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Notes on how this package can be tested.
────────────────────────────────────────
This package can be tested by running the provided test:
LC_ALL=C R --no-save <<EOT
require("VariantAnnotation") || stop("unable to load VariantAnnotation package")
VariantAnnotation:::.test()
EOT
in order to confirm its integrity.
To successfully run this test you need some BioConductor databases as
preconditions. Since these are not packaged for Debian the according
tests are removed from the test suite of this package.
If you want to install the as Debian packages you can use:
svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-txdb.hsapiens.ucsc.hg19.knowngene/trunk/
Further databases
http://bioconductor.org/packages/release/data/annotation/html/SIFT.Hsapiens.dbSNP132.html
http://bioconductor.org/packages/release/data/annotation/html/PolyPhen.Hsapiens.dbSNP131.html
http://bioconductor.org/packages/release/data/annotation/html/BSgenome.Hsapiens.UCSC.hg19.html
will be needed as well but these are not yet packaged.
Finally you would need to re-activate the according tests by moving the
original files from inst/unitTests to the installation directory or you
rebuild this package by deactivating the patch in the series file.
ATTENTION: There will be one failed test until the package
r-bioc-snpstats
will be available.
-- Andreas Tille <tille@debian.org> Thu, 24 Jul 2014 08:35:54 +0200
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