Re: [Nix-dev] Automatically locking the screen with xautolock

Nice! I'm currently binding gksu 'i3lock -c00 pm-suspend' to a hotkey using i3, but this is better. Is there a standard way to get it in my fork of nixpkgs, which is tracking the release-14.12 branch? (I could just copy and paste but if there's a better way now would be a good time to

Re: [Nix-dev] Disallowed host while building Python packages?

-packages-generated.nix? They're formatted just like the non-generated ones so I'm thinking generated means some other process? Jeff On Mon, 16 Feb 2015 09:30:16 +0100 Rok Garbas r...@garbas.si wrote: Quoting Jeffrey David Johnson (2015-02-16 04:56:35) I've had this happen a couple times now when

Re: [Nix-dev] Unstable Nixpkgs on stable NixOS (was: Automatically locking the screen with xautolock)

, Jeffrey David Johnson wrote: Nice! I'm currently binding gksu 'i3lock -c00 pm-suspend' to a hotkey using i3, but this is better. Is there a standard way to get it in my fork of nixpkgs, which is tracking the release-14.12 branch? (I could just copy and paste but if there's a better way

Re: [Nix-dev] Regex in manifest breaks nix-env

profile for testing and have my long-term package lists in a separate git repo. Jeff On Tue, 17 Mar 2015 18:26:26 +0100 Eelco Dolstra eelco.dols...@logicblox.com wrote: Hi, On 17/03/15 18:11, Jeffrey David Johnson wrote: Hi all! My nix-env commands recently stopped working. For example

[Nix-dev] NixOps doesn't work with EC2 anymore?

I'm trying to set up a server for my lab to do bioinformatics. I'm following the manual here: http://hydra.nixos.org/build/20346360/download/1/manual/manual.html#sec-deploying-to-ec2 I got to the `deploy` step but then Amazon gives me an this error: error: EC2ResponseError: 400 Bad Request

[Nix-dev] Regex in manifest breaks nix-env

Hi all! My nix-env commands recently stopped working. For example if I try to `nix-env -q`, it says: error: syntax error, unexpected $undefined, expecting '', at /nix/store/ar83fv0d68frfyifz2wl1dm97m6jvxnn-env-manifest.nix:1:153 The contents of

[Nix-dev] Using R with Bioconductor

Do any of you guys/gals use R and Bioconductor? The only page I can find related to setting it up is https://nixos.org/wiki/R. Bioconductor is a whole additional ecosystem on top of R/CRAN, with its own installer. You normally use it like: source(http://bioconductor.org/biocLite.R;)

Re: [Nix-dev] Getting started with nix-build

Yeah I'd like to know this too. I suspect there's a flag for it but not sure what it would be called. Also if you're building the latext nixpkgs from github hydra might not have cought up yet. I think standard practice is to stay a few commits back so can get binaries. I asked a semi-related

[Nix-dev] Help packaging BLAST?

Hi! The existing BLAST package (https://github.com/NixOS/nixpkgs/blob/master/pkgs/applications/science/biology/ncbi-tools/default.nix) isn't working for me. Probably because it's broken on x64. So I'm trying to package the standalone executables from http://www.ncbi.nlm.nih.gov/books/NBK52640/

Re: [Nix-dev] [***SPAM***] git:// repositories in nixpkgs

At least on github there's always an equivalent https:// url right? On Fri, 27 Mar 2015 12:49:04 -0400 Shea Levy s...@shealevy.com wrote: fetchurl has a concept of multiple urls and mirrors, I’m not sure if fetchgit does but it would be nice for this use case. git:// should be preferred when

[Nix-dev] What am I doing wrong with ssh-substitutor-hosts?

I've got two computers with nixos, and I can ssh between them without a password. But if I do a nixos-rebuild with `--option ssh-substitutor-hosts hostname` they still just download everything from cache.nixos.org. I think I have the sshServe set up in my configuration.nix: # nixServeKeys are

[Nix-dev] buildPythonPackage: add src to PYTHONPATH before build?

I'm trying to package a python application (https://github.com/dagraham/etm-tk). I made an initial package with python2nix, but when I try to install it I get: installing ‘python2.7-etm’ these derivations will be built: /nix/store/a1xn163ms6rg3w9k901lr6fga4lawqx9-python2.7-etm.drv building

Re: [Nix-dev] Haskell NG: Local packages

It's not specific to Haskell (and I haven't tried haskellng at all yet) but for personal packages I have mypkgs/pkgname/default.nix, and then a top-level mypkgs/default.nix: let nixpkgs = import nixpkgs {}; callPkg = nixpkgs.newScope ( nixpkgs //

Re: [Nix-dev] How to bootstrap a server using Nixops?

On Fri, 1 May 2015 08:46:14 + Rob Vermaas rob.verm...@gmail.com wrote: Hi Jeff, On Thu, Apr 30, 2015 at 11:17 PM, Jeffrey David Johnson jef...@gmail.com wrote: It's possible I'm getting the wrong idea about what nixops is for, but I used it to set up an Amazon EC2 instance

[Nix-dev] How to bootstrap a server using Nixops?

It's possible I'm getting the wrong idea about what nixops is for, but I used it to set up an Amazon EC2 instance with the idea of logging into the server and administering it using local commands afterward. The initial install goes fine. Afterward I clone my nixcfg repo (including nixpkgs

Re: [Nix-dev] What am I doing wrong with ssh-substitutor-hosts?

‘download-via-ssh’ died unexpectedly If I ssh in manually bash is found fine. Jeff On Tue, 07 Apr 2015 11:45:12 +0200 Eelco Dolstra eelco.dols...@logicblox.com wrote: Hi, On 02/04/15 20:56, Jeffrey David Johnson wrote: I've got two computers with nixos, and I can ssh between them without

[Nix-dev] R package name can't be used in variable substitution?

I put together an example package that generates a bash script: # default.nix with import nixpkgs {}; stdenv.mkDerivation { name = varSubTest; src = ./.; inherit R; rByAnotherName = R; builder = ./builder.sh; } # builder.sh #!/usr/bin/env bash source $stdenv/setup mkdir -p $out/bin

Re: [Nix-dev] Best practices for replacing channels with my own package set?

James Cook james.c...@utoronto.ca wrote: I have a symlink from ~/.nix-defexpr/myhead to the nixpkgs tree I want to use. James On 1 June 2015 at 17:35, Jeffrey David Johnson jef...@gmail.com wrote: Nevermind, that sets NIX_PATH but nix-env still errors out with: nix-env: src/libexpr

Re: [Nix-dev] funding nixos documentation

...@gmail.com wrote: I have thought about opening small bounties for nixos. Probably only 20-50 dollars a month though. Not clear how far that would go though. On Wed, Jun 3, 2015 at 2:37 PM, Tomasz Kontusz tomasz.kont...@gmail.com wrote: On 06/03/2015 08:21 PM, Jeffrey David Johnson wrote

Re: [Nix-dev] Using R with Bioconductor

...@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

Re: [Nix-dev] Using R with Bioconductor

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

Re: [Nix-dev] funding nixos documentation

Oops, replying to the whole list now. Begin forwarded message: Date: Wed, 3 Jun 2015 11:20:10 -0700 From: Jeffrey David Johnson jef...@gmail.com To: Joachim Schiele j...@lastlog.de Subject: Re: [Nix-dev] funding nixos documentation I like the idea but can't personally pay for it :( I see you

Re: [Nix-dev] Shape configuration.nix differently

Isn't that the same as ``` { imports = [ ./hardware-configuration.nix ./boot/grub.nix ]; } ``` ? I think you can still access config and pkgs from each file. Jeff On Fri, 29 May 2015 01:55:34 +0200 Nicolas Pierron nicolas.b.pier...@gmail.com wrote: I am not sure to understand your

[Nix-dev] Best practices for replacing channels with my own package set?

I'd like all the nix tools to reference my package repository, which is called mypkgs and re-exports nixpkgs with some custom ones added. I base it on the latest nixos-unstable revision so there should be binaries available. Currently I set NIX_PATH using `environment.interactiveShellInit`. That

Re: [Nix-dev] Using R with Bioconductor

unioned. Jeff On Tue, 26 May 2015 09:31:35 -0700 Jeffrey David Johnson jef...@gmail.com wrote: 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

Re: [Nix-dev] Best practices for replacing channels with my own package set?

Nevermind, that sets NIX_PATH but nix-env still errors out with: nix-env: src/libexpr/eval.hh:57: void nix::Bindings::push_back(const nix::Attr): Assertion `size_ capacity' failed. Aborted Unless explicitly given the -f option. Jeff On Tue, 2 Jun 2015 00:31:35 +0200 Herwig Hochleitner

Re: [Nix-dev] Best practices for replacing channels with my own package set?

Thanks, the mkForce was what I was missing! Jeff On Tue, 2 Jun 2015 00:31:35 +0200 Herwig Hochleitner hhochleit...@gmail.com wrote: I set NIX_PATH in environment.sessionVariables (with an mkForce, to override the builtin one). nix-env and everything else should pick it up, that way, since

Re: [Nix-dev] Garbled man pages/incomplete environment

Cook james.c...@utoronto.ca wrote: On 4 July 2015 at 09:24, Jeffrey David Johnson jef...@gmail.com wrote: I'm having the same issue described here on the Gentoo forums: https://forums.gentoo.org/viewtopic-t-670013.html Man pages are hard to read because they're full of control characters

Re: [Nix-dev] Garbled man pages/incomplete environment

infrastructure is supposed to take care of the // part for you. I think the infinite recursion happens because config.environment.variables is partly based on the value you define for environment.variables. James On 5 July 2015 at 10:51, Jeffrey David Johnson jef...@gmail.com wrote: Thanks, you're

Re: [Nix-dev] Garbled man pages/incomplete environment

wrote: Hi, On 04/07/15 18:24, Jeffrey David Johnson wrote: Man pages are hard to read because they're full of control characters. For example: NIXOS-REBUILD(8) NixOS Reference Pages NIXOS-REBUILD(8) ESC[1mNAMEESC[0m This can be a symptom

[Nix-dev] Garbled man pages/incomplete environment

I'm having the same issue described here on the Gentoo forums: https://forums.gentoo.org/viewtopic-t-670013.html Man pages are hard to read because they're full of control characters. For example: NIXOS-REBUILD(8) NixOS Reference Pages NIXOS-REBUILD(8)

Re: [Nix-dev] Using R with Bioconductor

and make a pull request? I've attached the bash script I made to list remaining dependencies. After I ran it I had to go through and manually correct some things it doesn't pick up, like packages that exist but are known not to build. Jeff On Sun, 8 Mar 2015 12:00:27 -0700 Jeffrey David Johnson jef

Re: [Nix-dev] Python packages with __future__ imports broken by wrapper?

Kožar do...@dev.si wrote: Are you using unstable branch or 14.12? I think we'll need to drop use of sed and go with Python AST parsing for injecting program name. On Thu, May 21, 2015 at 6:11 PM, Jeffrey David Johnson jef...@gmail.com wrote: I installed python27Packages.googlecl

[Nix-dev] Python packages with __future__ imports broken by wrapper?

I installed python27Packages.googlecl, and when running `google` it says: File /nix/store/1ksk91s0kd1sv2clrkwcvzcmr67smgps-python2.7-googlecl-0.9.14/bin/.google-wrapped, line 45 from __future__ import with_statement SyntaxError: from __future__ imports must occur at the beginning of the

Re: [Nix-dev] Using R with Bioconductor

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

Re: [Nix-dev] Mark two packages incompatible, but with the same priority?

Nevermind, just noticed the same behavior with plain bitcoin vs bitcoind, so maybe it's OK as is? On Tue, 18 Aug 2015 11:11:40 -0700 Jeffrey David Johnson jef...@gmail.com wrote: I'm trying to add BitcoinXT support. Changes here: https://github.com/NixOS/nixpkgs/compare/master

[Nix-dev] Mark two packages incompatible, but with the same priority?

I'm trying to add BitcoinXT support. Changes here: https://github.com/NixOS/nixpkgs/compare/master...jefdaj:bitcoinxt-pullreq It works as long as you only install bitcoin or bitcoin-xt, but trying one after the other they collide. Is there a way to set it up so installing either one overrides

Re: [Nix-dev] Logo improvement ideas

I like logo-slant-half best. They're all good though! On Mon, 24 Aug 2015 03:20:20 + Luke Clifton ltclif...@gmail.com wrote: Hi Tim, Nice work, I quite like the look of the 'hex' variations. Regards, Luke On Mon, 24 Aug 2015 at 13:14 Tim Cuthbertson t...@gfxmonk.net wrote:

Re: [Nix-dev] /etc/nixos/configuration.nix vs ~/.nixpkgs/config.nix

I do that too, here's my repo (of course also messy): https://github.com/jefdaj/nixcfg In particular the installDotfiles function here: https://github.com/jefdaj/nixcfg/blob/master/modules/util.nix works for probably half of the dotfiles I wanted to install. The rest were more complicated and

[Nix-dev] Nix-prefetch-git from branch?

How do I nix-prefetch-git from a branch other than master? I've tried the -m, -t, and -f flags but none of them seems to work with a commit id or branch name. I just get: error: hash ‘repourlhere’ has wrong length for hash type ‘sha256’ ___ nix-dev

[Nix-dev] How do I get the system crontab to work?

I see here that there are upstream issues with cron as far as setting user crontab entries: http://lists.science.uu.nl/pipermail/nix-dev/2014-September/014120.html But I'm having trouble setting the system ones as well. I think if they didn't work at all a lot of other things would fail, so I

[Nix-dev] imported archive lacks a signature?

What does this error mean? $ nix-copy-closure --to jefdaj@server $(type -tP labwiki) copying 166 missing paths (1820.22 MiB) to ‘jefdaj@server’... exporting path ‘/nix/store/cgddwzz9hkdgprvbymphv8yprc66zxk7-ghc-7.10.1’ exporting path

[Nix-dev] How to debug 'error: getting status of ... no such file or directory'?

I have what seems like a straightforward issue with paths, but am not sure how to debug it. I run my usual "update everything" script, which looks like this and is located at /git/hub/nixcfg/install.sh: #!/usr/bin/env bash # Automates rebuilding nixos from my repos. # Takes the same args as

Re: [Nix-dev] How to debug 'error: getting status of ... no such file or directory'?

everything! Fixed by deleting /etc/nixos. Jeff On Tue, 1 Sep 2015 12:07:12 -0700 Jeffrey David Johnson <jef...@gmail.com> wrote: > I have what seems like a straightforward issue with paths, but am not > sure how to debug it. I run my usual "update everything" scri

Re: [Nix-dev] Tablet stylus stopped working

gt; - Alexei > > On Mon, Sep 14, 2015, at 08:57 AM, Jeffrey David Johnson wrote: > > My wacom stylus recently stopped working. I wasn't doing anything > > nix-related at the time (just working in Inkscape) and booting into > > older generations doesn't fix it. The eraser tip a

[Nix-dev] Tablet stylus stopped working

My wacom stylus recently stopped working. I wasn't doing anything nix-related at the time (just working in Inkscape) and booting into older generations doesn't fix it. The eraser tip and side button keep working but nothing from the main tip. I can't get it to show up in xev or

Re: [Nix-dev] Tablet stylus stopped working

Solution in case someone has the same issue in the future: it's nothing to do with NixOS. Alexei was correct. Got a new stylus (HP instead of a knock-off this time) and it works again. Jeff On Sun, 13 Sep 2015 18:37:39 -0700 Jeffrey David Johnson <jef...@gmail.com> wrote: > Yeah I thi

Re: [Nix-dev] imported archive lacks a signature?

Thanks, that works! On Fri, 28 Aug 2015 10:45:06 +0200 Peter Simons sim...@cryp.to wrote: Hi Jeffrey, $ nix-copy-closure --to jefdaj@server $(type -tP labwiki) [...] error: imported archive of ‘/nix/store/cgddwzz9hkdgprvbymphv8yprc66zxk7-ghc-7.10.1’ lacks a signature to remedy

[Nix-dev] Wrap Debian packages with buildFHSUserEnv

I read this post by Anders J Papitto: http://anderspapitto.com/posts/2015-02-28-deb-installation-nixos.html and got excited. You can actually install Debian packages? Even complex ones like Steam? I started refactoring his example and surprisingly it wasn't hard to put in an automation-friendly

[Nix-dev] python2nix requires old pip?

What's the current state of the py*2nix helpers? I just tried to run python2nix and got this: $ python2nix Traceback (most recent call last): File "/nix/store/mpzwan1fyraps3kmigpda76lzyj9r9qy-python2nix-20140927/bin/.python2nix-wrapped", line 8, in from python2nix import main File

Re: [Nix-dev] Latex package to handle unicode characters?

, Jeffrey David Johnson wrote: > > I get the following error when exporting some markdown to PDF with pandoc: > > > > An error occured: PDF creation failed: > > ! Package inputenc Error: Unicode char \u8:  not set up for use with > > LaTeX. > > &

Re: [Nix-dev] Raspberry-Pi NixOS

I tried a few months ago and wasn't able to get it working. It runs, but I wasn't able to upgrade Nix. May have been a temporary problem fixed in recent versions though. Jeff On Wed, 15 Jun 2016 15:19:19 +0200 Matthias Beyer wrote: > On 15-06-2016 14:52:22, Lluís Batlle i

[Nix-dev] Latex package to handle unicode characters?

I get the following error when exporting some markdown to PDF with pandoc: An error occured: PDF creation failed: ! Package inputenc Error: Unicode char \u8:  not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help.

Re: [Nix-dev] Unwanted, unannounced reboot

I have a probably-unrelated issue, but mentioning it just in case. Mine involves VirtualBox. When starting up I will log in and open my email or something, but in the background the vboxnet0 service will be failing to start via systemd. When it times out after 90 sec the X server is killed