To deploy GN we have packages in Guix itself (that comes with a distribution), in guix-bioinformatics and in guix-past (for older packages).
Typically run a guix pull to get the latest guix:
mkdir -p ~/opt guix package -i guix -p ~/opt/guix
and checkout guix-past and guix-bioinformatics using git.
Now Guix should be happy with
~/opt/guix-pull/bin/guix package -L ~/guix-bioinformatics/ -L ~/guix-past/modules/ -A genenetwork genenetwork1 0.0.0-2.acf65ac out /home/wrk/guix-bioinformatics/gn/past/genenetwork1.scm:148:4 genenetwork2 3.11-2.1328932 out /home/wrk/guix-bioinformatics/gn/packages/genenetwork.scm:452:4 genenetwork3 0.1.0-2.e781996 out /home/wrk/guix-bioinformatics/gn/packages/genenetwork.scm:107:4
and we can try building
~/opt/guix-pull/bin/guix build -L ~/guix-bioinformatics/ -L ~/guix-past/modules/ genenetwork2
Any errors at either command means that we have to fix packages.
Note that you can use tux02 as a substitute server, see the README in guix-bioinformatics. That means that any package you build on tux02 can be downloaded from guix.genenetwork.org. So, best to build on tux02 - so everyone can share!
On tux02, to ramp up parallel building speed, you may want to use `-c 24 -M 24 -k` switches.
Here python-pingouin failed. Which is pulled in by
tux02:~/guix-bioinformatics$ grep -r pingouin * gn/packages/genenetwork.scm: python-pingouin
git blame shows it was added in summer by Arun as part of the genenetwork3 package. A check of genenetwork3 shows
tux02:~/genenetwork3$ git blame gn3/computations/correlations.py
it was added by Alex in 2021.
Now it is not puzzling why the tests fail for this package as the Guix package does not build on the build farm, see
I am going to disable it for testing. By introducing the override
(define python-pingouin-without-tests (package (inherit python-pingouin) (arguments (substitute-keyword-arguments (package-arguments python-pingouin) ((#:tests? _ #f) #f)))))