message on this page --
2016-12-27 9:14 [PATCH] Add r-scran 1.2.0 and all its dependencies Ra
2016-12-27 16:02 ` Ricardo Wurmus
2016-12-27 16:34 ` Ra
2016-12-27 16:59 ` Ricardo Wurmus
2016-12-27 17:06 ` Ra
2016-12-27 21:25 ` Ra
2016-12-28 9:26 ` Ra
2016-12-29 21:52 ` Ricardo Wurmus
2017-01-31 21:47 ` Ricardo Wurmus
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