Re: Reproducible rust builds

[Joe Hillenbrand]

On Mon, Oct 15, 2018 at 1:21 PM Joe Hillenbrand  wrote:
>
> I've pulled your repo and started a build with 4 rounds just to check.
> It will probably take a couple of days.
>

FYI, the build completed without issue.

Re: Trying to crosscompile for POWER9

[Marius Bakke]

Jonathan Brielmaier  writes:

> On 10/16/18 8:08 PM, Tobias Platen wrote:
>> Hello,
>> 
>> When I try to compile GUIX for POWER9 an old version of GCC is used.
>> How do I use the gcc version used for cross compiling.
>> 
>> ./pre-inst-env guix build --target=powerpc64le-linux hello
>> 
>> checking if powerpc64le-linux-gcc supports
>> binary128 floating point type... no
>> checking if the target machine is at least POWER8... yes
>> 
>> configure: error: ***
>> binary128 floating point type (GCC >= 6.2) is required on powerpc64le.
>> 
>> Tobias "Tomoko" Platen
>> 
>
> Note that Marius Bakke started a branch to update guix to gcc7:
> https://git.savannah.gnu.org/cgit/guix.git/log/?h=wip-gcc7
>
> This could be maybe a good starting point. The bug number is: bug#32953

Note that the cross-toolchain is broken in that branch, so it won't get
very far.  I hope to resolve that in the coming weeks and merge it to
'core-updates-next'.

Efraims suggestion is probably the best bet for now.


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Re: [outreach] Help trying to create R package

[Laura Lazzati]

On Wed, Oct 17, 2018 at 2:13 PM Clément Lassieur  wrote:
>
> Hi Laura,
>
> Laura Lazzati  writes:
>
> > You were right. I took a look at my .bashrc file, and I had an:
> > export PATH="/home/laura/.guix-profile/bin${PATH:+:}$PATH"
> > I ran $guix pull, did the PATH export in my CLI, then checked the output of
> > $which guix, that was the same that was mentioned by you,
> > commented that previous line in .bashrc,
> > added  export PATH="/home/laura/.config/guix/current/bin${PATH:+:}$PATH"
> > and ran again the command to check the available R packages, made a
> > diff with the previous one, and now at least r-bae appears.
>
> You should export environment variables such as PATH in
> ‘~/.bash_profile’ instead of ‘~/.bashrc’.  :-)
>
> Quoting the documentation[1]:
>
> Users sometimes wrongfully augment environment variables such as
> ‘PATH’ in their ‘~/.bashrc’ file.  As a consequence, when ‘guix
> environment’ launches it, Bash may read ‘~/.bashrc’, thereby
> introducing “impurities” in these environment variables.  It is an
> error to define such environment variables in ‘.bashrc’; instead,
> they should be defined in ‘.bash_profile’, which is sourced only by
> log-in shells.  See ‘Bash Startup Files[2]’, for details on Bash
> start-up files.
Thanks! I am reading that part now, specially [2].
I have deleted the env variables from .bashrc and have just set them
in .profile, since my distro is Ubuntu, and I am reading that Ubuntu
does not use .bash_profile. Everything seems to be working fine. Thank
you again :)

> Cheers,
> Clément
>
> [1]: 
> https://www.gnu.org/software/guix/manual/en/html_node/Invoking-guix-environment.html#FOOT15
> [2]: 
> https://www.gnu.org/software/bash/manual/html_node/Bash-Startup-Files.html#Bash-Startup-Files

Re: Packaging Inferno

[Diego Nicola Barbato]

Hello Nils,

Nils Gillmann  writes:

> Diego Nicola Barbato transcribed 12K bytes:
>> Hello,
>> 
>> Thank you for your feedback.
>> 
>> Nils Gillmann  writes:
>> 
>> > Ludovic Courtès transcribed 1.9K bytes:
>> >> Hello Diego,
>> >> 
>> >> Diego Nicola Barbato  skribis:

[...snip...]

>> >> >  ;; build mk
>> >> >  (invoke "./makemk.sh")
>> >> 
>> >> It would be ideal if we had a separate package for ‘mk’ (I suppose it
>> >> can run on POSIX systems, right?).
>> 
>> @Ludo:  This is Plan 9's mk (their version of make), which, I believe,
>> can run on POSIX systems.  Though, if we were to add mk to Guix, i would
>> rather package the one provided by Plan 9 from Userspace [7] since that
>> project seems to be more active than Inferno.
>> 
>> > I can finish my mk package and send it in.
>> > My mk is the canonical set of mk files as used by bmake.
>> > Sources are from http://crufty.net/help/sjg/mk-files.htm
>> > and/or places linked from there.
>> >
>> > If this matches the mk mentioned here, I can create this patch.
>> 
>> @Nils:  Your mk package seems to be unrelated to Plan 9's mk.
>
> Aha! I have it in 9base, which I have also packaged. At least according
> to the README in the 9base/mk/ folder it should be compatible.
>
> Now I don't know if we want all of 9base... I would leave analyis of
> that to you. If 9base on its own does not work, I can extract mk or
> create a package which just builds mk and gets rid of the other files.
>
> https://git.suckless.org/9base
>
> I haven't checked but would assume that differences exist between
> 9base (altough it states plan9 + inferno os) and inferno os mk.

AFAICT it should be possible to build inferno using 9base's mk.  In fact
I think 9base is better suited for this purpose than Plan 9 from
Userspace (plan9port), which was where I suggested we should get mk
from, since it is much smaller.

I can not tell from the source if it will be necessary to extract mk, so
I will try to build inferno using 9base's mk as soon as you send in your
patch and get back to you should I encounter any problems caused by one
of the other commands provided by 9base.

Thanks!

Diego

Re: [outreach] Help trying to create R package

[Clément Lassieur]

Hi Laura,

Laura Lazzati  writes:

> You were right. I took a look at my .bashrc file, and I had an:
> export PATH="/home/laura/.guix-profile/bin${PATH:+:}$PATH"
> I ran $guix pull, did the PATH export in my CLI, then checked the output of
> $which guix, that was the same that was mentioned by you,
> commented that previous line in .bashrc,
> added  export PATH="/home/laura/.config/guix/current/bin${PATH:+:}$PATH"
> and ran again the command to check the available R packages, made a
> diff with the previous one, and now at least r-bae appears.

You should export environment variables such as PATH in
‘~/.bash_profile’ instead of ‘~/.bashrc’.  :-)

Quoting the documentation[1]:

Users sometimes wrongfully augment environment variables such as
‘PATH’ in their ‘~/.bashrc’ file.  As a consequence, when ‘guix
environment’ launches it, Bash may read ‘~/.bashrc’, thereby
introducing “impurities” in these environment variables.  It is an
error to define such environment variables in ‘.bashrc’; instead,
they should be defined in ‘.bash_profile’, which is sourced only by
log-in shells.  See ‘Bash Startup Files[2]’, for details on Bash
start-up files.

Cheers,
Clément

[1]: 
https://www.gnu.org/software/guix/manual/en/html_node/Invoking-guix-environment.html#FOOT15
[2]: 
https://www.gnu.org/software/bash/manual/html_node/Bash-Startup-Files.html#Bash-Startup-Files

Re: Guix & IPFS

[Pierre Neidhardt]

I've started writing "gx-download.scm", it's on the wip-ipfs branch.

On the ipfs-go-ipfs-cmdkit example, I get this error:

--8<---cut here---start->8---
> ./pre-inst-env guix build -K ipfs-go-ipfs-cmdkit
;;; note: source file /home/ambrevar/projects/guix/guix/gx-download.scm
;;;   newer than compiled 
/home/ambrevar/.cache/guile/ccache/2.2-LE-8-3.A/home/ambrevar/projects/guix/guix/gx-download.scm.go
substitute: updating substitutes from 'https://mirror.hydra.gnu.org'... 100.0%
building 
/gnu/store/rnwbwvks2imzzs5av5p0ihab6qynfgi8-module-import-compiled.drv...
[ 1/ 2] Compiling './guix/build/gx.scm'...
[ 2/ 2] Compiling './guix/build/utils.scm'...
successfully built 
/gnu/store/rnwbwvks2imzzs5av5p0ihab6qynfgi8-module-import-compiled.drv
building 
/gnu/store/pwjnh2sp30plxbw12zmwg4p5w0wfh5fy-ipfs-go-ipfs-cmdkit-1.1.3-1.QmSP88r-checkout.drv...
what language will the project be in? initializing package 
3nbb94ssalhxdas7vz2bv8n6dpz3mdw2-ipfs-go-ipfs-cmdkit-1.1.3-1.QmSP88r-checkout...
where should users go to report issues? notice: no helper tool found for 
ERROR: from shell.Get(): Post 
https://ipfs.io/api/v0/get?arg=QmSP88ryZkHSRn1fnngAaV2Vcn63WUJzAavnRM9CVdU1Ky=true:
 x509: failed to load system roots and no roots provided
retrying fetch QmSP88ryZkHSRn1fnngAaV2Vcn63WUJzAavnRM9CVdU1Ky after a second...
ERROR: from shell.Get(): Post 
https://ipfs.io/api/v0/get?arg=QmSP88ryZkHSRn1fnngAaV2Vcn63WUJzAavnRM9CVdU1Ky=true:
 x509: failed to load system roots and no roots provided
retrying fetch QmSP88ryZkHSRn1fnngAaV2Vcn63WUJzAavnRM9CVdU1Ky after a second...
ERROR: from shell.Get(): Post 
https://ipfs.io/api/v0/get?arg=QmSP88ryZkHSRn1fnngAaV2Vcn63WUJzAavnRM9CVdU1Ky=true:
 x509: failed to load system roots and no roots provided
ERROR: (install): failed to fetch package: 
QmSP88ryZkHSRn1fnngAaV2Vcn63WUJzAavnRM9CVdU1Ky: Post 
https://ipfs.io/api/v0/get?arg=QmSP88ryZkHSRn1fnngAaV2Vcn63WUJzAavnRM9CVdU1Ky=true:
 x509: failed to load system roots and no roots provided 
Backtrace:
   2 (primitive-load "/gnu/store/gpnysp8v5nv1l3yklbv0y5fvb0r?")
In guix/build/gx.scm:
52:10  1 (gx-fetch _ _ #:gx-command _)
In unknown file:
   0 (scm-error misc-error #f "~A" ("Cannot import gx pack?") ?)

ERROR: In procedure scm-error:
Cannot import gx package
note: keeping build directory 
`/tmp/guix-build-ipfs-go-ipfs-cmdkit-1.1.3-1.QmSP88r-checkout.drv-1'
builder for 
`/gnu/store/pwjnh2sp30plxbw12zmwg4p5w0wfh5fy-ipfs-go-ipfs-cmdkit-1.1.3-1.QmSP88r-checkout.drv'
 failed with exit code 1
build of 
/gnu/store/pwjnh2sp30plxbw12zmwg4p5w0wfh5fy-ipfs-go-ipfs-cmdkit-1.1.3-1.QmSP88r-checkout.drv
 failed
View build log at 
'/var/log/guix/drvs/pw/jnh2sp30plxbw12zmwg4p5w0wfh5fy-ipfs-go-ipfs-cmdkit-1.1.3-1.QmSP88r-checkout.drv.bz2'.
cannot build derivation 
`/gnu/store/1prmx5jgzm4wzm23zzwbc1af0r593zhj-ipfs-go-ipfs-cmdkit-1.1.3-1.QmSP88r.drv':
 1 dependencies couldn't be built
guix build: error: build failed: build of 
`/gnu/store/1prmx5jgzm4wzm23zzwbc1af0r593zhj-ipfs-go-ipfs-cmdkit-1.1.3-1.QmSP88r.drv'
 failed
--8<---cut here---end--->8---

My understanding is that I need to pass certificates to the fetcher.
Does anyone know how to do that?

-- 
Pierre Neidhardt
https://ambrevar.xyz/


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Re: [outreach] Help trying to create R package

[Laura Lazzati]

On Wed, Oct 17, 2018 at 11:27 AM Laura Lazzati
 wrote:
>
> On Wed, Oct 17, 2018 at 5:21 AM Gábor Boskovits  wrote:
> >
> > ÜHi Laura,
> >
> >
> >
> > Björn Höfling  ezt írta (időpont: 2018. 
> > okt. 17., Sze 9:17):
> >>
> >> Hi Laura,
> >>
> >> On Tue, 16 Oct 2018 22:01:58 -0300
> >> Laura Lazzati  wrote:
> >>
> >> > On Tue, Oct 16, 2018 at 7:19 PM Björn Höfling
> >> >  wrote:
> >> > >
> >> > > Hi Laura,
> >> > Hi! I had not answered yet because I thought I would be too verbose.
> >> > If so, please do a Laura -v instead of Laura -vvv.
> >> > Thanks for writing :) it encourages me a lot.
> >>
> >> You're welcome. It's nice to hear from your progress. Verbosity-level
> >> is fine :-)
> Thanks :) Hope you enjoy my nerd jokes
>
> >> [..]
> >>
> >> > > Here is another one:
> >> > >
> >> > > guix package -s "^r-" | recsel -p name| grep '\S' | sort >r.txt
> >> >
> >> > Something I faced after writing, was that in the link one of you
> >> > provided: [1]https://guix.mdc-berlin.de/
> >> > I have all the packages that are already available in guix. I like
> >> > using the guix package command to practice that too, but i found it
> >> > practical to see packages easier. I found out that package aspi
> >> > (https://CRAN.R-project.org/package=aspi) is not available, and I
> >> > would like to ask you if you believe it is a good candidate.
> >> > One available package, according to [1] is r-abe
> >> > (https://cran.r-project.org/web/packages/abe/index.html)
> >>
> >> Sorry I have no clue of R at all. Could someone else please answer that
> >> question, is r-aspi a good candidate?
> >>
> >> https://cran.r-project.org/web/packages/aspi/index.html
> >>
> >>
> >> > I wanted to see the template, so I ran:
> >> > $ guix import cran abe
> >> > And got the template, that matches even the version, and everything
> >> > stated in the site.
> >> > But then I tried:
> >> > $ guix package -i r-abe and got no results.
> >
> > This happens, as the installed guix doesn't know where to find the package 
> > definition. There are several ways around that, for example see the -f flag 
> > of guix package, in the invoking guix package section of the manual.
> >>
> >> > In fact, after running the command you have just provided, r-abe is
> >> > not appearing in the r.txt file.
> >> > I can't understand why that is happening. Am I missing something, or
> >> > is there maybe an inconsistency between [1] and the guix installed in
> >> > my foreign distro?
> >>
> >> Concerning r-abe: I don't know how the list at guix-hpc is created
> >> , how often it is updated or if there are extra packages in there. In
> >> your case, I suppose you lack behind:
> >>
> >> There is a commit for r-abe from 2019-09-13, so it is only a month old.
> >> I think you are lacking behind. Have you done a `guix pull`? That's the
> >> command used to update the package definitions.
> >>
> >> In case you already did a guix pull recently, and you still don't see
> >> it, there could be a problem with your $PATH, that the wrong guix is
> >> coming first. Do a `which guix`.
> >> Guix should be the one in ~/.config/guix/current/bin/guix
> >
> >
> > Yes, please run guix pull, and check which guix output.
> I have to take a look at my .bash_history, but I guess somewhere I ran
> guix pull because I recall seing something about the $PATH stuff. I
> did not run guix output. It doesn'matter, I save my machine state and
> run all that now.
You were right. I took a look at my .bashrc file, and I had an:
export PATH="/home/laura/.guix-profile/bin${PATH:+:}$PATH"
I ran $guix pull, did the PATH export in my CLI, then checked the output of
$which guix, that was the same that was mentioned by you,
commented that previous line in .bashrc,
added  export PATH="/home/laura/.config/guix/current/bin${PATH:+:}$PATH"
and ran again the command to check the available R packages, made a
diff with the previous one, and now at least r-bae appears.
> >
> >>
> >>
> >> > Just wanted to install it to run guix edit to check if the suggested
> >> > packages were already available or if I needed to package them too,
> >> > but I have installed r-ade4, which has both imports and suggests, and
> >> > I have just run:
> >> > $guix import cran ade4
> >> > And noticed that it only states in the template the Import package
> >> > (MASS)
> >>
> >> If I see that right, for R we only add the "Imports" packages, as they
> >> are absolutely needed for compiling/running. All "Suggests" can be
> >> installed/used just at runtime. Please correct me anyone if I'm wrong,
> >> I'm not into R.
> >>
> >>
> >> > Here is my template for aspi (I named it for myself r-aspi.scm). I ran
> >> > guix download from its site, and also guix hash to convert it to
> >> > base32:
> >> >
> >> > (define-public r-aspi
> >> > (package
> >> >   (name "r-aspi")
> >> >   (version "0.2.0")
> >> >   (source
> >> > (origin
> >> >   (method url-fetch)
> >> >   (uri (cran-uri "aspi" version))
> >> >   (sha256
> >> > 

Call for talks: Minimalistic Languages Devroom at FOSDEM 2019

[Ludovic Courtès]

Hello Guilers & Guix!

Guile, Guix, and Lua fellows are organizing the “Minimalistic Languages”
track at this year’s FOSDEM:

  https://fosdem.org/2019

Consider submitting a talk about what you’ve been hacking on!

Ludo’.


* Minimalistic Languages Devroom call for talks @ FOSDEM 2019

(posted at https://libreplanet.org/wiki/FOSDEM2019-devroom-minimalism)

We are excited to announce a devroom on minimalistic languages (with
big ideas) at FOSDEM on Saturday February 2nd 2019!

FOSDEM is one of the most important free software conferences and is
hosted annually at Université libre de Bruxelles in Brussels,
Belgium. FOSDEM is fantastic, check last year's schedule for Saturday
(https://archive.fosdem.org/2018/schedule/day/saturday/)

Minimalism matters. Minimalism allows for smaller systems that take
less resources and consume less energy. More importantly, free and
open source minimalism allows for secure systems that are easy to
understand. Finally, we believe that minimalism is educational and
brings back the fun of the early days of computing where people learn
to understand systems from the ground up. Speakers will be asked to
accentuate the educational side of their projects.

We have a room Saturday 2 February 2019. We want to invite you to
submit a talk on the use of minimalistic languages that fits that
description. We are especially happy to receive talk submissions from
members of any underrepresented groups.

If you have something you’d like to share with your fellow developers,
please head to pentabarf at

  - https://penta.fosdem.org/submission/FOSDEM19

The deadline for submission is November 25th. If you have a FOSDEM
pentabarf account from a previous year, please use that
account. Otherwise add one on
https://penta.fosdem.org/user/new_account. Reach out to
pjotr.public...@thebird.nl if you run into any trouble.

When submitting your talk make doubly sure to select "Minimalistic
Languages devroom" as track (if you don't we won't find it), and
include the following information:

  * The title and subtitle of your talk
  * A short abstract of one paragraph
  * A longer description if you wish to do so
  * Links to related websites/blogs etc

Let's make this a fun day!

** Organisers

Pjotr Prins, Manolis Ragkousis, Hisham Muhammad, Ricardo Wurmus,
Ludovic Courtès, Jan Nieuwenhuizen, Alex Sassmannshausen, and Amirouche Boubekki

** Code of conduct

  - https://fosdem.org/2019/practical/conduct/

** Original proposal

  - https://libreplanet.org/wiki/FOSDEM2019-devroom-proposal

** Important dates:

  - Nov 25th 2018:  submission deadline for talk proposals
  - Dec 17th 2018:  announcement of the final schedule
  - Feb  2nd 2019:  FOSDEM!


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Re: [outreach] Help trying to create R package

[Laura Lazzati]

On Wed, Oct 17, 2018 at 5:21 AM Gábor Boskovits  wrote:
>
> ÜHi Laura,
>
>
>
> Björn Höfling  ezt írta (időpont: 2018. 
> okt. 17., Sze 9:17):
>>
>> Hi Laura,
>>
>> On Tue, 16 Oct 2018 22:01:58 -0300
>> Laura Lazzati  wrote:
>>
>> > On Tue, Oct 16, 2018 at 7:19 PM Björn Höfling
>> >  wrote:
>> > >
>> > > Hi Laura,
>> > Hi! I had not answered yet because I thought I would be too verbose.
>> > If so, please do a Laura -v instead of Laura -vvv.
>> > Thanks for writing :) it encourages me a lot.
>>
>> You're welcome. It's nice to hear from your progress. Verbosity-level
>> is fine :-)
Thanks :) Hope you enjoy my nerd jokes

>> [..]
>>
>> > > Here is another one:
>> > >
>> > > guix package -s "^r-" | recsel -p name| grep '\S' | sort >r.txt
>> >
>> > Something I faced after writing, was that in the link one of you
>> > provided: [1]https://guix.mdc-berlin.de/
>> > I have all the packages that are already available in guix. I like
>> > using the guix package command to practice that too, but i found it
>> > practical to see packages easier. I found out that package aspi
>> > (https://CRAN.R-project.org/package=aspi) is not available, and I
>> > would like to ask you if you believe it is a good candidate.
>> > One available package, according to [1] is r-abe
>> > (https://cran.r-project.org/web/packages/abe/index.html)
>>
>> Sorry I have no clue of R at all. Could someone else please answer that
>> question, is r-aspi a good candidate?
>>
>> https://cran.r-project.org/web/packages/aspi/index.html
>>
>>
>> > I wanted to see the template, so I ran:
>> > $ guix import cran abe
>> > And got the template, that matches even the version, and everything
>> > stated in the site.
>> > But then I tried:
>> > $ guix package -i r-abe and got no results.
>
> This happens, as the installed guix doesn't know where to find the package 
> definition. There are several ways around that, for example see the -f flag 
> of guix package, in the invoking guix package section of the manual.
>>
>> > In fact, after running the command you have just provided, r-abe is
>> > not appearing in the r.txt file.
>> > I can't understand why that is happening. Am I missing something, or
>> > is there maybe an inconsistency between [1] and the guix installed in
>> > my foreign distro?
>>
>> Concerning r-abe: I don't know how the list at guix-hpc is created
>> , how often it is updated or if there are extra packages in there. In
>> your case, I suppose you lack behind:
>>
>> There is a commit for r-abe from 2019-09-13, so it is only a month old.
>> I think you are lacking behind. Have you done a `guix pull`? That's the
>> command used to update the package definitions.
>>
>> In case you already did a guix pull recently, and you still don't see
>> it, there could be a problem with your $PATH, that the wrong guix is
>> coming first. Do a `which guix`.
>> Guix should be the one in ~/.config/guix/current/bin/guix
>
>
> Yes, please run guix pull, and check which guix output.
I have to take a look at my .bash_history, but I guess somewhere I ran
guix pull because I recall seing something about the $PATH stuff. I
did not run guix output. It doesn'matter, I save my machine state and
run all that now.
>
>>
>>
>> > Just wanted to install it to run guix edit to check if the suggested
>> > packages were already available or if I needed to package them too,
>> > but I have installed r-ade4, which has both imports and suggests, and
>> > I have just run:
>> > $guix import cran ade4
>> > And noticed that it only states in the template the Import package
>> > (MASS)
>>
>> If I see that right, for R we only add the "Imports" packages, as they
>> are absolutely needed for compiling/running. All "Suggests" can be
>> installed/used just at runtime. Please correct me anyone if I'm wrong,
>> I'm not into R.
>>
>>
>> > Here is my template for aspi (I named it for myself r-aspi.scm). I ran
>> > guix download from its site, and also guix hash to convert it to
>> > base32:
>> >
>> > (define-public r-aspi
>> > (package
>> >   (name "r-aspi")
>> >   (version "0.2.0")
>> >   (source
>> > (origin
>> >   (method url-fetch)
>> >   (uri (cran-uri "aspi" version))
>> >   (sha256
>> > (base32
>> >   "a7izhueiqsdjs2eo7dfyb63cqje7mbqz6ennlyoynxxucbhpdnta"
>> >   (build-system r-build-system)
>> >(home-page
>> > "https://cran.r-project.org/web/packages/aspi/;)
>> >   (synopsis
>> > "Analysis of Symmetry of Parasitic Infections")
>> >   (description
>> > "Tools for the analysis and visualization of bilateral asymmetry
>> > in parasitic infections.")
>> >   (license gpl3+)))
>> > And that's were I ended up today (it is still Tuesday, almost 10pm)
>>
>> I haven't done a full review, but that looks good. Next you need to get
>> the guix sources and prepare a patch.
Thanks, I took a look at most of the R packages in cran site, and
chose it because of two reasons: it has to do with bioinformatics due
to its description, and as it does not 

Re: openssh vulnerability

[Christopher Lemmer Webber]

Leo Famulari writes:

> On Wed, Oct 17, 2018 at 12:47:26AM -0400, Mike Gerwitz wrote:
>> On Tue, Oct 16, 2018 at 21:20:30 -0400, Christopher Lemmer Webber wrote:
>> > https://www.libssh.org/2018/10/16/libssh-0-8-4-and-0-7-6-security-and-bugfix-release/
>> >
>> > seems serious?
>> 
>> Very... Fortunately that's libssh and not OpenSSH[0], but with that said,
>> it does appear to be packaged in Guix and there are a couple packages
>> that use it.

Ha, sorry for the scare.

> Patch at 

Yay, thanks Leo!

Re: [outreach] Help trying to create R package

[Gábor Boskovits]

ÜHi Laura,



Björn Höfling  ezt írta (időpont: 2018.
okt. 17., Sze 9:17):

> Hi Laura,
>
> On Tue, 16 Oct 2018 22:01:58 -0300
> Laura Lazzati  wrote:
>
> > On Tue, Oct 16, 2018 at 7:19 PM Björn Höfling
> >  wrote:
> > >
> > > Hi Laura,
> > Hi! I had not answered yet because I thought I would be too verbose.
> > If so, please do a Laura -v instead of Laura -vvv.
> > Thanks for writing :) it encourages me a lot.
>
> You're welcome. It's nice to hear from your progress. Verbosity-level
> is fine :-)
>
> [..]
>
> > > Here is another one:
> > >
> > > guix package -s "^r-" | recsel -p name| grep '\S' | sort >r.txt
> >
> > Something I faced after writing, was that in the link one of you
> > provided: [1]https://guix.mdc-berlin.de/
> > I have all the packages that are already available in guix. I like
> > using the guix package command to practice that too, but i found it
> > practical to see packages easier. I found out that package aspi
> > (https://CRAN.R-project.org/package=aspi) is not available, and I
> > would like to ask you if you believe it is a good candidate.
> > One available package, according to [1] is r-abe
> > (https://cran.r-project.org/web/packages/abe/index.html)
>
> Sorry I have no clue of R at all. Could someone else please answer that
> question, is r-aspi a good candidate?
>
> https://cran.r-project.org/web/packages/aspi/index.html
>
>
> > I wanted to see the template, so I ran:
> > $ guix import cran abe
> > And got the template, that matches even the version, and everything
> > stated in the site.
> > But then I tried:
> > $ guix package -i r-abe and got no results.
>
This happens, as the installed guix doesn't know where to find the package
definition. There are several ways around that, for example see the -f flag
of guix package, in the invoking guix package section of the manual.

> > In fact, after running the command you have just provided, r-abe is
> > not appearing in the r.txt file.
> > I can't understand why that is happening. Am I missing something, or
> > is there maybe an inconsistency between [1] and the guix installed in
> > my foreign distro?
>
> Concerning r-abe: I don't know how the list at guix-hpc is created
> , how often it is updated or if there are extra packages in there. In
> your case, I suppose you lack behind:
>
> There is a commit for r-abe from 2019-09-13, so it is only a month old.
> I think you are lacking behind. Have you done a `guix pull`? That's the
> command used to update the package definitions.
>
> In case you already did a guix pull recently, and you still don't see
> it, there could be a problem with your $PATH, that the wrong guix is
> coming first. Do a `which guix`.
> Guix should be the one in ~/.config/guix/current/bin/guix
>

Yes, please run guix pull, and check which guix output.


>
> > Just wanted to install it to run guix edit to check if the suggested
> > packages were already available or if I needed to package them too,
> > but I have installed r-ade4, which has both imports and suggests, and
> > I have just run:
> > $guix import cran ade4
> > And noticed that it only states in the template the Import package
> > (MASS)
>
> If I see that right, for R we only add the "Imports" packages, as they
> are absolutely needed for compiling/running. All "Suggests" can be
> installed/used just at runtime. Please correct me anyone if I'm wrong,
> I'm not into R.
>
>
> > Here is my template for aspi (I named it for myself r-aspi.scm). I ran
> > guix download from its site, and also guix hash to convert it to
> > base32:
> >
> > (define-public r-aspi
> > (package
> >   (name "r-aspi")
> >   (version "0.2.0")
> >   (source
> > (origin
> >   (method url-fetch)
> >   (uri (cran-uri "aspi" version))
> >   (sha256
> > (base32
> >   "a7izhueiqsdjs2eo7dfyb63cqje7mbqz6ennlyoynxxucbhpdnta"
> >   (build-system r-build-system)
> >(home-page
> > "https://cran.r-project.org/web/packages/aspi/;)
> >   (synopsis
> > "Analysis of Symmetry of Parasitic Infections")
> >   (description
> > "Tools for the analysis and visualization of bilateral asymmetry
> > in parasitic infections.")
> >   (license gpl3+)))
> > And that's were I ended up today (it is still Tuesday, almost 10pm)
>
> I haven't done a full review, but that looks good. Next you need to get
> the guix sources and prepare a patch.
>
> That's described here:
>
>
> https://www.gnu.org/software/guix/manual/en/html_node/Contributing.html#Contributing
>
>
> Björn
>

Best regards,
g_bor

>

Re: Video Documentation for GNU GUIX (an Outreachy project)

[Gábor Boskovits]

Hello Lakshmi,
Welcome to Guix!

Björn Höfling  ezt írta (időpont: 2018.
okt. 17., Sze 8:45):

> Hi Lakshmi,
>
> On Wed, 17 Oct 2018 09:04:40 +0530
> Lakshmi Prasannakumar  wrote:
>
> > Hi  Björn,
> > I write to you in regards to the project description seen at the
> > Outreachy project list. I would like to join your community and start
> > contributing to the documentation part of it.
>
> Welcome to Guix! I'm adding the public mailing list on CC, so other
> community members can also answer if necessary. Also adding Gabor on
> CC, who is the main mentor.
>
> >  Though I have joined
> > the IRC channel for GNU GUIX, I'm continually receiving the error
> > message as below on sending messages:
> > == Cannot send to nick/channel
>
> There was recently a spam attack on the freenode IRC network. Since
> then you need to register your nick name before it is possible to join
> the #guix channel. If you haven't done that yet, here are the
> instructions:
>
> https://freenode.net/kb/answer/registration
>
> You can also join the mailing list and write there.
>
> > My understanding regarding the project contribution is to make
> > video tutorials on how to install and use GNU GUIX.
> > Could you kindly direct me with some initial task so that I can start
> > working on it and get familiar with the environment?
>
> Yes, that's right, video documentation is the job. One requirement for
> Outreachy is to make a first, formal contribution to the project. For
> Guix that means you could add a new package.
>
> But the very first step is to install Guix and get used to it. You can
> install Guix either on top of another Linux-Distribution or standalone,
> in a virtual mashine or on real hardware. On top of an existing distro
> is probably the easiest step.
>
> The docs for installation should be linked from the Outreachy Project
> site, I post it also here:
>
>
> https://www.gnu.org/software/guix/manual/en/html_node/Binary-Installation.html#Binary-Installation


Yes, installation would be the first step.


>
> If you have any questions feel free to ask (preferably on the mailing
> list, or if it works for you, on IRC).
>
> Yours,
>
> Björn
>

Best regards,
g_bor

>

Re: [outreach] Help trying to create R package

[Björn Höfling]

Hi Laura,

On Tue, 16 Oct 2018 22:01:58 -0300
Laura Lazzati  wrote:

> On Tue, Oct 16, 2018 at 7:19 PM Björn Höfling
>  wrote:
> >
> > Hi Laura,  
> Hi! I had not answered yet because I thought I would be too verbose.
> If so, please do a Laura -v instead of Laura -vvv.
> Thanks for writing :) it encourages me a lot.

You're welcome. It's nice to hear from your progress. Verbosity-level
is fine :-)

[..]

> > Here is another one:
> >
> > guix package -s "^r-" | recsel -p name| grep '\S' | sort >r.txt  
> 
> Something I faced after writing, was that in the link one of you
> provided: [1]https://guix.mdc-berlin.de/
> I have all the packages that are already available in guix. I like
> using the guix package command to practice that too, but i found it
> practical to see packages easier. I found out that package aspi
> (https://CRAN.R-project.org/package=aspi) is not available, and I
> would like to ask you if you believe it is a good candidate.
> One available package, according to [1] is r-abe
> (https://cran.r-project.org/web/packages/abe/index.html)

Sorry I have no clue of R at all. Could someone else please answer that
question, is r-aspi a good candidate?

https://cran.r-project.org/web/packages/aspi/index.html


> I wanted to see the template, so I ran:
> $ guix import cran abe
> And got the template, that matches even the version, and everything
> stated in the site.
> But then I tried:
> $ guix package -i r-abe and got no results.
> In fact, after running the command you have just provided, r-abe is
> not appearing in the r.txt file.
> I can't understand why that is happening. Am I missing something, or
> is there maybe an inconsistency between [1] and the guix installed in
> my foreign distro?

Concerning r-abe: I don't know how the list at guix-hpc is created
, how often it is updated or if there are extra packages in there. In
your case, I suppose you lack behind:

There is a commit for r-abe from 2019-09-13, so it is only a month old.
I think you are lacking behind. Have you done a `guix pull`? That's the
command used to update the package definitions.

In case you already did a guix pull recently, and you still don't see
it, there could be a problem with your $PATH, that the wrong guix is
coming first. Do a `which guix`.
Guix should be the one in ~/.config/guix/current/bin/guix


> Just wanted to install it to run guix edit to check if the suggested
> packages were already available or if I needed to package them too,
> but I have installed r-ade4, which has both imports and suggests, and
> I have just run:
> $guix import cran ade4
> And noticed that it only states in the template the Import package
> (MASS)

If I see that right, for R we only add the "Imports" packages, as they
are absolutely needed for compiling/running. All "Suggests" can be
installed/used just at runtime. Please correct me anyone if I'm wrong,
I'm not into R.

 
> Here is my template for aspi (I named it for myself r-aspi.scm). I ran
> guix download from its site, and also guix hash to convert it to
> base32:
> 
> (define-public r-aspi
> (package
>   (name "r-aspi")
>   (version "0.2.0")
>   (source
> (origin
>   (method url-fetch)
>   (uri (cran-uri "aspi" version))
>   (sha256
> (base32
>   "a7izhueiqsdjs2eo7dfyb63cqje7mbqz6ennlyoynxxucbhpdnta"
>   (build-system r-build-system)
>(home-page
> "https://cran.r-project.org/web/packages/aspi/;)
>   (synopsis
> "Analysis of Symmetry of Parasitic Infections")
>   (description
> "Tools for the analysis and visualization of bilateral asymmetry
> in parasitic infections.")
>   (license gpl3+)))
> And that's were I ended up today (it is still Tuesday, almost 10pm)

I haven't done a full review, but that looks good. Next you need to get
the guix sources and prepare a patch.

That's described here:

https://www.gnu.org/software/guix/manual/en/html_node/Contributing.html#Contributing


Björn


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Description: OpenPGP digital signature

Re: Video Documentation for GNU GUIX (an Outreachy project)

[Björn Höfling]

Hi Lakshmi,

On Wed, 17 Oct 2018 09:04:40 +0530
Lakshmi Prasannakumar  wrote:

> Hi  Björn,
> I write to you in regards to the project description seen at the
> Outreachy project list. I would like to join your community and start
> contributing to the documentation part of it.

Welcome to Guix! I'm adding the public mailing list on CC, so other
community members can also answer if necessary. Also adding Gabor on
CC, who is the main mentor.

>  Though I have joined
> the IRC channel for GNU GUIX, I'm continually receiving the error
> message as below on sending messages:
> == Cannot send to nick/channel

There was recently a spam attack on the freenode IRC network. Since
then you need to register your nick name before it is possible to join
the #guix channel. If you haven't done that yet, here are the
instructions:

https://freenode.net/kb/answer/registration

You can also join the mailing list and write there.

> My understanding regarding the project contribution is to make
> video tutorials on how to install and use GNU GUIX.
> Could you kindly direct me with some initial task so that I can start
> working on it and get familiar with the environment?

Yes, that's right, video documentation is the job. One requirement for
Outreachy is to make a first, formal contribution to the project. For
Guix that means you could add a new package.

But the very first step is to install Guix and get used to it. You can
install Guix either on top of another Linux-Distribution or standalone,
in a virtual mashine or on real hardware. On top of an existing distro
is probably the easiest step.

The docs for installation should be linked from the Outreachy Project
site, I post it also here:

https://www.gnu.org/software/guix/manual/en/html_node/Binary-Installation.html#Binary-Installation

If you have any questions feel free to ask (preferably on the mailing
list, or if it works for you, on IRC).

Yours,

Björn


pgpCFoSHnUplx.pgp
Description: OpenPGP digital signature