[Bioc-devel] "'BiocInstaller' package not in repository" error during nightly build

[Dan Tenenbaum]

----- Original Message -----
> From: "Robert Castelo" <robert.castelo at upf.edu>
> To: "Kevin Rue-Albrecht" <kevin.rue at ucdconnect.ie>
> Cc: bioc-devel at r-project.org
> Sent: Thursday, October 16, 2014 3:24:32 AM
> Subject: Re: [Bioc-devel] "'BiocInstaller' package not in repository" error during nightly build
> 
> hi Kevin,
> 
> if you're talking about the devel version of BiocInstaller, the SVN
> logs
> show a commit yesterday with some correction on the BiocInstaller
> package, just svn the last version if you don't want to wait until
> the
> newer version gets built:
> 
> vn export --username readonly --password readonly
> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/BiocInstaller
> BiocInstaller
> 
> and R CMD build and INSTALL this newer version (1.17.1).
> 

Yes, this was an issue with the build system, resolved now. 

I wouldn't worry too much about the brand new devel builds; they usually start off a bit unstable.

BTW, I don't advise that you have an evaluated vignette chunk that calls biocLite(). 

Dan


> 
> cheers,
> 
> robert.
> 
> On 10/16/2014 11:45 AM, Kevin Rue-Albrecht wrote:
> > Hi Bioconductors,
> >
> > I got the *BUILD* ERROR report below on all platforms last night.
> >
> > Given the fact that I didn't update my package since the last
> > (successful)
> > build, and the error ''BiocInstaller' package not in repository'',
> >  I have
> > a feeling this is due to a problem on the build platforms ?
> > In which case, I wonder how many other packages may be affected the
> > same
> > way. Most of the packages seem fine though.
> >
> > I can see that the BiocInstaller package got *CHECK* ERROR on all
> > platforms
> > in the most recent report. Could that be the origin of the problem?
> > In my vignette, I give the typical installation code
> > "biocLite(GOexpress)"
> > which likely caused the build error when trying to load the
> > BiocInstaller
> > library.
> >
> > Thanks in advance for advising me
> >
> > Kind regards,
> > Kevin
> >
> >
> > ##############################################################################
> > ##############################################################################
> > ###
> > ### Running command:
> > ###
> > ###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD build
> > --keep-empty-dirs
> > --no-resave-data GOexpress
> > ###
> > ##############################################################################
> > ##############################################################################
> >
> >
> > * checking for file ‘GOexpress/DESCRIPTION’ ... OK
> > * preparing ‘GOexpress’:
> > * checking DESCRIPTION meta-information ... OK
> > * installing the package to build vignettes
> > * creating vignettes ... ERROR
> > Bioconductor version 3.1 (BiocInstaller 1.17.0), ?biocLite for help
> >
> > Error: processing vignette 'GOexpress-UsersGuide.Rnw' failed with
> > diagnostics:
> >   chunk 2
> > Error : ''BiocInstaller' package not in repository' while trying
> >    http://bioconductor.org/packages/3.1/bioc
> > Execution halted
> >
> >
> 
> --
> Robert Castelo, PhD
> Associate Professor
> Dept. of Experimental and Health Sciences
> Universitat Pompeu Fabra (UPF)
> Barcelona Biomedical Research Park (PRBB)
> Dr Aiguader 88
> E-08003 Barcelona, Spain
> telf: +34.933.160.514
> fax: +34.933.160.550
> 
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