[Nix-commits] [NixOS/nixpkgs] fb4a53: saga: 2.2.2 -> 2.3.1
Branch: refs/heads/master Home: https://github.com/NixOS/nixpkgs Commit: fb4a53b1c14def4490a9e8af559e432008f3 https://github.com/NixOS/nixpkgs/commit/fb4a53b1c14def4490a9e8af559e432008f3 Author: Michel Kuhlmann Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M pkgs/applications/gis/saga/default.nix Log Message: --- saga: 2.2.2 -> 2.3.1 ___ nix-commits mailing list nix-comm...@lists.science.uu.nl http://lists.science.uu.nl/mailman/listinfo/nix-commits
[Nix-dev] Documenting the R language (was: Using R with Bioconductor)
Hi, I started to write something up [1], which needs to be extended. There was also a discussion [2], if we should use a README and splice it into the documentation with pandoc. Indeed, a section on how to handle personal packages would be great. Greetings, Michel [1]: https://github.com/michelk/nixpkgs/blob/a0b93d7959bc1fba65aa08d8cc8d03f78e44da09/pkgs/development/r-modules/README.md [2]: https://github.com/NixOS/nixpkgs/pull/8154 ___ nix-dev mailing list nix-dev@lists.science.uu.nl http://lists.science.uu.nl/mailman/listinfo/nix-dev
[Nix-dev] Adding documentation to nixpkgs
Hi, I just wanted to update the R-CRAN-packages and I always forget how to check if the resulting expression could be evaluated. Therefor I created a basic README.md [1] directly within nixpkgs. So is this desirable or do you think this clutters up the source-tree? Greetings, Michel P.S.: For me, the wiki is not really accessible (I like to work offline in the train) and despite of that I don't like to write in mediawiki markup. [1]: https://raw.githubusercontent.com/michelk/nixpkgs/r-modules/update/pkgs/development/r-modules/README.md ___ nix-dev mailing list nix-dev@lists.science.uu.nl http://lists.science.uu.nl/mailman/listinfo/nix-dev
[Nix-dev] QGIS: Mismatch between compiled and running libpng
Hi, I'm just trying to update QGIS to version 2.6 [1]. I have two issues, when running the compiled executable: -libpng warning: Application was compiled with png.h from libpng-1.6.13 Application is running with png.c from libpng-1.2.50 error: Incompatible libpng version in application and library - an error: python ImportError: No module named _sysconfigdata_nd The first issue is also present in the current version. Could anyone assist? Thanks, Michel [1]: https://github.com/michelk/nixpkgs/commit/2097a72f8e6ed3f4ef2f16bd09f2643b61285975 ___ nix-dev mailing list nix-dev@lists.science.uu.nl http://lists.science.uu.nl/mailman/listinfo/nix-dev
Re: [Nix-dev] Developing R modules with nix
Thanks Peter for the very helpful answers. I have some follow-up
questions:
- Is it possible to make the package-executables available in the
search-PATH, when installing with `nix`? For example me, I put the
executables which are based on the package-library into the
`exec`-folder (see 1.1.5 [1]). My scripts usually use
`#!/usr/bin/env Rscript`; I guess this would have to be patched.
[1]: http://cran.r-project.org/doc/manuals/R-exts.html
- Workflow for developing personal R-package projects. In Haskell I've
seen the following pattern:
/projects/foobar/shell.nix
let
pkgs = import {};
haskellPackages = pkgs.haskellPackages.override {
extension = self: super: {
foobar = self.callPackage ./. {};
};
};
in
pkgs.lib.overrideDerivation haskellPackages.foobar(attrs: {
buildInputs = [ haskellPackages.cabalInstall ] ++
attrs.buildInputs;
})
/projects/foobar/default.nix
{ cabal, text, attoparsec }:
cabal.mkDerivation (self: {
pname = "foobar";
src = ./.;
version = "1.0";
buildDepends = [ text attoparsec ];
})
$HOME/.nixpkgs/config.nix
haskellProjects = { self, super, callPackage }: rec {
foobar = callPackage /projects/foobar {};
};
haskellPackages_wrapper = hp: self.recurseIntoAttrs (hp.override {
extension = this: super: haskellProjects {
self = this;
super = super;
callPackage = self.lib.callPackageWith this;
};
});
haskellPackages_ghc783 =
haskellPackages_wrapper (recurseIntoAttrs
haskell.packages_ghc783.noProfiling);
Then I could install foobar with
nix-env -iA nixpkgs.haskellPackages.foobar
Could you give me a hint how to accomplish an analog behavior for my personal
R-packages?
Thanks, Michel
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[Nix-dev] [nix-dev] Re: Developing R modules with nix
> if you write that code like so instead:
>
> packageOverrides = super: let self = super.pkgs; in
> {
> rWrapper = super.rWrapper.override {
> packages = with self.rPackages; [ Defaults data_table ];
> };
> };
>
> then it should work just fine. 'super' refers to the package set before
> the overrides are applied and 'self' is the package set after the
> overrides have been applied. This distinction is important, because an
> override like
>
> rWrapper = self.rWrapper.override { ...}
>
> tries to replace itself with its value after having replaced itself with
> its value after having replaced itself ... a.k.a. infinite recursion. :-)
Thanks Peter for clarification; is this the preferred way to declare
user-packages? Could you argue about benefits or drawbacks of the *Wrapper
vs *ToolsEnv approach?
-Michel
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Re: [Nix-dev] Developing R modules with nix
Hi Peter,
> what do you mean by "didn't work out"? What exactly didn't work?
I guess I mixed up my config; I already had John's *ToolsEnv-pattern for
haskell in my config:
{ pkgs }: {
packageOverrides = self: with pkgs; rec {
haskellToolsEnv = pkgs.buildEnv {
name = "haskellTools";
paths = with haskellPackages; [
ghc
cabalInstall_1_20_0_3
ghcMod_5_0_1_2
hlint
hasktags
cabal2nix
stylishHaskell
pandoc
hindent
ghcServer
];
};
rWrapper = pkgs.rWrapper.override {
packages = with pkgs.rPackages; [ Defaults data_table ];
};
};
}
Then using `rWrapper` lead to
error: infinite recursion encountered
(use ‘--show-trace’ to show detailed location information)
Greetings, Michel
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Re: [Nix-dev] Developing R modules with nix
Hi Peter,
> > Currently I have in my `.nixpkgs/config.nix` an entry with
> >
> > rToolsEnv = pkgs.buildEnv {
> > name = "rTools";
> > paths = with rPackages; [
> > devtools
> > ggplot2
> > ];
> > };
> >
> > and I am installing it with `nix-env -i rTools`
>
> interesting ... why do you prefer that approach? I would have used
>
> rWrapper = super.rWrapper.override {
> packages = with self.rPackages; [ devtools ggplot2 ]
> };
>
In the first place I was trying the approach listed on the mailing list [1]:
{
packageOverrides = pkgs: {
rWrapper = pkgs.rWrapper.override {
packages = with pkgs.rPackages; [ Defaults data_table ];
};
};
}
which didn't immediately work out; this is why I used John's [2] approach,
which did.
[1]: http://www.mail-archive.com/nix-dev%40lists.science.uu.nl/msg11757.html
[2]: https://github.com/jwiegley/nix-config/blob/master/config.nix
> I'm not much of an R developer, so I cannot say much about this subject.
> A default.nix that you could use to build your local project with Nix
> is:
>
> | let
> |
> | pkgs = import {};
> | buildRPackage = import
> pkgs.R;
> |
> | in
> |
> | with pkgs.rPackages;
> |
> | {
> | foobar = buildRPackage {
> | name = "your-package-name-1.0";
> | src = ./.;
> | propagatedBuildInputs = [/* required dependencies go here */];
> | };
> | }
>
> The command "nix-build . -A foobar" would then compile it.
>
> I hope this helps,
Thanks a lot; this helped,
Michel
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[Nix-dev] Developing R modules with nix
Hi,
I have two issues related to using R with nix:
- Fixing the CRAN-mirror
- a `default.nix`-file for an R-package.
Fixing the CRAN-mirror
--
Currently I have in my `.nixpkgs/config.nix` an entry with
rToolsEnv = pkgs.buildEnv {
name = "rTools";
paths = with rPackages; [
devtools
ggplot2
];
};
and I am installing it with `nix-env -i rTools`
Could I somehow fix the CRAN-mirror to use eg. with
`cranMirror = "http://stat.ethz.ch/CRAN/src/contrib/"`
default.nix
---
I'm looking for an example default.nix file, which I can put into my R-package
directory; could someone suggest me a common workflow for developing the
R-package?
Thanks, Michel
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