From mboxrd@z Thu Jan 1 00:00:00 1970 From: Lakshmi Prasannakumar Subject: Help required for installation of GUIX Date: Thu, 18 Oct 2018 10:20:15 +0530 Message-ID: References: Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="0000000000009a713905787986e9" Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:60314) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1gD0Gd-0008CT-GX for guix-devel@gnu.org; Thu, 18 Oct 2018 00:50:43 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1gD0GZ-000812-Gq for guix-devel@gnu.org; Thu, 18 Oct 2018 00:50:39 -0400 Received: from mail-ot1-x335.google.com ([2607:f8b0:4864:20::335]:35319) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1gD0GX-0007cI-K1 for guix-devel@gnu.org; Thu, 18 Oct 2018 00:50:35 -0400 Received: by mail-ot1-x335.google.com with SMTP id 14so24522335oth.2 for ; Wed, 17 Oct 2018 21:50:29 -0700 (PDT) In-Reply-To: List-Id: "Development of GNU Guix and the GNU System distribution." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-devel-bounces+gcggd-guix-devel=m.gmane.org@gnu.org Sender: "Guix-devel" To: guix-devel@gnu.org --0000000000009a713905787986e9 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable 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 ISTgpg: using RSA key 090B11993D9AEBB5gpg: Good signature from "Ludovic Court=C3=A8s >" [unknown]gpg: aka "Ludovic Court=C3=A8s >" [unknown]gpg: aka "Ludovic Court=C3=A8s (Inria) >" [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 On Wed, Oct 17, 2018 at 11:21 PM wrote: > Send Guix-devel mailing list submissions to > guix-devel@gnu.org > > To subscribe or unsubscribe via the World Wide Web, visit > https://lists.gnu.org/mailman/listinfo/guix-devel > or, via email, send a message with subject or body 'help' to > guix-devel-request@gnu.org > > You can reach the person managing the list at > guix-devel-owner@gnu.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Guix-devel digest..." > > > 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 > To: G?bor Boskovits > Cc: Bj?rn H?fling , Guix-devel > , Ricardo Wurmus < > ricardo.wurmus@mdc-berlin.de> > Subject: Re: [outreach] Help trying to create R package > Message-ID: > < > CAPNLzUM8EM2k0c2a4eOkygT4WMzuzxuGfoTj4PXNun_wODFtsg@mail.gmail.com> > Content-Type: text/plain; charset=3D"UTF-8" > > On Wed, Oct 17, 2018 at 11:27 AM Laura Lazzati > wrote: > > > > On Wed, Oct 17, 2018 at 5:21 AM G?bor Boskovits > wrote: > > > > > > ?Hi Laura, > > > > > > > > > > > > Bj?rn H?fling ezt ?rta (id?pont: > 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 Bj?rn H?fling > > >> > wrote: > > >> > > > > >> > > Hi Laura, > > >> > Hi! I had not answered yet because I thought I would be too verbos= e. > > >> > 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-leve= l > > >> 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 i= t > > >> > practical to see packages easier. I found out that package aspi > > >> > (https://CRAN.R-project.org/package=3Daspi) 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 everythin= g > > >> > 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 t= he > -f flag of guix package, in the invoking guix package section of the manu= al. > > >> > > >> > In fact, after running the command you have just provided, r-abe i= s > > >> > 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. I= n > > >> 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 se= e > > >> 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 $PATH stuff. I > > did not run guix output. It doesn'matter, I save my machine state and > > run all that now. > You were right. I took a look at my .bashrc file, and I had an: > export PATH=3D"/home/laura/.guix-profile/bin${PATH:+:}$PATH" > I ran $guix pull, did the PATH export in my CLI, then checked the output = of > $which guix, that was the same that was mentioned by you, > commented that previous line in .bashrc, > added export PATH=3D"/home/laura/.config/guix/current/bin${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 suggest= ed > > >> > 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 th= ey > > >> are absolutely needed for compiling/running. All "Suggests" can be > > >> installed/used just at runtime. Please correct me anyone if I'm wron= g, > > >> 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 asymmet= ry > > >> > 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#C= ontributing > > >> > > >> > > >> 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 > To: Leo Famulari > Cc: Ludovic Court?s , Guix-devel > Subject: Re: Guix & IPFS > Message-ID: <87r2goecf5.fsf@ambrevar.xyz> > Content-Type: text/plain; charset=3D"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/gu= ix/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.Q= mSP88r-checkout.drv... > what language will the project be in? initializing package > 3nbb94ssalhxdas7vz2bv8n6dpz3mdw2-ipfs-go-ipfs-cmdkit-1.1.3-1.QmSP88r-chec= kout... > 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=3DQmSP88ryZkHSRn1fnngAaV2Vcn63WUJzAavnRM9C= VdU1Ky&create=3Dtrue: > 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=3DQmSP88ryZkHSRn1fnngAaV2Vcn63WUJzAavnRM9C= VdU1Ky&create=3Dtrue: > 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=3DQmSP88ryZkHSRn1fnngAaV2Vcn63WUJzAavnRM9C= VdU1Ky&create=3Dtrue: > 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=3DQmSP88ryZkHSRn1fnngAaV2Vcn63WUJzAavnRM9C= VdU1Ky&create=3Dtrue: > 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.Q= mSP88r-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/ > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: signature.asc > Type: application/pgp-signature > Size: 487 bytes > Desc: not available > URL: < > http://lists.gnu.org/archive/html/guix-devel/attachments/20181017/a73842e= e/attachment.pgp > > > > ------------------------------ > > Message: 3 > Date: Wed, 17 Oct 2018 19:13:28 +0200 > From: Cl?ment Lassieur > To: Laura Lazzati > Cc: G?bor Boskovits , Guix-devel > , Ricardo Wurmus > > Subject: Re: [outreach] Help trying to create R package > Message-ID: <87y3aw339j.fsf@lassieur.org> > Content-Type: text/plain; charset=3Dutf-8 > > Hi Laura, > > Laura Lazzati writes: > > > You were right. I took a look at my .bashrc file, and I had an: > > export PATH=3D"/home/laura/.guix-profile/bin${PATH:+:}$PATH" > > I ran $guix pull, did the PATH export in my CLI, then checked the outpu= t > of > > $which guix, that was the same that was mentioned by you, > > commented that previous line in .bashrc, > > added export PATH=3D"/home/laura/.config/guix/current/bin${PATH:+:}$PA= TH" > > 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-envir= onment.html#FOOT15 > [2]: > https://www.gnu.org/software/bash/manual/html_node/Bash-Startup-Files.htm= l#Bash-Startup-Files > > > > ------------------------------ > > Message: 4 > Date: Wed, 17 Oct 2018 19:35:07 +0200 > From: Diego Nicola Barbato > To: Nils Gillmann > Cc: guix-devel@gnu.org > Subject: Re: Packaging Inferno > Message-ID: <87k1mgjx2s.fsf@GlaDOS.home> > Content-Type: text/plain; charset=3Dutf-8 > > Hello Nils, > > Nils Gillmann writes: > > > Diego Nicola Barbato transcribed 12K bytes: > >> Hello, > >> > >> Thank you for your feedback. > >> > >> Nils Gillmann writes: > >> > >> > Ludovic Court?s 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 wou= ld > >> rather package the one provided by Plan 9 from Userspace [7] since tha= t > >> 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 > To: clement@lassieur.org > Cc: G?bor Boskovits , Guix-devel > , Ricardo Wurmus < > ricardo.wurmus@mdc-berlin.de> > Subject: Re: [outreach] Help trying to create R package > Message-ID: > cMd8awOYi65b3gWpQkoXoON9qiTmpjKd4fLcag@mail.gmail.com> > Content-Type: text/plain; charset=3D"UTF-8" > > On Wed, Oct 17, 2018 at 2:13 PM Cl?ment Lassieur > wrote: > > > > Hi Laura, > > > > Laura Lazzati writes: > > > > > You were right. I took a look at my .bashrc file, and I had an: > > > export PATH=3D"/home/laura/.guix-profile/bin${PATH:+:}$PATH" > > > I ran $guix pull, did the PATH export in my CLI, then checked the > output of > > > $which guix, that was the same that was mentioned by you, > > > commented that previous line in .bashrc, > > > added export > PATH=3D"/home/laura/.config/guix/current/bin${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-envir= onment.html#FOOT15 > > [2]: > https://www.gnu.org/software/bash/manual/html_node/Bash-Startup-Files.htm= l#Bash-Startup-Files > > > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > Guix-devel mailing list > Guix-devel@gnu.org > https://lists.gnu.org/mailman/listinfo/guix-devel > > > ------------------------------ > > End of Guix-devel Digest, Vol 64, Issue 57 > ****************************************** > --0000000000009a713905787986e9 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hi,

While trying to install GUIX using Binary installation, I'= ;m getting the following error at verifying sig file using the below comman= d.

$ 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:= =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0 using RSA key 090B11993D9AEBB5
gpg: Good signature from = "Ludovic Court=C3=A8s <ludo@gnu.org= >" [unknown]
gpg:=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 aka "Ludovic Co= urt=C3=A8s <ludo@chbouib.org>= " [unknown]
gpg:=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 aka "Ludovic Court=C3=A8= s (Inria) <ludovic.courtes@i= nria.fr>" [unknown]
gpg: WARNING: This key is not certified = with a trusted signature!
gpg:=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0 There is no indication that the signature belongs to the owner= .
Primary key fingerprint: 3CE4 6455 8A84 FDC6 9DB4=C2=A0 0CFB 090B 1199= 3D9A EBB5

Tried downloadin= g the public key, still getting this=C2=A0error. Could you please help ?
Running the .sh script had crashed my= standalone ubuntu system, hence I'm trying to do it step by step.
<= br>
Thanks,


Thanks,


Lakshmi= Prasannakumar
Bangalore
=


On Wed, Oct 17, 2= 018 at 11:21 PM <guix-deve= l-request@gnu.org> wrote:
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When replying, please edit your Subject line so it is more specific
than "Re: Contents of Guix-devel digest..."


Today's Topics:

=C2=A0 =C2=A01. Re: [outreach] Help trying to create R package (Laura Lazza= ti)
=C2=A0 =C2=A02. Re: Guix & IPFS (Pierre Neidhardt)
=C2=A0 =C2=A03. Re: [outreach] Help trying to create R package (Cl?ment Las= sieur)
=C2=A0 =C2=A04. Re: Packaging Inferno (Diego Nicola Barbato)
=C2=A0 =C2=A05. Re: [outreach] Help trying to create R package (Laura Lazza= ti)


----------------------------------------------------------------------

Message: 1
Date: Wed, 17 Oct 2018 13:38:53 -0300
From: Laura Lazzati <laura.lazzati.15@gmail.com>
To: G?bor Boskovits <boskovits@gmail.com>
Cc: Bj?rn H?fling <bjoern.hoefling@bjoernhoefling.de>,=C2=A0 Guix-dev= el
=C2=A0 =C2=A0 =C2=A0 =C2=A0 <guix-devel@gnu.org>,=C2=A0 =C2=A0Ricardo Wurmus <ricardo.wurm= us@mdc-berlin.de>
Subject: Re: [outreach] Help trying to create R package
Message-ID:
=C2=A0 =C2=A0 =C2=A0 =C2=A0 <CAPNLzUM8EM2k0= c2a4eOkygT4WMzuzxuGfoTj4PXNun_wODFtsg@mail.gmail.com>
Content-Type: text/plain; charset=3D"UTF-8"

On Wed, Oct 17, 2018 at 11:27 AM Laura Lazzati
<laura.l= azzati.15@gmail.com> wrote:
>
> On Wed, Oct 17, 2018 at 5:21 AM G?bor Boskovits <boskovits@gmail.com> wrote: > >
> > ?Hi Laura,
> >
> >
> >
> > Bj?rn H?fling <bjoern.hoefling@bjoernhoefling.de> ezt ?rta = (id?pont: 2018. okt. 17., Sze 9:17):
> >>
> >> Hi Laura,
> >>
> >> On Tue, 16 Oct 2018 22:01:58 -0300
> >> Laura Lazzati <laura.lazzati.15@gmail.com> wrote:
> >>
> >> > On Tue, Oct 16, 2018 at 7:19 PM Bj?rn H?fling
> >> > <bjoern.hoefling@bjoernhoefling.de> 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| g= rep '\S' | sort >r.txt
> >> >
> >> > Something I faced after writing, was that in the link on= e of you
> >> > provided: [1]https://guix.mdc-berlin.de/
> >> > I have all the packages that are already available in gu= ix. I like
> >> > using the guix package command to practice that too, but= i found it
> >> > practical to see packages easier. I found out that packa= ge aspi
> >> > (https://CRAN.R-project.org/package=3Das= pi) is not available, and I
> >> > would like to ask you if you believe it is a good candid= ate.
> >> > 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 a= nswer 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 fin= d the package definition. There are several ways around that, for example s= ee the -f flag of guix package, in the invoking guix package section of the= manual.
> >>
> >> > In fact, after running the command you have just provide= d, r-abe is
> >> > not appearing in the r.txt file.
> >> > I can't understand why that is happening. Am I missi= ng 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 i= s created
> >> , how often it is updated or if there are extra packages in t= here. 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 d= on'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 $PATH stuff. I > did not run guix output. It doesn'matter, I save my machine state = and
> run all that now.
You were right. I took a look at my .bashrc file, and I had an:
export PATH=3D"/home/laura/.guix-profile/bin${PATH:+:}$PATH"
I ran $guix pull, did the PATH export in my CLI, then checked the output of=
$which guix, that was the same that was mentioned by you,
commented that previous line in .bashrc,
added=C2=A0 export PATH=3D"/home/laura/.config/guix/current/bin${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 t= he suggested
> >> > packages were already available or if I needed to packag= e 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 Impo= rt package
> >> > (MASS)
> >>
> >> If I see that right, for R we only add the "Imports"= ; packages, as they
> >> are absolutely needed for compiling/running. All "Sugges= ts" 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-as= pi.scm). I ran
> >> > guix download from its site, and also guix hash to conve= rt it to
> >> > base32:
> >> >
> >> > (define-public r-aspi
> >> > (package
> >> >=C2=A0 =C2=A0(name "r-aspi")
> >> >=C2=A0 =C2=A0(version "0.2.0")
> >> >=C2=A0 =C2=A0(source
> >> >=C2=A0 =C2=A0 =C2=A0(origin
> >> >=C2=A0 =C2=A0 =C2=A0 =C2=A0(method url-fetch)
> >> >=C2=A0 =C2=A0 =C2=A0 =C2=A0(uri (cran-uri "aspi"= ; version))
> >> >=C2=A0 =C2=A0 =C2=A0 =C2=A0(sha256
> >> >=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0(base32
> >> >=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0"a7izhueiqs= djs2eo7dfyb63cqje7mbqz6ennlyoynxxucbhpdnta"))))
> >> >=C2=A0 =C2=A0(build-system r-build-system)
> >> >=C2=A0 =C2=A0 (home-page
> >> >=C2=A0 =C2=A0 =C2=A0"https://cra= n.r-project.org/web/packages/aspi/")
> >> >=C2=A0 =C2=A0(synopsis
> >> >=C2=A0 =C2=A0 =C2=A0"Analysis of Symmetry of Parasit= ic Infections")
> >> >=C2=A0 =C2=A0(description
> >> >=C2=A0 =C2=A0 =C2=A0"Tools for the analysis and visu= alization of bilateral asymmetry
> >> > in parasitic infections.")
> >> >=C2=A0 =C2=A0(license gpl3+)))
> >> > And that's were I ended up today (it is still Tuesda= y, almost 10pm)
> >>
> >> I haven't done a full review, but that looks good. Next y= ou 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<= br> > 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<= br> > go on packaging more complicated R packages.
>
> >> That's described here:
> >>
> >> ht= tps://www.gnu.org/software/guix/manual/en/html_node/Contributing.html#Contr= ibuting
> >>
> >>
> >> 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 <mail@ambrevar.xyz>
To: Leo Famulari <leo@famulari.name>
Cc: Ludovic Court?s <l= udo@gnu.org>, Guix-devel=C2=A0 <guix-devel@gnu.org>
Subject: Re: Guix & IPFS
Message-ID: <87r2goecf5.fsf@ambrevar.xyz>
Content-Type: text/plain; charset=3D"us-ascii"

I've started writing "gx-download.scm", it's on the wip-i= pfs 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
;;;=C2=A0 =C2=A0 =C2=A0 =C2=A0newer than compiled /home/ambrevar/.cache/gui= le/ccache/2.2-LE-8-3.A/home/ambrevar/projects/guix/guix/gx-download.scm.go<= br> substitute: updating substitutes from 'https://mirror.hydra.gnu.org<= /a>'... 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-impor= t-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 3nbb94ssalhxdas7= vz2bv8n6dpz3mdw2-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=3DQmSP88ryZkHSRn1= fnngAaV2Vcn63WUJzAavnRM9CVdU1Ky&create=3Dtrue: x509: failed to load= system roots and no roots provided
retrying fetch QmSP88ryZkHSRn1fnngAaV2Vcn63WUJzAavnRM9CVdU1Ky after a secon= d...
ERROR: from shell.Get(): Post https://ipfs.io/api/v0/get?arg=3DQmSP88ryZkHSRn1= fnngAaV2Vcn63WUJzAavnRM9CVdU1Ky&create=3Dtrue: x509: failed to load= system roots and no roots provided
retrying fetch QmSP88ryZkHSRn1fnngAaV2Vcn63WUJzAavnRM9CVdU1Ky after a secon= d...
ERROR: from shell.Get(): Post https://ipfs.io/api/v0/get?arg=3DQmSP88ryZkHSRn1= fnngAaV2Vcn63WUJzAavnRM9CVdU1Ky&create=3Dtrue: x509: failed to load= system roots and no roots provided
ERROR: (install): failed to fetch package: QmSP88ryZkHSRn1fnngAaV2Vcn63WUJz= AavnRM9CVdU1Ky: Post https://ipfs.io/api/v0/get?arg=3DQmSP88ryZkHSRn1fnngAaV2V= cn63WUJzAavnRM9CVdU1Ky&create=3Dtrue: x509: failed to load system r= oots and no roots provided
Backtrace:
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A02 (primitive-load "/gnu/store= /gpnysp8v5nv1l3yklbv0y5fvb0r?")
In guix/build/gx.scm:
=C2=A0 =C2=A0 52:10=C2=A0 1 (gx-fetch _ _ #:gx-command _)
In unknown file:
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A00 (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-cmdki= t-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-g= o-ipfs-cmdkit-1.1.3-1.QmSP88r.drv': 1 dependencies couldn't be buil= t
guix build: error: build failed: build of `/gnu/store/1prmx5jgzm4wzm23zzwbc= 1af0r593zhj-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
http= s://ambrevar.xyz/
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------------------------------

Message: 3
Date: Wed, 17 Oct 2018 19:13:28 +0200
From: Cl?ment Lassieur <clement@lassieur.org>
To: Laura Lazzati <laura.lazzati.15@gmail.com>
Cc: G?bor Boskovits <boskovits@gmail.com>, Guix-devel
=C2=A0 =C2=A0 =C2=A0 =C2=A0 <guix-devel@gnu.org>, Ricardo Wurmus <ricardo.wurmus@mdc-berli= n.de>
Subject: Re: [outreach] Help trying to create R package
Message-ID: <87y3aw339j.fsf@lassieur.org>
Content-Type: text/plain; charset=3Dutf-8

Hi Laura,

Laura Lazzati <laura.lazzati.15@gmail.com> writes:

> You were right. I took a look at my .bashrc file, and I had an:
> export PATH=3D"/home/laura/.guix-profile/bin${PATH:+:}$PATH"=
> I ran $guix pull, did the PATH export in my CLI, then checked the outp= ut of
> $which guix, that was the same that was mentioned by you,
> commented that previous line in .bashrc,
> added=C2=A0 export PATH=3D"/home/laura/.config/guix/current/bin${= 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?.=C2=A0 :-)

Quoting the documentation[1]:

=C2=A0 =C2=A0 Users sometimes wrongfully augment environment variables such= as
=C2=A0 =C2=A0 ?PATH? in their ?~/.bashrc? file.=C2=A0 As a consequence, whe= n ?guix
=C2=A0 =C2=A0 environment? launches it, Bash may read ?~/.bashrc?, thereby<= br> =C2=A0 =C2=A0 introducing ?impurities? in these environment variables.=C2= =A0 It is an
=C2=A0 =C2=A0 error to define such environment variables in ?.bashrc?; inst= ead,
=C2=A0 =C2=A0 they should be defined in ?.bash_profile?, which is sourced o= nly by
=C2=A0 =C2=A0 log-in shells.=C2=A0 See ?Bash Startup Files[2]?, for details= on Bash
=C2=A0 =C2=A0 start-up files.

Cheers,
Cl?ment

[1]: http= s://www.gnu.org/software/guix/manual/en/html_node/Invoking-guix-environment= .html#FOOT15
[2]: ht= tps://www.gnu.org/software/bash/manual/html_node/Bash-Startup-Files.html#Ba= sh-Startup-Files



------------------------------

Message: 4
Date: Wed, 17 Oct 2018 19:35:07 +0200
From: Diego Nicola Barbato <dnbarbato@posteo.de>
To: Nils Gillmann <ng0@n0= .is>
Cc: guix-devel@gnu.= org
Subject: Re: Packaging Inferno
Message-ID: <87k1mgjx2s.fsf@GlaDOS.home>
Content-Type: text/plain; charset=3Dutf-8

Hello Nils,

Nils Gillmann <ng0@n0.is<= /a>> writes:

> Diego Nicola Barbato transcribed 12K bytes:
>> Hello,
>>
>> Thank you for your feedback.
>>
>> Nils Gillmann <n= g0@n0.is> writes:
>>
>> > Ludovic Court?s transcribed 1.9K bytes:
>> >> Hello Diego,
>> >>
>> >> Diego Nicola Barbato <dnbarbato@posteo.de> skribis:

[...snip...]

>> >> >=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 ;; b= uild mk
>> >> >=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 (inv= oke "./makemk.sh")
>> >>
>> >> It would be ideal if we had a separate package for ?mk? (= I suppose it
>> >> can run on POSIX systems, right?).
>>
>> @Ludo:=C2=A0 This is Plan 9's mk (their version of make), whic= h, I believe,
>> can run on POSIX systems.=C2=A0 Though, if we were to add mk to Gu= ix, 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 patc= h.
>>
>> @Nils:=C2=A0 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 accordin= g
> 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<= br> > 9base (altough it states plan9 + inferno os) and inferno os mk.

AFAICT it should be possible to build inferno using 9base's mk.=C2=A0 I= n 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 you= r
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 <laura.lazzati.15@gmail.com>
To: clement@lassi= eur.org
Cc: G?bor Boskovits <boskovits@gmail.com>,=C2=A0 =C2=A0 =C2=A0 Guix-devel
=C2=A0 =C2=A0 =C2=A0 =C2=A0 <guix-devel@gnu.org>,=C2=A0 =C2=A0Ricardo Wurmus <ricardo.wurm= us@mdc-berlin.de>
Subject: Re: [outreach] Help trying to create R package
Message-ID:
=C2=A0 =C2=A0 =C2=A0 =C2=A0 <CAPNLzUPBPEw=3DcMd8awOYi65b= 3gWpQkoXoON9qiTmpjKd4fLcag@mail.gmail.com>
Content-Type: text/plain; charset=3D"UTF-8"

On Wed, Oct 17, 2018 at 2:13 PM Cl?ment Lassieur <clement@lassieur.org> wrote:
>
> Hi Laura,
>
> Laura Lazzati <laura.lazzati.15@gmail.com> writes:
>
> > You were right. I took a look at my .bashrc file, and I had an: > > export PATH=3D"/home/laura/.guix-profile/bin${PATH:+:}$PATH&= quot;
> > I ran $guix pull, did the PATH export in my CLI, then checked the= output of
> > $which guix, that was the same that was mentioned by you,
> > commented that previous line in .bashrc,
> > added=C2=A0 export PATH=3D"/home/laura/.config/guix/current/= bin${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?.=C2=A0 :-)
>
> Quoting the documentation[1]:
>
>=C2=A0 =C2=A0 =C2=A0Users sometimes wrongfully augment environment vari= ables such as
>=C2=A0 =C2=A0 =C2=A0?PATH? in their ?~/.bashrc? file.=C2=A0 As a conseq= uence, when ?guix
>=C2=A0 =C2=A0 =C2=A0environment? launches it, Bash may read ?~/.bashrc?= , thereby
>=C2=A0 =C2=A0 =C2=A0introducing ?impurities? in these environment varia= bles.=C2=A0 It is an
>=C2=A0 =C2=A0 =C2=A0error to define such environment variables in ?.bas= hrc?; instead,
>=C2=A0 =C2=A0 =C2=A0they should be defined in ?.bash_profile?, which is= sourced only by
>=C2=A0 =C2=A0 =C2=A0log-in shells.=C2=A0 See ?Bash Startup Files[2]?, f= or details on Bash
>=C2=A0 =C2=A0 =C2=A0start-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-enviro= nment.html#FOOT15
> [2]: https://www.gnu.org/software/bash/manual/html_node/Bash-Startup-Files.ht= ml#Bash-Startup-Files



------------------------------

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