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

[Roel Janssen]

Ricardo Wurmus writes:

> Roel Janssen <address@hidden> 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 <address@hidden>
>> 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