From mboxrd@z Thu Jan 1 00:00:00 1970 From: =?UTF-8?Q?G=C3=A1bor_Boskovits?= Subject: Re: [outreach] Help trying to create R package Date: Tue, 16 Oct 2018 10:28:54 +0200 Message-ID: References: <20181016074412.54757b18@alma-ubu> <20181016082350.75757e6b@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 ([208.118.235.92]:42292) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1gCKqS-0000qP-4o for guix-devel@gnu.org; Tue, 16 Oct 2018 04:36:54 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1gCKiy-0008Nm-Bg for guix-devel@gnu.org; Tue, 16 Oct 2018 04:29:57 -0400 Received: from mail-oi1-x232.google.com ([2607:f8b0:4864:20::232]:36329) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1gCKiy-0008LA-3I for guix-devel@gnu.org; Tue, 16 Oct 2018 04:29:08 -0400 Received: by mail-oi1-x232.google.com with SMTP id p125-v6so17338205oic.3 for ; Tue, 16 Oct 2018 01:29:07 -0700 (PDT) In-Reply-To: <20181016082350.75757e6b@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 Hello Bj=C3=B6rn, Bj=C3=B6rn H=C3=B6fling ezt =C3=ADrta (= id=C5=91pont: 2018. okt. 16., K, 8:24): > > On Tue, 16 Oct 2018 07:44:12 +0200 > Bj=C3=B6rn H=C3=B6fling wrote: > > > 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. > > > > > > 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 > > > > > > 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 # _ # _) > > > > > > guix/build/download.scm:296:6: In procedure tls-wrap: > > > X.509 certificate of 'bioconductor.org' could not be verified: > > > signer-not-found > > > invalid > > > > > > 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-Certifi= cates > > > > 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. > > > 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 > > Bj=C3=B6rn > Thanks for having a look at this. > 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? >