Re: Updating to latest Bioconductor release

On Thu, 2020-11-19 at 22:13 +0100, Ricardo Wurmus wrote: > Hi, > > > > > http://logs.guix.gnu.org/guix/2020-11-19.log#182349 > > > > > Right, so I shouldn't have pushed to "wip-r" in the first place. > > > > Well, I think it is a lack of synchronisation between all of 3; > > especially with this

Re: GNU Guix 1.2.0rc2 available for testing!

Hi Ludo, On Thu, 19 Nov 2020 at 03:24, zimoun wrote: >> You can also check the ‘NEWS’ file and the draft blog post at >> >> to make sure your favorite feature is mentioned and/or to discuss t

Re: GNU Guix 1.2.0rc2 available for testing!

Ryan Prior writes: > I'm glad for the "without-tests" option because when I'm working on > packages with a test suite that takes more than a few seconds, I like to > make sure that the rest of everything is working before I start running > the tests. Exactly, that was my original thought. > Ano

Re: Thoughts on building things for substitutes and the Guix Build Coordinator

Hi Chris, Christopher Baines skribis: >>> Another feature supported by the Guix Build Coordinator is retries. If a >>> build fails, the Guix Build Coordinator can automatically retry it. In a >>> perfect world, everything would succeed first time, but because the >>> world isn't perfect, there s

Re: GNU Guix 1.2.0rc2 available for testing!

Hi, zimoun skribis: > On Thu, 19 Nov 2020 at 03:24, zimoun wrote: > >>> You can also check the ‘NEWS’ file and the draft blog post at >>> >>> to make sure your favorite feature is mentioned

/etc/passwd & co. in Docker images

Hi, Danny Milosavljevic skribis: > After Ryan Prior's E-Mail I'm pretty sure my workaround of creating /tmp, > /etc/passwd, /etc/group etc is what Docker actually expects one to do. I’ve been pondering whether to create those files in ‘guix pack -f docker’ and… > ADD etc/passwd /etc > ADD etc/

Re: A plan for parameterized packages

Hi, Denis 'GNUtoo' Carikli skribis: > Last time I looked into how LibreCMC/OpenWRT did that, they had much > more optimization than that. If I recall well, they use at least: > - sstrip to strip binaries as much as they could. sstrip produces > smaller binaries than with strip. > - compilation

reproducibility related grants

This is about grants being given to software projects considered as infrastructure for reproducibility in scentific research I thought hte Guix community could be interested https://cziscience.medium.com/scaling-open-infrastructure-and-reproducibility-in-biomedicine-69546a399747

Re: Updating to latest Bioconductor release

Roel Janssen writes: > On Thu, 2020-11-19 at 22:13 +0100, Ricardo Wurmus wrote: >> Hi, >> >> > > > http://logs.guix.gnu.org/guix/2020-11-19.log#182349 >> > >> > > Right, so I shouldn't have pushed to "wip-r" in the first place. >> > >> > Well, I think it is a lack of synchronisation between

Re: Updating to latest Bioconductor release

Ricardo Wurmus writes: > There are some open questions: the changes to r-mutationalpatterns > invalidate the comment > >;; These two packages are suggested packages > > above r-bsgenome-hsapiens-1000genomes-hs37d5 and > r-bsgenome-hsapiens-ucsc-hg19. Would be good to adjust the comment or

New French PO file for 'guix-manual' (version 1.2.0-pre3)

Hello, gentle maintainer. This is a message from the Translation Project robot. A revised PO file for textual domain 'guix-manual' has been submitted by the French team of translators. The file is available at: https://translationproject.org/latest/guix-manual/fr.po (We can arrange things

Re: Updating to latest Bioconductor release

Hi, On Fri, 20 Nov 2020 at 14:37, Ricardo Wurmus wrote: > > It'd be great if you could reset the branch pointer! :) > > Done! I rebased onto master and pushed to r-wip. Nice! Thanks. (You mean wip-r, right?) > Many of the commit messages were incomplete (didn’t mention all changed > input

Re: Updating to latest Bioconductor release

Hi Ricardo, On Fri, 20 Nov 2020 at 14:40, Ricardo Wurmus wrote: > The commit that updates %bioconductor-version (“import: cran: Update the > Bioconductor version to 3.12.”) should also change “bioconductor-uri” in > (guix build-system r). This is still at 3.11. When should this commit be done?

Re: Updating to latest Bioconductor release

On Fri, 2020-11-20 at 14:42 +0100, Ricardo Wurmus wrote: > > Ricardo Wurmus writes: > > > There are some open questions: the changes to r-mutationalpatterns > > invalidate the comment > > > >    ;; These two packages are suggested packages > > > > above r-bsgenome-hsapiens-1000genomes-hs37d5 a

Re: Updating to latest Bioconductor release

zimoun writes: > (You mean wip-r, right?) Oof, yes, of course :) >> Many of the commit messages were incomplete (didn’t mention all changed >> inputs) and used the wrong heading “gnu: Update r-foo to 1.2.3.” instead >> of the more greppable “gnu: r-foo: Update to 1.2.3.”. > > Just to understa

Re: A plan for parameterized packages

Hi, On Fri, 20 Nov 2020 at 12:40, Ludovic Courtès wrote: > > The issue is that despite all that, the size of the images tend to > > increase too rapidly over time[1]. > > Yeah, that’s also the problem here: we have ‘guix size’ to profile a > package at one point in time, but it’s easy to unwilli

Re: Updating to latest Bioconductor release

On Fri, 20 Nov 2020 at 15:26, Ricardo Wurmus wrote: > > Just to understand for the next time: when should the commit upgrading > > the %bioconductor-version be done? First one or last one? > > > > (I am speaking of this kind of commit: > > ac6a55e68a6ed675a55abc5339f776613648cb9d) > > It doesn’

Re: /etc/passwd & co. in Docker images

On November 20, 2020, "Ludovic Courtès" wrote: > … what you’re doing here suggest that ‘guix pack’ should indeed create > those files. Oh I think it should be an option. Many Docker containers do not need those things, but it would be great to have the option to include them. Another option that

Re: A plan for parameterized packages

Ludovic Courtès writes: > Hi, > > Denis 'GNUtoo' Carikli skribis: > >> The issue is that despite all that, the size of the images tend to >> increase too rapidly over time[1]. > > Yeah, that’s also the problem here: we have ‘guix size’ to profile a > package at one point in time, but it’s easy