[Bioc-devel] Upcoming release: *Please* revise your Depends and Suggests of DESCRIPTION

[Herve Pages]

Hi developers,

Henrik Bengtsson wrote:
[...]
> Finally, if one want to install all packages including those in
> 'Suggests', one can do:
> 
>  biocLite("<pkg/group>", dependencies=c("Depends", "Suggests", "Imports"))

Note that currently, when I do:

  biocLite("<somepackage>", dependencies=TRUE)  # equivalent to the above

I end up with tons of packages that I'm not necessarily interested in.

This is because the behaviour of install.packages() (the backend of biocLite)
when "Suggests" is specified in the 'dependencies' argument is to follow
recursively the Suggests field. This is obviously the right thing to do for
the Depends and Imports fields but IMO the Suggests field should be treated
differently i.e. only packages *directly* suggested by <somepackage> should be
installed (+ the packages that those suggested packages depend on or import,
recursively, of course), but not the packages that the suggested packages
suggest :-P

It could be that this behaviour of install.packages() is partly responsible
of the too many installed packages that the user experiences sometimes...

Cheers,
H.

> 
> Cheers
> 
> Henrik
> 
>>
>>
>> L.
>>
>>
>>
>> On Wed, 2008-10-15 at 13:11 -0700, Henrik Bengtsson wrote:
>>> Hi *all* package developers
>>>
>>> for the upcoming Bioc release, as a developer, could you please revise
>>> what packages you put under 'Depends' in your DESCRIPTION files.
>>>
>>> In many cases packages listed there are only used occationally in a
>>> few rarely called functions.  In such cases it is recommended to put
>>> such packages under 'Suggests' instead and use require("<pkg>") where
>>> ever they are needed.   This will decrease the download/installation
>>> footprint.
>>>
>>> Without picking on a particular package (I've used a different package
>>> before), here is an illustrative example involving several packages
>>> with large package footprints:
>>>
>>> In order to use the runBioHMM() segmentation method in the snapCGH package:
>>>
>>> Package: snapCGH
>>> Depends: limma, tilingArray, DNAcopy, GLAD, cluster, methods, aCGH
>>> Suggests:
>>> Imports:
>>>
>>> this is what you need to download and install (illustrated package by package):
>>>
>>>> biocLite("limma");
>>> trying URL 'http://bioconductor.org/packages/2.3/bioc/bin/windows/contrib/2.8/limma_2.15.15.zip'
>>> Content type 'application/zip' length 1499394 bytes (1.4 Mb)
>>> opened URL
>>> downloaded 1016 Kb
>>>
>>>
>>>> biocLite("tilingArray");
>>> trying URL 'http://cran.fhcrc.org/bin/windows/contrib/2.8/xtable_1.5-4.zip'
>>> Content type 'application/zip' length 215584 bytes (210 Kb)
>>> opened URL
>>> downloaded 210 Kb
>>>
>>> trying URL 'http://cran.fhcrc.org/bin/windows/contrib/2.8/DBI_0.2-4.zip'
>>> Content type 'application/zip' length 442504 bytes (432 Kb)
>>> opened URL
>>> downloaded 432 Kb
>>>
>>> trying URL 'http://cran.fhcrc.org/bin/windows/contrib/2.8/RSQLite_0.7-0.zip'
>>> Content type 'application/zip' length 599395 bytes (585 Kb)
>>> opened URL
>>> downloaded 585 Kb
>>>
>>> trying URL 'http://cran.fhcrc.org/bin/windows/contrib/2.8/zoo_1.5-4.zip'
>>> Content type 'application/zip' length 872593 bytes (852 Kb)
>>> opened URL
>>> downloaded 852 Kb
>>>
>>> trying URL 'http://cran.fhcrc.org/bin/windows/contrib/2.8/sandwich_2.1-0.zip'
>>> Content type 'application/zip' length 758762 bytes (740 Kb)
>>> opened URL
>>> downloaded 740 Kb
>>>
>>> trying URL 'http://bioconductor.org/packages/2.3/bioc/bin/windows/contrib/2.8/annotate_1.19.3.zip'
>>> Content type 'application/zip' length 1966201 bytes (1.9 Mb)
>>> opened URL
>>> downloaded 1.3 Mb
>>>
>>> trying URL 'http://bioconductor.org/packages/2.3/bioc/bin/windows/contrib/2.8/AnnotationDbi_1.3.12.zip'
>>> Content type 'application/zip' length 1517547 bytes (1.4 Mb)
>>> opened URL
>>> downloaded 1.4 Mb
>>>
>>> trying URL 'http://cran.fhcrc.org/bin/windows/contrib/2.8/strucchange_1.3-4.zip'
>>>
>>> Content type 'application/zip' length 937367 bytes (915 Kb)
>>> opened URL
>>> downloaded 915 Kb
>>>
>>> trying URL 'http://bioconductor.org/packages/2.3/bioc/bin/windows/contrib/2.8/vsn_3.7.7.zip'
>>> Content type 'application/zip' length 1328450 bytes (1.3 Mb)
>>> opened URL
>>> downloaded 1.3 Mb
>>>
>>> trying URL 'http://bioconductor.org/packages/2.3/bioc/bin/windows/contrib/2.8/genefilter_1.21.5.zip'
>>> Content type 'application/zip' length 483979 bytes (472 Kb)
>>> opened URL
>>> downloaded 472 Kb
>>>
>>> trying URL 'http://bioconductor.org/packages/2.3/bioc/bin/windows/contrib/2.8/geneplotter_1.19.6.zip'
>>> Content type 'application/zip' length 1446820 bytes (1.4 Mb)
>>> opened URL
>>> downloaded 1.4 Mb
>>>
>>> trying URL 'http://cran.fhcrc.org/bin/windows/contrib/2.8/pixmap_0.4-9.zip'
>>> Content type 'application/zip' length 118653 bytes (115 Kb)
>>> opened URL
>>> downloaded 115 Kb
>>>
>>> trying URL 'http://bioconductor.org/packages/2.3/bioc/bin/windows/contrib/2.8/tilingArray_1.19.2.zip'
>>> Content type 'application/zip' length 2291041 bytes (2.2 Mb)
>>> opened URL
>>> downloaded 2.2 Mb
>>>
>>>
>>>> biocLite("DNAcopy");
>>> trying URL 'http://bioconductor.org/packages/2.2/bioc/bin/windows/contrib/2.7/DNAcopy_1.14.0.zip'
>>> Content type 'application/zip' length 389689 bytes (380 Kb)
>>> opened URL
>>> downloaded 380 Kb
>>>
>>>
>>>> biocLite("GLAD");
>>> trying URL 'http://bioconductor.org/packages/2.2/bioc/bin/windows/contrib/2.7/GLAD_1.16.0.zip'
>>> Content type 'application/zip' length 1821831 bytes (1.7 Mb)
>>> opened URL
>>> downloaded 1.7 Mb
>>>
>>>
>>>> biocLite("cluster");
>>> trying URL 'http://cran.fhcrc.org/bin/windows/contrib/2.7/cluster_1.11.11.zip'
>>> Content type 'application/zip' length 517782 bytes (505 Kb)
>>> opened URL
>>> downloaded 505 Kb
>>>
>>>
>>>> biocLite("aCGH");
>>> trying URL 'http://cran.fhcrc.org/bin/windows/contrib/2.7/multtest_1.21.1.zip'
>>> Content type 'application/zip' length 1653667 bytes (1.6 Mb)
>>> opened URL
>>> downloaded 1.6 Mb
>>>
>>> trying URL 'http://cran.fhcrc.org/bin/windows/contrib/2.7/sma_0.5.15.zip'
>>> Content type 'application/zip' length 3070300 bytes (2.9 Mb)
>>> opened URL
>>> downloaded 2.9 Mb
>>>
>>> trying URL 'http://bioconductor.org/packages/2.2/bioc/bin/windows/contrib/2.7/aCGH_1.14.0.zip'
>>> Content type 'application/zip' length 6692045 bytes (6.4 Mb)
>>> opened URL
>>> downloaded 6.4 Mb
>>>
>>>> biocLite("snapCGH");
>>> trying URL 'http://bioconductor.org/packages/2.3/bioc/bin/windows/contrib/2.8/snapCGH_1.9.5.zip'
>>> Content type 'application/zip' length 1308714 bytes (1.2 Mb)
>>> opened URL
>>> downloaded 1.2 Mb
>>>
>>>
>>> POINT MADE?
>>>
>>> Cheers
>>>
>>> Henrik
>>>
>>> PS. I'd like to suggest that is is checked as part of the initial
>>> package review. DS.
>>>
>>> _______________________________________________
>>> Bioc-devel at stat.math.ethz.ch mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
> 
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