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