From mboxrd@z Thu Jan 1 00:00:00 1970 From: Laura Lazzati Subject: Re: [outreach] Help trying to create R package Date: Fri, 2 Nov 2018 16:44:38 -0300 Message-ID: References: <20181016074412.54757b18@alma-ubu> <20181016082350.75757e6b@alma-ubu> Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="0000000000004237eb0579b3c64c" Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:50727) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1gIfO3-0001r3-2d for guix-devel@gnu.org; Fri, 02 Nov 2018 15:45:44 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1gIfO0-00037q-IF for guix-devel@gnu.org; Fri, 02 Nov 2018 15:45:42 -0400 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?= , =?UTF-8?Q?G=C3=A1bor_Boskovits?= , =?UTF-8?Q?Ludovic_Court=C3=A8s?= , rekado@elephly.net Cc: Guix-devel , Ricardo Wurmus --0000000000004237eb0579b3c64c Content-Type: text/plain; charset="UTF-8" > > > 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=bioconductor rtracklayer > Sorry for writing again on this topic. Today I wanted to practice packaging an r package belonging to bioconductor, to then go on and read and work with texinfo. After writing on IRC channel, I realized I already had this exact problem, but thought it was a problem of other packages. I ran again this same command, and I am getting: $guix import cran -a bioconductor rtracklayer guile: warning: failed to install locale hint: Consider installing the `glibc-utf8-locales' or `glibc-locales' package and defining `GUIX_LOCPATH', along these lines: guix package -i glibc-utf8-locales export GUIX_LOCPATH="$HOME/.guix-profile/lib/locale" See the "Application Setup" section in the manual, for more info. Starting download of /tmp/guix-file.kBVFop From https://bioconductor.org/packages/release/bioc/src/contrib/rtracklayer_1.40.6.tar.gz. .. download failed " https://bioconductor.org/packages/release/bioc/src/contrib/rtracklayer_1.40.6.tar.gz" 404 "Not Found" failed to download "/tmp/guix-file.kBVFop" from " https://bioconductor.org/packages/release/bioc/src/contrib/rtracklayer_1.40.6.tar.gz " Backtrace (and the backtrace is the same). I am also new to schemas, but opened guix/import/cran.scm and saw what Bjorn was saying. I don't know why if it is not the latest package there should be a false condition, but I don't know either why I am not getting the latest version from bioconductor if it is real that, for tracklayer the latest is 42 and that file does not exist. Any ideas? Should I spend more time trying to figure this out or should I move on to another task, like knowing guix more deeply or learning texinfo? Regards! Laura --0000000000004237eb0579b3c64c Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable

I tracked it down:

The cause is that:

guix/import/cran.scm:

(define (latest-bioconductor-package-version name)
=C2=A0 "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
Sorry for writing again on this topic.
Today I wanted= to practice packaging an r package belonging to bioconductor, to then go o= n and read and work with texinfo.
After writing on IRC channel, I= realized I already had this exact problem, but thought it was a problem of= other packages.
I ran again this same command, and I am getting:=

$guix import cran -a bioconductor rtracklayer guile: warning: failed to install locale
hint: Consider installing the = `glibc-utf8-locales' or `glibc-locales' package and defining `GUIX_= LOCPATH', along these lines:

=C2=A0=C2=A0=C2=A0=C2=A0 guix packa= ge -i glibc-utf8-locales
=C2=A0=C2=A0=C2=A0=C2=A0 export GUIX_LOCPATH=3D= "$HOME/.guix-profile/lib/locale"

See the "Application= Setup" section in the manual, for more info.



Starting = download of /tmp/guix-file.kBVFop
From https://bi= oconductor.org/packages/release/bioc/src/contrib/rtracklayer_1.40.6.tar.gz.= ..
download failed "https://bioconductor.= org/packages/release/bioc/src/contrib/rtracklayer_1.40.6.tar.gz" 4= 04 "Not Found"
failed to download "/tmp/guix-file.kBVFop&= quot; from "https://bioconductor.org/packages/re= lease/bioc/src/contrib/rtracklayer_1.40.6.tar.gz"
Backtrace
(and the backtrace is the same).

I am = also new to schemas, but opened guix/import/cran.scm and saw what Bjorn was= saying. I don't know why if it is not the latest package there should = be a false condition, but I don't know either why I am not getting the = latest version from bioconductor if it is real that, for tracklayer the lat= est is 42 and that file does not exist.
Any ideas? Should I spend= more time trying to figure this out or should I move on to another task, l= ike knowing guix more deeply or learning texinfo?

=
Regards!
Laura
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