From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ricardo Wurmus Subject: Re: [PATCH 7/7] gnu: Add r-bioccheck. Date: Wed, 19 Oct 2016 19:09:14 +0200 Message-ID: <87mvi0s1tx.fsf@elephly.net> References: <87bmzps87x.fsf@gnu.org> <87d1k0m5ek.fsf@elephly.net> <87oa2ggzvr.fsf@gnu.org> Mime-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:43671) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1bwuMq-00014i-D4 for guix-devel@gnu.org; Wed, 19 Oct 2016 13:09:29 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1bwuMp-0007ST-6i for guix-devel@gnu.org; Wed, 19 Oct 2016 13:09:28 -0400 In-reply-to: <87oa2ggzvr.fsf@gnu.org> 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: Roel Janssen Cc: guix-devel@gnu.org Roel Janssen writes: > Ricardo Wurmus writes: > >> Roel Janssen writes: >> >>> * gnu/packages/bioinformatics.scm (r-bioccheck): New variable. >>> --- >>> gnu/packages/bioinformatics.scm | 29 +++++++++++++++++++++++++++++ >>> 1 file changed, 29 insertions(+) >>> >>> diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm >>> index 902d1d2..00a4161 100644 >>> --- a/gnu/packages/bioinformatics.scm >>> +++ b/gnu/packages/bioinformatics.scm >>> @@ -5426,6 +5426,35 @@ like automatically generated help option and usage, support for default >>> values, positional argument support, etc.") >>> (license license:gpl2+))) >>> >>> +(define-public r-bioccheck >>> + (package >>> + (name "r-bioccheck") >>> + (version "1.8.2") >>> + (source (origin >>> + (method url-fetch) >>> + (uri (bioconductor-uri "BiocCheck" version)) >>> + (sha256 >>> + (base32 >>> + "0bvkhxmr25nb0gkncifbc3x48i5zgls3737g3xais6jx16wd4q35")))) >>> + (properties >>> + `((upstream-name . "BiocCheck"))) >>> + (build-system r-build-system) >>> + (inputs >>> + `(("which" ,which))) >> >> Is this a native input? > > Ah, yes it is. > >>> + (propagated-inputs >>> + `(("r-graph" ,r-graph) >>> + ("r-knitr" ,r-knitr) >>> + ("r-httr" ,r-httr) >>> + ("r-optparse" ,r-optparse) >>> + ("r-devtools" ,r-devtools) >>> + ("r-biocinstaller" ,r-biocinstaller) >>> + ("r-biocviews" ,r-biocviews))) >>> + (home-page "http://bioconductor.org/packages/BiocCheck") >>> + (synopsis "Executes Bioconductor-specific package checks") >>> + (description "This package executes Bioconductor-specific >>> +package checks.") >> >> Well… okay. :) It would be nice if it was a little more specific. >> >> Maybe: >> >> This package contains tools to perform quality checks on R packages >> that are to be submitted to the Bioconductor repository. >> >> WDYT? > > I used your description, but added "additional" to it. I also added a > custom build phase to make "R CMD BiocCheck" work. > > Here's the new patch: > >>From 1d9248098fc507876d77cddc890ea906aef7b83d Mon Sep 17 00:00:00 2001 > From: Roel Janssen > Date: Wed, 19 Oct 2016 16:43:04 +0200 > Subject: [PATCH] gnu: Add r-bioccheck. > > * gnu/packages/bioinformatics.scm (r-bioccheck): New variable. > --- > gnu/packages/bioinformatics.scm | 48 +++++++++++++++++++++++++++++++++++++++++ > 1 file changed, 48 insertions(+) > > diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm > index 3fe7b5f..d21781f 100644 > --- a/gnu/packages/bioinformatics.scm > +++ b/gnu/packages/bioinformatics.scm > @@ -5936,6 +5936,54 @@ Bioconductor PDF and HTML documents. Package vignettes illustrate use and > functionality.") > (license license:artistic2.0))) > > +(define-public r-bioccheck > + (package > + (name "r-bioccheck") > + (version "1.10.0") > + (source (origin > + (method url-fetch) > + (uri (bioconductor-uri "BiocCheck" version)) > + (sha256 > + (base32 > + "1rfy37xg1nc2cmgbclvzsi7sgmdcdjiahsx9crgx3yaw7kxgiack")))) > + (properties > + `((upstream-name . "BiocCheck"))) > + (build-system r-build-system) > + (arguments > + '(#:phases > + (modify-phases %standard-phases > + ;; This package can be used by calling BiocCheck() from > + ;; within R, or by running R CMD BiocCheck . This phase > + ;; makes sure the latter works. For this to work, the BiocCheck > + ;; script must be somewhere on the PATH (not the R bin directory). > + (add-after 'install 'install-bioccheck-subcommand > + (lambda _ > + (let ((dest-dir (string-append %output "/bin")) > + (script-dir > + (string-append %output "/site-library/BiocCheck/script/"))) We usually prefer to do this (lambda* (#:key outputs #:allow-other-keys) (let* ((out (assoc-ref outputs "out")) … out …))) instead of using the magical “%output”. > + (mkdir-p dest-dir) > + (zero? (system* "ln" "--symbolic" > + (string-append script-dir "/checkBadDeps.R") > + (string-append dest-dir "/checkBadDeps.R"))) > + (zero? (system* "ln" "--symbolic" > + (string-append script-dir "/BiocCheck") > + (string-append dest-dir "/BiocCheck"))))))))) Would it work to use “install-file” here (or to use Guile’s “symlink oldpath newpath”) instead of shelling out? ~~ Ricardo