[Bioc-devel] CRAN package with Bioconductor dependencies
hpages at fredhutch.org
Tue Mar 3 00:32:31 CET 2015
On 03/02/2015 03:18 PM, Laurent Gatto wrote:
> Dear all,
> I had never realised that CRAN packages that depended on Bioc packages
> could actually not be installed with install.packages without setting a
> repo or using BiocInstaller::bioLite. Here is an example using a fresh R
> Depends: amap, clValid, cluster, fpc, mzR, xcms
> $ docker run --rm -ti rocker/r-base R
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> Installing package into ‘/usr/local/lib/R/site-library’
> (as ‘lib’ is unspecified)
> Warning: dependencies ‘mzR’, ‘xcms’ are not available
> also installing the dependencies ‘modeltools’, ‘DEoptimR’, ‘mclust’, ‘flexmix’, ‘prabclus’, ‘diptest’, ‘mvtnorm’, ‘robustbase’, ‘kernlab’, ‘trimcluster’, ‘amap’, ‘clValid’, ‘fpc’
> ERROR: dependencies ‘mzR’, ‘xcms’ are not available for package ‘MSeasy’
> * removing ‘/usr/local/lib/R/site-library/MSeasy’
> The downloaded source packages are in
> Warning message:
> In install.packages("MSeasy") :
> installation of package ‘MSeasy’ had non-zero exit status
> This does sound really counter-intuitive. Am I missing anything?
I don't think you are. By default install.packages() doesn't know
about the BioC repos so...
But the CRAN builds do know about the BioC repos so CRAN packages
that depend on us do pass check (or not... but that's another story).
And sometimes we receive notifications from the CRAN maintainer that
some changes in our packages break some of their packages.
Also I'm not sure what version of BioC they depend on for their
builds. Our release schedules are different: 1 release per year
for them, 2 for us. If they use BioC release for their release builds,
then we can break CRAN packages when we release. It's unavoidable
Having CRAN packages that depend on us is just not a good situation
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