Re: [PATCH] import: Update Bioconductor release to 3.5.

[Roel Janssen <roel@gnu.org>]

Ricardo Wurmus writes:

> Roel Janssen <roel@gnu.org> writes:
>
>> From de9f486828827b1d024cad4918eed3ed96202cc0 Mon Sep 17 00:00:00 2001
>> From: Roel Janssen <roel@gnu.org>
>> Date: Wed, 26 Apr 2017 10:30:52 +0200
>> Subject: [PATCH] import: Update Bioconductor release to 3.5.
>>
>> * guix/import/cran.scm: Change Bioconductor release to 3.5.
>>  guix/import/cran.scm | 4 ++--
>>  1 file changed, 2 insertions(+), 2 deletions(-)
>
> Excellent!  I planned to do this next week, but I’m glad you beat me to
> it :)

Awesome.  Good that I can finally help by taking some of the work. :)

>>
>> +(define-public r-bookdown
>> +  (package
>> +  (name "r-bookdown")
>> +  (version "0.3")
>> +  (source (origin
>> +            (method url-fetch)
>> +            (uri (cran-uri "bookdown" version))
>> +            (sha256
>> +             (base32
>> +              "0r9bchzg7im6psc3jphvshzbidc5bv5xaih1qg7b5518jy4iyvb9"))))
>> +  (build-system r-build-system)
>> +  (propagated-inputs
>> +   `(("r-htmltools" ,r-htmltools)
>> +     ("r-knitr" ,r-knitr)
>> +     ("r-rmarkdown" ,r-rmarkdown)
>> +     ("r-yaml" ,r-yaml)))
>> +  (home-page "https://github.com/rstudio/bookdown")
>> +  (synopsis "Authoring books and technical documents with R markdown")
>> +  (description "This package provides output formats and utilities for
>> +authoring books and technical documents with R Markdown.")
>> +  (license license:gpl3)))
>> +
>
> LGTM.  Sadly, it does indeed seem to be GPLv3 only.
>
>> From f661fce758f3f051f4f951c4c7384c69268169d9 Mon Sep 17 00:00:00 2001
>> From: Roel Janssen <roel@gnu.org>
>> Date: Wed, 26 Apr 2017 11:02:28 +0200
>> Subject: [PATCH] gnu: Add r-delayedarray.
>>
>> * gnu/packages/bioinformatics.scm (r-delayedarray): New variable.
> […]
>> +(define-public r-delayedarray
>> +  (package
>> +    (name "r-delayedarray")
>> +    (version "0.2.0")
>> +    (source (origin
>> +              (method url-fetch)
>> +              (uri (bioconductor-uri "DelayedArray" version))
>> +              (sha256
>> +               (base32
>> +                "0pcsk0f2dg2ldzprs1cccqrk53jrysmm6ccgjj5wh6z3x17g7g2r"))))
>> +    (properties
>> +     `((upstream-name . "DelayedArray")))
>> +    (build-system r-build-system)
>> +    (propagated-inputs
>> +     `(("r-biocgenerics" ,r-biocgenerics)
>> +       ("r-s4vectors" ,r-s4vectors)
>> +       ("r-iranges" ,r-iranges)
>> +       ("r-matrixstats" ,r-matrixstats)))
>> +    (home-page "http://bioconductor.org/packages/DelayedArray")
>> +    (synopsis "Delayed operations on array-like objects")
>> +    (description
>> +     "Wrapping an array-like object (typically an on-disk object) in a
>> +DelayedArray object allows one to perform common array operations on
>> it
>
> @code{DelayedArray}
>
>> +without loading the object in memory.  In order to reduce memory usage
>> +and optimize performance, operations on the object are either delayed
>> +or executed using a block processing mechanism.  Note that this also
>> +works on in-memory array-like objects like DataFrame objects
>> (typically
>
> @code{DataFrame}
>
>> +with Rle columns), Matrix objects, and ordinary arrays and data frames.")
>> +    (license license:artistic2.0)))
>> +
>
> Okay with these changes.

Great!

>> From d4313b287e05efcf54f87160d6e34ea60bfbadf6 Mon Sep 17 00:00:00 2001
>> From: Roel Janssen <roel@gnu.org>
>> Date: Wed, 26 Apr 2017 11:01:23 +0200
>> Subject: [PATCH] gnu: Add r-genomeinfodbdata.
>>
>> * gnu/packages/bioinformatics.scm (r-genomeinfodbdata): New variable.
>> ---
> […]
>
>> +(define-public r-genomeinfodbdata
>> +  (package
>> +    (name "r-genomeinfodbdata")
>> +    (version "0.99.0")
>> +    (source (origin
>> +              (method url-fetch)
>> +              (uri (bioconductor-uri "GenomeInfoDbData" version))
>> +              (sha256
>> +               (base32
>> +                "120qvhb0pvkzd65lsgja62vyrgc37si6fh68q4cg4w5x9f04jw25"))))
>> +    (properties
>> +     `((upstream-name . "GenomeInfoDbData")))
>> +    (build-system r-build-system)
>> +    (home-page "http://bioconductor.org/packages/GenomeInfoDbData")
>> +    (synopsis "Species and taxonomy ID look up tables for GenomeInfoDb")
>> +    (description
>> +     "This package contains data for mapping between NCBI taxonomy ID and
>> +species.  It is used by functions in the GenomeInfoDb package.")
>> +    (license license:artistic2.0)))
>> +
>
> LGTM!
>
> I’d be happy if you could take care of the mass update.  I should note
> that sometimes new inputs are required.  To find them I usually run the
> update in a separate branch where I’ve applied changes to import anew
> and compare with the existing package expression when updating.  It’s on
> my list to clean this all up and submit my changes for review.  It’s
> ugly but it works pretty well.  If you’re interested I could send you a
> patch.

How do you test which inputs are required?  I built all the bioconductor
packages and fixed their builds by adding inputs wherever that was
needed.  This does not take care of inputs that are no longer needed (if
any..).  Any way I can test that in a convenient way?

I'll process the mass-update on Friday, taking your changes into
account.

Thanks!

Kind regards,
Roel Janssen