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: Tue, 16 Oct 2018 08:23:50 +0200 Message-ID: <20181016082350.75757e6b@alma-ubu> References: <20181016074412.54757b18@alma-ubu> Mime-Version: 1.0 Content-Type: multipart/signed; micalg=pgp-sha1; boundary="Sig_/P4MQMenxytcdayOpG.Oja2n"; protocol="application/pgp-signature" Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:35831) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1gCIlw-0006j7-90 for guix-devel@gnu.org; Tue, 16 Oct 2018 02:24:05 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1gCIlo-0001kV-KA for guix-devel@gnu.org; Tue, 16 Oct 2018 02:24:02 -0400 Received: from m4s11.vlinux.de ([83.151.27.109]:47582 helo=bjoernhoefling.de) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1gCIll-0001fn-T4 for guix-devel@gnu.org; Tue, 16 Oct 2018 02:23:54 -0400 In-Reply-To: <20181016074412.54757b18@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: Laura Lazzati Cc: Guix-devel , Ricardo Wurmus --Sig_/P4MQMenxytcdayOpG.Oja2n Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable On Tue, 16 Oct 2018 07:44:12 +0200 Bj=C3=B6rn H=C3=B6fling wrote: > Hi Laura, >=20 > On Mon, 15 Oct 2018 19:47:38 -0300 > Laura Lazzati wrote: >=20 > > I've reading the documentation as well as trying some commands,and > > there are some problems I am facing. I don't know what I am doing > > wrong. > >=20 > > First, I ran: > > $ guix package -s r-* | recsel -p name >> > > resultOfSearchingRpackages.txt And reading the output file, I found > > that the packages belonging to R that are available are: > > name: r-rtracklayer > > name: r-rcas > > name: r-qtl > > name: r-ggridges > > name: r-feather > > I also took a look at each of them with > > $guix package --show=3DPACKAGENAME > > Then, I tried: > > $ guix import cran --archive=3Dbioconductor tracklayer > >=20 > > But got this output: > > acktrace: > > 17 (apply-smob/1 #) > > In ice-9/boot-9.scm: > > 705:2 16 (call-with-prompt _ _ # > default-prompt-handle=E2=80=A6>) In ice-9/eval.scm: > > 619:8 15 (_ #(#(#))) > > In guix/ui.scm: > > 1578:12 14 (run-guix-command _ . _) > > In guix/scripts/import.scm: > > 114:11 13 (guix-import . _) > > In guix/scripts/import/cran.scm: > > 107:23 12 (guix-import-cran . _) > > In guix/memoization.scm: > > 98:0 11 (_ # ("tracklayer" #) _) > > In unknown file: > > 10 (_ # > =E2=80=A6> =E2=80=A6) In guix/import/cran.scm: > > 349:12 9 (_ _ _) > > 183:21 8 (fetch-description _ "tracklayer") > > 160:15 7 (latest-bioconductor-package-version _) > > In ice-9/boot-9.scm: > > 829:9 6 (catch _ _ # > guix/import/cra=E2=80=A6> =E2=80=A6) In guix/import/cran.scm: > > 153:36 5 (_) > > In ice-9/boot-9.scm: > > 829:9 4 (catch _ _ # > guix/http-client.scm=E2=80=A6> =E2=80=A6) In guix/http-client.scm: > > 182:20 3 (_) > > 88:25 2 (http-fetch _ #:port _ #:text? _ #:buffered? _ # _ # _ > > # =E2=80=A6) In guix/build/download.scm: > > 398:4 1 (open-connection-for-uri _ #:timeout _ # _) > > 296:6 0 (tls-wrap # _ # _) > >=20 > > guix/build/download.scm:296:6: In procedure tls-wrap: > > X.509 certificate of 'bioconductor.org' could not be verified: > > signer-not-found > > invalid > >=20 > > I don't know what's wrong, could you give me a hand? =20 >=20 > See the last message: "certificate could not be verified". >=20 > You need to install certificates first and setup some environment > variables. >=20 > That is described here: >=20 > https://www.gnu.org/software/guix/manual/en/guix.html#X_002e509-Certifica= tes >=20 > Can you get over that problem then? >=20 > Unfortunately, I'm getting then to another error: >=20 > guix import cran --archive=3Dbioconductor tracklayer > Backtrace: > 9 (primitive-load > "/home/bjoern/.config/guix/current/bin/=E2=80=A6") In guix/ui.scm: > 1583:12 8 (run-guix-command _ . _) > In guix/scripts/import.scm: > 115:11 7 (guix-import . _) > In guix/scripts/import/cran.scm: > 107:23 6 (guix-import-cran . _) > In guix/memoization.scm: > 98:0 5 (_ # ("tracklayer" #) _) > In unknown file: > 4 (_ # > =E2=80=A6) In guix/import/cran.scm: > 349:12 3 (_ _ _) > 184:26 2 (fetch-description _ _) > In guix/build-system/r.scm: > 53:8 1 (bioconductor-uri "tracklayer" #f) > In unknown file: > 0 (string-append "https://bioconductor.org/packages/rele=E2=80= =A6" > =E2=80=A6) >=20 > ERROR: In procedure string-append: > In procedure string-append: Wrong type (expecting string): #f >=20 >=20 > Currently, I don't have time to track that down further. >=20 > Either you don't have that second problem, someone else has a > solution, or I will come back to this back later. I tracked it down: The cause is that: guix/import/cran.scm: (define (latest-bioconductor-package-version name) "Return the version string corresponding to the latest release of the bioconductor package NAME, or #F if the package is unknown." actually returns #f. It's a bit said that this #f is not checked further down. The problem is the package name. If you add an "r" before the package name, it should work (suppose you fixed the first problem): guix import cran --archive=3Dbioconductor rtracklayer=20 Bj=C3=B6rn PS: I personally think the Scheme backtraces are a bit hard to read (I'm more used to Java), especially with the "In unknown file" parts, but anyway you can get your information out of it. Try to look at them, read the error message carefully. Find the lines in source code. Get your way up, where is that abnormal #f coming from? --Sig_/P4MQMenxytcdayOpG.Oja2n Content-Type: application/pgp-signature Content-Description: OpenPGP digital signature -----BEGIN PGP SIGNATURE----- Version: GnuPG v2 iEYEARECAAYFAlvFg/cACgkQvyhstlk+X/0TrwCggsdUlRVp0h24wTs5fbEDARJa mfEAni03YPe0dobwF18fJ8INkz4+oSRJ =z+qa -----END PGP SIGNATURE----- --Sig_/P4MQMenxytcdayOpG.Oja2n--