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

[Dan Tenenbaum]

----- Original Message -----
> From: "Kevin Rue-Albrecht" <kevin.rue at ucdconnect.ie>
> To: "Dan Tenenbaum" <dtenenba at fhcrc.org>
> Cc: "Robert Castelo" <robert.castelo at upf.edu>, bioc-devel at r-project.org
> Sent: Thursday, October 16, 2014 8:07:02 AM
> Subject: Re: [Bioc-devel] "'BiocInstaller' package not in repository" error during nightly build
> 
> 
> 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.
> 


Just to clarify, BiocInstaller is now available in R-devel by the usual means of running:

source('http://bioconductor.org/biocLite.R')

You don't need to install via svn.

Dan


> 
> 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
>