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

[Kevin Rue-Albrecht]

Hi Dan, Robert,

Thanks for the answer and fix, Dan. I thought it might be to do with the
recent release.  I just wanted to make sure whether I should be doing
something on my part. Setting the "biocLite" code in my vignette to
"eval=FALSE" crossed my mind, I was just afraid to raise a warning or
something during the build if I had unevaluated code. Since you say it's
fine, then I'll push that with the next substantial fix. It's added to my
GitHub issues to remind me.

Robert, I didn't want to update my local BiocInstaller package, but thanks
for your answer as well. Might be useful in the future for other types of
problems.

Cheers
Kevin



On 16 October 2014 15:34, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:

>
>
> ----- 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
> >
> > _______________________________________________
> > Bioc-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>



-- 
Kévin RUE-ALBRECHT
Wellcome Trust Computational Infection Biology PhD Programme
University College Dublin
Ireland
http://fr.linkedin.com/pub/k%C3%A9vin-rue/28/a45/149/en

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