From mboxrd@z Thu Jan 1 00:00:00 1970 From: Laura Lazzati Subject: Re: [outreach] Help trying to create R package Date: Tue, 16 Oct 2018 22:01:58 -0300 Message-ID: References: <20181016074412.54757b18@alma-ubu> <20181016082350.75757e6b@alma-ubu> <20181017001851.71543cc9@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]:35849) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1gCaEa-0006Cb-Ct for guix-devel@gnu.org; Tue, 16 Oct 2018 21:02:49 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1gCaEY-0001UY-17 for guix-devel@gnu.org; Tue, 16 Oct 2018 21:02:48 -0400 Received: from mail-pf1-x436.google.com ([2607:f8b0:4864:20::436]:42103) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1gCaEX-0001HP-JL for guix-devel@gnu.org; Tue, 16 Oct 2018 21:02:45 -0400 Received: by mail-pf1-x436.google.com with SMTP id f26-v6so12296184pfn.9 for ; Tue, 16 Oct 2018 18:02:36 -0700 (PDT) In-Reply-To: <20181017001851.71543cc9@alma-ubu> 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?B?QmrDtnJuIEjDtmZsaW5n?= Cc: Guix-devel , Ricardo Wurmus 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. > > On Tue, 16 Oct 2018 10:13:23 -0300 > Laura Lazzati wrote: > > [importing problems ...] > > Could you solve your certificate-problem? Have you been successfully in > importing a package? Yes! I love reading ALL the documentation, but I focused mainly in chapters 3 to 5, and the part about the certificate stuff is 6. That is why I did not know about it. > > Unfortunately the package of your choice is already part of guix: > > > $ guix package -s "rtracklayer$" > name: r-rtracklayer > version: 1.40.6 > outputs: out > systems: x86_64-linux i686-linux armhf-linux aarch64-linux mips64el-linux > dependencies: pkg-config@0.29.2 r-biocgenerics@0.26.0 r-biostrings@2.48.0 > + r-genomeinfodb@1.16.0 r-genomicalignments@1.16.0 r-genomicranges@1.32.6 > + r-iranges@2.14.11 r-rcurl@1.95-0.1.2 r-rsamtools@1.32.3 r-s4vectors@0.1= 8.3 > + r-xml@3.98-1.16 r-xvector@0.20.0 zlib@1.2.11 > location: gnu/packages/bioinformatics.scm:7696:2 > homepage: https://bioconductor.org/packages/rtracklayer > license: Artistic License 2.0 > synopsis: R interface to genome browsers and their annotation tracks > description: rtracklayer is an extensible framework for interacting with > + multiple genome browsers (currently UCSC built-in) and manipulating ann= otation > + tracks in various formats (currently GFF, BED, bedGraph, BED15, WIG, Bi= gWig > + and 2bit built-in). The user may export/import tracks to/from the supp= orted > + browsers, as well as query and modify the browser state, such as the cu= rrent > + viewport. > relevance: 4 > > Can you find another one? Yes! I knew that the package was already available for guix, but I just wanted to see the template, with guix import, to use it for others. > > > > I am trying to do my best. I am reading the documentation carefully, I > > recall mentioning that I am that kind of person, but I also know that > > time counts for the contributions. > > Yes, you mentioned that :-) The documentation is huge, with lots of > special concepts. I would recommend reading it only partially, whenever > you need more information. I have already answered this :( I know I don't have time to do things this way, at least for the contribution(s) > > > > And if I figure out how to package > > R packages, then I can also package more packages and, whatever the > > result of outreachy might be, well, there are more useful packages in > > guix. > > For instance, I tried, before of asking for help with the example > > shown with cairo and it worked fine, so I was not understanding very > > well what was happening, > > In addition, I have just run > > $ guix package -s "\" | recsel -p name,synopsis >> > > outputRwithNameAndSynopsis.txt > > and found even more R packages already installed. > > 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) 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? 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) 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) > > the carret-symbol "^" matches the beginning of the line. > There are some empty lines, which get sorted out with the grep. Thanks :) I knew about the regex, but everything is always welcome :) sometimes it is true that after reading too much info you end up messed up if you do not have enough time to practice and try everything. > > > > Well, time to work! > > Good luck! Thanks! > > Bj=C3=B6rn Regards, Laura