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 07:44:12 +0200 Message-ID: <20181016074412.54757b18@alma-ubu> References: Mime-Version: 1.0 Content-Type: multipart/signed; micalg=pgp-sha1; boundary="Sig_/gvgYm+H7v0wytyEuEQwhd1l"; protocol="application/pgp-signature" Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:44583) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1gCI9d-0000e4-KR for guix-devel@gnu.org; Tue, 16 Oct 2018 01:44:30 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1gCI9Z-0004Uf-Pj for guix-devel@gnu.org; Tue, 16 Oct 2018 01:44:29 -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_/gvgYm+H7v0wytyEuEQwhd1l Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Hi Laura, On Mon, 15 Oct 2018 19:47:38 -0300 Laura Lazzati wrote: > 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) 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 _ _ # > =E2=80=A6) In guix/import/cran.scm: > 153:36 5 (_) > In ice-9/boot-9.scm: > 829:9 4 (catch _ _ # > =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? See the last message: "certificate could not be verified". You need to install certificates first and setup some environment variables. That is described here: https://www.gnu.org/software/guix/manual/en/guix.html#X_002e509-Certificates Can you get over that problem then? Unfortunately, I'm getting then to another error: 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) ERROR: In procedure string-append: In procedure string-append: Wrong type (expecting string): #f Currently, I don't have time to track that down further. Either you don't have that second problem, someone else has a solution, or I will come back to this back later. Bj=C3=B6rn --Sig_/gvgYm+H7v0wytyEuEQwhd1l Content-Type: application/pgp-signature Content-Description: OpenPGP digital signature -----BEGIN PGP SIGNATURE----- Version: GnuPG v2 iEYEARECAAYFAlvFeq0ACgkQvyhstlk+X/2ccACfaFsDRewJUqThlRPX29FgLClo 7PsAn3qbAWInE863yN0ybSdKI8egh5eA =8pWJ -----END PGP SIGNATURE----- --Sig_/gvgYm+H7v0wytyEuEQwhd1l--