Re: [PATCH] gnu: simple-scan: Update to 3.19.91.

On Tue, Mar 08, 2016 at 08:39:37PM -0500, Leo Famulari wrote: > On Wed, Mar 09, 2016 at 01:25:04AM +0100, Tobias Geerinckx-Rice wrote: > > On 09/03/2016, Leo Famulari wrote: > > > [...] pass to ./configure '--disable-packagekit'. Would that work? > > > > So do ‘we’: > > > >

Re: should gnome-desktop-service really provide all of this to a profile?

l...@gnu.org (Ludovic Courtès) writes: > Pulseaudio also propagates a few things. Yes, I think it should be splited into “out” and “dev”, if we can make only the “dev” output propagating libcap and gdbm. > > Good point, this sounds undesirable (and shows that some packages would > benefit

Re: [PATCH] gnu: Add freebayes.

On Wed, Mar 09, 2016 at 07:53:20AM +0100, Pjotr Prins wrote: > On Tue, Mar 08, 2016 at 04:44:13PM +0100, Roel Janssen wrote: > > One of the problems with the patch is probably the bulk of dependencies > > dragged in (for example, vcflib). They use specific versions so they > > are tied to this

Re: [PATCH] gnu: Add freebayes.

On Tue, Mar 08, 2016 at 04:44:13PM +0100, Roel Janssen wrote: > One of the problems with the patch is probably the bulk of dependencies > dragged in (for example, vcflib). They use specific versions so they > are tied to this package (so that's why I cannot package them separately). This

Re: [PATCH] gnu: Add freebayes.

On Tue, Mar 08, 2016 at 06:55:15PM -0500, Leo Famulari wrote: > Thanks again for putting such a complicated patch together! We will find > the best way to add freebayes to the distribution :) +1. Freebayes is (in my opinion) one of the best variant callers out there, both for SNPs and somatic

Re: Guix vs GuixSD - upgrade Debian to Guix

g...@rcdrun.com writes: > Hello, > > I have read this: > >> I am saying you can "upgrade" your computer from, say, Guix on Debian to >> GuixSD by doing ... >> >> mount /dev/sdX /mnt >> guix system init /mnt/etc/config.scm /mnt >> >> ... where /dev/sdX is a new system disk. With more

Re: [PATCH] gnu: Add bioawk.

On Tue, Mar 08, 2016 at 09:10:14PM +0100, Roel Janssen wrote: > From 990eda92a62dc25d0f5792437a82e119c5e3579f Mon Sep 17 00:00:00 2001 > From: Roel Janssen > Date: Tue, 8 Mar 2016 21:06:53 +0100 > Subject: [PATCH] gnu: Add bioawk. > > * gnu/packages/bioinformatics.scm (bioawk): New

Re: [PATCH] gnu: simple-scan: Update to 3.19.91.

On Wed, Mar 09, 2016 at 01:25:04AM +0100, Tobias Geerinckx-Rice wrote: > On 09/03/2016, Leo Famulari wrote: > > [...] pass to ./configure '--disable-packagekit'. Would that work? > > So do ‘we’: > > On Tue, Mar 08, 2016 at 11:04:35PM +0100, Tobias Geerinckx-Rice wrote: > >

Re: [PATCH] gnu: simple-scan: Update to 3.19.91.

Firstly, thanks for the feedback! On 09/03/2016, Leo Famulari wrote: >> I therefore simply disabled it. > > I think that lots of software in our distribution has unused features or > portability "goop" that doesn't apply to us, but we don't delete that > code. Running

Re: [PATCH] gnu: simple-scan: Update to 3.19.91.

On Wed, Mar 09, 2016 at 12:43:52AM +0100, Tobias Geerinckx-Rice wrote: > Hullo Leo, > > On 09/03/2016, Leo Famulari wrote: > > Except where necessary for the new version to work, it's best to do > > updates in a separate commit from other changes. > > > > I can apply the

Re: [PATCH] gnu: Add freebayes.

On Tue, Mar 08, 2016 at 04:44:13PM +0100, Roel Janssen wrote: Thanks for the patch! This looks like a big one! [...] > + (native-inputs > + `(("cmake" ,cmake) > + ("htslib" ,htslib) > + ("zlib" ,zlib) > + ("python" ,python-2) > + ("perl" ,perl) > +

Re: [PATCH] gnu: simple-scan: Update to 3.19.91.

An addendum to the mentioning of upstream: they have been aware of the issue for some time, but it has yet to be fixed. The bug report[1] mentions some other workarounds, but I preferred a more explicit approach. Regards, T G-R [1] https://bugs.launchpad.net/simple-scan/+bug/1462769

Re: [PATCH] gnu: simple-scan: Update to 3.19.91.

Hullo Leo, On 09/03/2016, Leo Famulari wrote: > Except where necessary for the new version to work, it's best to do > updates in a separate commit from other changes. > > I can apply the update myself if you say it's okay to do on its own, or > feel free to submit a revised

Re: [PATCH] gnu: Include CodingQuarry gene predictor

Sure, I'll do that. Thanks for the feedback. -r On Wed, 9 Mar 2016, 07:40 Leo Famulari, wrote: > On Tue, Mar 08, 2016 at 05:13:34PM +0800, Rob Syme wrote: > > Thank you for the patch! > > > * gnu/packages/bioinformatics.scm: Add codingquarry package description > > When

Re: [PATCH] gnu: Include CodingQuarry gene predictor

On Tue, Mar 08, 2016 at 05:13:34PM +0800, Rob Syme wrote: Thank you for the patch! > * gnu/packages/bioinformatics.scm: Add codingquarry package description When adding packages, we have a preferred format for the commit message. It's either the GNU changelog format or a slightly modified

Re: [PATCH] gnu: simple-scan: Update to 3.19.91.

On Tue, Mar 08, 2016 at 11:04:35PM +0100, Tobias Geerinckx-Rice wrote: > * gnu/packages/gnome.scm (simple-scan): Update to 3.19.91. Thanks for your attention to this package! Except where necessary for the new version to work, it's best to do updates in a separate commit from other changes. I

[PATCH] gnu: simple-scan: Update to 3.19.91.

* gnu/packages/gnome.scm (simple-scan): Update to 3.19.91. [arguments]: Disable PackageKit support irrelevant for Guix. --- Thanks in advance for your loving corrections. :-) T G-R gnu/packages/gnome.scm | 12 ++-- 1 file changed, 10 insertions(+), 2 deletions(-) diff --git

Re: wip-rox.scm : ROX Desktop

Hi Nils, On Tue, 08 Mar 2016 09:16:41 +0100 Nils Gillmann wrote: > for me this part is checkout / pull latest merges, > make clean, ./configure --localstatedir=/var, make > etc > why bootstrap when we are talking about GuixSD (probably)? It just does automake and autoconf

Re: Guix vs GuixSD - upgrade Debian to Guix

Hello, I have read this: > I am saying you can "upgrade" your computer from, say, Guix on Debian to > GuixSD by doing ... > > mount /dev/sdX /mnt > guix system init /mnt/etc/config.scm /mnt > > ... where /dev/sdX is a new system disk. With more complicated maneuvers > you can no

[PATCH] gnu: Add bioawk.

>From 990eda92a62dc25d0f5792437a82e119c5e3579f Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Tue, 8 Mar 2016 21:06:53 +0100 Subject: [PATCH] gnu: Add bioawk. * gnu/packages/bioinformatics.scm (bioawk): New variable. --- gnu/packages/bioinformatics.scm | 38

Re: [PATCH] gnunet-gtk: adds --with-gnunet to configure-flags

Ricardo Wurmus writes: > Nils Gillmann writes: > >> I'll ask on gnunet-dev about this, but it might be that we have >> to decide wether to default to some svn of gnunet, as 0.10.1 is >> really old. Stable, but old.. Which possibly could affect

Re: Guix vs GuixSD

Chris Marusich writes: [...] Thank you for the helpful comments. I have revised the diagram accordingly. Please let me know if I missed something. >>> * "Guix system services": consider renaming "Guix" to "GuixSD". >> >> One issue with "GuixSD" is that GuixSD does not

Re: [PATCH] gnunet-gtk: adds --with-gnunet to configure-flags

Nils Gillmann writes: > I'll ask on gnunet-dev about this, but it might be that we have > to decide wether to default to some svn of gnunet, as 0.10.1 is > really old. Stable, but old.. Which possibly could affect the > experience for people who try to use gnunet now,

Re: should gnome-desktop-service really provide all of this to a profile?

iyzs...@member.fsf.org (宋文武) skribis: > l...@gnu.org (Ludovic Courtès) writes: > >> Andy Wingo skribis: >> >>> On Mon 07 Mar 2016 22:11, l...@gnu.org (Ludovic Courtès) writes: >>> Andy Wingo skribis: > I installed gnome using > > guix

Re: [PATCH] gnunet-gtk: adds --with-gnunet to configure-flags

On Tue, Mar 08, 2016 at 03:48:03PM +0100, Nils Gillmann wrote: > Following later this week: > > gnunet + gnunet-gtk SVN, co-authored work with Jookia. > > I'll ask on gnunet-dev about this, but it might be that we have > to decide wether to default to some svn of gnunet, as 0.10.1 is > really

Re: [PATCH] gnunet-gtk: adds --with-gnunet to configure-flags

Following later this week: gnunet + gnunet-gtk SVN, co-authored work with Jookia. I'll ask on gnunet-dev about this, but it might be that we have to decide wether to default to some svn of gnunet, as 0.10.1 is really old. Stable, but old.. Which possibly could affect the experience for people

[PATCH] gnu: Include CodingQuarry gene predictor

* gnu/packages/bioinformatics.scm: Add codingquarry package description --- gnu/packages/bioinformatics.scm | 31 +++ 1 file changed, 31 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 5d53dc9..2e665db 100644 ---

Re: should gnome-desktop-service really provide all of this to a profile?

l...@gnu.org (Ludovic Courtès) writes: > Andy Wingo skribis: > >> On Mon 07 Mar 2016 22:11, l...@gnu.org (Ludovic Courtès) writes: >> >>> Andy Wingo skribis: >>> I installed gnome using guix package --profile=/tmp/foo-profile -i gnome

Re: Yet another Hydra mirror: hydra-mirror.marusich.info

On Tue, Mar 08, 2016 at 10:04:33AM +0100, Andy Wingo wrote: > Right now hydra.gnu.org is in this weird situation where people who use > it have to trust it, modulo "guix challenge" of course. But really all > we have to trust is the mapping from the derivation (like the "foo" > package) to a hash

Re: [PATCH] gnu: Add tracker.

ren...@openmailbox.org skribis: > i made changes to the patch, i disable 'make check' because i found > two errors during this phase: > > a) "Tracker-WARNING **: Locale '0' is not set, defaulting to C locale" >For this case i set LANG "en_US.UTF-8". > b) "Unable to load

Re: should gnome-desktop-service really provide all of this to a profile?

Andy Wingo skribis: > On Mon 07 Mar 2016 22:11, l...@gnu.org (Ludovic Courtès) writes: > >> Andy Wingo skribis: >> >>> I installed gnome using >>> >>> guix package --profile=/tmp/foo-profile -i gnome >>> >>> There is a lot of stuff there. If

Re: Yet another Hydra mirror: hydra-mirror.marusich.info

Chris Marusich skribis: > I've set up a caching proxy to serve substitutes from Hydra. If you want > to use it, it's available here: > > http://hydra-mirror.marusich.info Nice! Are you using the nginx config that’s in guix-maintenance.git? > Full disclosure: I'm employed

Re: wip-rox.scm : ROX Desktop

Danny Milosavljevic skribis: > I have a work-in-progress for the ROX Desktop (the ROX-Filer and ROX-Session > parts work), see below; you can use it as a starting point. Nice, sounds like you’re almost there! Once you have polished the patches, feel free to send them

Re: [PATCH 0/6] Libreoffice CVE and update

Leo Famulari skribis: > On Mon, Mar 07, 2016 at 10:03:17PM +0200, Efraim Flashner wrote: >> On Mon, 7 Mar 2016 12:42:01 +0200 >> Efraim Flashner wrote: >> >> > Now that vigra is building again, I've put together a patch to update >> > libreoffice to

Re: Texlive-texmf

Eric Bavier skribis: > On Mon, 07 Mar 2016 17:41:44 +0100 > l...@gnu.org (Ludovic Courtès) wrote: > >> Andreas Enge skribis: >> >> > On Thu, Mar 03, 2016 at 06:04:17PM +0100, Ludovic Courtès wrote: >> >> Andreas Enge skribis:

Re: Yet another Hydra mirror: hydra-mirror.marusich.info

On Tue 08 Mar 2016 07:37, Chris Marusich writes: > I've set up a caching proxy to serve substitutes from Hydra. If you want > to use it, it's available here: > > http://hydra-mirror.marusich.info > > Behind the scenes, this endpoint is set up to distribute hydra.gnu.org's >

Re: 02/02: gnu: elogind: Update to 219.13.

On Tue 08 Mar 2016 02:46, Mark H Weaver writes: > Mark H Weaver writes: > >> Andy Wingo writes: >> >>> (define-public elogind >>>(package >>> (name "elogind") >>> -(version "219.12") >>> +(version "219.13") >>> (source

Re: should gnome-desktop-service really provide all of this to a profile?

On Mon 07 Mar 2016 22:11, l...@gnu.org (Ludovic Courtès) writes: > Andy Wingo skribis: > >> I installed gnome using >> >> guix package --profile=/tmp/foo-profile -i gnome >> >> There is a lot of stuff there. If gnome-desktop-service extends >> profile-service-type with gnome,

Re: Python 3.5 start of update

Diane Trout writes: > (If you're curious about my progress with jupyter, that's over here: > https://github.com/detrout/guix-detrout/blob/master/detrout/packages/py > data.scm) Oh, nice. I also have a couple of jupyter-related patches, but they are already a little older. I

Re: wip-rox.scm : ROX Desktop

Danny Milosavljevic writes: > To use it, with your normal user account do: > $ git clone git://git.sv.gnu.org/guix.git > $ cd guix > $ ./bootstrap ./bootstrap? for me this part is checkout / pull latest merges, make clean, ./configure --localstatedir=/var, make etc why

[RFCv2] install: Create a GC root during install-grub.

While previously creating a GC root for GRUB's resources was the caller's responsibility, it's much less repetitive to put it in install-grub now that it's wrapped by error handling. This also means we can replace the install-grub* function with a small definition inside perform-action named

wip-rox.scm : ROX Desktop

Hello Louis, well, writing the package declaration is easy - if you have the time, it would be nice. But I understand that you have to get guix working for you first. I have a work-in-progress for the ROX Desktop (the ROX-Filer and ROX-Session parts work), see below; you can use it as a