bug#44264: Doc and vignettes bundled from Bioconductor

On Tue, 27 Oct 2020 at 21:36, zimoun wrote: On part of the story, > --8<---cut here---start->8--- > (define-public r-diffcyt > (package > (name "r-diffcyt") [...] > (native-inputs `(("r-knitr" ,r-knitr) ("r-rmarkdown" ,r-rmarkdown)

bug#44264: Doc and vignettes bundled from Bioconductor

Dear, Let’s take the example: --8<---cut here---start->8--- $ guix import cran -a bioconductor diffcyt -r Starting download of /tmp/guix-file.qJmqja >From >https://bioconductor.org/packages/release/bioc/src/contrib/diffcyt_1.8.8.tar.gz... …8.8.tar.gz

bug#44262: Sphinx is out of date

Our Sphinx package is at version 2.3.1 (latest is 4.x.x), which causes problems for packages like python-matplotlib-documentation and python-numpy-documentation. (python-ipython-documentation still builds fine.) We should try to upgrade Sphinx to a more recent version, or perhaps add a new

bug#44261: running a daemon with userns in relocateble pack breaks

Jan Nieuwenhuizen writes: Hi! I tried the hint from Ludovic to use MS_PRIVATE in the attached patch and that works for me; not sure if we want a test and even less sure how to write that... Janneke >From fd3104608c3fa6a2375b6c7df0862e5479976b39 Mon Sep 17 00:00:00 2001 From: "Jan (janneke)

bug#44254: Performance of package input rewriting

Lars-Dominik Braun writes: > this issue is similar to https://issues.guix.gnu.org/41702, but I’m not sure > it’s exactly the same. For guix-science I’m trying to provide some packages > like python-jupyterlab, which depend on a mix of packages from guix proper and > newer versions of packages

bug#44261: running a daemon with userns in relocateble pack breaks

Hi! As mentioned on IRC, running a daemon from a guix relocatable pack on a foreign distro using the user namespace feature is troublesome: it looks as if the daemon "loses" (its view of) the file-system once the parent process that creates the daemon exits. I'm attatching a package description

bug#43850: cuirass: inconsistent SQL queries execution time.

> I don't really get why I/O pressure on /dev/sdb could impact /dev/sda. Turns out /tmp is mounted on /dev/sda, so all the building and ISO production are first written on /dev/sda before being copied to the store in /dev/sdb. Reducing the build activity of berlin, as Ludo proposed should help

bug#43565: cuirass: Fibers scheduling blocked.

Hey, > Yeah please go ahead if you want, or let me know if you’d rather let me > apply it. I applied your patch, thanks! I'm closing this one, because there's nothing much that can be done right now. Thanks, Mathieu

bug#43818: [PATCH] packages: Fix a bug in %patch-path.

Hello, Ludovic Courtès writes: > Hi, > > Maxim Cournoyer skribis: > >> Fixes . >> >> Having the Guix root trailed by a slash in the GUILE_LOAD_PATH would >> previously cause %patch-path to not return an entry with the patches >> sub-directory, leading to

bug#44257: guix boot stop

Hi Douglas, I think I've seen this before and the solution was to use the latest image, instead of the latest release because this issue was fixed after the last release. You can find more info on the latest installer at http://guix.gnu.org/en/download/latest/ Please tell us if it solves your

bug#44254: Performance of package input rewriting

Hi Lars, On Tue, 27 Oct 2020 at 14:26, Lars-Dominik Braun wrote: > Previously I have been doing this using package-input-rewriting, but starting > an environment containing python-jupyterlab alone took about 20s (warm caches, > all derivations in the store). Manually rewriting inputs by

bug#43850: cuirass: inconsistent SQL queries execution time.

Hello Chris, > I think Ricardo mentioned that the machine running Cuirass uses an SSD > for the root filesystem, so moving the database there may help? Looks like the database was already on the SSD before my tmpfs experiment. --8<---cut here---start->8---

bug#44256: “guix import cran -a bioconductor FOO” downloads twice

Dear, --8<---cut here---start->8--- $ guix import cran -a bioconductor CATALYST Starting download of /tmp/guix-file.OPtOW1 >From >https://bioconductor.org/packages/release/bioc/src/contrib/CATALYST_1.12.2.tar.gz... …12.2.tar.gz 10.2MiB

bug#44254: Performance of package input rewriting

Hi, this issue is similar to https://issues.guix.gnu.org/41702, but I’m not sure it’s exactly the same. For guix-science I’m trying to provide some packages like python-jupyterlab, which depend on a mix of packages from guix proper and newer versions of packages already included in guix proper.

bug#43850: cuirass: inconsistent SQL queries execution time.

Ludovic Courtès writes: > Hi, > > Mathieu Othacehe skribis: > >>> I have now copied the database to a tmpfs mounted directory to make sure >>> that those inconsistent duration are only caused by the I/O pressure on >>> berlin. >> >> This helps a lot. The Cuirass web service has been running