Quoting Jeffrey David Johnson (2015-06-18 06:20:57)
Wonderful, thanks for pushing it forward! I did some more on it but
then got sidetracked by grad school and kind of dropped the ball. There
is one more thing though...
After splitting CRAN and BIOC packages up, I discovered that
many of
Nope just that really, but it could use a little more explanation: when
downloading the new packages I found them to be unreliable. That is
each time some of the curl calls would fail but it would be different
ones. I think that might have to do with my heavily refactored
generate-r-packages.R, or
Hi Jeffrey,
we now have full Bioconductor support in master. According to
http://hydra.cryp.to/jobset/nixpkgs/r-updates, we can build about
7000 packages for R in Nix. Thank you very much for your help!
Best regards,
Peter
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Wonderful, thanks for pushing it forward! I did some more on it but
then got sidetracked by grad school and kind of dropped the ball. There
is one more thing though...
After splitting CRAN and BIOC packages up, I discovered that
many of the BIOC ones require other Annotation or Experiment data
Finally got around to writing it!
https://github.com/NixOS/nixpkgs/compare/master...jefdaj:bioc-pullreq-twofiles
I'm getting an error when installing a Bioconductor package with CRAN
dependency though... is that just me? I think they should be able to
find each other since the two sets get
Hi Jeffrey,
https://github.com/NixOS/nixpkgs/compare/master...jefdaj:bioc-pullreq
this looks good to me. Thank you very much for figuring this out!
The only thing I'd prefer is to have packages from CRAN and Bioconductor
in two separate files so that it's possible to re-generate them
Sure that sounds good. It would make storing the mirror type for each
package unneccesary too. I'll see if I can set it up later today so
the script takes 'cran' or 'bioc' as an argument and reads/writes
cran-packages.nix or bioc-packages.nix, then default.nix can read both
sets and map the right
OK, turns out it's not so bad! We can skip biocLite and install packages
directly, same as from CRAN. Draft changes here:
https://github.com/NixOS/nixpkgs/compare/master...jefdaj:bioc-pullreq
Opinions? I considered splitting off a separate
bioc-modules folder, but then I noticed the majority of
