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

[laurent]

Henrik,

I agree that the installation footprint is/has been issue, and I would
think that it could be addressed more efficiently than going the "less
dependencies" route.

Having code and data mixed into one package, and the absence of common
recommended data source for data types, are probably responsible for a
much larger fraction of the footprint than the dependencies are.

Regarding the example you picked this time, it can be seen as
disputable. "snapCGH" is clearly advertised as an "umbrella" package,
unifying several other aCGH-related packages under one common framework.
One should still be interested in the package, one should also suspect
that is it going to require other packages (and their respective
dependencies in turn), shouldn't he ?

As a side note, it can seem difficult to objectively judge what
functions are "rarely called" in a package without actual usage data.



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.
> 
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