RE: guix and mirroring dataset

>> Does the guix project and members suggest best guix-ish practices for >> managing on premise mirrors of large file-based data-sets such as >> appear in genomics HPC evironments? > >From my understanding, it is still “unsolved“ and there is no clear >answer. > >Basically, the /gnu/store is not d

guix and mirroring dataset

HI, Does the guix project and members suggest best guix-ish practices for managing on premise mirrors of large file-based data-sets such as appear in genomics HPC evironments? Perhaps a guix-ish response to [Go Get Data \(GGD\) is a framework that facilitates reproducible access to genomic da

RE: Free software telemetry and the Guix System

> Bone Baboon writes: > > What types of telemetry in free software programs are compatible with > > the Guix System? > > The relevant text in the GNU FSDG is here: > > > "No Malwa

RE: GWL 0.3.0 released

Do we know if a video recording Ricardo’s FOSDEM talk is/will be available? I don’t (yet?) see it in FOSDEM’s Youtube channel. Thanks!

Re: [Guix Website] A Search Page for Packages

A few quick thoughts – * There should be a link documenting the search language. Are there Booleans allowed? Is “stemming” automatic? Do quote characters do anything? Is proximity searching available? Regular expressions? What columns are searched? License? Version? Author? * I

Re: good practices in science

> I would like to find a community where I can do science in a good way. > I want to use free software and would like to collaborate through > version control, IRC, Jitsi, well formatted e-mails. Does such a > community exist? Look into [Center for Open Science](https://cos.io/) I the R world, t

FW: Guix: A most advanced operating system

FWIW: Discussion of this article https://ambrevar.xyz/guix-advance/index.html occurring on hacker news now at https://news.ycombinator.com/item?id=18902823

RE: Promoting the GNU Kind Communication Guidelines?

This so very well said - thank you Alex - were there a vote to recast mine flows thusly: > I'm so glad you brought this up, because it seems equally plausible to me > that the other party could be reacting overly sensitively. > > This is precisely why it is a bad idea to set up an authority

RE: website: say what Guix is at the very top

t: Monday, January 29, 2018 4:20 PM > To: Cook, Malcolm > Cc: Pjotr Prins ; myg...@gmail.com; guix- > de...@gnu.org; sirgazil > Subject: Re: website: say what Guix is at the very top > > > Hi Malcolm, > > > I entirely agree that with the right educational mater

RE: website: say what Guix is at the very top

Pjotr, that was excellently put! I entirely agree that with the right educational materials you are going to see have the possibility of appealing to other groups/cultures/biases. Having a section for each of the 2**3 type of user might be the perfect compromise. Perhaps try to appeal to each

RE: Guix Workflow Language ?

Hi, Watching this thread and trying to take the pulse of GWL. Where should I look? https://git.roelj.com/guix/gwl has little documentation - it does say " GWL has a built-in getting-started guide. To use it, run: guix workflow --web-interface" - but supposing we just want to read some document

guix in discussion on ycombinator hacker news

In case you missed it: https://news.ycombinator.com/item?id=13914260

RE: How to get the package metadata as structured data?

Hi, Could the guix project please make available the results of `guix package -s .` that would list all available packages in recutils format for those who do not (yet) have fully functioning guix install? Thanks? > -Original Message- > From: Guix-devel [mailto:guix-devel-bounces+me

RE: Test suite failures building 0.10.0 on CentOS7

PASS: tests/guix-build.sh PASS: tests/guix-environment.sh PASS: tests/builders.scm > -Original Message- > From: Ludovic Courtès [mailto:l...@gnu.org] > Sent: Wednesday, March 30, 2016 4:14 PM > To: Cook, Malcolm > Cc: Guix-devel > Subject: Re: Test suite failure

Test suite failures building 0.10.0 on CentOS7

Hi Guix Devel, I am (again) having (new) test suite failures while building guix version 0.10.0 on Cent0S-7 and would appreciate your help. I am building and testing as follows: env -i PATH=${PATH} bash ## build in a clean shell bld=$(mktemp -d) ## in a clean, new, empty directory cd $bld git c

http://xkcd.com/1654/

Perish the thought! ~ malcolm_c...@stowers.org

RE: Making the case for GNU Guix ... advice sought

guix-devel- > bounces+mec=stowers....@gnu.org] On Behalf Of Cook, Malcolm > Sent: Monday, February 29, 2016 10:55 AM > To: 'Ricardo Wurmus' > Cc: guix-devel@gnu.org; 'bio-packag...@mailman.open-bio.org' packag...@mailman.open-bio.org> > Subject: RE: Makin

RE: Making the case for GNU Guix ... advice sought

> Cook, Malcolm writes: > > > Hi Ricardo, > > > > Great specifics. If you can help me solve a few of my remaining > > questions, in-line below, I'd be much obliged > > Hi Malcolm, > > I see that others have already replied to some of

RE: Making the case for GNU Guix ... advice sought

Pjotr! > > Yes. Agreed. However, my emphasis here was intended to be that > > Guix can be used to obviate the need for rbenv, virtualenv, and > > friends.I thought that `guix environment` was going to be an > > effective replacement for them. Am I mistaken in this? > > I have dropped

RE: Making the case for GNU Guix ... advice sought

Hi Ricardo, Great specifics. If you can help me solve a few of my remaining questions, in-line below, I'd be much obliged.... > Cook, Malcolm writes: > > > I have been asked to write up an argument for the advantages that GNU > > Guix confers for deploying lin

RE: Making the case for GNU Guix ... advice sought

gt; bounces+mec=stowers@gnu.org] On Behalf Of Cook, Malcolm > Sent: Wednesday, February 10, 2016 10:02 AM > To: 'Ludovic Courtès' ; 'Ricardo Wurmus' > ; 'Pjotr Prins' ; 'Leo > Famulari' > Cc: 'Guix-devel' ; 'bio-packag

RE: Making the case for GNU Guix ... advice sought

Hi, Thanks everyone for the many valuable suggestions and education. Next week I intend to incorporate the suggested improvements as best I can and follow up with an edit that I will use in-house, and share back out via git-hub. Though the document is aimed at my particular internal "project ju

Making the case for GNU Guix ... advice sought

Hi, I have been asked to write up an argument for the advantages that GNU Guix confers for deploying linux software, especially scientific computing and including bioinformatics software. To that end I have written up this document https://github.com/malcook/sce/blob/master/Ma

RE: Funding the build farm

11. > -Original Message- > From: Ludovic Courtès [mailto:l...@gnu.org] > Sent: Wednesday, November 18, 2015 3:21 PM > To: Cook, Malcolm > Cc: Pjotr Prins ; guix-devel@gnu.org > Subject: Re: Funding the build farm > > "Cook, Malcolm" skribis:

RE: Funding the build farm

Hi, I don't know what kind of $ we're talking about, nor quite how to interpret all those up and down thumbs at lwn.net, but (once I've finally deployed guix) I'll certainly go to bat with my institute to free up some funding. Back to Pjotr's Q: How much would it cost to get some decent hardwa

RE: Should we start a Guix users wiki?

breplanet.org/wiki/Group:Guix/> for instance, but the > >> manual should clearly remain the primary source of documentation, > >> without any ambiguity. > Thank you for your feedback on this, I agree with your points, and that in > this > case the manual is the b

RE: New ‘guix graph’ command

Hi, I like the request. I think the dependent packages should be pointed to. In this way, each node in the graph and its outgoing arrows reflect the contents of a single package. ~Malco > -Original Message- > From: guix-devel-bounces+mec=stowers@gnu.org [mailto:guix-devel- > bo

RE: warning: failed to install locale: Invalid argument

> "Cook, Malcolm" skribis: > > > With each call to guix I get > > > > warning: failed to install locale: Invalid argument > > See > <http://www.gnu.org/software/guix/manual/html_node/Application- > Setup.html#Locales-1>. Thanks Ludo, I sh

RE: warning: guix collision encountered

Hi, > "Cook, Malcolm" skribis: > > > warning: collision encountered: > > /gnu/store/4zmkk7mwn4v2iid4nqldlxx9g6nszc5l-dconf- > 0.22.0/share/icons/h > > icolor/icon-theme.cache > > /gnu/store/1qrbdgrk7p6c1z80kz49gj6gsfk444wf-emacs- > 24.5/share/i

RE: How to handle required plugins and dbus services for GNOME Programs?

> On Thu, Jul 23, 2015 at 8:16 PM, Cook, Malcolm wrote: > > Hi, > > > > What fortune... > > > >> IMO, given that every GLib based program needs it, the right thing to > >> do is to make it an implicit input of 'glib-or-gtk-build-system'

warning: failed to install locale: Invalid argument

With each call to guix I get warning: failed to install locale: Invalid argument I am using fresh binary install of 0.8.3 into clean CentOS7 following http://www.gnu.org/software/guix/manual/html_node/Binary-Installation.html Can anyone provide guidance on how to proceed on this? Thx

RE: TIP: untar binary install tarball using option `--warning=no-timestamp`

> > > Hi, in Cent0S7 vendor supplies me with: > > > > tar --version > > tar (GNU tar) 1.26 > > Running ‘git blame’ on tar’s src/extract.c shows that warnings about zeroed > timestamps are no longer issued starting from tar 1.27, released in Oct. 2013. > I’ve amended the manual to mention that.

warning: guix collision encountered

Hi, In https://gnunet.org/bot/log/guix/2014-12-08 I read I just installed my second binary package (emacs) and I get this warning: [19:33:50] warning: collision encountered: /gnu/store/wsa1hpnqa9rzpw3irkr03ad6q3xblpmj-info-dir I too am getting collisions, for me wh

RE: How to handle required plugins and dbus services for GNOME Programs?

Hi, What fortune... > IMO, given that every GLib based program needs it, the right thing to do is to > make it an implicit input of 'glib-or-gtk-build-system'. > > In a similar way, every GLib based program/library makes use of sound > themes. For this to work it needs access to 'libcanberra'.

RE: TIP: untar binary install tarball using option `--warning=no-timestamp`

activity on selected "watched" bugs. Any such thing exists? Thanks! ~Malcolm > -Original Message- > From: Ludovic Courtès [mailto:l...@gnu.org] > Sent: Wednesday, July 22, 2015 4:49 PM > To: Cook, Malcolm > Cc: 'Guix-devel' > Subject: Re: TIP: unt

TIP: untar binary install tarball using option `--warning=no-timestamp`

Doing so avoids boatloads of warnings

RE: Using a shared Guix store (was RE: [Bio-packaging] testing out guix)

Original Message- > From: Cook, Malcolm > Sent: Monday, July 20, 2015 5:38 PM > To: 'Ludovic Courtès' > Cc: 'Ricardo Wurmus'; 'Guix-devel'; 'Pjotr Prins'; 'bio- > packag...@mailman.open-bio.org' > Subject: RE: Using a sha

RE: Using a shared Guix store (was RE: [Bio-packaging] testing out guix)

> > However > > > > ./pre-inst-env guix package -i hello > > > > Gives me > > > > guix package: error: build failed: the build users group > > `guix-builder' has no members > > > > But, but, I do have a group `guix-builder` > > > > I think the problem may be that my guix-builder group was d

RE: Using a shared Guix store (was RE: [Bio-packaging] testing out guix)

> I hope to chime in further with a big WOOHOO once I have this configuration > working Not quite WOOHOO yet. Getting close Here is where I am: I have built guix-0.8.2 on centOS7 passing all checks However ./pre-inst-env guix package -i hello Gives me guix package: e

RE: Test suite failures

11:46 AM > To: Cook, Malcolm > Cc: Guix-devel > Subject: Test suite failures > > (Stripping the list of recipients.) > > "Cook, Malcolm" skribis: > > > In that thread, you suggested "What about installing Guix in /gnu/bin (say) > and sharing i

RE: Using a shared Guix store (was RE: [Bio-packaging] testing out guix)

> Cook, Malcolm writes: > > > Also, you discussed need for setting NIX_STATE_DIR. This should not > > be needed if guix was already installed with configuration of > > --localstatedir=/guix/var (with /guix being nfs mounted), right? > > NIX_STATE_DIR is used to

RE: Formatting lists in descriptions

> Yes, why not; it’s still not very pleasant to the eye but at least it > formatting > will be preserved (except for guix-web, but we can fix it > later.) > > > And as I have an unhealthy desire to organize the same things in the > > same manner, what variant to choose for formatting lists? Shou

RE: Using a shared Guix store (was RE: [Bio-packaging] testing out guix)

Ludovic, and Ricardo, > Yes, one way to help would be by trying a simple setup using Guix as it > currently exists, coupled with socat: > > http://debbugs.gnu.org/cgi/bugreport.cgi?bug=20381 > > If you could test this and provide feedback about the other options discussed > there, that would b

RE: Using a shared Guix store (was RE: [Bio-packaging] testing out guix)

Hi Ludovic and Ricardo, > Ricardo Wurmus skribis: > > > Even then, /gnu would be mounted read-only on all but the management > > host, because there would still only be one daemon writing to the > > store and the localstatedir – even if it would take requests from > > multiple remote guix client

RE: Using a shared Guix store (was RE: [Bio-packaging] testing out guix)

Hi! > >> > Can anyone elaborate a little on what are the obstacles to having > >> > `/gnu` mounted read-write network wide? > >> > >> Yes, the primary problem is that the daemon assumes that it is the > >> only thing writing to the store and the localstatedir. Any > >> modification of profiles an

security concerns of using guix packages

Hello Guixen (Guixers? Guix-noscenti?) The sys admin at my institute expresses concern that we would potentially expose ourselves to additional security risk by building scientific software stack in Guix where we might depend on alternate versions of, say, openssl. Do you agree this is a reaso

RE: Using a shared Guix store (was RE: [Bio-packaging] testing out guix)

Ricardo, Thanks for your complete and easy-to-understand response to my inquiries. > > Can anyone elaborate a little on what are the obstacles to having > > `/gnu` mounted read-write network wide? > > Yes, the primary problem is that the daemon assumes that it is the only thing > writing to the

Using a shared Guix store (was RE: [Bio-packaging] testing out guix)

Ricardo, Pj, et al, ... Hi - I am resending this message as I omitted Guix-devel at first and would like to cast a broader net I am interested in understanding details behind Ricardo's observation: "Guix is not designed to be run in a centralised manner. A Guix daemon is supposed to run