Re: Ruby on Rails (web-application framework) (and the wip-rails branch)

Hi Chris, On 07/02/18 18:30, Christopher Baines wrote: $ git remote set-url cbaines http://git.cbaines.net/guix $ git fetch cbaines error: wrong index v2 file size in .git/objects/pack/pack-739d9ab6fbe9233657458397a3ab1f0ad30107f1.idx.temp error: Unable to find 289e6cffc4ed9a6658e85b22635ea2f

Re: Ruby on Rails (web-application framework) (and the wip-rails branch)

On 06/02/18 08:34, Christopher Baines wrote: Ben Woodcroft writes: On 31/01/18 05:50, Christopher Baines wrote: I think it would be good to see these packages in the master branch, and would be up for trying to help towards this. Ben, do you have any thoughts on the wip-rails branch? My

Re: 03/03: gnu: python-dateutil: Update to 2.6.1.

On 31/01/18 16:18, Alex Vong wrote: Ben Woodcroft writes: Hi Mark, Marius, On 31/01/18 12:52, Mark H Weaver wrote: Hi, mba...@fastmail.com (Marius Bakke) writes: mbakke pushed a commit to branch master in repository guix. commit b94502bed69c0fb5033d702fd0308209efb8815c Author: Alex

Re: 03/03: gnu: python-dateutil: Update to 2.6.1.

Hi Mark, Marius, On 31/01/18 12:52, Mark H Weaver wrote: Hi, mba...@fastmail.com (Marius Bakke) writes: mbakke pushed a commit to branch master in repository guix. commit b94502bed69c0fb5033d702fd0308209efb8815c Author: Alex Vong Date: Sat Jan 27 22:58:58 2018 +0800 gnu: python-dat

Re: Ruby on Rails (web-application framework) (and the wip-rails branch)

Hi Chris, On 31/01/18 05:50, Christopher Baines wrote: Hey, So I had a go at rebasing and using the wip-rails [1] branch recently, and I was very successful. One minor conflict needed resolving, a few extra packages, a few update and a few disabled test suites [2] and I was able to start a Rai

Re: [bug#27438] [PATCH] guix: build: ruby-build-system: Install to the vendor directory

Hi Chris, On 18/12/17 00:19, Christopher Baines wrote: Hey, It's been a while since I looked at this, but I think it's still relevant. As a reminder, currently the search paths for the Ruby packages in Guix are a bit off [1], which makes it difficult to use Ruby gems with different versions o

Re: ISO image available for testing!

On 06/12/17 10:52, Mark H Weaver wrote: Hi Ludovic, l...@gnu.org (Ludovic Courtès) writes: 91c9b5d01 * packages: 'package-grafts' trims native inputs. [...] Long story short: we were flagging native inputs as potential sources of grafts even though, by definition, native inputs are not ref

Re: ‘staging’ branch

On 21/09/17 12:31, Ben Woodcroft wrote: On 21/09/17 11:28, Kei Kebreau wrote: Marius Bakke writes: Ludovic Courtès writes: Hello! Marius, what’s the status of ‘staging’? (Sorry I had to pick someone as the staging master, so to speak. :-)) I've shepherded the last few itera

Re: ‘staging’ branch

On 21/09/17 11:28, Kei Kebreau wrote: Marius Bakke writes: Ludovic Courtès writes: Hello! Marius, what’s the status of ‘staging’? (Sorry I had to pick someone as the staging master, so to speak. :-)) I've shepherded the last few iterations, so I guess it's only fair! Thank you. If p

Re: Optionally using more advanced CPU features

Hi, On 21/08/17 22:23, Ricardo Wurmus wrote: Hi Guix, I was wondering how we should go about optionally building software for more advanced CPU features. Currently, we build software for the lowest common feature set among x86_64 CPUs. That’s good for portability, but not so good for perform

Re: 'core-updates' status

Hi Marius, On 19/08/17 07:24, Marius Bakke wrote: Hello! 'core-updates' has finished building on x86_64 and i686. There are a few failing packages still, but nothing too scary. Please try to fix some if you can! I went to look at blast+ on armhf, and came across this: /tmp/guix-build-blast

Re: git cannot be built

On 09/08/17 18:02, Ricardo Wurmus wrote: Mark H Weaver writes: Ricardo Wurmus writes: Commit 7f171fdaadb15bb1b313b25e9be3d1988b0f650f broke git for me. I cannot build it from source because one of the many tests appears to fail. This is on x86_64. I have not tried this on other archite

Re: core-updates failing packages

On 20/07/17 16:17, Ricardo Wurmus wrote: Ben Woodcroft writes: I have a patch ready but will push this as a part of a series that updates htslib to 1.5. Just to say that I'm working on it and noone else should spend time on this, I'm almost there. Thanks for letting me know. I w

Re: core-updates failing packages

Hi Leo, Thanks for taking the time to list these issues - helpful. On 15/07/17 02:50, Leo Famulari wrote: metabat fails: https://hydra.gnu.org/build/2171756 This fails due to the issue described at https://bitbucket.org/berkeleylab/metabat/issues/28/compilation-fail-with-boost-164 I have a

Re: [PATCH] Makefile.am: add a target that lists patches no longer used

Hi Eric, On 22/04/17 03:41, Leo Famulari wrote: On Thu, Apr 20, 2017 at 11:20:23PM -0500, Eric Bavier wrote: ---BEGIN test-suite.log FAIL: tests/patches === test-name: distributed patches are used location: /home/bavier/projects/guix/tests/patches.scm:

Re: Rails

On 12/07/17 18:47, ng0 wrote: Pjotr Prins transcribed 0.4K bytes: On Wed, Jul 12, 2017 at 08:03:48AM +, ng0 wrote: While I was working on it (or occasionally do) I wonder why we have so little rails packages? What happened there? Ruby support is great in Guix. But we don't use Rails much,

Re: 01/02: gnu: blast+: Update to 2.6.0.

On 07/07/17 09:39, Leo Famulari wrote: On Fri, Jul 07, 2017 at 09:33:26AM +1000, Ben Woodcroft wrote: Hi Ludo, On 07/07/17 02:54, Ludovic Courtès wrote: Hi Ben, donttrust...@gmail.com (Ben Woodcroft) skribis: commit 18dea67dc3a42d782b34b551304748346f173184 Author: Ben Woodcroft Date

Re: 01/02: gnu: blast+: Update to 2.6.0.

Hi Ludo, On 07/07/17 02:54, Ludovic Courtès wrote: Hi Ben, donttrust...@gmail.com (Ben Woodcroft) skribis: commit 18dea67dc3a42d782b34b551304748346f173184 Author: Ben Woodcroft Date: Mon Jul 3 23:00:14 2017 +1000 gnu: blast+: Update to 2.6.0. * gnu/packages

Re: [PATCH 01/26] gnu: Add perl-file-pushd.

Hi, On 24/03/17 18:13, Alex Sassmannshausen wrote: Hi Kei, Kei Kebreau writes: This series of packages builds and lints fine for me. There are over 200 dependent packages that would have to be rebuilt though, and core-updates is frozen to my knowledge. We can save this for the next core-upda

Re: [PATCH 35/35] gnu: Add r-seurat.

Hi Raoul, On 20/01/17 04:55, Raoul Bonnal wrote: + +(define-public r-seurat + (let ((commit "e1eae2da82ada2211e84fbc471615e8d3921b539")) +(package + (name "r-seurat") + (version (string-append "1.4." (string-take commit 7))) Apologies for the long delay on getting these recipes re

Re: [PATCH 0/15]: Add pplacer and OCaml dependencies.

Hi Ludo, On 10/02/17 08:32, Ludovic Courtès wrote: Hi Ben, Ben Woodcroft skribis: I'm quite happy to send these patches in, pplacer has been near the top of my most wanted list since I started contributing. There's two parts that are a little out of the ordinary: 1) Unfortunate

Re: bug#25177: python-tests: python-oslosphinx fixed. Please evaluate.

Hi Ricardo, On 22/02/17 03:47, Leo Famulari wrote: On Tue, Feb 21, 2017 at 06:30:12PM +0100, Ricardo Wurmus wrote: From 1ac5166df11766b47cd1ac723a464063a89afc96 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 21 Feb 2017 18:28:21 +0100 Subject: [PATCH] gnu: python-dendropy: Disable

Re: Packaging leiningen (feedback desired)

Hi Danny, Alex, On 07/02/17 18:19, Danny Milosavljevic wrote: Hmmm... works for me with: $ java -cp "${HOME}/.guix-profile/share/java/clojure-1.8.0.jar" clojure.main (Note: java -> /gnu/store/4lnjmsr4szhqyixy238xjl83k8h5f0ck-icedtea-3.2.0/bin/java) Also works within guix environment --ad-hoc

Re: [PATCH 00/10] ocaml patches

Hi Julien, On 08/02/17 06:16, Julien Lepiller wrote: On Tue, 31 Jan 2017 21:58:05 +0100 Julien Lepiller wrote: Here is the next series of patches. I think I took into account all of your previous remarks, so it should be faster. Julien Lepiller (10): gnu: Add ocaml-fieldslib. gnu: Add

[PATCH 0/15]: Add pplacer and OCaml dependencies.

ges/ocaml.scm index 9a0bc9112..2026def09 100644 --- a/gnu/packages/ocaml.scm +++ b/gnu/packages/ocaml.scm @@ -7,6 +7,7 @@ ;;; Copyright © 2016 Jan Nieuwenhuizen ;;; Copyright © 2016 Efraim Flashner ;;; Copyright © 2016, 2017 Julien Lepiller +;;; Copyright © 2017 Ben Woodcroft ;;; ;;;

Re: [PATCH] gnu: Add python-pprofile.

Hi Danny, On 06/02/17 19:05, Danny Milosavljevic wrote: * gnu/packages/python.scm (python-pprofile, python2-pprofile): New variables. LGTM, thanks. ben

Re: [PATCH] gnu: rustc: Add LIBRARY_PATH search path.

On 29/01/17 11:57, Chris Marusich wrote: Ben Woodcroft writes: I didn't have any problem compiling and linking pure rust programs - that commit fixed that issue, but when trying to link rust programs to non-rust libraries such as zlib the linker did not look in the lib of the pr

Re: [PATCH] gnu: rustc: Add LIBRARY_PATH search path.

On 28/01/17 09:22, Ludovic Courtès wrote: Marius Bakke skribis: Hi Ben, Ben Woodcroft writes: * gnu/packages/rust.scm (rustc)[native-search-paths]: New field. [...] +(native-search-paths + (list (search-path-specification +(variable "LIBRARY

Re: [PATCH] gnu: rustc: Add LIBRARY_PATH search path.

Hi Marius, On 28/01/17 06:21, Marius Bakke wrote: Hi Ben, Ben Woodcroft writes: * gnu/packages/rust.scm (rustc)[native-search-pat hs]: New field. [...] +(native-search-paths + (list (search-path-specification +(variable "LIBRARY_PATH") +(fi

[PATCH] gnu: rustc: Add LIBRARY_PATH search path.

Hi, This helps compiling when rustc is in one's profile and gcc is not. Thanks, ben.

[PATCH] gnu: rustc: Add LIBRARY_PATH search path.

@@ ;;; Copyright © 2016 David Craven ;;; Copyright © 2016 Eric Le Bihan ;;; Copyright © 2016 ng0 +;;; Copyright © 2016 Ben Woodcroft ;;; ;;; This file is part of GNU Guix. ;;; @@ -272,6 +273,10 @@ rustc-bootstrap and cargo-bootstrap packages.") (wrap-program (string-a

Re: [PATCH 0/1] Help wanted fixing a ruby-minitar bug

qOn 26/01/17 03:42, Leo Famulari wrote: On Wed, Jan 25, 2017 at 09:32:22AM +1000, Ben Woodcroft wrote: Well, it is unpacking a .gem file rather than a tar.gz, and patching rubygem sources has never worked. It might be worth fixing this in general, or perhaps packaging minitar from GitHub rather

Re: [PATCH 0/1] Help wanted fixing a ruby-minitar bug

Hi Leo, On 25/01/17 07:40, Ludovic Courtès wrote: Leo Famulari skribis: I tried using this patch to fix a bug in ruby-minitar, but the build fails as shown below. Any ideas? $ ./pre-inst-env guix build ruby-minitar The following derivations will be built: /gnu/store/naprvm320mvzlhv4ciax

Re: Fwd: 16/35: gnu: r-ggplot2: Update to 2.2.0.

On 23/01/17 21:42, Ricardo Wurmus wrote: Ben Woodcroft writes: [..] I wonder if the importer could import the previous version again and compare to those, rather than just the current definition to avoid other situations like this. Would this have helped in this instance? Did the previous

Re: Fwd: 16/35: gnu: r-ggplot2: Update to 2.2.0.

On 23/01/17 18:57, Ricardo Wurmus wrote: Ben Woodcroft writes: Forwarded Message Subject:16/35: gnu: r-ggplot2: Update to 2.2.0. Date: Thu, 29 Dec 2016 20:49:25 + (UTC) From: Ricardo Wurmus Reply-To: Ricardo Wurmus To: guix-comm...@gnu.org

Fwd: 16/35: gnu: r-ggplot2: Update to 2.2.0.

Hi Ricardo, Forwarded Message Subject:16/35: gnu: r-ggplot2: Update to 2.2.0. Date: Thu, 29 Dec 2016 20:49:25 + (UTC) From: Ricardo Wurmus Reply-To: Ricardo Wurmus To: guix-comm...@gnu.org rekado pushed a commit to branch master in repository gui

Re: GitHub updater broken?

Hi Ludo, On 11/01/17 00:37, Ludovic Courtès wrote: Hi Ben, The GitHub updater always returns 403 (“Forbidden”) now. I tried passing a token and that didn’t help, but maybe I did not check the right boxes at . Any idea what can be done about it? It se

Re: [PATCH 09/96] gnu: Add camlzip

On 09/01/17 03:40, Julien Lepiller wrote: On Sun, 8 Jan 2017 22:16:05 +1000 Ben Woodcroft wrote: Hi Julien, Thanks for all your efforts in this patch series - impressive stuff, and thanks to David for reviewing them. On 04/01/17 05:10, Julien Lepiller wrote: [...] +(arguments

Re: [PATCH 09/96] gnu: Add camlzip

ution is necessary? I have a downstream OCaml package (pplacer) which is failing to compile because of it (though with OCaml 4.01.0). I've attached my unpolished, convoluted patch series to get to pplacer, for reference. Thanks, ben. >From 8151b508dc3550bde6ad00d9997f16673999b5b2 Mon Sep 1

Re: Cross-distro reproducible build patches

Hi, On 05/01/17 19:00, Ludovic Courtès wrote: Hello Guix! A new initiative to share repro-build patches has started as a followup to the Reproducible Build Summit: http://lists.reproducible-builds.org/pipermail/rb-general/2017-January/000222.html https://github.com/distropatches/reprod

Re: Ruby 2.4.0 update

Hi Marius, On 26/12/16 23:18, Ben Woodcroft wrote: On 26/12/16 03:09, Marius Bakke wrote: In good tradition, ruby made a new release today (25/12)[0]. I tried building some packages with the new version, but ruby-minitest complains that Rake 12 is too new (even with the latest minitest

Re: 77 Rust Crates, fluid, roboto-font, libpsyc rust bindings

Lotsa packages, nice. On 04/01/17 09:35, ng0 wrote: [...] I have not run any of the 81 packages through guix lint, I would if I would know a way to mass lint a list of packages. How about using parallel? $ cat list_of_packages |parallel -j1 guix lint ben

Re: [PATCH 4/4] gnu: ocaml-findlib: Update to 1.7.1.

uot; (string-append destdir "/ld.conf")) #t)) I've been preparing a few ocaml packages, and it is getting to the point that it might be worth adding an ocaml-build-system, much like gnu-build-system except perhaps with a few tweaks such as the above (prelimin

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

Hi Raoul, On 28/12/16 23:13, Ra wrote: 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 ? I just pushed an update to 0.9

Re: Per-package updaters?

Hi Ricardo, On 27/12/16 01:00, Ricardo Wurmus wrote: Hi Guix, we have a couple of generic package updaters (CPAN, CRAN, Bioconductor, Github, GNU, etc), but they don’t nearly cover all of our packages. I wonder if we should add one-off updaters for individual packages that don’t fall into any

Re: Ruby 2.4.0 update

Thanks Marius, an enjoyable xmas read of all the new features it was. On 26/12/16 03:09, Marius Bakke wrote: In good tradition, ruby made a new release today (25/12)[0]. I tried building some packages with the new version, but ruby-minitest complains that Rake 12 is too new (even with the late

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

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 w

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

ar are in the attached patch. Thanks, ben. >From d1c70ba0a701a31469dcae2b1a0efb624e5409d1 Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Fri, 23 Dec 2016 22:13:33 +1000 Subject: [PATCH] gnu: multiqc: Update to 0.9. * gnu/packages/bioinformatics.scm (multiqc): Update to 0.9. [origin]: Add patch.

Re: [PATCH] gnu: Add python-xopen.

On 18/12/16 11:00, Tobias Geerinckx-Rice wrote: Marius, On 16/12/16 17:09, Marius Bakke wrote: Pypi archives are sometimes smaller than the raw sources Oh, I didn't know that. or otherwise "prepared", but I guess no inherent benefits. Good point. I can certainly see people relying too hea

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

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

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

On 17/12/16 23:28, Ben Woodcroft wrote: Hi, On 17/12/16 18:25, Ra wrote: --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) Thanks for the patch. I pushed this as 'c9e9154e993f055a438e2e43518bbd0740aaaf24' after modifying the commit m

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

Hi, On 17/12/16 18:25, Ra wrote: --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) Thanks for the patch. I pushed this as 'c9e9154e993f055a438e2e43518bbd0740aaaf24' after modifying the commit message and removing the extra precompiled binary it i

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

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 a

Re: [PATCH 1/2] gnu: Add r-bit.

On 14/12/16 02:30, Ricardo Wurmus wrote: [..] Okay with these changes. Thanks! Quite right. I made a few more changes to the description and push the series ending in 'ce3f92e7018e140f5e6b7333a604f26506de6c2a'. Thanks for the prompt review. ben

[PATCH 1/2] gnu: Add r-bit.

* gnu/packages/statistics.scm (r-bit): 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 36f1889ef..ea9ef0e39 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/

[PATCH 2/2] gnu: Add r-bit64.

* gnu/packages/statistics.scm (r-bit64): New variable. --- gnu/packages/statistics.scm | 26 ++ 1 file changed, 26 insertions(+) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index ea9ef0e39..8af94e6af 100644 --- a/gnu/packages/statistics.scm +++ b

Re: [PATCH 0/1] Update pardre source hash.

On 09/12/16 00:45, Marius Bakke wrote: Ricardo Wurmus writes: Marius Bakke writes: Ben Woodcroft writes: Hi, It seems that the pardre source has been updated in place. I'm not sure what the procedure is for verifying that nothing untoward has taken place, since I cannot downloa

Re: ruby-sdoc failing on staging

On 10/12/16 02:44, Ludovic Courtès wrote: Leo Famulari skribis: There are several Ruby packages failing to build on the staging branch: https://hydra.gnu.org/eval/109387?compare=master#tabs-now-fail Fixed in d99ee3d923b822828394167b51a1178ec0996a27! Thanks Ludo. I updated ruby-sdoc and f

[PATCH] gnu: pardre: Update source hash.

* gnu/packages/bioinformatics.scm (pardre)[source]: Update hash. --- gnu/packages/bioinformatics.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 625935dfd..eac42e7ac 100644 --- a/gnu/packages/bioinforma

[PATCH 0/1] Update pardre source hash.

Hi, It seems that the pardre source has been updated in place. I'm not sure what the procedure is for verifying that nothing untoward has taken place, since I cannot download and old version from the hydra content addressed mirror - it does not seem to exist there either. So I just assume all is

[PATCH 1/4] gnu: Add perl-time-piece.

* gnu/packages/perl.scm (perl-time-piece): New variable. --- gnu/packages/perl.scm | 22 ++ 1 file changed, 22 insertions(+) diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm index 6b4370d..55982ab 100644 --- a/gnu/packages/perl.scm +++ b/gnu/packages/perl.scm @@ -716

[PATCH 3/4] gnu: Add barrnap.

* gnu/packages/bioinformatics.scm (barrnap): New variable. --- gnu/packages/bioinformatics.scm | 67 + 1 file changed, 67 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 961f0b2..4541791 100644 --- a/gnu/pa

[PATCH 4/4] gnu: Add prokka.

* gnu/packages/bioinformatics.scm (prokka): New variable. --- gnu/packages/bioinformatics.scm | 110 1 file changed, 110 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 4541791..c4f421c 100644 --- a/gnu/pa

[PATCH 2/4] gnu: Add ncbi-tools.

* gnu/packages/bioinformatics.scm (ncbi-tools): New variable. --- gnu/packages/bioinformatics.scm | 62 + 1 file changed, 62 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 415024f..961f0b2 100644 --- a/gnu

Re: [PATCH] gnu: Add newick-utils.

On 27/11/16 19:29, Marius Bakke wrote: Ben Woodcroft writes: * gnu/packages/bioinformatics.scm (newick-utils): New variable. --- gnu/packages/bioinformatics.scm | 40 1 file changed, 40 insertions(+) LGTM! Thanks, pushed as

[PATCH] gnu: Add newick-utils.

* gnu/packages/bioinformatics.scm (newick-utils): New variable. --- gnu/packages/bioinformatics.scm | 40 1 file changed, 40 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 8d2cb93..f04acc0 100644 --- a/gn

Re: [PATCH] gnu: Add proteinortho.

On 26/11/16 16:11, Leo Famulari wrote: On Sat, Nov 26, 2016 at 03:14:16PM +1000, Ben Woodcroft wrote: * gnu/packages/bioinformatics.scm (proteinortho): New variable. LGTM Pushed, thanks for the quick review.

[PATCH] gnu: Add proteinortho.

* gnu/packages/bioinformatics.scm (proteinortho): New variable. --- gnu/packages/bioinformatics.scm | 52 + 1 file changed, 52 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 773b590..31e9533 100644 --- a/g

Re: [PATCH 09/18] gnu: Add r-wgcna.

On 25/11/16 02:51, Ricardo Wurmus wrote: [..] +(home-page + "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/";) This line is a bit long, I don't remember, should it be split over two lines? +(synopsis "Weighted correlation network analysis") +

Re: [PATCH] gnu: ruby: Replace with 2.3.2 [fixes CVE-2015-3900].

On 20/11/16 01:28, Leo Famulari wrote: On Sat, Nov 19, 2016 at 09:32:09AM +1000, Ben Woodcroft wrote: * gnu/packages/ruby.scm (ruby)[replacement]: New field. (ruby-2.3.2): New variable. --- gnu/packages/ruby.scm | 20 1 file changed, 20 insertions(+) diff --git a/gnu

Re: Guix on clusters and in HPC

Hi Ludo, I hope the proposal is/was working out. On 03/11/16 23:44, Ludovic Courtès wrote: Hi! Ben Woodcroft skribis: I'm a little late here, but please do all of the things on that list :) :-) With this suggestion: + for [[https://lists.gnu.org/archive/html/guix-devel/20

Re: [PATCH] gnu: ruby-net-http-digest-auth: Add new package

Hi Frederick, On 17/11/16 21:47, Frederick Muriithi wrote: On 17 Nov 2016 1:56 p.m., "Ben Woodcroft" wrote: Hi Frederick, thanks for the updated patch. I didn't see any functional issues with this patch, but I had some trouble testing this out - can I ask how to test it?

[PATCH] gnu: ruby: Replace with 2.3.2 [fixes CVE-2015-3900].

* gnu/packages/ruby.scm (ruby)[replacement]: New field. (ruby-2.3.2): New variable. --- gnu/packages/ruby.scm | 20 1 file changed, 20 insertions(+) diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm index e4c1ef0..f2b5de9 100644 --- a/gnu/packages/ruby.scm +++ b/gnu/

[PATCH 0/1]: Replace ruby with ruby-2.3.2.

Hi there, Ruby 2.3.2 was just released, and since it entails >300 rebuilds it is a good candidate for staging I think. I do not know of an easy way to check exactly which security fixes have been applied beyond text searching the CHANGELOG, which isn't optimal so I believe there are other fixes t

Re: [PATCH] gnu: ruby-net-http-digest-auth: Add new package

Hi Frederick, thanks for the updated patch. I didn't see any functional issues with this patch, but I had some trouble testing this out - can I ask how to test it? My problem was simply that I didn't know of a http-only server with this authentication method. I ask because the last commit to t

Re: Guix on clusters and in HPC

On 26/10/16 21:51, Ludovic Courtès wrote: Ricardo Wurmus skribis: Ludovic Courtès writes: What they suggest is to add Guix support simply by using Guix inside of Docker… Obviously, I’m not a fan of this because of how inelegant this all seems. When it comes to bringing Guix to Galaxy I thi

Re: Guix on clusters and in HPC

Hi, I'm a little late here, but please do all of the things on that list :) With this suggestion: + for [[https://lists.gnu.org/archive/html/guix-devel/2016-10/msg5.html][CPU-specific optimizations]] + somehow support -mtune=native (and even profile-guided optimizations?)

Re: CPU-specific builds

is ignored, is that unexpected? 2) Is something amiss with gcc-toolchain-6? Compiling with it, diamond complains of a missing stdlib.h. Thanks, ben ;;; Copyright © 2016 Ben Woodcroft ;;; ;;; This code is free software; you can redistribute it and/or modify it ;;; under the terms of the

CPU-specific builds

Hi, Currently, we build a single set of x86_64 packages assuming SSE but not SSE2 instructions, but sometimes it would be nice to use more recent instructions like AVX. So I'm wondering if there is some way to specify a system more specific than 'X86_64'? I tried simply adding '--with-arch=ha

Re: Ruby / OpenSSL security issue

On 01/10/16 03:32, Leo Famulari wrote: On Wed, Sep 21, 2016 at 11:19:45AM +1000, Ben Woodcroft wrote: On 21/09/16 05:05, Leo Famulari wrote: On Tue, Sep 20, 2016 at 03:17:42PM +1000, Ben Woodcroft wrote: On 20/09/16 12:06, Leo Famulari wrote: Ruby users, There is a bug report on Ruby&#

Re: [PATCH 2/3] gnu: Add python-pyxb.

On 27/09/16 04:32, Marius Bakke wrote: Ben Woodcroft writes: On 24/09/16 13:15, Marius Bakke wrote: Ben Woodcroft writes: Htslib is propagated because it is included by the installed samtools and bcftools headers; at least one of pysams dependencies failed to build when it was a regular

Re: [PATCH 2/3] gnu: Add python-pyxb.

On 24/09/16 13:15, Marius Bakke wrote: Ben Woodcroft writes: Htslib is propagated because it is included by the installed samtools and bcftools headers; at least one of pysams dependencies failed to build when it was a regular input. Ah, I see. Can this be avoided with patchelf? I don&#

Re: [PATCH 2/2] gnu: perl: Enable threading support.

On 24/09/16 15:05, Ludovic Courtès wrote: Ben Woodcroft skribis: * gnu/packages/perl.scm (perl)[arguments]: Enable threading support. * gnu/packages/commencement.scm (perl-boot0): Do not inherit 'configure' phase from perl. [...] "-Uin

Re: [PATCH 2/3] gnu: Add python-pyxb.

On 24/09/16 01:56, Marius Bakke wrote: Ben Woodcroft writes: Also, I notice that pysam bundles htslib, bcftools and samtools C code. Hopefully it should be straightforward enough to remove htslib as there are install instructions, I'm not sure about the other two. This shouldn't

Re: [PATCH 2/3] gnu: Add python-pyxb.

On 09/23/2016 01:15 AM, Marius Bakke wrote: Ben Woodcroft writes: Subject: [PATCH 1/3] gnu: python-pysam: Update to 0.9.1.4. I'm not sure whether this is a product of the upgrade or not, but I notice this in the build log. I think it is harmless though, WDYT? starting phase `val

Re: Definite article in synopsis

On 09/23/2016 10:15 AM, Leo Famulari wrote: On Wed, Sep 21, 2016 at 12:59:51PM +0200, John Darrington wrote: I thought we had a policy that the synopsis field must not start with an article. However running grep 'synopsis *"The' *.scm shows that we have many instances where this po

Re: Writing recipe for Crypto++, and getting build errors

Hi, On 09/23/2016 12:49 AM, Adonay Felipe Nogueira wrote: I tried your suggestions, and the unpack phase doesn't seem to be working as expected. Inspecting **all** the directories created with --keep-failed shows that the "source" directory wasn't made. I believe the problem now is the snippet,

Re: Writing recipe for Crypto++, and getting build errors

On 09/22/2016 11:18 AM, Ben Woodcroft wrote: Welcome Adoney, Also, I forgot to say, make sure to remove the "-mtune=native" flag from the gcc calls, and there is no need to set 'gcc' as an input if you are using the gnu-build-system. ben

Re: Writing recipe for Crypto++, and getting build errors

Welcome Adoney, On 09/22/2016 01:24 AM, Adonay Felipe Nogueira wrote: [..] Doing: $ guix build --fallback "cryptopp" ... outputs: # Begin of output starting phase `build' make: *** No rule to make target 'dynamic'. Stop. phase `build' failed after 0.2 seconds builder for `/gnu/store/k863vf0

Re: [PATCH 2/3] gnu: Add python-pyxb.

On 22/09/16 07:14, Marius Bakke wrote: [..] Hi Ben, Thanks for the review. Updated patches attached. Hi, Subject: [PATCH 1/3] gnu: python-pysam: Update to 0.9.1.4. I'm not sure whether this is a product of the upgrade or not, but I notice this in the build log. I think it is harmless though

Re: Ruby / OpenSSL security issue

On 21/09/16 05:05, Leo Famulari wrote: On Tue, Sep 20, 2016 at 03:17:42PM +1000, Ben Woodcroft wrote: On 20/09/16 12:06, Leo Famulari wrote: Ruby users, There is a bug report on Ruby's OpenSSL module regarding IV re-use in AES-GCM mode [0]. Does anyone volunteer to investigate the bug r

Re: [PATCH 2/3] gnu: Add python-pyxb.

Hi again, On 20/09/16 16:34, Ben Woodcroft wrote: Oops, forgot to cc the list. On 20/09/16 16:02, Ben Woodcroft wrote: Hi Marius, Thanks for the patches. On 17/09/16 20:10, Marius Bakke wrote: [..] + (add-after 'unpack 'fix-tests + (lambda _ + ;;

Re: [PATCH 2/3] gnu: Add python-pyxb.

Oops, forgot to cc the list. On 20/09/16 16:02, Ben Woodcroft wrote: Hi Marius, Thanks for the patches. On 17/09/16 20:10, Marius Bakke wrote: [..] + (add-after 'unpack 'fix-tests + (lambda _ + ;; See https://github.com/pabigot/pyxb

Re: Ruby / OpenSSL security issue

On 20/09/16 12:06, Leo Famulari wrote: Ruby users, There is a bug report on Ruby's OpenSSL module regarding IV re-use in AES-GCM mode [0]. Does anyone volunteer to investigate the bug report and decide what to do about it for our Ruby package? Thanks for the report Leo. I don't think much

[PATCH 1/2] gnu: perl: Split configure phase.

* gnu/packages/perl.scm (perl)[arguments]: Split 'configure' phase into 'setup-configure' and 'configure' phases. --- gnu/packages/perl.scm | 24 +--- 1 file changed, 13 insertions(+), 11 deletions(-) diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm index 0a26e51..f0

[PATCH 0/2] Perl: Enable threading support.

Hi, I found that our Perl was giving "Error: This Perl not built to support threads" when trying to use threads. I added '-Dusethreads' to the configure phase, but had to copy across the old configure phase to the inheriting 'perl-boot0' where we cannot use threads as pthreads is apparently unava

[PATCH 2/2] gnu: perl: Enable threading support.

012 Nikita Karetnikov ;;; Copyright © 2014, 2015 Mark H Weaver +;;; Copyright © 2016 Ben Woodcroft ;;; ;;; This file is part of GNU Guix. ;;; @@ -269,24 +270,44 @@ (package-native-inputs gcc)) (define perl-boot0 - (let ((perl (package -(in

Re: [PATCH] gnu: Add python-cachecontrol.

Hi Marius, thanks for the patch. I added a 'python2-variant' line and pushed as 'b30565b'. The thing is, the list has already seen this package before, in this thread where I tried packaging scikit-bio (I suspect you are trying to do the same): https://lists.gnu.org/archive/html/guix-devel/20

Re: [PATCH] gnu: Add seqtk.

On 09/09/16 22:37, Marius Bakke wrote: Ben Woodcroft writes: Well, despite the lightness of my touch, it seems the licensing is in now in order. I've updated the package, here's an updated patch. Better? I don't think this was intended to be a commit message? :) N

Re: R

On 08/09/16 23:02, Ricardo Wurmus wrote: Ben Woodcroft writes: Hi, I thought I'd respond to this old thread now that the openblas eigen error seems to be fixed. I'm interested in using openblas so that the (as yet not in master) WGCNA package works faster, among other thin

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