Hi,
While trying to install GUIX using Binary installation, I'm getting the following error at verifying sig file using the below command.
$ sudo gpg --verify guix-binary-0.15.0.x86_64-linux.tar.xz.sig
gpg: WARNING: unsafe ownership on homedir '/home/lakshmi/.gnupg'
gpg: assuming signed data in 'guix-binary-0.15.0.x86_64-linux.tar.xz'
gpg: Signature made Friday 06 July 2018 02:50:33 PM IST
gpg: using RSA key 090B11993D9AEBB5
gpg: Good signature from "Ludovic Courtès <address@hidden>" [unknown]
gpg: aka "Ludovic Courtès <address@hidden>" [unknown]
gpg: aka "Ludovic Courtès (Inria) <address@hidden>" [unknown]
gpg: WARNING: This key is not certified with a trusted signature!
gpg: There is no indication that the signature belongs to the owner.
Primary key fingerprint: 3CE4 6455 8A84 FDC6 9DB4 0CFB 090B 1199 3D9A EBB5
Tried downloading the public key, still getting this error. Could you please help ?
Running the .sh script had crashed my standalone ubuntu system, hence I'm trying to do it step by step.
Thanks,
Thanks,
Lakshmi Prasannakumar
Bangalore
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Today's Topics:
1. Re: [outreach] Help trying to create R package (Laura Lazzati)
2. Re: Guix & IPFS (Pierre Neidhardt)
3. Re: [outreach] Help trying to create R package (Cl?ment Lassieur)
4. Re: Packaging Inferno (Diego Nicola Barbato)
5. Re: [outreach] Help trying to create R package (Laura Lazzati)
----------------------------------------------------------------------
Message: 1
Date: Wed, 17 Oct 2018 13:38:53 -0300
From: Laura Lazzati <address@hidden>
To: G?bor Boskovits <address@hidden>
Cc: Bj?rn H?fling <address@hidden>, Guix-devel
<address@hidden>, Ricardo Wurmus <address@hidden>
Subject: Re: [outreach] Help trying to create R package
Message-ID:
<address@hidden>
Content-Type: text/plain; charset="UTF-8"
On Wed, Oct 17, 2018 at 11:27 AM Laura Lazzati
<address@hidden> wrote:
>
> On Wed, Oct 17, 2018 at 5:21 AM G?bor Boskovits <address@hidden> wrote:
> >
> > ?Hi Laura,
> >
> >
> >
> > Bj?rn H?fling <address@hidden> ezt ?rta (id?pont: 2018. okt. 17., Sze 9:17):
> >>
> >> Hi Laura,
> >>
> >> On Tue, 16 Oct 2018 22:01:58 -0300
> >> Laura Lazzati <address@hidden> wrote:
> >>
> >> > On Tue, Oct 16, 2018 at 7:19 PM Bj?rn H?fling
> >> > <address@hidden> 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 -vvvvvvv.
> >> > 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
> >> > (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 mention imports so I found it
> easy for a first R package contribution. If it works fine, then I can
> go on packaging more complicated R packages.
>
> >> That's described here:
> >>
> >> https://www.gnu.org/software/guix/manual/en/html_node/Contributing.html#Contributing
> >>
> >>
> >> Bj?rn
> >
> >
> > Best regards,
> > g_bor
>
> Thanks both!
> Regards,
> Laura
Thanks again, time to read how to go on with my contribution :)
Laura
------------------------------
Message: 2
Date: Wed, 17 Oct 2018 19:00:14 +0200
From: Pierre Neidhardt <address@hidden>
To: Leo Famulari <address@hidden>
Cc: Ludovic Court?s <address@hidden>, Guix-devel <address@hidden>
Subject: Re: Guix & IPFS
Message-ID: <address@hidden>
Content-Type: text/plain; charset="us-ascii"
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&create=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&create=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&create=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&create=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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------------------------------
Message: 3
Date: Wed, 17 Oct 2018 19:13:28 +0200
From: Cl?ment Lassieur <address@hidden>
To: Laura Lazzati <address@hidden>
Cc: G?bor Boskovits <address@hidden>, Guix-devel
<address@hidden>, Ricardo Wurmus <address@hidden>
Subject: Re: [outreach] Help trying to create R package
Message-ID: <address@hidden>
Content-Type: text/plain; charset=utf-8
Hi Laura,
Laura Lazzati <address@hidden> 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,
Cl?ment
[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
------------------------------
Message: 4
Date: Wed, 17 Oct 2018 19:35:07 +0200
From: Diego Nicola Barbato <address@hidden>
To: Nils Gillmann <address@hidden>
Cc: address@hidden
Subject: Re: Packaging Inferno
Message-ID: <address@hidden>
Content-Type: text/plain; charset=utf-8
Hello Nils,
Nils Gillmann <address@hidden> writes:
> Diego Nicola Barbato transcribed 12K bytes:
>> Hello,
>>
>> Thank you for your feedback.
>>
>> Nils Gillmann <address@hidden> writes:
>>
>> > Ludovic Court?s transcribed 1.9K bytes:
>> >> Hello Diego,
>> >>
>> >> Diego Nicola Barbato <address@hidden> 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
------------------------------
Message: 5
Date: Wed, 17 Oct 2018 14:50:14 -0300
From: Laura Lazzati <address@hidden>
To: address@hidden
Cc: G?bor Boskovits <address@hidden>, Guix-devel
<address@hidden>, Ricardo Wurmus <address@hidden>
Subject: Re: [outreach] Help trying to create R package
Message-ID:
<CAPNLzUPBPEw=address@hidden>
Content-Type: text/plain; charset="UTF-8"
On Wed, Oct 17, 2018 at 2:13 PM Cl?ment Lassieur <address@hidden> wrote:
>
> Hi Laura,
>
> Laura Lazzati <address@hidden> 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,
> Cl?ment
>
> [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
------------------------------
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