Oops, I've noticed that an unsupported repo was not handled gracefully.
On Thu, Jun 25, 2015 at 8:33 PM, Federico Beffa be...@ieee.org wrote:
Thanks for the review!
I've made the suggested changes, except for the comments below.
On Wed, Jun 24, 2015 at 11:06 PM, Ludovic Courtès l...@gnu.org
Ricardo Wurmus ricardo.wur...@mdc-berlin.de skribis:
From 8d131f66ba0378738e5b837f78c411edb241d35a Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus ricardo.wur...@mdc-berlin.de
Date: Tue, 16 Jun 2015 16:24:24 +0200
Subject: [PATCH] gnu: Add Blast+.
* gnu/packages/bioinformatics.scm (blast+):
Alex Kost alez...@gmail.com skribis:
From e93d21889bdcbed02a517f30d8401a3bb144cce4 Mon Sep 17 00:00:00 2001
From: Claes Wallin claes.wal...@greatsinodevelopment.com
Date: Fri, 19 Jun 2015 20:12:09 +0200
Subject: [PATCH] gnu: Add pv.
* gnu/package/pv.scm (pv): New file.
* gnu-system.am
From 0039b2d36f77d19c92e07e02c7b3e829c485f355 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus rek...@elephly.net
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
Federico Beffa be...@ieee.org skribis:
On Thu, Jun 25, 2015 at 2:33 PM, Ludovic Courtès l...@gnu.org wrote:
Federico Beffa be...@ieee.org skribis:
[...]
The problem is that this forcefully introduces bindings in an opaque way
(that is, regardless of whether the ‘outputs’ binding appears in
Federico Beffa be...@ieee.org skribis:
From 56c460213d76ff2b88fd771b48997c3e03200234 Mon Sep 17 00:00:00 2001
From: Federico Beffa be...@fbengineering.ch
Date: Tue, 16 Jun 2015 10:50:06 +0200
Subject: [PATCH 1/6] import: Add 'elpa' importer.
* guix/import/elpa.scm: New file.
*
Ricardo Wurmus ricardo.wur...@mdc-berlin.de skribis:
From 85811f556f0db843f2c699465d317c10d4e85807 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus ricardo.wur...@mdc-berlin.de
Date: Thu, 25 Jun 2015 12:04:05 +0200
Subject: [PATCH] gnu: Add plink.
* gnu/packages/bioinformatics.scm (plink): New
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: Ricardo
Federico Beffa be...@ieee.org skribis:
From 84bded85e25fd8130f222d30442027219fa8f642 Mon Sep 17 00:00:00 2001
From: Federico Beffa be...@fbengineering.ch
Date: Wed, 17 Jun 2015 10:42:09 +0200
Subject: [PATCH 5/5] gnu: Add emacs-mmm-mode.
* gnu/packages/emacs.scm (emacs-mmm-mode): New
Federico Beffa be...@ieee.org skribis:
From c17c181a5663a29fdc84942c90d6b90549a9f76e Mon Sep 17 00:00:00 2001
From: Federico Beffa be...@fbengineering.ch
Date: Mon, 15 Jun 2015 14:51:06 +0200
Subject: [PATCH 4/5] gnu: Add emacs-auctex.
* gnu/packages/emacs.scm: New variable.
[...]
+
On 27/06/15 20:40, Ricardo Wurmus wrote:
+(synopsis Protein-coding gene prediction for Archaea and Bacteria)
Shouldn’t “Archaea” and “Bacteria” both be lower-cased?
I don't believe so. As I understand it you can use bacterial and
archaeal with lower case, but here we are referring to
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
Ben Woodcroft b.woodcr...@uq.edu.au 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
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?
~~
On 27/06/15 20:14, Ludovic Courtès wrote:
Ricardo Wurmus ricardo.wur...@mdc-berlin.de skribis:
From 8d131f66ba0378738e5b837f78c411edb241d35a Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus ricardo.wur...@mdc-berlin.de
Date: Tue, 16 Jun 2015 16:24:24 +0200
Subject: [PATCH] gnu: Add Blast+.
*
I feel a bit uncomfortable that I added my name to AUTHORS :-)
From 5f610f3b84e6024b686e310bbaa402ed25e2d4df Mon Sep 17 00:00:00 2001
From: Alex Kost alez...@gmail.com
Date: Sat, 27 Jun 2015 20:42:32 +0300
Subject: [PATCH] Clean up 'THANKS' and 'AUTHORS'.
* AUTHORS: Add Alex Kost.
Align Paul
On Sat, Jun 27, 2015 at 08:53:29PM +0300, Alex Kost wrote:
I feel a bit uncomfortable that I added my name to AUTHORS :-)
Well, it definitely belongs there. Probably everybody assumed it was there
already and did not bother to check.
Andreas
Ricardo Wurmus ricardo.wur...@mdc-berlin.de writes:
It would be great to get the tests working, even if we have to disable
some of them. Otherwise we have no way of knowing that we're not
distributing broken garbage :)
It's hard to know in this case even with the tests, because it's only
Out of pure curiosity, why are we not thanking so many people any more?
I don't have any vested interest, i'm really just idly wondering.
signature.asc
Description: PGP signature
Hello!
The ‘wip-diet’ branch removes extra weight from a few packages:
• Remove dependency from MySQL, Mutt, and cups-filters on GCC 4.9.
• Remove 32 MiB of useless binaries from MySQL.
• Remove reference to qt-4:doc (280 MiB) from qt-4.
• Move Ghostscript documentation (16 MiB) to
Andreas Enge andr...@enge.fr writes:
On Sat, Jun 27, 2015 at 08:53:29PM +0300, Alex Kost wrote:
I feel a bit uncomfortable that I added my name to AUTHORS :-)
Well, it definitely belongs there. Probably everybody assumed it was there
already and did not bother to check.
Agreed :)
Mark
Paul van der Walt p...@denknerd.org writes:
Out of pure curiosity, why are we not thanking so many people any
more?
Alex explained in the commit log:
* THANKS: Remove Federico Beffa, Marek Benc, John Darrington, Alex Kost,
Cyrill Schenkel and Andy Wingo because they are placed in AUTHORS.
I
On 2015-06-28 at 01:48, quoth Mark H Weaver:
Alex explained in the commit log:
Oops, that'll teach me not to read everything exhaustively
:shame:. Thanks!
p.
From: Eric Bavier bav...@member.fsf.org
The following patches add the deal.II finite element library and some of its
dependencies. Also included are some non-trivial package upgrades.
I've tested builds on both x86_64 and i686, but cannot comment on mips or arm.
Stylistic or other comments are
From: Eric Bavier bav...@member.fsf.org
* gnu/packages/mpi.scm (openmpi): Upgrade to 1.8.5.
[native-inputs]: Add perl.
[arguments]: Add configure flags for thread support.
---
gnu/packages/mpi.scm | 19 +++
1 file changed, 11 insertions(+), 8 deletions(-)
diff --git
From: Eric Bavier bav...@member.fsf.org
* gnu/packages/patches/hwloc-gather-topology-lstopo.patch: New patch.
* gnu/packages/mpi.scm (hwloc): Upgrade to 1.10.1.
[source]: Use patch.
[propagated-inputs]: Remove libpci.
[inputs]: Add libpciaccess.
* gnu-system.am (dist_patch_DATA): Add patch.
From: Eric Bavier bav...@member.fsf.org
* gnu/packages/maths.scm (deal.II, deal.II-openmpi): New variables.
* gnu/packages/patches/deal.II-p4est-interface.patch: New patch.
* gnu-system.am (dist_patch_DATA): Add it.
---
gnu-system.am | 1 +
From: Eric Bavier bav...@member.fsf.org
* gnu/packages/maths.scm (slepc, slepc-complex, slepc-openmpi)
(slepc-complex-openmpi): New variables.
---
gnu/packages/maths.scm | 98 ++
1 file changed, 98 insertions(+)
diff --git
From: Eric Bavier bav...@member.fsf.org
* gnu/packages/maths.scm (mumps, mumps-metis, mumps-openmpi)
(mumps-metis-openmpi): New variables.
* gnu/packages/patches/mumps-build-parallelism.patch: New patch.
* gnu-system.am (dist_patch_DATA): Add it.
---
gnu-system.am
From: Eric Bavier bav...@member.fsf.org
* gnu/packages/maths.scm (arpack-ng-openmpi): New variable.
---
gnu/packages/maths.scm | 9 +
1 file changed, 9 insertions(+)
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index a6c4bba..343b56c 100644
--- a/gnu/packages/maths.scm
From: Eric Bavier bav...@member.fsf.org
* gnu/packages/maths.scm (petsc): Upgrade to 3.6.0.
* gnu/packages/patches/petsc-fix-threadcomm.patch: Delete patch.
* gnu-system.am (dist_patch_DATA): Remove it.
---
gnu-system.am | 1 -
gnu/packages/maths.scm
From: Eric Bavier bav...@member.fsf.org
* gnu/packages/maths.scm (p4est, p4est-openmpi): New variables.
---
gnu/packages/maths.scm | 46 ++
1 file changed, 46 insertions(+)
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index
From: Eric Bavier bav...@member.fsf.org
* gnu/packages/maths.scm (scotch, pt-scotch)[arguments]: Use modify-phases.
---
gnu/packages/maths.scm | 70 ++
1 file changed, 31 insertions(+), 39 deletions(-)
diff --git a/gnu/packages/maths.scm
From: Eric Bavier bav...@member.fsf.org
* gnu/packages/maths.scm (scalapack): New variable.
---
gnu/packages/maths.scm | 29 +
1 file changed, 29 insertions(+)
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 765a111..b67ae9c 100644
---
From: Eric Bavier bav...@member.fsf.org
* gnu/packages/maths.scm (scotch)[arguments]: Add 'build-esmumps
phase. Install esmumps libraries and headers in 'install phase.
(pt-scotch)[arguments]: Build ptesmumps in 'build phase. Add
make parallelism.
---
gnu/packages/maths.scm | 22
From: Eric Bavier bav...@member.fsf.org
* gnu/packages/maths.scm (metis): New variable.
---
gnu/packages/maths.scm | 30 ++
1 file changed, 30 insertions(+)
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 3852311..bc13fd5 100644
---
From: Eric Bavier bav...@member.fsf.org
* gnu/packages/maths.scm (scotch): Update to 6.0.4.
[arguments]: Add -fPIC to CFLAGS.
* gnu/packages/patches/scotch-test-threading.patch: Adjust patch for a
new set of test fixes.
* gnu/packages/patches/pt-scotch-build-parallelism.patch: New patch.
*
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