[Bioc-devel] Can't seem to use useDevel(); biocLite() for BioC 3.1

Leonardo Collado Torres lcollado at jhu.edu
Mon Nov 3 03:32:46 CET 2014


I can't seem to install devel packages via biocLite() and I wonder if
something is broken or if I'm missing something. For example, take
GenomeInfoDb which is at 1.3.6 and is passing all checks.

The usual code using a fresh R 3.1.2-patched install isn't working as
it downloads the latest release version (1.2.2):

> source("http://bioconductor.org/biocLite.R")
Bioconductor version 3.0 (BiocInstaller 1.16.0), ?biocLite for help
## Was expecting 3.1 here
> useDevel()
Error: 'devel' version already in use
> biocLite('GenomeInfoDb')
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.0 (BiocInstaller 1.16.0), R version 3.1.2.
Installing package(s) 'GenomeInfoDb'
trying URL 'http://bioconductor.org/packages/3.0/bioc/bin/macosx/contrib/3.1/GenomeInfoDb_1.2.2.tgz'
Content type 'application/x-gzip' length 404120 bytes (394 KB)
opened URL
downloaded 394 KB

The downloaded binary packages are in
> sessionInfo()
R version 3.1.2 Patched (2014-11-01 r66923)
## Note that it matches the current R version used by the Bioc-devel
build machines
Platform: x86_64-apple-darwin10.8.0 (64-bit)

[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] BiocInstaller_1.16.0 colorout_1.0-2

loaded via a namespace (and not attached):
[1] tools_3.1.2

For my computer it's not problem because I can download the pkg via
svn and install locally. But it breaks my tests in TravisCI which
relies on biocLite().


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