Re: [Nix-dev] Nix expression for OpenModelica

2015-06-18 Thread Rok Garbas
Quoting Sergey Mironov (2015-06-14 00:38:05)
 Hi! I've started to write Nix expression for building OpenModelica
 (https://openmodelica.org/index.php) the open source simulation
 environment. Currently, I have several 'standalone' nix expressions located at
 https://github.com/grwlf/nixcfg/tree/openmodelica/src/pkgs/OpenModelica
 
 At the moment, builder is able to pass configuration stage, but
 it runs out of memory somewhere in the middle of compilation:
 OpenModelica is a big thing, but my machine is not. If anyone has
 interest in building the tool, you are welcome to join the initiative!
 

i would suggest you open a pull request against github.com/NixOS/nixpkgs so
that others can test it easier.


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Re: [Nix-dev] Using R with Bioconductor

2015-06-18 Thread Rok Garbas
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 the BIOC ones require other Annotation or Experiment data
 packages. So I added those too. They're hosted on the same bioconductor
 servers but under different subdirectories. I added them as separate
 files because it was easier with my existing code, but hoped to
 integrate them into the same BIOC file and update the broken packages
 list before doing a pull request. Then I didn't get around to it.
 
 This is a working implementation (just missing the updated broken
 list) that shows the new subdirectories in default.nix around line 50:
 
 https://github.com/jefdaj/nixpkgs/tree/master/pkgs/development/r-modules
 
 Any chance that could make it into the release too?
 Jeff
 

Hi Jeffrey,

This really looks nice, I would love to see this in 15.06.

I see 3 TODO items here [1] I we want to remove them. Is there anythigs left on
you todo list?

And maybe R language should get a short section in the manual [2] since there
is no mention of language support of R. Instructions how to update the manual
are here [3].



[1] 
https://github.com/NixOS/nixpkgs/compare/master...jefdaj:master#diff-789598f937b7fe2f8e737d7e3f4e206dR3
[2] http://nixos.org/nixpkgs/manual/#chap-language-support
[3] https://nixos.org/wiki/Contributing_to_Nix_documentation



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Re: [Nix-dev] Using R with Bioconductor

2015-06-18 Thread Jeffrey David Johnson
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 with my university internet. It works slower
but more reliably from my laptop off campus. Best guess is that
either I triggered some kind of limit on concurrent or daily downloads
from bioconductor.statistik.tu-dortmund.de, or I was downloading faster
than my hard drive could write (such a first world problem!). I
partially fixed it by running the script repeatedly.

I'd also like to write something short in the manual/wiki.
Embarassingly I haven't figured out how to write/build my own R
packages using buildRPackage yet though. It never came up because my
current project is a mess of R + python + bash code glued together with
makefiles. But any of the pre-hashed R packages can be installed or used
in a shell like you'd expect:

with import nixpkgs {};
stdenv.mkDerivation {
  buildInputs = with rPackages; [ package1 package2 ... ];
}

Jeff

On Thu, 18 Jun 2015 14:04:41 +0200
Rok Garbas r...@garbas.si wrote:

 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 the BIOC ones require other Annotation or Experiment data
  packages. So I added those too. They're hosted on the same bioconductor
  servers but under different subdirectories. I added them as separate
  files because it was easier with my existing code, but hoped to
  integrate them into the same BIOC file and update the broken packages
  list before doing a pull request. Then I didn't get around to it.
  
  This is a working implementation (just missing the updated broken
  list) that shows the new subdirectories in default.nix around line 50:
  
  https://github.com/jefdaj/nixpkgs/tree/master/pkgs/development/r-modules
  
  Any chance that could make it into the release too?
  Jeff
  
 
 Hi Jeffrey,
 
 This really looks nice, I would love to see this in 15.06.
 
 I see 3 TODO items here [1] I we want to remove them. Is there anythigs left 
 on
 you todo list?
 
 And maybe R language should get a short section in the manual [2] since there
 is no mention of language support of R. Instructions how to update the manual
 are here [3].
 
 
 
 [1] 
 https://github.com/NixOS/nixpkgs/compare/master...jefdaj:master#diff-789598f937b7fe2f8e737d7e3f4e206dR3
 [2] http://nixos.org/nixpkgs/manual/#chap-language-support
 [3] https://nixos.org/wiki/Contributing_to_Nix_documentation
 
 
 
 --
 Rok Garbas - http://www.garbas.si
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[Nix-dev] nixops deploying to libvirtd

2015-06-18 Thread Richard Wallace
Hello all,

I'm trying to get a project setup to deploy to libvirtd locally instead of
VirtualBox because I've grown a bit tired of VirtualBox being so buggy.
But I'm having issues getting the libvirtd deployment going and I'm hoping
someone can help me along.

I'm running NixOS on the host, so in my configuration.nix I added
virtualisation.libvirtd.enabled = true; and added my user into the
libvirtd group.

When trying to deploy the first time, I received the error

error: [Errno 13] Permission denied: '/var/lib/libvirt/images'

So I went off and created it with 770 perms owned by root:libvirtd. After
trying to deploy again, I get

error: [Errno 2] No such file or directory:
'/var/lib/libvirt/dnsmasq/default.leases'

I'm not sure what I need to do now, so I'm a bit stuck. Any advice?

Thanks,
Rich
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