Re: [PATCH] gnu: r: Add which to propagated-inputs.

2017-01-24 Thread Ra 
Hi Ludo,

On Tue, Jan 24, 2017 at 10:04 PM Ludovic Courtès  wrote:

Hi,

Raoul Bonnal  skribis:

> From: Raoul Jean Pierre Bonnal 
>
> * gnu/packages/statistics.scm (r)[propagated-inputs]: Add which.
> ---
>
> Notes:
> In my local installation of R
>
> Sys.which(c("bash"))
>
> was not working properly, inspecting the function(below) I had not
installed which beforehand.
> > Sys.which
> function (names)
> {
> res <- character(length(names))
> names(res) <- names
> which <-
"/gnu/store/cn670s29lsf2nr5axd8gmhl8sb9qpyiq-which-2.21/bin/which"

This function contains the absolute file name of ‘which’, so everything
should work?


That is what I expected. The R function was not working till I explicitly
installed the package 'which', maybe it was something strange on my side.


Doing this (modifying the code to refer to external commands by absolute
file names) is preferable over propagating inputs, because it avoids
clobbering user profiles.


Thanks.
Ra

Re: [PATCH] gnu: Add kallisto.

2017-01-19 Thread Ra 
Hi Ricardo,

On Wed, Jan 18, 2017 at 9:31 PM Ricardo Wurmus  wrote:

>
> Alex Vong  writes:
>
> > Looking at the license text:
> >
> > Copyright ©2015. The Regents of the University of California (Regents).
> All
> > Rights Reserved. Permission to use, copy, modify, and distribute this
> software
> > and its documentation for educational and research not-for-profit
> purposes,
> > without fee and without a signed licensing agreement, is hereby granted,
> > provided that the above copyright notice, this paragraph and the
> following two
> > paragraphs appear in all copies, modifications, and distributions.
> Contact The
> > Office of Technology Licensing, UC Berkeley, 2150 Shattuck Avenue, Suite
> 510,
> > Berkeley, CA 94720-1620, (510) 643-7201, for commercial licensing
> > opportunities.
> >
> >
> > It seems the license is {fsf, dfsg} non-free because it does not allow
> > commercial usage. More precisely, it violates freedom 0 (the freedom to
> > run the program as you wish, for any purpose).
>
> Correct.  Kallisto is non-free software.
>
> > Does anybody know of any fork or should we use an old version?
>
> I don’t know of any version that is free software.
>

Looking around, I saw that you are using Kallisto at BIMSB and you have
other software I need (latest rsem);  Other software I want to work/port to
guix are https://github.com/tderrien/FEELnc,
https://github.com/Teichlab/tracer ( and Trinity). Does it make sense to
contribute to https://github.com/BIMSBbioinfo/ or do you suggest to go with
a personal/independent repo ?

--
Ra


> --
> Ricardo
>
> GPG: BCA6 89B6 3655 3801 C3C6  2150 197A 5888 235F ACAC
> https://elephly.net
>
>

Re: [PATCH] gnu: Add kallisto.

2017-01-18 Thread Ra 
Hi Alex,

On Wed, Jan 18, 2017 at 12:09 PM Alex Vong  wrote:

> Hello,
>
>
> Looking at the license text:
>
> Copyright ©2015. The Regents of the University of California (Regents). All
> Rights Reserved. Permission to use, copy, modify, and distribute this
> software
> and its documentation for educational and research not-for-profit purposes,
> without fee and without a signed licensing agreement, is hereby granted,
> provided that the above copyright notice, this paragraph and the following
> two
> paragraphs appear in all copies, modifications, and distributions. Contact
> The
> Office of Technology Licensing, UC Berkeley, 2150 Shattuck Avenue, Suite
> 510,
> Berkeley, CA 94720-1620, (510) 643-7201, for commercial licensing
> opportunities.
>
>
> It seems the license is {fsf, dfsg} non-free because it does not allow
> commercial usage. More precisely, it violates freedom 0 (the freedom to
> run the program as you wish, for any purpose).
>
>
> Does anybody know of any fork or should we use an old version?
>
>
Do you mean that this package can not be included or I need to fall back to
an older version ?  In both cases, I should find a way to have a different
branch/repo for "special" packages.

--
Ra




>
> Cheers,
> Alex
>
>
> Ra  writes:
>
> > Hi,
> > I think I need your help to identify the right license for this package,
> I set bsd-3 only for
> > convenience this is the original license
> > (https://github.com/pachterlab/kallisto/blob/master/license.txt)
> >
> > Do I need to use something like :
> > (license (license:non-copyleft "file://src/COPYING"
> >"See src/COPYING in the
> distribution."
> >
> > * gnu/packages/bioinformatics.scm (kallisto): New variable.
> > ---
> > gnu/packages/bioinformatics.scm | 28 
> > 1 file changed, 28 insertions(+)
> >
> > diff --git a/gnu/packages/bioinformatics.scm
> b/gnu/packages/bioinformatics.scm
> > index c60bedc..86026fd 100644
> > --- a/gnu/packages/bioinformatics.scm
> > +++ b/gnu/packages/bioinformatics.scm
> > @@ -8502,3 +8502,31 @@ a specified false discovery rate. It also
> contains a number of utilities
> > to
> > explore the MS/MS results and assess missed and irregular enzymatic
> cleavages,
> > mass measurement accuracy, etc.")
> > (license license:artistic2.0)))
> > +
> > +(define-public kallisto
> > + (package
> > + (name "kallisto")
> > + (version "0.43.0")
> > + (source (origin
> > + (method url-fetch)
> > + (uri (string-append
> > + "https://github.com/pachterlab/kallisto/archive/v";
> > + version ".tar.gz"))
> > + (file-name (string-append name "-" version ".tar.gz"))
> > + (sha256
> > + (base32
> > + "1d9cqf3lz6mm9kmqn47d99c6byn6q9l4ppgcafxrhcnrb2davhv9"
> > + (build-system cmake-build-system)
> > + (arguments
> > + '(#:tests? #f)) ; no "check" target
> > + (inputs
> > + `(("zlib" ,zlib)
> > + ("hdf5" ,hdf5)))
> > + (home-page "https://pachterlab.github.io/kallisto";)
> > + (synopsis "Near-optimal RNA-Seq quantification")
> > + (description
> > + "Kallisto is a program for quantifying abundances of transcripts from
> > +RNA-Seq data, or more generally of target sequences using
> high-throughput
> > +sequencing reads. It is based on the novel idea of pseudoalignment for
> rapidly
> > +determining the compatibility of reads with targets, without the need
> for alignment.")
> > + (license license:bsd-3)))
> > --
> > 1.9.1
> >
> > From f30c6b20e2564f3617ab3dde40af10bfbe790749 Mon Sep 17 00:00:00 2001
> > From: Raoul Jean Pierre Bonnal 
> > Date: Wed, 18 Jan 2017 10:46:49 +0100
> > Subject: [PATCH] gnu: Add kallisto.
> >
> > * gnu/packages/bioinformatics.scm (kallisto): New variable.
> > ---
> >  gnu/packages/bioinformatics.scm | 28 
> >  1 file changed, 28 insertions(+)
> >
> > diff --git a/gnu/packages/bioinformatics.scm
> b/gnu/packages/bioinformatics.scm
> > index c60bedc..86026fd 100644
> > --- a/gnu/packages/bioinformatics.scm
> > +++ b/gnu/packages/bioinformatics.scm
> > @@ -8502,3 +8502,31 @@ a specified false discovery rate.  It also
> contains a number of utilities to
> >  explore the MS/MS results and assess missed and irregular enzymatic
> cleavages,
> >  mass measurement accuracy, etc.")
> >  (license

[PATCH] gnu: Add kallisto.

2017-01-18 Thread Ra 
Hi,
I think I need your help to identify the right license for this package, I
set bsd-3 only for convenience this is the original license (
https://github.com/pachterlab/kallisto/blob/master/license.txt)

Do I need to use something like :

(license (license:non-copyleft "file://src/COPYING"
   "See src/COPYING in the distribution."




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

diff --git a/gnu/packages/bioinformatics.scm
b/gnu/packages/bioinformatics.scm
index c60bedc..86026fd 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8502,3 +8502,31 @@ a specified false discovery rate.  It also contains
a number of utilities to
 explore the MS/MS results and assess missed and irregular enzymatic
cleavages,
 mass measurement accuracy, etc.")
 (license license:artistic2.0)))
+
+(define-public kallisto
+  (package
+(name "kallisto")
+(version "0.43.0")
+(source (origin
+  (method url-fetch)
+  (uri (string-append
+"https://github.com/pachterlab/kallisto/archive/v";
+version ".tar.gz"))
+  (file-name (string-append name "-" version ".tar.gz"))
+  (sha256
+   (base32
+"1d9cqf3lz6mm9kmqn47d99c6byn6q9l4ppgcafxrhcnrb2davhv9"
+(build-system cmake-build-system)
+(arguments
+ '(#:tests? #f)) ; no "check" target
+(inputs
+ `(("zlib" ,zlib)
+   ("hdf5" ,hdf5)))
+(home-page "https://pachterlab.github.io/kallisto";)
+(synopsis "Near-optimal RNA-Seq quantification")
+(description
+ "Kallisto is a program for quantifying abundances of transcripts from
+RNA-Seq data, or more generally of target sequences using high-throughput
+sequencing reads. It is based on the novel idea of pseudoalignment for
rapidly
+determining the compatibility of reads with targets, without the need for
alignment.")
+(license license:bsd-3)))
--
1.9.1


0001-gnu-Add-kallisto.patch
Description: Binary data

Re: [PATCH] gnu: Add r-gmodels

2017-01-16 Thread Ra 
On Sat, Jan 14, 2017 at 8:51 PM Ra  wrote:

> Ouch ,
> actually I just cut and pasted the text from a shell and sending it with
> inbox. Sorry for that and thanks for spot it.
>
> Ra
>
> Il sab 14 gen 2017 18:19 Ludovic Courtès  ha scritto:
>
> Hi!
>
> Ricardo Wurmus  skribis:
>
> > Ra  writes:
> >
> >> * gnu/packages/statistics.scm (r-gmodels): New variable.
> >> ---
> >>  gnu/packages/statistics.scm | 19 +++
> >>  1 file changed, 19 insertions(+)
> >
> > Thanks for the patch, but I get the same problem as with your other
> > patch:
> >
> > error: corrupt patch at line 10
> >
> > I don’t know if this is a problem on my end or with your email.
>
> The message contains both a text/html and a text/plain version.
>
> Ra: Could you turn off HTML altogether, or use ‘git send-email’?  I
> think that’s the best way to make sure it works for everyone.
>
> Thanks,
> Ludo’.
>
>
The patch file works as expected.
I will follow Ludo's advice next time.


Cheers
--
Ra

Re: [PATCH] gnu: Add r-gmodels

2017-01-14 Thread Ra 
Ouch ,
actually I just cut and pasted the text from a shell and sending it with
inbox. Sorry for that and thanks for spot it.

Ra

Il sab 14 gen 2017 18:19 Ludovic Courtès  ha scritto:

> Hi!
>
> Ricardo Wurmus  skribis:
>
> > Ra  writes:
> >
> >> * gnu/packages/statistics.scm (r-gmodels): New variable.
> >> ---
> >>  gnu/packages/statistics.scm | 19 +++
> >>  1 file changed, 19 insertions(+)
> >
> > Thanks for the patch, but I get the same problem as with your other
> > patch:
> >
> > error: corrupt patch at line 10
> >
> > I don’t know if this is a problem on my end or with your email.
>
> The message contains both a text/html and a text/plain version.
>
> Ra: Could you turn off HTML altogether, or use ‘git send-email’?  I
> think that’s the best way to make sure it works for everyone.
>
> Thanks,
> Ludo’.
>

[PATCH] gnu: Add r-rann.

2017-01-13 Thread Ra 
* gnu/packages/statistics.scm (r-rann): New variable.
---
 gnu/packages/statistics.scm | 21 +
 1 file changed, 21 insertions(+)

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index db1a687..695f6ed 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -4004,3 +4004,24 @@ generalized linear model functions that implement
secure convergence,
 dispersion modeling and Tweedie power-law families.")
 ;; Statmod is distributed under either license
 (license (list license:gpl2 license:gpl3
+
+(define-public r-rann
+  (package
+(name "r-rann")
+(version "2.5")
+(source (origin
+  (method url-fetch)
+  (uri (cran-uri "RANN" version))
+  (sha256
+   (base32
+"007cgqg9bybg2zlljbv5m6cmlm3r6i251018rpgjcn0xnm9sjsj7"
+(properties
+ `((upstream-name . "RANN")))
+(build-system r-build-system)
+(home-page "https://github.com/jefferis/RANN";)
+(synopsis "Fast nearest neighbour search")
+(description
+ "This package finds the k nearest neighbours for every point in a
given
+dataset in O(N log N) time using Arya and Mount's ANN library. Provides
approximate,
+exact searches, fixed radius searches, bd and kb trees.")
+(license license:gpl3+)))
--
1.9.1


0001-gnu-Add-r-rann.patch
Description: Binary data

Re: [PATCH] gnu: Add r-gmodels

2017-01-13 Thread Ra 
On Fri, Jan 13, 2017 at 11:31 PM Leo Famulari  wrote:

> On Fri, Jan 13, 2017 at 10:55:29PM +0100, Ricardo Wurmus wrote:
> >
> > Ra  writes:
> >
> > > * gnu/packages/statistics.scm (r-gmodels): New variable.
> > > ---
> > >  gnu/packages/statistics.scm | 19 +++
> > >  1 file changed, 19 insertions(+)
> >
> > Thanks for the patch, but I get the same problem as with your other
> > patch:
> >
> > error: corrupt patch at line 10
> >
> > I don’t know if this is a problem on my end or with your email.
>
> It works for me.
>

Do I need to resend the patch or perform some kind of test  ?

--
Ra

Re: [PATCH] gnu: Add r-sva

2017-01-13 Thread Ra 
Hi Ricardo,

On Fri, Jan 13, 2017 at 10:52 PM Ricardo Wurmus  wrote:

> Ra  writes:
>
> > * gnu/packages/bioinformatics.scm (r-sva): New variable.
> > ---
> >  gnu/packages/bioinformatics.scm | 35 +++
> >  1 file changed, 35 insertions(+)
>
> Thanks for the patch.  I tried to apply this but got this error:
>
> error: corrupt patch at line 12
>
> Could you resend the patch please?
>
> > +(description
> > + "This package contains functions for removing batch effects and
> > +other unwanted variation in high-throughput experiment. Specifically,
> > +the sva package contains functions for the identifying and building
> > +surrogate variables for high-dimensional data sets. Surrogate variables
> > +are covariates constructed directly from high-dimensional data (like
> gene
> > +expression/RNA sequencing/methylation/brain imaging data) that can be
> used
> > +in subsequent analyses to adjust for unknown, unmodeled, or latent
> sources
> > +of noise. The sva package can be used to remove artifacts in three ways:
> > +1. identifying and estimating surrogate variables for unknown sources of
> > +variation in high-throughput experiments Leek and Storey 2007 PLoS
> > Genetics,
> > + 2008 PNAS,2. directly removing known batch effects using ComBat
> > +Johnson et al. 2007 Biostatistics and 3. removing batch effects with
> known
> > +control probes Leek 2014 biorXiv. Removing batch effects and using
> > surrogate
> > +variables in differential expression analysis have been shown to reduce
> > +dependence, stabilize error rate estimates, and improve reproducibility,
> > +see Leek and Storey 2007 PLoS Genetics, 2008 PNAS or Leek et al. 2011
> Nat.
> > Reviews Genetics.")
> > +(license license:artistic2.0)))
>
> Could you please shorten the description?  A paragraph or two would be
> sufficient.  We also don’t need the references to publications.  If you
> decide to keep (a shortened variant of) the enumeration, please use
> texinfo syntax.
>
>
follows the patch with the reduced description, sorry for the long version.
I do not know why you get the "corrupt" message, I hope that attaching the
patch file could solve the issue.



* gnu/packages/bioinformatics.scm (r-sva): New variable.
---
 gnu/packages/bioinformatics.scm | 26 ++
 1 file changed, 26 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm
b/gnu/packages/bioinformatics.scm
index d82b6c0..867a72e 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7995,3 +7995,29 @@ immunoprecipitation and target enrichment on small
gene panels.  Thereby,
 CopywriteR constitutes a widely applicable alternative to available copy
 number detection tools.")
 (license license:gpl2)))
+
+(define-public r-sva
+  (package
+(name "r-sva")
+(version "3.22.0")
+(source
+ (origin
+   (method url-fetch)
+   (uri (bioconductor-uri "sva" version))
+   (sha256
+(base32
+ "1wc1fjm6dzlsqqagm43y57w8jh8nsh0r0m8z1p6ximcb5gxqh7hn"
+(build-system r-build-system)
+(propagated-inputs
+ `(("r-genefilter" ,r-genefilter)))
+(home-page "http://bioconductor.org/packages/sva";)
+(synopsis "Surrogate variable analysis")
+(description
+ "This package contains functions for removing batch effects and
+other unwanted variation in high-throughput experiment. The package
+contains functions for identifying and building surrogate variables
+for high-dimensional data sets. Surrogate variables are covariates
+constructed directly from high-dimensional data like gene expression/RNA
+sequencing/methylation/brain imaging data that can be used in subsequent
+analyses to adjust for unknown, unmodeled, or latent sources of noise.")
+(license license:artistic2.0)))
--
1.9.1


0001-gnu-Add-r-sva.patch
Description: Binary data

[PATCH] gnu: Add r-sva

2017-01-13 Thread Ra 
* gnu/packages/bioinformatics.scm (r-sva): New variable.
---
 gnu/packages/bioinformatics.scm | 35 +++
 1 file changed, 35 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm
b/gnu/packages/bioinformatics.scm
index d82b6c0..c6acab1 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7995,3 +7995,38 @@ immunoprecipitation and target enrichment on small
gene panels.  Thereby,
 CopywriteR constitutes a widely applicable alternative to available copy
 number detection tools.")
 (license license:gpl2)))
+
+(define-public r-sva
+  (package
+(name "r-sva")
+(version "3.22.0")
+(source
+ (origin
+   (method url-fetch)
+   (uri (bioconductor-uri "sva" version))
+   (sha265
+(base32
+ "1wc1fjm6dzlsqqagm43y57w8jh8nsh0r0m8z1p6ximcb5gxqh7hn"
+(build-system r-build-system)
+(propagated-inputs
+ `(("r-genefilter" ,r-genefilter)))
+(home-page "http://bioconductor.org/packages/sva";)
+(synopsis "Surrogate variable analysis")
+(description
+ "This package contains functions for removing batch effects and
+other unwanted variation in high-throughput experiment. Specifically,
+the sva package contains functions for the identifying and building
+surrogate variables for high-dimensional data sets. Surrogate variables
+are covariates constructed directly from high-dimensional data (like gene
+expression/RNA sequencing/methylation/brain imaging data) that can be used
+in subsequent analyses to adjust for unknown, unmodeled, or latent sources
+of noise. The sva package can be used to remove artifacts in three ways:
+1. identifying and estimating surrogate variables for unknown sources of
+variation in high-throughput experiments Leek and Storey 2007 PLoS
Genetics,
+ 2008 PNAS,2. directly removing known batch effects using ComBat
+Johnson et al. 2007 Biostatistics and 3. removing batch effects with known
+control probes Leek 2014 biorXiv. Removing batch effects and using
surrogate
+variables in differential expression analysis have been shown to reduce
+dependence, stabilize error rate estimates, and improve reproducibility,
+see Leek and Storey 2007 PLoS Genetics, 2008 PNAS or Leek et al. 2011 Nat.
Reviews Genetics.")
+(license license:artistic2.0)))
--
1.9.1


0001-gnu-Add-r-sva.patch
Description: Binary data

[PATCH] gnu: Add r-gmodels

2017-01-13 Thread Ra 
* gnu/packages/statistics.scm (r-gmodels): New variable.
---
 gnu/packages/statistics.scm | 19 +++
 1 file changed, 19 insertions(+)

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index db1a687..45d8d23 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -4004,3 +4004,22 @@ generalized linear model functions that implement
secure convergence,
 dispersion modeling and Tweedie power-law families.")
 ;; Statmod is distributed under either license
 (license (list license:gpl2 license:gpl3
+
+(define-public r-gmodels
+  (package
+(name "r-gmodels")
+(version "2.16.2")
+(source (origin
+  (method url-fetch)
+  (uri (cran-uri "gmodels" version))
+  (sha256
+   (base32
+"0zf4krlvdywny5p5hnkr0r0hync6dvzc9yy4dfywaxmkpna8h0db"
+(build-system r-build-system)
+(propagated-inputs
+ `(("r-gdata" ,r-gdata)))
+(home-page "http://www.sf.net/projects/r-gregmisc";)
+(synopsis "Various R programming tools for model fitting")
+(description
+ "This package provides various R programming tools for model
fitting.")
+(license license:gpl2)))
--
1.9.1


0001-gnu-Add-r-gmodels.patch
Description: Binary data

Re: [PATCH] gnu: Add perl-parallel-forkmanager.

2017-01-12 Thread Ra 
Hi Marius,

On Thu, Jan 12, 2017 at 9:27 PM Marius Bakke  wrote:

> Ra  writes:
>
> > * gnu/packages/perl.scm (perl-parallel-forkmanager): New variable.
>
> Thanks! This looks mostly good, see comments below. Can you send an
> updated patch that also includes copyright information? Thanks in
> advance!
>
> > ---
> >  gnu/packages/perl.scm | 26 ++
> >  1 file changed, 26 insertions(+)
> >
> > diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm
> > index 8f103ec..532e360 100644
> > --- a/gnu/packages/perl.scm
> > +++ b/gnu/packages/perl.scm
> > @@ -7770,3 +7770,29 @@ interface to File::Find::Object.")
> >(description "Test::TrailingSpace tests for trailing spaces
> >  in Perl source files.")
> >(license x11)))
> > +
> > +(define-public perl-parallel-forkmanager
>
> There is a pledge at the top of perl.scm asking to add packages in
> alphabetic order. Can you adjust the location of this expression
> accordingly?
>
> > +  (package
> > +(name "perl-parallel-forkmanager")
> > +(version "1.19")
> > +(source
> > + (origin
> > +   (method url-fetch)
> > +   (uri (string-append
> > +
>  "mirror://cpan/authors/id/Y/YA/YANICK/Parallel-ForkManager-"
> > + version
> > + ".tar.gz"))
> > +   (sha256
> > +(base32
> > + "0wm4wp6p3ah5z212jl12728z68nmxmfr0f03z1jpvdzffnc2xppi"
> > +(build-system perl-build-system)
> > +(native-inputs
> > + `(("perl-test-warn" ,perl-test-warn)))
> > +(home-page
> > + "http://search.cpan.org/dist/Parallel-ForkManager";)
> > +(synopsis
> > + "A simple parallel processing fork manager")
>
> Synopsis should not start with an article. `guix lint` will complain
> about this ;-)
>
> Also, the line breaks after home-page and synopsis are not necessary.
>
> > +  (description "Parallel::ForkManager is intended for use in
>^^^
>Please use @code{Parallel::ForkManager} here.
>
> > +operations that can be done in parallel where the number of
> > +processes to be forked off should be limited.")
> > +  (license (package-license perl
>
> Otherwise LGTM!
>
Thanks for helping me in creating a right patch.
I think I did everything, below and attached the patch.

* gnu/packages/perl.scm (perl-parallel-forkmanager): New variable.
---
 gnu/packages/perl.scm | 25 +
 1 file changed, 25 insertions(+)

diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm
index 8f103ec..4e8ed9a 100644
--- a/gnu/packages/perl.scm
+++ b/gnu/packages/perl.scm
@@ -12,6 +12,7 @@
 ;;; Copyright © 2016 Roel Janssen 
 ;;; Copyright © 2016 Ben Woodcroft 
 ;;; Copyright © 2016 Jan Nieuwenhuizen 
+;;; Copyright @ 2017 Raoul J.P. Bonnal 
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -5014,6 +5015,30 @@ show those variables which are in scope at the point
of the call.  PadWalker
 is particularly useful for debugging.")
 (license (package-license perl

+(define-public perl-parallel-forkmanager
+  (package
+(name "perl-parallel-forkmanager")
+(version "1.19")
+(source
+ (origin
+   (method url-fetch)
+   (uri (string-append
+ "mirror://cpan/authors/id/Y/YA/YANICK/Parallel-ForkManager-"
+ version
+ ".tar.gz"))
+   (sha256
+(base32
+ "0wm4wp6p3ah5z212jl12728z68nmxmfr0f03z1jpvdzffnc2xppi"
+(build-system perl-build-system)
+(native-inputs
+ `(("perl-test-warn" ,perl-test-warn)))
+(home-page "http://search.cpan.org/dist/Parallel-ForkManager";)
+(synopsis "Simple parallel processing fork manager")
+(description "@code{Parallel::ForkManager} is intended for use in
+operations that can be done in parallel where the number of
+processes to be forked off should be limited.")
+  (license (package-license perl
+
 (define-public perl-params-util
   (package
 (name "perl-params-util")
--
1.9.1

Ciao
--
Ra


0001-gnu-Add-perl-parallel-forkmanager.patch
Description: Binary data

[PATCH] gnu: Add perl-parallel-forkmanager.

2017-01-12 Thread Ra 
* gnu/packages/perl.scm (perl-parallel-forkmanager): New variable.
---
 gnu/packages/perl.scm | 26 ++
 1 file changed, 26 insertions(+)

diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm
index 8f103ec..532e360 100644
--- a/gnu/packages/perl.scm
+++ b/gnu/packages/perl.scm
@@ -7770,3 +7770,29 @@ interface to File::Find::Object.")
   (description "Test::TrailingSpace tests for trailing spaces
 in Perl source files.")
   (license x11)))
+
+(define-public perl-parallel-forkmanager
+  (package
+(name "perl-parallel-forkmanager")
+(version "1.19")
+(source
+ (origin
+   (method url-fetch)
+   (uri (string-append
+ "mirror://cpan/authors/id/Y/YA/YANICK/Parallel-ForkManager-"
+ version
+ ".tar.gz"))
+   (sha256
+(base32
+ "0wm4wp6p3ah5z212jl12728z68nmxmfr0f03z1jpvdzffnc2xppi"
+(build-system perl-build-system)
+(native-inputs
+ `(("perl-test-warn" ,perl-test-warn)))
+(home-page
+ "http://search.cpan.org/dist/Parallel-ForkManager";)
+(synopsis
+ "A simple parallel processing fork manager")
+  (description "Parallel::ForkManager is intended for use in
+operations that can be done in parallel where the number of
+processes to be forked off should be limited.")
+  (license (package-license perl
--
1.9.1


0001-gnu-Add-perl-parallel-forkmanager.patch
Description: Binary data

[PATCH] gnu: Add r-randomforest.

2017-01-12 Thread Ra 
* gnu/packages/statistics.scm (r-randomforest): New variable.
---
 gnu/packages/statistics.scm | 23 +++
 1 file changed, 23 insertions(+)

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 40a511b..f5041a8 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -3979,3 +3979,26 @@ generalized linear model functions that implement
secure convergence,
 dispersion modeling and Tweedie power-law families.")
 ;; Statmod is distributed under either license
 (license (list license:gpl2 license:gpl3
+
+(define-public r-randomforest
+  (package
+(name "r-randomforest")
+(version "4.6-12")
+(source
+ (origin
+   (method url-fetch)
+   (uri (cran-uri "randomForest" version))
+   (sha256
+(base32
+ "1i43idaihhl6nwqw42v9dqpl6f8z3ykcn2in32lh2755i27jylbf"
+(properties `((upstream-name . "randomForest")))
+(build-system r-build-system)
+(home-page "https://www.stat.berkeley.edu/~breiman/RandomForests/";)
+(native-inputs
+ `(("gfortran" ,gfortran)))
+(synopsis
+ "Breiman and Cutler's random forests for classification and
regression")
+(description
+ "This package provides algorithm for classification and regression
based
+on a forest of trees using random inputs.")
+(license license:gpl2+)))
--
1.9.1


0001-gnu-Add-r-randomforest.patch
Description: Binary data

Re: [PATCH 2/2] gnu: multiqc: Update to 0.8.

2016-12-28 Thread Ra 
Hi Ben,
reading the comments from https://github.com/ewels/MultiQC/issues/376
it seems that in the upcoming release they will solve the problem.
Are we going to wait for the next v. 1.0 or include it now and update later
?

--
Ra

On Mon, Dec 26, 2016 at 1:18 PM Ben Woodcroft  wrote:

> Hi Raoul,
>
>
> On 26/12/16 20:45, Ra wrote:
> > Hi Ben,
> > thanks I will investigate. Does it mean that multiqc is in stand by
> > for now ?
>
> It would be ideal I think to add tests, and because they are failing it
> would be good to know why. I thought the easiest simply to ask the
> maintainers if they knew why the tests were failing:
> https://github.com/ewels/MultiQC/issues/376
>
> I also submitted the exception catching patch here, which we should add
> to our patch if we decide to keep it before pushing our changes.
> https://github.com/ewels/MultiQC/pull/377
>
> I figure it makes sense to give them a week or two to respond, and
> reevaluate after that. I presume you have not observed any problems
> using multiqc after this update?
> Thanks,
> ben
>

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

2016-12-28 Thread Ra 
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  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  wrote:
>
> On Tue, Dec 27, 2016 at 6:00 PM Ricardo Wurmus  wrote:
>
>
> Ra  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
>
>


0006-gnu-Add-r-shiny.patch
Description: Binary data


0005-gnu-Add-r-statmod.patch
Description: Binary data


0010-gnu-Add-r-scater.patch
Description: Binary data


0008-gnu-Add-r-tximport.patch
Description: Binary data


0003-gnu-Add-r-sourcetools.patch
Description: Binary data


0001-gnu-Add-r-vipor.patch
Description: Binary data


0002-gnu-Add-r-beeswarm.patch
Description: Binary data


0007-gnu-Add-r-shinydashboard.patch
Description: Binary data


0004-gnu-Add-r-ggbeeswarm.patch
Description: Binary data


0009-gnu-Add-r-rhdf5.patch
Description: Binary data


0011-gnu-Add-r-scran.patch
Description: Binary data

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

2016-12-27 Thread Ra 
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  wrote:

> On Tue, Dec 27, 2016 at 6:00 PM Ricardo Wurmus  wrote:
>
>
> Ra  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
>
>


0001-gnu-Add-r-vipor.patch
Description: Binary data


0004-gnu-Add-r-ggbeeswarm.patch
Description: Binary data


0002-gnu-Add-r-beeswarm.patch
Description: Binary data


0005-gnu-Add-r-statmod.patch
Description: Binary data


0006-gnu-Add-r-shiny.patch
Description: Binary data


0008-gnu-Add-r-tximport.patch
Description: Binary data


0007-gnu-Add-r-shinydashboard.patch
Description: Binary data


0003-gnu-Add-r-sourcetools.patch
Description: Binary data


0009-gnu-Add-r-rhdf5.patch
Description: Binary data


0011-gnu-Add-r-scran.patch
Description: Binary data


0010-gnu-Add-r-scater.patch
Description: Binary data

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

2016-12-27 Thread Ra 
On Tue, Dec 27, 2016 at 6:00 PM Ricardo Wurmus  wrote:

>
> Ra  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
>
>

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

2016-12-27 Thread Ra 
Hi Ricardo,

On Tue, Dec 27, 2016 at 5:02 PM Ricardo Wurmus  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

Re: Re: [PATCH 2/2] gnu: multiqc: Update to 0.8.

2016-12-26 Thread Ra 
Hi Ben,
thanks I will investigate. Does it mean that multiqc is in stand by for now
?

On Fri, Dec 23, 2016 at 2:30 PM Ben Woodcroft  wrote:

> Hi Raoul,
>
> Thanks for the patches.
>
> On 19/12/16 07:36, Ra wrote:
> > [PATCH] gnu: multiqc: Update to 0.8.
> > is [PATCH 1/2] for this message, sorry for the mistake.
> > Running multiqc without [PATCH 2/2] systems say that matplotlib
> > requires nose>=0.11.1, so I added it to the propagated inputs.
> I notice that 0.9 is out too, so I tried updating to that version. I
> also added "python-nose" as a native-input rather than a
> propagated-input since it is only used at build time.
>
> However, the tests fail with this error:
>
> FileNotFoundError: [Errno 2] No such file or directory: 'git'
>
> The check phase is still successful so it doesn't stop - this problem is
> being fixed by others. I added a patch to ignore the FileNotFoundError,
> but then after all that the tests fail. Would you mind investigating
> further, perhaps by raising an issue on the multiqc GitHub? My efforts
> so far are in the attached patch.
>
> Thanks, ben.
>
>

Re: [PATCH] doc: Mention "guix pull" during installation.

2016-12-19 Thread Ra 
Hi Theodoros,

On Sun, Dec 18, 2016 at 1:12 PM Theodoros Foradis <
theodoros@openmailbox.org> wrote:

>
> Petter writes:
>
> > Hi,
> >
> > Some new users don't run `guix pull` before installing, and can have a
> > less good experience because of this. Proposing a patch to add this to
> > the manual.
> >
> > Thanks,
> > Petter
>
> Just a sidenote here, that I mentioned in #guix irc channel the other
> time. I tried to `guix pull` from the 0.11 USB installer, and it would
> fail because some package couldn't be substituted,
> module-import-compiled if I recall correctly.
>
> Guix suggested as normal, that `--fallback` flag should be used, which
> is a non-accepted flag for `guix pull`. I had to `guix system init
> --fallback`, until that package was built, and then `guix pull`. Not
> having run `guix pull`, building from source was failing anyway.


Last week I tried to follow the manual (binary install with Ubuntu) and use
`guix pull` without success, `--fallback` option was there and I had a lot
of troubles with [module-import-compiled](
https://gist.github.com/helios/6d13037a7ae7be40f118573545cbccb3)
In #guix irc I found valuable helps (cbaines, rekado)  and I ended up using
the git source


git clone --recurse git://git.savannah.gnu.org/guix.git
cd guix

guix environment --fallback --pure --container -N guix --ad-hoc guile-cairo
guile-charting guile-rsvg -- sh -c "make clean; ./bootstrap &&
./configure --localstatedir=/var
&& make -j4"

ln -s ~/guix ~/.config/guix/latest
guix package -u

maybe the git/source install should be documented as well or at least
tested from scratch for newbies such as me.

--
Ra

[PATCH 2/2] gnu: multiqc: Update to 0.8.

2016-12-18 Thread Ra 
[PATCH] gnu: multiqc: Update to 0.8.
is [PATCH 1/2] for this message, sorry for the mistake.
Running multiqc without [PATCH 2/2] systems say that matplotlib requires
nose>=0.11.1, so I added it to the propagated inputs.

---
 gnu/packages/bioinformatics.scm | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/bioinformatics.scm
b/gnu/packages/bioinformatics.scm
index 43bf701..1167df5 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7863,7 +7863,8 @@ replacement for strverscmp.")
("python-pyyaml" ,python-pyyaml)
("python-click" ,python-click)
("python-matplotlib" ,python-matplotlib)
-   ("python-numpy" ,python-numpy)))
+   ("python-numpy" ,python-numpy)
+   ("python-nose" ,python-nose )))
 (home-page "http://multiqc.info";)
 (synopsis "Aggregate bioinformatics analysis reports")
 (description
--
1.9.1

[PATCH 1/2] gnu: multiqc: Update to 0.8.

2016-12-18 Thread Ra 
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm
b/gnu/packages/bioinformatics.scm
index 3e9c82f..43bf701 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7848,14 +7848,14 @@ replacement for strverscmp.")
 (define-public multiqc
   (package
 (name "multiqc")
-(version "0.6")
+(version "0.8")
 (source
  (origin
(method url-fetch)
(uri (pypi-uri "multiqc" version))
(sha256
 (base32
- "0avw11h63ldpxy5pizc3wl1wa01ha7q10wb240nggsjz3jaqvyiy"
+ "0fpzhby0g36h14l0lrxhpcp8czv6lrv8v8fsbl0ksxmdgmn176i6"
 (build-system python-build-system)
 (propagated-inputs
  `(("python-jinja2" ,python-jinja2)
--
1.9.1

Re: [PATCH] gnu: r: Update to 3.3.2

2016-12-18 Thread Ra 
Hi Ben,
thanks for reviewing the patch. I am very happy to contribute even if this
is minimal :)

Hope to provide more patch and new software and use in production in our
infra.

On Sun, Dec 18, 2016 at 1:07 AM Ben Woodcroft  wrote:

> On 17/12/16 17:52, Ben Woodcroft wrote:
>
> Hi Raoul, good to see you here.
>
> On 17/12/16 03:16, Ra wrote:
>
> * gnu/packages/statistics.scm (r): Update to 3.3.2.
>
> I successfully built R and all of its 243 dependencies on x86_64, and
> except for the previously failing shogun, all built successfully. So I
> think it is OK for master.
>
> Unless anyone objects, I'll push it to master tomorrow.
>
>
> I added at attribution line and pushed as
> a1814e4a27aa2e99283d381ec7e090706fa1031d.
>
>

[PATCH] gnu: star: Update to 2.5.2b.

2016-12-17 Thread Ra 
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm
b/gnu/packages/bioinformatics.scm
index 3e9c82f..1b6532b 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -4924,7 +4924,7 @@ application of SortMeRNA is filtering rRNA from
metatranscriptomic data.")
 (define-public star
   (package
 (name "star")
-(version "2.5.2a")
+(version "2.5.2b")
 (source (origin
   (method url-fetch)
   (uri (string-append "
https://github.com/alexdobin/STAR/archive/";
@@ -4932,7 +4932,7 @@ application of SortMeRNA is filtering rRNA from
metatranscriptomic data.")
   (file-name (string-append name "-" version ".tar.gz"))
   (sha256
(base32
-"0xjlsm4p9flln111hv4xx7xy94c2nl53zvdvbk9winmiradjsdra"))
+"1na6np880r1zaamiy00hy8bid5anpy0kgf63587v2yl080krk2zq"))
   (modules '((guix build utils)))
   (snippet
'(begin
-- 
1.9.1

[PATCH] gnu: r: Update to 3.3.2

2016-12-16 Thread Ra 
* gnu/packages/statistics.scm (r): Update to 3.3.2.
---
  gnu/packages/statistics.scm | 4 ++--
  1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 6cdd694..72c5430 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -101,7 +101,7 @@ be output in text, PostScript, PDF or HTML.")
  (define-public r
(package
  (name "r")
-(version "3.3.1")
+(version "3.3.2")
  (source (origin
(method url-fetch)
(uri (string-append "mirror://cran/src/base/R-"
@@ -109,7 +109,7 @@ be output in text, PostScript, PDF or HTML.")
version ".tar.gz"))
(sha256
 (base32
-"1qm9znh8akfy9fkzzi6f1vz2w1dd0chsr6qn7kw80lqzhgjrmi9x"
+"0k2i9qdd83g09fcpls2198q4ykxkii5skczb514gnx7mx4hsv56j"
  (build-system gnu-build-system)
  (arguments
   `(#:make-flags
--
1.9.1

[PATCH] gnu: r: Update to 3.3.2

2016-12-16 Thread Ra 
* gnu/packages/statistics.scm (r): Update to 3.3.2.
---
 gnu/packages/statistics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 6cdd694..72c5430 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -101,7 +101,7 @@ be output in text, PostScript, PDF or HTML.")
 (define-public r
   (package
 (name "r")
-(version "3.3.1")
+(version "3.3.2")
 (source (origin
   (method url-fetch)
   (uri (string-append "mirror://cran/src/base/R-"
@@ -109,7 +109,7 @@ be output in text, PostScript, PDF or HTML.")
   version ".tar.gz"))
   (sha256
(base32
-"1qm9znh8akfy9fkzzi6f1vz2w1dd0chsr6qn7kw80lqzhgjrmi9x"
+"0k2i9qdd83g09fcpls2198q4ykxkii5skczb514gnx7mx4hsv56j"
 (build-system gnu-build-system)
 (arguments
  `(#:make-flags
--
1.9.1