[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/packag

[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

[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

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

2016-12-18 Thread Ra
, 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

[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,

[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(+),

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

2016-12-19 Thread Ra
"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

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

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 >

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 “

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

2016-12-27 Thread Ra
: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 c

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 no

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 Ra

[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 +

[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/package

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 i

[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/pack

[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/b

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 insertio

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/stati

[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/packa

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/package

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

[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"

Re: [PATCH] gnu: Add kallisto.

2017-01-18 Thread Ra
er 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 onl

Re: [PATCH] gnu: Add kallisto.

2017-01-19 Thread Ra
hub.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: r: Add which to propagated-inputs.

2017-01-24 Thread Ra
mething 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