diff mbox

[7/7] gnu: Add r-bioccheck.

Message ID 87twc856ze.fsf@gnu.org
State New
Headers show

Commit Message

Roel Janssen Oct. 19, 2016, 10:06 p.m. UTC
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(+)

Comments

Ricardo Wurmus Oct. 20, 2016, 6:16 a.m. UTC | #1
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
Roel Janssen Oct. 20, 2016, 7:59 a.m. UTC | #2
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
diff mbox

Patch

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")