From mboxrd@z Thu Jan 1 00:00:00 1970 From: =?UTF-8?B?QmrDtnJuIEjDtmZsaW5n?= Subject: Re: [outreach] Help trying to create R package Date: Wed, 17 Oct 2018 09:17:50 +0200 Message-ID: <20181017091750.1c408b8d@alma-ubu> References: <20181016074412.54757b18@alma-ubu> <20181016082350.75757e6b@alma-ubu> <20181017001851.71543cc9@alma-ubu> Mime-Version: 1.0 Content-Type: multipart/signed; micalg=pgp-sha1; boundary="Sig_/9PZgewqpTkg2GPcW8IsTdpK"; protocol="application/pgp-signature" Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:59945) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1gCg5e-00086Q-7I for guix-devel@gnu.org; Wed, 17 Oct 2018 03:17:59 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1gCg5a-0002Bo-TH for guix-devel@gnu.org; Wed, 17 Oct 2018 03:17:58 -0400 Received: from m4s11.vlinux.de ([83.151.27.109]:47672 helo=bjoernhoefling.de) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1gCg5a-000285-B7 for guix-devel@gnu.org; Wed, 17 Oct 2018 03:17:54 -0400 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: Laura Lazzati Cc: Guix-devel , Ricardo Wurmus --Sig_/9PZgewqpTkg2GPcW8IsTdpK Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable 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, =20 > 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 :-) [..] > > Here is another one: > > > > guix package -s "^r-" | recsel -p name| grep '\S' | sort >r.txt =20 >=20 > 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. > 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. =20 > 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: >=20 > (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#Con= tributing Bj=C3=B6rn --Sig_/9PZgewqpTkg2GPcW8IsTdpK Content-Type: application/pgp-signature Content-Description: OpenPGP digital signature -----BEGIN PGP SIGNATURE----- Version: GnuPG v2 iEYEARECAAYFAlvG4h8ACgkQvyhstlk+X/3DGACgqhS+zS4OnLLkG1uIIFjQBk2j nVUAn2Bn9LLPdod22mYP2mkQU3rthyL/ =HWg1 -----END PGP SIGNATURE----- --Sig_/9PZgewqpTkg2GPcW8IsTdpK--