7bc4454a90d2c Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus
Date: Sat, 23 May 2015 14:06:17 +0200
Subject: [PATCH 1/3] gnu: Add GCR.
* gnu/packages/gnome.scm (gcr): New variable.
---
gnu/packages/gnome.scm | 45 +
1 file changed, 45 insertions(+)
diff --
Alexander Shendi writes:
> Googling I realized that this was CUPS' way to tell me it could not write to
> the spool directory
> or the log files.
> Indeed I found the following lines in /var/log/messages.
>
> May 26 05:26:13 localhost cupsd: Unable to change ownership of
> "/gnu/store/543kjj82r
>> From 9243823abad3943bd3f4ebe4f6d18cc53c2143e0 Mon Sep 17 00:00:00 2001
>> From: Ricardo Wurmus
>> Date: Thu, 21 May 2015 15:24:11 +0200
>> Subject: [PATCH] gnu: python-ipython: Add optional dependencies.
>>
>> * gnu/packages/python.scm (python-ipython
Hi Guix,
attached is a patch for "Entrez Direct" a tool for accessing the vast
online databases of NCBI.
>From 1808a6000260418ce7a3433cb75e904b854fcc53 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus
Date: Wed, 27 May 2015 15:14:19 +0200
Subject: [PATCH] gnu: Add edirect.
*
Federico Beffa writes:
> Out of curiosity, could you outline how OpenBLAS is optimized for a
> specific CPU architecture while being compiled on a different CPU (and
> hence allowing to be substituted)?
The Quick Install instructions[1] say that when OpenBLAS is compiled
with DYNAMIC_ARCH=1
>From bbd4a72d89762f93816cfe4ed917c55ffe19bac8 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus
Date: Thu, 28 May 2015 15:53:14 +0200
Subject: [PATCH] gnu: Add libsvm.
* gnu/packages/machine-learning.scm: New file.
* gnu-system.am (GNU_SYSTEM_MODULES): Add it.
---
gnu-system
>> + (uri (string-append
>> + "https://github.com/cjlin1/libsvm/archive/v";
>> + (string-join (string-split version #\.) "") ".tar.gz"))
>
> (string-delete #\. version)
Oh, that's better, indeed!
> Also, please add a 'file-name' field so that the source filename in
> 6. Build package: ./pre-inst-env.in guix build ipcalc -K
This is wrong. "./pre-inst-env.in" is a template that is used to
produce the script "./pre-inst-env" at build time. If you do not have
"./pre-inst-env" you probably have not actually built Guix yet.
~~ Ricardo
hould thus fix the build
of sra-tools on i686.
>From 6d3e22354c767f76711e3f73a2e26d7d7783f57a Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus
Date: Mon, 1 Jun 2015 11:31:29 +0200
Subject: [PATCH] gnu: ncbi-vdb: Use "i386" instead of "i686" in directory
name.
* gnu/package
>From 708093dc001d46a2ec487873e8150861b05872da Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus
Date: Mon, 1 Jun 2015 15:06:04 +0200
Subject: [PATCH] gnu: Add HTSlib.
* gnu/packages/bioinformatics.scm (htslib): New variable.
---
gnu/packages/bioinformatics.scm |
Ricardo Wurmus writes:
> python-numpy currently depends on Atlas, which means that it cannot be
> substituted with a binary built elsewhere. OpenBLAS is an alternative
> to Atlas and the binary can be used on all supported CPUs at runtime.
> This makes it possible for us t
> We should aim to blur the distinction between developers and users, and
> I think we have the right technical environment for that
> (“configuration” files that happen to actually be Scheme, “package
> recipes” that happen to be Scheme as well, etc.) So I’m in favor of
> keeping the technical in
>From 66133f87b988417ba9207ac5d101a94a7ed601b4 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus
Date: Tue, 2 Jun 2015 16:35:23 +0200
Subject: [PATCH 1/2] gnu: Add IO::String.
* gnu/packages/perl.scm (perl-io-string): New variable.
---
gnu/packages/perl.scm | 19 +++
1 file chan
uot;.
>
> My apologies for the confusion! I'll send an updated patch soon.
Attached are two patches for libsvm and python-libsvm (only available
for Python 3), taking the comments into consideration.
>From 6a17d83d4bc2512f8089477e70c485e9ca93377a Mon Sep 17 00:00:00 2001
From: Ri
>From d4f171912387304e61f2536a2eb167c7321e7663 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus
Date: Tue, 2 Jun 2015 15:47:22 +0200
Subject: [PATCH 1/2] gnu: Add randomjungle.
* gnu/packages/machine-learning.scm (randomjungle): New variable.
---
gnu/packages/machine-learning.scm |
>From e8cffdb9e7a2447657b3f700b2f0beb00ad0f98e Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus
Date: Wed, 3 Jun 2015 17:44:20 +0200
Subject: [PATCH] gnu: Add BioPerl.
* gnu/packages/bioinformatics.scm (bioperl-minimal): New variable.
---
gnu/packages/bioinformatics.scm |
>>> We currently do not have a working OpenBLAS on MIPS, so the attached
>>> patch selects OpenBLAS as an input only when not on MIPS. Some
>>> additional configuration happens only unless "atlas" is among the
>>> inputs.
>>
>> If there are no objections I'd like to go ahead and push this patch t
>From da77c25e8c32243ca2bd77bd76de41312aafaac1 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus
Date: Mon, 25 May 2015 22:13:27 +0200
Subject: [PATCH 1/6] gnu: Add withershins.
* gnu/packages/code.scm (withershins): New variable.
---
gnu/packages/code.scm |
Ludovic Courtès writes:
> Ricardo Wurmus skribis:
>
>> From e8cffdb9e7a2447657b3f700b2f0beb00ad0f98e Mon Sep 17 00:00:00 2001
>> From: Ricardo Wurmus
>> Date: Wed, 3 Jun 2015 17:44:20 +0200
>> Subject: [PATCH] gnu: Add BioPerl.
>>
>> * gnu/packages
The attached patch removes icedtea6 from the inputs of icedtea7.
IcedTea7 can now be built with just GCJ.
>From d4c04d81e4c8b43636e5f9adb279e8ef6a0b8752 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus
Date: Tue, 9 Jun 2015 12:53:23 +0200
Subject: [PATCH] gnu: icedtea7: Bootstrap with GCJ.
*
rfM.
* gnu/packages/bioinformatics.scm (orfm): New variable.
Signed-off-by: Ricardo Wurmus
---
gnu/packages/bioinformatics.scm | 21 +
1 file changed, 21 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 8d59768..55b2ff6 100644
--
python-scipy use
OpenBLAS and Lapack instead of ATLAS.
The final patch replaces "atlas" with "openblas" in the
python-scikit-learn package definition.
~~ Ricardo
>From aeb4f541486d5bb02d4002380e8f7be49967b10d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus
Date: Fri, 12
>From 0026435cc8c1c4eea0c616a55ff54c6421cd6756 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus
Date: Fri, 12 Jun 2015 15:39:40 +0200
Subject: [PATCH] gnu: python-scikit-learn: Update to 0.16.1.
* gnu/packages/python.scm (python-scikit-learn): Update to 0.16.1.
---
gnu/packages/python.scm
Ludovic Courtès writes:
> Ricardo Wurmus skribis:
>
>> From da77c25e8c32243ca2bd77bd76de41312aafaac1 Mon Sep 17 00:00:00 2001
>> From: Ricardo Wurmus
>> Date: Mon, 25 May 2015 22:13:27 +0200
>> Subject: [PATCH 1/6] gnu: Add withershins.
>>
>>
Hi Ben,
> $ guix import pypi GroopM
[...]
> ERROR: In procedure scm-error:
> ERROR: no code for module (json)
This means that guile-json cannot be found. It is needed to parse the
JSON metadata for a given Python module.
You initially installed guix with the binary tarball method, did you
not
>From 612b8503d5b473f8a7416b0b9c9287102fa72bb8 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus
Date: Sat, 13 Jun 2015 19:53:48 +0200
Subject: [PATCH] gnu: Add Qsynth.
* gnu/packages/audio.scm (qsynth): New variable.
---
gnu/packages/audio.scm | 23 +++
1 file changed,
>From 20497fda2366acbce8314588d4871fff3b4621f0 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus
Date: Sun, 14 Jun 2015 10:04:50 +0200
Subject: [PATCH] gnu: lv2: Update to 1.12.0.
* gnu/packages/audio.scm (lv2): Update to 1.12.0.
---
gnu/packages/audio.scm | 6 +++---
1 file changed, 3 inserti
>From 14a14d312198f4c3a0cac7c308c925b35a80c5cd Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus
Date: Sun, 14 Jun 2015 10:05:38 +0200
Subject: [PATCH] gnu: Add Raul.
* gnu/packages/audio.scm (raul): New variable.
---
gnu/packages/audio.scm | 27 +++
1 file changed,
>From 7d0f4d6702cf6ed370e534862244fb65c414f46d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus
Date: Sun, 14 Jun 2015 15:00:37 +0200
Subject: [PATCH 1/3] gnu: Add Faust.
* gnu/packages/audio.scm (faust): New variable.
---
gnu/packages/audio.scm | 31 +++
1 file chan
Alex Kost writes:
> However I think that a running ssh server is the expected default for
> '%desktop-services'.
l...@gnu.org (Ludovic Courtès) writes:
> However, the idea was that ‘%desktop-services’ would provide you the
> typical set of services you get by default when installing another
> “de
Pjotr Prins writes:
> Is there a way guix could quickly print out the information it now gives after
> a successful package install:
>
> The following environment variable definitions may be needed:
>export
> PATH="/home/pjotrp/.guix-profile/bin:/home/pjotrp/.guix-profile/sbin"
>export
Ludovic Courtès writes:
> Ricardo Wurmus skribis:
>
>> attached are three more patches to replace ATLAS with OpenBLAS in
>> python.scm.
[...]
>> From 79d29126037cd227b01b3a193bf016ec9e12b4fb Mon Sep 17 00:00:00 2001
>> From: Ricardo Wurmus
>> Date: Fri, 1
>From 815a5e24f43f61c4beb243d98beb0659bbd74b3a Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus
Date: Tue, 16 Jun 2015 11:33:26 +0200
Subject: [PATCH] gnu: Add idr.
* gnu/packages/bioinformatics.scm (idr): New variable.
---
gnu/packages/bioinformatics.scm |
> in a package for AUCTeX that I'm preparing, I'm trying to replace any
> reference to '/bin/sh' in '.el' files with
>
> (with-directory-excursion el-dir
> (substitute* (find-files "." "\\.el$") (("/bin/sh") (which "sh"
>
> A particular file causes Guile to produce the following error:
>
>From 81cbb9bfa523d56c68d5f9f4feed3676edb5a414 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus
Date: Tue, 16 Jun 2015 16:24:24 +0200
Subject: [PATCH] gnu: Add Blast+.
* gnu/packages/bioinformatics.scm (blast+): New variable.
---
gnu/packages/bioinformatics.scm |
he protocol of the tarball URL from http to
https; pypi redirects to https.
~~ Ricardo
>From b8c6ece9d658969a0ce8054e368df96ce293c30f Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus
Date: Wed, 17 Jun 2015 12:14:39 +0200
Subject: [PATCH 1/2] gnu: miso: Install executables.
* gnu/packages/bioinfo
they are
> listed as ‘native-inputs’.
>
> Should it instead explicitly list SciPy, NumPy, and Matplotlib?
You are right. Is the attached patch better?
>From 37db5b51fe4a09496e149d59b64aa0b69ae42fd1 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus
Date: Tue, 16 Jun 2015 11
t that
includes the native-input "perl-test-most" and the paths to its
dependencies. I don't know how to do this nicely in any other way,
though, because I need not only the direct inputs to be in this list of
paths, but also their propagated inputs.
Is there a better way to make sure
;Guitarix is a virtual guitar amplifier running JACK.")
>
> Could you expound a bit, for instance using the second paragraph on the
> web page?
Done. Attached is a new patch.
Thanks!
~~ Ricardo
>From 444196dc501dad2ee793d5b1a20116fee799fb2f Mon Sep 17 00:00:00 2001
From:
Alex Kost writes:
> Ricardo Wurmus (2015-06-14 19:25 +0300) wrote:
>
> [...]
>> +(synopsis "Real-time audio utility library")
>> +(description
>> + "Raul (Real-time Audio Utility Library) is a C++ utility library
>> primarily
>
David Hashe writes:
> * gnu/packages/gnome.scm (rhythmbox): New variable.
[...]
> +(define-public rhythmbox
> + (package
> + (name "rhythmbox")
> + (version "3.2.1")
> + (source (origin
> +(method url-fetch)
> +(uri (string-append "mirror://gnome/sources/rhythmbox
Attached is a patch for an organ emulation. As I built it I noticed
that ftgl should propagate its input “freetype” as its pkg-config file
contains this line:
Requires.private: freetype2
>From 00bd892e00e2f8d1261f4fffaf2a9ba31d5961e8 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus
Date:
Cook, Malcolm writes:
> Can anyone elaborate a little on what are the obstacles to having
> `/gnu` mounted read-write network wide?
Yes, the primary problem is that the daemon assumes that it is the only
thing writing to the store and the localstatedir. Any modification of
profiles and the sto
> +(define-public hmmer
> + (package
> +(name "hmmer")
> +(version "3.1b2")
> +(source (origin
> + (method url-fetch)
> + (uri (string-append
> +"http://selab.janelia.org/software/hmmer3/3.1b2/hmmer-";
> + version ".tar.gz"
Pjotr Prins writes:
> It is quite common in bioinformatics tools to include foreign code.
> One reason in favour of including the original setup that is it is
> THAT what the authors and others test and run. Bringing in our own
> dependencies is bound to open a can of worms - there often is a re
bapi/driver/odbc/unix_odbc/
* ASL 2.0:
* ncbi-blast-2.2.30+-src/c++/src/corelib/teamcity_*
I could not find mention of any other licenses. Is this correct, then:
;; Most of the sources are in the public domain, with the following
exceptions:
;; ...(the above list)...
(license (list
>From 7e0352fad776f1c491882647ee3ad5f5319e1164 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus
Date: Tue, 23 Jun 2015 10:54:00 +0200
Subject: [PATCH] gnu: Add preseq.
* gnu/packages/bioinformatics.scm (preseq): New variable.
---
gnu/packages/bioinformatics.scm |
>From b88c44394c1a6e2e9a5932ac2a3a9b431408c742 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus
Date: Fri, 12 Jun 2015 15:46:40 +0200
Subject: [PATCH 1/2] gnu: Add python2-pysnptools.
* gnu/packages/python.scm (python2-pysnptools): New variable.
---
gnu/packages/python.scm |
Ludovic Courtès writes:
> Don’t hesitate to push non-controversial changes like these after a
> couple of days have passed.
Thank you, I'll do that.
~~ Ricardo
Ludovic Courtès writes:
>> +(propagated-inputs `(("freetype" ,freetype)))
>
> Please explain the reason (Requires.private) in a comment above.
Oh, right.
>> From 0110a38d7c1fcf47ffc5691f97966addd379f50c Mon Sep 17 00:00:00 2001
>> From: Ricardo Wurmus
>From bac01c1b64ed14fc1c26f35961f1c8fd29caabcb Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus
Date: Tue, 23 Jun 2015 21:25:19 +0200
Subject: [PATCH 1/2] gnu: Add sfarklib.
* gnu/packages/compression.scm (sfarklib): New variable.
---
gnu/packages/compression.scm |
Currently, R cannot be built because the default GCC is now 4.9 but R
depends on gfortran 4.8.
These two patches add gfortran-4.9 and update the R package to use it.
>From 6c25bf3435fc690c75ba7bbf2b98c60bf5261cfc Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus
Date: Wed, 24 Jun 2015 11:36
> On Wed, Jun 24, 2015 at 11:40:31AM +0200, Ricardo Wurmus wrote:
>> These two patches add gfortran-4.9 and update the R package to use it.
>
> If it works, this looks like a patch to push.
I successfully built R 3.2.0 on my workstation with these changes
(whereas before the b
> I must reiterate my concern about this approach to the wider
> guix-devel audience. From what I can see, the gem archives hosted on
> rubygems.org are build artifacts and should probably be treated like
> pre-built binaries. They are not the complete, corresponding source
> code. Can anyone e
Ludovic Courtès writes:
> A simple way to test the latter is with ‘socat’, something along the
> lines of what I described at:
>
> https://lists.gnu.org/archive/html/guix-devel/2015-02/msg00680.html
>
> It would be great if you could check whether something like this works
> for you.
>
> Then
Note: this is not PuTTY's plink, but a bioinformatics tool with the same
name.
>From d60d727bd9c2955c70ebf8cd3ee44becab64624e Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus
Date: Thu, 25 Jun 2015 12:04:05 +0200
Subject: [PATCH] gnu: Add plink.
* gnu/packages/bioinformatics.scm (pli
Forgot to add the patch this recipe is referring to. New patch
attached.
>From 85811f556f0db843f2c699465d317c10d4e85807 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus
Date: Thu, 25 Jun 2015 12:04:05 +0200
Subject: [PATCH] gnu: Add plink.
* gnu/packages/bioinformatics.scm (plink): New varia
Ludovic Courtès writes:
> Cyril Roelandt skribis:
>
>> +(define (run-shell shell env-name)
>> + "Run the given SHELL, adding '(ENV-NAME) ' at the start of the prompt."
>> + (cond ((string=? shell "/bin/bash")
>> + (let* ((directory (or (getenv "TMPDIR") "/tmp"))
>> +(t
a hurry to push this.
~~ Ricardo
>From 3ffe6847848f6ba107e0757728f1c6a6e7807d56 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus
Date: Tue, 23 Jun 2015 10:54:00 +0200
Subject: [PATCH] gnu: Add preseq.
* gnu/packages/bioinformatics.scm (preseq): New variable.
---
gnu/packages/
Thompson, David writes:
> On Thu, Jun 25, 2015 at 8:02 AM, Ricardo Wurmus
> wrote:
>>
>> Would it be feasible to give "GUIX_ENVIRONMENT" the package name as a
>> value instead of just "t"?
>
> Not really, because 'guix environment' ac
s all "gfortran-4.x" inputs to just "gfortran".
~~ Ricardo
>From de44275012ad3443b4da463eb1cc4b1c20db9b34 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus
Date: Thu, 25 Jun 2015 17:52:10 +0200
Subject: [PATCH 1/2] gnu: Add default GCC and default gfortran.
* gnu/packages/gcc.scm (
Thompson, David writes:
> This will work against our goals. It will create a lot of duplicated
> files which will eat up extra disk space and make it difficult to
> apply security patches. The job of a distribution is to deduplicate,
> not bundle. Furthermore, it will cover up the lack of su
Ludovic Courtès writes:
> Eric Bavier skribis:
>
>> I think the convention would be to collapse the files references, and
>> just list the variables, e.g.:
>>
>> * gnu/packages/maths.scm (arpack-ng, lapack, petsc, superlu)
>> (superlu-dist, openblas, openspecfun, atlas)[inputs]: Likewise.
>>
> Updated patch attached.
So, I applied the patch, built rhythmbox, and installed it into a
separate profile. It starts up fine and begins importing files from
~/Music but I get a *lot* of import errors:
“Couldn’t create ‘uridecodebin’ element”
I see this for a great many ogg and mp3 files i
>From 0039b2d36f77d19c92e07e02c7b3e829c485f355 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus
Date: Sat, 27 Jun 2015 11:45:01 +0200
Subject: [PATCH] gnu: Add libtar.
* gnu/packages/compression.scm (libtar): New variable.
---
gnu/packages/compression.scm | 21 +
1 file chan
GCC 4.8.4 is the last GCC containing libiberty.a. The attached patch
adds a package generator that creates a libiberty package for a given
GCC package. It also adds a libiberty package for the default “gcc”.
>From 848a6b91a48abcfdc2eb0d9bbde6a0f22b019090 Mon Sep 17 00:00:00 2001
From: Rica
Hi Ben,
> Oops, now all lines <= 80 chars.
looks good to me, except for the synopsis:
> +(synopsis "Protein-coding gene prediction for Archaea and Bacteria")
Shouldn’t “Archaea” and “Bacteria” both be lower-cased?
~~ Ricardo
Hi again,
another thing just occurred to me. Instead of replacing the install
phase you might just overwrite the INSTALLDIR variable, something like
this:
#:make-flags (list (string-append "INSTALLDIR="
(assoc-ref %outputs "out")))
What do you think?
~
Ben Woodcroft writes:
> 2.2.31+ just got released, maybe upgrade first?
Ah, good to know. I’ll build the latest version on Monday and push that
if there are no further objections.
~~ Ricardo
This patch depends on my previous patch adding a separate “libiberty”
package.
>From 8f6dd7a290d32b154cc353b69373d5a0225d88e5 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus
Date: Sun, 28 Jun 2015 10:22:45 +0200
Subject: [PATCH] gnu: withershins: Use new "libiberty" package.
*
>> +(synopsis "Collection of subroutines used by various GNU programs")))
>
> Maybe add a short description.
Okay.
>> +(define-public libiberty
>> + (make-libiberty gcc))
>
> s/gcc/gcc-4.8/ if 4.8 is the last package installing it.
I wanted to provide a default libiberty package for the def
> OK with these changes!
Thanks for the review. I updated the descriptions and pushed them.
~~ Ricardo
+(define-public libiberty
+ (make-libiberty gcc))
>>>
>>> s/gcc/gcc-4.8/ if 4.8 is the last package installing it.
>>
>> I wanted to provide a default libiberty package for the default “gcc”.
>> Otherwise any change to the default GCC version would require packages
>> to update their li
>> Following the GCC version automatically dependent on whatever value the
>> variable "gcc" has is just a bonus to simplify upgrades to the default
>> version of GCC (as the recent move from 4.8 to 4.9).
>
> I don’t get it. If we use ‘gcc’ instead of ‘gcc-4.8’, it doesn’t work,
> because ‘gcc’ is
Hi Guix,
there are two things related to the installation of Python modules that
I would like to see changed; but as I may not understand what side
effects the proposed changes might have I'd like to gather some opinions
first.
1) Nosetests
Installing Python modules that have an input "python-no
Mark H Weaver writes:
>> + (snippet
>> + '(begin
>> + ;; Remove bundled bzip2 and zlib
>> + (delete-file-recursively "c++/src/util/compress/bzip2")
>> + (delete-file-recursively "c++/src/util/compress/zlib")
>> +
>From 0362c7d01134a46530f9fe01a477c28fd3ae15ff Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus
Date: Wed, 17 Jun 2015 12:22:19 +0200
Subject: [PATCH] gnu: Add WarpedLMM.
* gnu/packages/bioinformatics.scm (python2-warpedlmm): New variable.
---
gnu/packages/bioinformatics.scm |
>From 795a43bf73a3a3417e095a5f88c48603e2a67ad7 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus
Date: Mon, 29 Jun 2015 18:26:43 +0200
Subject: [PATCH] gnu: Add Hydrogen.
* gnu/packages/music.scm (hydrogen): New variable.
---
gnu/packages/music.scm |
Federico Beffa writes:
>> 2) lib/python$version/site-packages/site.{py,pyc}
>>
>> Another file that frequently causes conflicts is "site.py" (and its
>> compiled cousin). It seems to me that "site.py" doesn't contain any
>> module-specific information and is probably the same for all modules.
Hi,
> * gnu/packages/statistics.scm (r)[arguments]: make and install info files
>
> diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
> index 0b9e081..0dfe25d 100644
> --- a/gnu/packages/statistics.scm
> +++ b/gnu/packages/statistics.scm
> @@ -63,7 +63,23 @@
> 'check
> Attached is a new version that includes support for BAM files, but
> without using the bundled version of samtools. Two patches were
> necessary that I have submitted upstream.
>
> I'm still testing this with a user, and I'm waiting for upstream to
> comment on the patches, so I'm not in a hurry
Ludovic Courtès writes:
>> + (snippet
>> + ;; Remove bundled samtools. Leave the headers.
>> + '(for-each delete-file
>> + (find-files "preseq-master/samtools"
>> + "\\.c$")
>
> Why leave
>From 2d11dfa79d388e409965cda8f05d77b3eafcee86 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus
Date: Sat, 4 Jul 2015 11:11:19 +0200
Subject: [PATCH 1/2] gnu: powertabeditor: Enable tests.
* gnu/packages/music.scm (powertabeditor)[arguments]: Run "pte_tests" in
"check" phas
Alex Kost writes:
> Ricardo is a Master of bioinformatics
Haha! :)
Mark already pushed it. I simply forgot about this patch, my apologies!
~~ Ricardo
c1969e0390674844c85982575c305 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus
Date: Sun, 5 Jul 2015 10:45:15 +0200
Subject: [PATCH] cmake-build-system: Enable BUILD_WITH_INSTALL_RPATH.
* guix/build/cmake-build-system.scm (configure): Set BUILD_WITH_INSTALL_RPATH
to TRUE.
---
guix/build/cmake-build-
>> So, I applied the patch, built rhythmbox, and installed it into a
>> separate profile. It starts up fine and begins importing files from
>> ~/Music but I get a *lot* of import errors:
>>
>>“Couldn’t create ‘uridecodebin’ element”
>>
>> I see this for a great many ogg and mp3 files in my ~/
>From 1f5f4de3da2f8158884116746ed00435a317b6c6 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus
Date: Sun, 5 Jul 2015 19:58:38 +0200
Subject: [PATCH] gnu: Add emacs-pdf-tools.
* gnu/packages/emacs.scm (emacs-pdf-tools): New variable.
---
gnu/packages/emacs.scm |
The attached patch should fix the build of setbfree on MIPS64. The
default value for OPTIMIZATIONS contains flags for x86 systems.
I have not tested this as I don’t have access to a MIPS64 system.
>From 87a5264e54d93cfd84b3c886e2d6ee5fbe69cce7 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus
D
Ludovic Courtès writes:
>> I found that setting BUILD_WITH_INSTALL_RPATH=TRUE helped when the
>> INSTALL_RPATH was also set to contain all inputs, like this:
>>
>> (string-append "-DCMAKE_INSTALL_RPATH="
>> (string-join (map (match-lambda
>>
Attached is a new patch, leaving the optimizations unaltered only on
i686 and x86_64.
>From 50536b6e40eed40822b65aba2c296809e5bfbc1e Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus
Date: Sun, 5 Jul 2015 20:40:56 +0200
Subject: [PATCH] gnu: setbfree: Disable unsupported optimizations on non-
(I failed to send this email out before the one containing a corrected
patch.)
>> + ;; Disable unsupported optimization flags on MIPS64
>> + ,@(if (string-prefix? "mips64" (or (%current-target-system)
>> +(%current-system)))
>
Hi Arun,
> Please find attached patch to add new package 'bwm-ng' to (gnu packages
> admin).
thanks for the patch. I’ve made a couple of cosmetic changes and
removed the list of supported operating systems from the description. I
also moved it from admin.scm to networking.scm where we already
Arun Isaac writes:
>> thanks for the patch. I’ve made a couple of cosmetic changes and
>> removed the list of supported operating systems from the description. I
>> also moved it from admin.scm to networking.scm where we already have a
>> couple of network monitoring packages.
>
> Sure.
>
>> I
gno writes:
> On Mon, 22 Aug 2016 21:39:12 +0200
> Ricardo Wurmus wrote:
>
>> * gnu/packages/lua.scm (lua)[arguments]: Use regular build phase and
>> add make-flags.
>> ---
>> gnu/packages/lua.scm | 10 ++
>> 1 file changed, 6 insertions(+),
Leo Famulari writes:
> On Mon, Aug 22, 2016 at 09:39:18PM +0200, Ricardo Wurmus wrote:
>> * gnu/packages/messaging.scm (prosody): New variable.
>
>> +(inputs
>> + `(("libidn" ,libidn)
>> + ("openssl" ,openssl)
>> +
Ludovic Courtès writes:
> I had the pleasant surprise to be invited to give a talk about Guix at
> the Scheme Workshop in September in Japan:
>
> http://scheme2016.snow-fort.org/
>
> While I was at it, I submitted another talk to the Commercial(!) Users
> of Functional Programming conference,
Ludovic Courtès writes:
> Ricardo Wurmus skribis:
>
>> Ricardo Wurmus writes:
>>
>>> Ludovic Courtès writes:
>>>
>>>> Ricardo Wurmus skribis:
>>>>
>>>>> * guix/import/cran.scm (description->package): R
knx...@onionmail.info writes:
> On https://git.dthompson.us/guix-web.git/blob/HEAD:/README.md
>
> there is a dead link to
> http://media.dthompson.us/mgoblin_media/media_entries/20/Screenshot_from_2014-08-13_180724.png
>
> - so no visible screenshot of the web interface to the GNU Guix package
>
ng0 writes:
> Ricardo Wurmus writes:
>
>> knx...@onionmail.info writes:
>>
>>> On https://git.dthompson.us/guix-web.git/blob/HEAD:/README.md
>>>
>>> there is a dead link to
>>> http://media.dthompson.us/mgoblin_media/media_entries/20
Hi Tobias,
> I tried to package a speech syntesizer framework called WORLD for Guix,
> which I had earlier packaged for Trisquel. The guix build process does
> not find , even if I declared a dependency on libsndfile.
That’s because actually you added pulseaudio, not libsndfile :)
> (define-pub
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