Re: [PATCH 7/7] gnu: Add r-bioccheck.
Ricardo Wurmus writes: > Roel Janssenwrites: > +(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”. >> >> Ofcourse! Sorry, I should've known this. >> >> + (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? >> >> I prefer symlinking. Sorry for being a shell-out. I updated the patch >> to use Guile's @code{symlink} instead (I wasn't aware of this function!). >> >> Here's the new patch: >> >>>From cce8a9580645011cf8f6b259296a4779633aa2af Mon Sep 17 00:00:00 2001 >> From: Roel Janssen >> Date: Thu, 20 Oct 2016 00:00:33 +0200 >> Subject: [PATCH] gnu: Add r-bioccheck. >> >> * gnu/packages/bioinformatics.scm (r-bioccheck): New variable. >> --- >> gnu/packages/bioinformatics.scm | 46 >> + >> 1 file changed, 46 insertions(+) >> >> diff --git a/gnu/packages/bioinformatics.scm >> b/gnu/packages/bioinformatics.scm >> index 3fe7b5f..8e426d0 100644 >> --- a/gnu/packages/bioinformatics.scm >> +++ b/gnu/packages/bioinformatics.scm >> @@ -5936,6 +5936,52 @@ 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* (#:key outputs #:allow-other-keys) >> + (let ((dest-dir (string-append (assoc-ref outputs "out") >> "/bin")) >> + (script-dir >> +(string-append %output >> "/site-library/BiocCheck/script/"))) > > You missed one “%output” :) > I’d bind “out” it in the “let*” so that you don’t need to “assoc-ref” twice. Aha! That's why you suggested binding "out" in the "let*".. I applied your suggestion. >> + (mkdir-p dest-dir) >> + (symlink (string-append script-dir "/checkBadDeps.R") >> +(string-append dest-dir "/checkBadDeps.R")) >> + (symlink (string-append script-dir "/BiocCheck") >> +(string-append dest-dir "/BiocCheck" > > One last thing: please let the lambda end with #t. > Other than that it’s all good. Right. The return value of @code{symlink} is unspecified, so I just added #t to the end of the lambda. I pushed the patch with these
Re: [PATCH 7/7] gnu: Add r-bioccheck.
Ricardo Wurmus writes: > Roel Janssenwrites: >> >> 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”. Ofcourse! Sorry, I should've known this. >> + (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? I prefer symlinking. Sorry for being a shell-out. I updated the patch to use Guile's @code{symlink} instead (I wasn't aware of this function!). Here's the new patch: >From cce8a9580645011cf8f6b259296a4779633aa2af Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Thu, 20 Oct 2016 00:00:33 +0200 Subject: [PATCH] gnu: Add r-bioccheck. * gnu/packages/bioinformatics.scm (r-bioccheck): New variable. --- gnu/packages/bioinformatics.scm | 46 + 1 file changed, 46 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 3fe7b5f..8e426d0 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5936,6 +5936,52 @@ 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* (#:key outputs #:allow-other-keys) + (let ((dest-dir (string-append (assoc-ref outputs "out") "/bin")) + (script-dir +(string-append %output "/site-library/BiocCheck/script/"))) + (mkdir-p dest-dir) + (symlink (string-append script-dir "/checkBadDeps.R") +(string-append dest-dir "/checkBadDeps.R")) + (symlink (string-append script-dir
Re: [PATCH 7/7] gnu: Add r-bioccheck.
Roel Janssenwrites: > 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
Re: [PATCH 7/7] gnu: Add r-bioccheck.
Ricardo Wurmus writes: > Roel Janssenwrites: > >> * 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/"))) + (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") +(native-inputs + `(("which" ,which))) +(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 contains tools to perform additional quality +checks on R packages that are to be submitted to the Bioconductor repository.") +(license license:artistic2.0))) + (define-public r-getopt (package
Re: [PATCH 7/7] gnu: Add r-bioccheck.
Roel Janssenwrites: > * 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? > +(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? ~~ Ricardo
[PATCH 7/7] gnu: Add r-bioccheck.
* 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))) +(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.") +(license license:artistic2.0))) + (define-public r-dnacopy (package (name "r-dnacopy") -- 2.10.0