From mboxrd@z Thu Jan 1 00:00:00 1970 From: Laura Lazzati Subject: Re: [outreach] Help trying to create R package Date: Wed, 17 Oct 2018 11:27:24 -0300 Message-ID: References: <20181016074412.54757b18@alma-ubu> <20181016082350.75757e6b@alma-ubu> <20181017001851.71543cc9@alma-ubu> <20181017091750.1c408b8d@alma-ubu> Mime-Version: 1.0 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:51086) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1gCmnz-0006ok-Cx for guix-devel@gnu.org; Wed, 17 Oct 2018 10:28:12 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1gCmnx-0008C4-Cy for guix-devel@gnu.org; Wed, 17 Oct 2018 10:28:11 -0400 Received: from mail-pl1-x644.google.com ([2607:f8b0:4864:20::644]:35065) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1gCmnt-00081m-L7 for guix-devel@gnu.org; Wed, 17 Oct 2018 10:28:07 -0400 Received: by mail-pl1-x644.google.com with SMTP id f8-v6so12802996plb.2 for ; Wed, 17 Oct 2018 07:28:02 -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: =?UTF-8?Q?G=C3=A1bor_Boskovits?= Cc: Guix-devel , Ricardo Wurmus On Wed, Oct 17, 2018 at 5:21 AM G=C3=A1bor Boskovits = wrote: > > =C3=9CHi Laura, > > > > Bj=C3=B6rn H=C3=B6fling ezt =C3=ADrta= (id=C5=91pont: 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=C3=B6rn H=C3=B6fling >> > 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=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 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 packag= e definition. There are several ways around that, for example see the -f fl= ag 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 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=C3=B6rn > > > Best regards, > g_bor Thanks both! Regards, Laura