[Bioc-devel] Build error: Dependency 'Biobase' is not available

Hervé Pagès hpages at fredhutch.org
Wed Oct 26 21:32:43 CEST 2016

Hi Shraddha,

On 10/26/2016 11:12 AM, Shraddha Pai wrote:
> Hello BioC developers,
> I'm not sure why the nightly build of my package IdeoViz is reporting this
> error on tokay (see message below). It seems to me that not having Biobase
> installed is such a fundamental problem that the package should have been
> flagged when it first got submitted (sometime in 2014). What am I missing?

If you look at the full report


you'll see that hundreds of packages were victims of that problems
during yesterday builds. This is a problem we see sometimes on the
Windows builders. We're working on it.

The problem should clear out in a couple of hours when the report
gets updated with the results of today's builds.

Sorry for the inconvenience.

> Separately, I got a message about 10 days back reporting a build error on
> malbec1, but that seems to have resolved without my intervention. Does
> anyone know what the case could have been there?

Hard to know for sure without knowing the details of the build error but
if your package is trying to access some remote resource then it could
be that it failed 10 days ago because that resource was momentarily


> ----
> * checking for file 'IdeoViz/DESCRIPTION' ... OK
> * preparing 'IdeoViz':
> * checking DESCRIPTION meta-information ... OK
> * installing the package to build vignettes
> Warning: running command
> '"C:/Users/biocbuild/bbs-3.5-bioc/R/bin/x64/Rcmd.exe" INSTALL -l
> "C:\Users\biocbuild\bbs-3.5-bioc\tmpdir\Rtmpu0feNb\Rinst1230396730de"
> --no-multiarch "C:/Users/biocbuild/bbs-3.5-bioc/tmpdir/Rtmpu0feNb/Rbuild123010852598/IdeoViz"'
> had status 1
>       -----------------------------------
> ERROR: dependency 'Biobase' is not available for package 'IdeoViz'
> * removing 'C:/Users/biocbuild/bbs-3.5-bioc/tmpdir/Rtmpu0feNb/Rinst1230396730de/IdeoViz'
>       -----------------------------------
> ERROR: package installation failed
> ---
> Thanks for your time,
> Shraddha
> ----
> Shraddha Pai
> Post-doctoral Fellow, http://baderlab.org
> The Donnelly Center, University of Toronto
> 	[[alternative HTML version deleted]]
> _______________________________________________
> Bioc-devel at r-project.org mailing list
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Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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E-mail: hpages at fredhutch.org
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