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

[Robert Gentleman]

Hi Henrik,
   Good points.  I would also like people to consider Imports for things 
that are infrastructure and hence should not end up on the search path.

   And to answer your last point - the number of dependencies and where 
they are is something we do check (as several recent submitters can 
attest).  We also review packages that are in the repository for a 
number of things (excessive dependencies being one of them).

  best wishes
    Robert


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
> 

-- 
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
206-667-7700
rgentlem at fhcrc.org