[PATCH 12/14] gnu: Add arpack-ng-openmpi.

From: Eric Bavier * 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 +++ b/gnu/packages/math

[PATCH 11/14] gnu: petsc: Upgrade to 3.6.0.

From: Eric Bavier * 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 | 26 ++

[PATCH 10/14] gnu: Add MUMPS.

From: Eric Bavier * 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 | 1 + gnu/p

[PATCH 08/14] gnu: Add p4est.

From: Eric Bavier * 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 b67ae9c..3852311 100644 --- a/gnu

[PATCH 09/14] gnu: Add METIS.

From: Eric Bavier * 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 --- a/gnu/packages/maths.scm +++ b/gnu/pa

[PATCH 14/14] gnu: Add deal.II.

From: Eric Bavier * 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 + gnu/packages/maths.scm

[PATCH 05/14] gnu: scotch, pt-scotch: Use modify-phases.

From: Eric Bavier * 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 b/gnu/packages/maths.scm index

[PATCH 07/14] gnu: Add ScaLAPACK.

From: Eric Bavier * 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 --- a/gnu/packages/maths.scm +++ b/gnu

[PATCH 06/14] gnu: scotch, pt-scotch: Build esmumps libraries.

From: Eric Bavier * 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 -- 1 file

[PATCH 13/14] gnu: Add SLEPc.

From: Eric Bavier * 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 a/gnu/packages/maths.scm b/gnu/packages/math

[PATCH 04/14] gnu: Update scotch to 6.0.4.

From: Eric Bavier * 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. * gnu-system.am (dist_patc

[PATCH 01/14] gnu: hwloc: Upgrade to 1.10.1.

From: Eric Bavier * 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. --- gnu-system.am

[PATCH 03/14] gnu: openmpi: Upgrade to 1.8.5.

From: Eric Bavier * 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 a/gnu/packages/mpi.scm b/gnu/p

[PATCH 00/14] Add deal.II and some dependencies.

From: Eric Bavier 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 most welcome. Eric B

[PATCH 02/14] gnu: hwloc: Move numactl to inputs.

From: Eric Bavier * gnu/packages/mpi.scm (hwloc)[propagated-inputs]: Move numactl from here... [inputs]: ...to here. [arguments]: New 'refine-libnuma' phase. --- gnu/packages/mpi.scm | 16 +--- 1 file changed, 13 insertions(+), 3 deletions(-) diff --git a/gnu/packages/mpi.scm b/

Re: [PATCH] Clean up 'THANKS' and 'AUTHORS'.

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.

Re: [PATCH] Clean up 'THANKS' and 'AUTHORS'.

Paul van der Walt 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 guess that no o

Re: [PATCH] Clean up 'THANKS' and 'AUTHORS'.

Andreas Enge 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

Diet branch

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 sep

Re: [PATCH] Clean up 'THANKS' and 'AUTHORS'.

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

Re: [PATCH] Add Blast+.

Ricardo Wurmus 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 > three tests and they

Re: [PATCH] Clean up 'THANKS' and 'AUTHORS'.

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

[PATCH] Clean up 'THANKS' and 'AUTHORS'.

I feel a bit uncomfortable that I added my name to AUTHORS :-) >From 5f610f3b84e6024b686e310bbaa402ed25e2d4df Mon Sep 17 00:00:00 2001 From: Alex Kost Date: Sat, 27 Jun 2015 20:42:32 +0300 Subject: [PATCH] Clean up 'THANKS' and 'AUTHORS'. * AUTHORS: Add Alex Kost. Align Paul van der Walt name

Re: [PATCH] Add Blast+.

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

Re: [PATCH] Add Blast+.

On 27/06/15 20:14, Ludovic Courtès wrote: Ricardo Wurmus skribis: From 8d131f66ba0378738e5b837f78c411edb241d35a 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.

Re: [PATCH] Add prodigal.

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

Re: [PATCH] Add prodigal.

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? ~

Re: [PATCH] Add prodigal.

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

Re: [PATCH] Add plink.

Ricardo Wurmus skribis: > 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 variable. > * gnu/packages/patches/plink-1.07-uncl

Re: [PATCH] gnu/package/pv.scm (pv): New file, new variable

Alex Kost skribis: >> From e93d21889bdcbed02a517f30d8401a3bb144cce4 Mon Sep 17 00:00:00 2001 >> From: Claes Wallin >> Date: Fri, 19 Jun 2015 20:12:09 +0200 >> Subject: [PATCH] gnu: Add pv. >> >> * gnu/package/pv.scm (pv): New file. >> * gnu-system.am (GNU_SYSTEM_MODULES): Add it. > > Thank you

Re: [PATCH] Add Blast+.

Ricardo Wurmus skribis: > From 8d131f66ba0378738e5b837f78c411edb241d35a 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. Mark, do you have anything to add on

Re: [PATCH 5/5] gnu: Add emacs-mmm-mode

Federico Beffa skribis: > From 84bded85e25fd8130f222d30442027219fa8f642 Mon Sep 17 00:00:00 2001 > From: Federico Beffa > 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 variable. [...] > +(synopsis >

Re: [PATCH 4/5] gnu: Add emacs-auctex

Federico Beffa skribis: > From c17c181a5663a29fdc84942c90d6b90549a9f76e Mon Sep 17 00:00:00 2001 > From: Federico Beffa > Date: Mon, 15 Jun 2015 14:51:06 +0200 > Subject: [PATCH 4/5] gnu: Add emacs-auctex. > > * gnu/packages/emacs.scm: New variable. [...] > +(synopsis "Integrated environme

Re: [PATCH 1/5] import: Add 'elpa' importer

Federico Beffa skribis: > From 56c460213d76ff2b88fd771b48997c3e03200234 Mon Sep 17 00:00:00 2001 > From: Federico Beffa > Date: Tue, 16 Jun 2015 10:50:06 +0200 > Subject: [PATCH 1/6] import: Add 'elpa' importer. > > * guix/import/elpa.scm: New file. > * guix/scripts/import.scm: Add "elpa" to 'im

Re: [PATCH 3/5] build: Add 'emacs-build-system'

Federico Beffa skribis: > On Thu, Jun 25, 2015 at 2:33 PM, Ludovic Courtès wrote: >> Federico Beffa skribis: [...] >> The problem is that this forcefully introduces bindings in an opaque way >> (that is, regardless of whether the ‘outputs’ binding appears in the >> source, there’s an ‘outputs

[PATCH] Add libiberty.

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 Wu

[PATCH] Add libtar.

>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 changed,

Re: [PATCH 1/5] import: Add 'elpa' importer

Oops, I've noticed that an unsupported repo was not handled gracefully. On Thu, Jun 25, 2015 at 8:33 PM, Federico Beffa 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 wrote: >> Federico Bef