* [PATCH 7/7] gnu: Add r-bioccheck.
@ 2016-09-15 11:39 Roel Janssen
2016-09-19 12:37 ` Ricardo Wurmus
0 siblings, 1 reply; 7+ messages in thread
From: Roel Janssen @ 2016-09-15 11:39 UTC (permalink / raw)
To: guix-devel
* 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
^ permalink raw reply related [flat|nested] 7+ messages in thread* Re: [PATCH 7/7] gnu: Add r-bioccheck.
2016-09-15 11:39 [PATCH 7/7] gnu: Add r-bioccheck Roel Janssen
@ 2016-09-19 12:37 ` Ricardo Wurmus
2016-10-19 14:46 ` Roel Janssen
0 siblings, 1 reply; 7+ messages in thread
From: Ricardo Wurmus @ 2016-09-19 12:37 UTC (permalink / raw)
To: Roel Janssen; +Cc: guix-devel
Roel Janssen <roel@gnu.org> 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?
> + (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
^ permalink raw reply [flat|nested] 7+ messages in thread* Re: [PATCH 7/7] gnu: Add r-bioccheck.
2016-09-19 12:37 ` Ricardo Wurmus
@ 2016-10-19 14:46 ` Roel Janssen
2016-10-19 17:09 ` Ricardo Wurmus
0 siblings, 1 reply; 7+ messages in thread
From: Roel Janssen @ 2016-10-19 14:46 UTC (permalink / raw)
To: Ricardo Wurmus; +Cc: guix-devel
Ricardo Wurmus writes:
> Roel Janssen <roel@gnu.org> 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 <roel@gnu.org>
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(<package>) from
+ ;; within R, or by running R CMD BiocCheck <package>. 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
(name "r-getopt")
--
2.10.0
^ permalink raw reply related [flat|nested] 7+ messages in thread* Re: [PATCH 7/7] gnu: Add r-bioccheck.
2016-10-19 14:46 ` Roel Janssen
@ 2016-10-19 17:09 ` Ricardo Wurmus
2016-10-19 22:06 ` Roel Janssen
0 siblings, 1 reply; 7+ messages in thread
From: Ricardo Wurmus @ 2016-10-19 17:09 UTC (permalink / raw)
To: Roel Janssen; +Cc: guix-devel
Roel Janssen <roel@gnu.org> writes:
> Ricardo Wurmus writes:
>
>> Roel Janssen <roel@gnu.org> 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 <roel@gnu.org>
> 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(<package>) from
> + ;; within R, or by running R CMD BiocCheck <package>. 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
^ permalink raw reply [flat|nested] 7+ messages in thread* Re: [PATCH 7/7] gnu: Add r-bioccheck.
2016-10-19 17:09 ` Ricardo Wurmus
@ 2016-10-19 22:06 ` Roel Janssen
2016-10-20 6:16 ` Ricardo Wurmus
0 siblings, 1 reply; 7+ messages in thread
From: Roel Janssen @ 2016-10-19 22:06 UTC (permalink / raw)
To: Ricardo Wurmus; +Cc: guix-devel
Ricardo Wurmus writes:
> Roel Janssen <roel@gnu.org> writes:
>>
>> Here's the new patch:
>>
>>From 1d9248098fc507876d77cddc890ea906aef7b83d Mon Sep 17 00:00:00 2001
>> From: Roel Janssen <roel@gnu.org>
>> 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(<package>) from
>> + ;; within R, or by running R CMD BiocCheck <package>. 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 <roel@gnu.org>
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(<package>) from
+ ;; within R, or by running R CMD BiocCheck <package>. 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 "/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
(name "r-getopt")
--
2.10.0
Kind regards,
Roel Janssen
^ permalink raw reply related [flat|nested] 7+ messages in thread* Re: [PATCH 7/7] gnu: Add r-bioccheck.
2016-10-19 22:06 ` Roel Janssen
@ 2016-10-20 6:16 ` Ricardo Wurmus
2016-10-20 7:59 ` Roel Janssen
0 siblings, 1 reply; 7+ messages in thread
From: Ricardo Wurmus @ 2016-10-20 6:16 UTC (permalink / raw)
To: Roel Janssen; +Cc: guix-devel
Roel Janssen <roel@gnu.org> writes:
>>> +(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(<package>) from
>>> + ;; within R, or by running R CMD BiocCheck <package>. 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 <roel@gnu.org>
> 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(<package>) from
> + ;; within R, or by running R CMD BiocCheck <package>. 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.
> + (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.
Thanks!
~~ Ricardo
^ permalink raw reply [flat|nested] 7+ messages in thread* Re: [PATCH 7/7] gnu: Add r-bioccheck.
2016-10-20 6:16 ` Ricardo Wurmus
@ 2016-10-20 7:59 ` Roel Janssen
0 siblings, 0 replies; 7+ messages in thread
From: Roel Janssen @ 2016-10-20 7:59 UTC (permalink / raw)
To: Ricardo Wurmus; +Cc: guix-devel
Ricardo Wurmus writes:
> Roel Janssen <roel@gnu.org> writes:
>
>>>> +(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(<package>) from
>>>> + ;; within R, or by running R CMD BiocCheck <package>. 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 <roel@gnu.org>
>> 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(<package>) from
>> + ;; within R, or by running R CMD BiocCheck <package>. 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 changes.
Thanks a lot for your time!
Kind regards,
Roel Janssen
^ permalink raw reply [flat|nested] 7+ messages in thread
end of thread, other threads:[~2016-10-20 7:58 UTC | newest]
Thread overview: 7+ messages (download: mbox.gz follow: Atom feed
-- links below jump to the message on this page --
2016-09-15 11:39 [PATCH 7/7] gnu: Add r-bioccheck Roel Janssen
2016-09-19 12:37 ` Ricardo Wurmus
2016-10-19 14:46 ` Roel Janssen
2016-10-19 17:09 ` Ricardo Wurmus
2016-10-19 22:06 ` Roel Janssen
2016-10-20 6:16 ` Ricardo Wurmus
2016-10-20 7:59 ` Roel Janssen
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