[Bioc-devel] fatal error when installing BioC devel on R devel

[Dan Tenenbaum]

----- Original Message -----
> From: "Martin Rijlaarsdam" <m.a.rijlaarsdam at gmail.com>
> To: "bioc-devel" <bioc-devel at r-project.org>
> Sent: Thursday, March 13, 2014 1:52:20 AM
> Subject: [Bioc-devel] fatal error when installing BioC devel on R devel
> 
> Dear Sirs,
> 
> When trying to install the devel version of Bioconductor on a clean
> install
> of R devel I got the following errors:
> 
> *source("http://bioconductor.org/biocLite.R
> <http://bioconductor.org/biocLite.R>")*
> *Warning in install.packages :*
> *  package 'BiocInstaller' is not available (for R Under
> development)*
> *Installing package into 'C:/Users/lepo/Documents/R/win-library/3.2'*
> *(as 'lib' is unspecified)*
> *Warning in install.packages :*
> *  cannot open: HTTP status was '404 Not Found'*
> *Warning in install.packages :*
> *  cannot open: HTTP status was '404 Not Found'*
> *Warning in install.packages :*
> *  unable to access index for repository
> http://www.bioconductor.org/packages/2.14/bioc/bin/windows/contrib/3.2
> <http://www.bioconductor.org/packages/2.14/bioc/bin/windows/contrib/3.2>*
> 
> *   package 'BiocInstaller' is available as a source package but not
> as a
> binary*
> 
> *Warning in install.packages :*
> *  package 'BiocInstaller' is not available (for R Under
> development)*
> *'biocLite.R' failed to install 'BiocInstaller', use
> 'install.packages("BiocInstaller",*
> *  repos="http://www.bioconductor.org/packages/2.14/bioc
> <http://www.bioconductor.org/packages/2.14/bioc>")'*
> 
> Next, I tried:
> *install.packages("BiocInstaller",repos="http://www.bioconductor.org/packages/2.14/bioc
> <http://www.bioconductor.org/packages/2.14/bioc>", type="source")*
> *Installing package into 'C:/Users/lepo/Documents/R/win-library/3.2'*
> *(as 'lib' is unspecified)*
> *trying URL
> 'http://www.bioconductor.org/packages/2.14/bioc/src/contrib/BiocInstaller_1.13.3.tar.gz
> <http://www.bioconductor.org/packages/2.14/bioc/src/contrib/BiocInstaller_1.13.3.tar.gz>'*
> *Content type 'application/x-gzip' length 14183 bytes (13 Kb)*
> *opened URL*
> *downloaded 13 Kb*
> 
> ** installing *source* package 'BiocInstaller' ...*
> *** R*
> *** inst*
> *** preparing package for lazy loading*
> *** help*
> **** installing help indices*
> *** building package indices*
> *** testing if installed package can be loaded*
> **** arch - i386*
> *Bioconductor version 2.14 (BiocInstaller 1.13.3), ?biocLite for
> help*
> **** arch - x64*
> *Bioconductor version 2.14 (BiocInstaller 1.13.3), ?biocLite for
> help*
> ** DONE (BiocInstaller)*
> 
> *The downloaded source packages are in*
> * 'C:\Users\lepo\AppData\Local\Temp\RtmpoRLBWv\downloaded_packages'*
> 
> I then tried to install the default packages and the Gviz package:
> 
> *source("http://bioconductor.org/biocLite.R
> <http://bioconductor.org/biocLite.R>")*
> *Bioconductor version 2.14 (BiocInstaller 1.13.3), ?biocLite for
> help*
> 
> *biocLite()*
> *Error: 'no packages in repository (no internet connection?)' while
> trying
> http://bioconductor.org/packages/2.14/bioc
> <http://bioconductor.org/packages/2.14/bioc>*
> 
> *biocLite("Gviz")*
> *Error: 'no packages in repository (no internet connection?)' while
> trying
> http://bioconductor.org/packages/2.14/bioc
> <http://bioconductor.org/packages/2.14/bioc>*
> 
> Am I doing something fundamentally wrong here? Or is it a
> Bioconductor
> issue?
> 
> I am using Windows 7 64 bits and have no firewall enabled. Several
> other
> (non-devel) versions of R and Bioconductor work find on this machine.
> The
> problem occurs in both the 64bits and 32bits version of R devel.
> 
> Thanks for any help!


We've added some symlinks to enable this to work now. Try again and let us know if you run into any problems.
Dan


> 
> Best wishes,
> Martin
> 
> *sessionInfo()*
> *R Under development (unstable) (2014-03-12 r65176)*
>  *Platform: x86_64-w64-mingw32/x64 (64-bit)*
> 
> *locale:*
> *[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United
> States.1252    LC_MONETARY=English_United States.1252*
> *[4] LC_NUMERIC=C                           LC_TIME=English_United
> States.1252    *
> 
> *attached base packages:*
> *[1] stats     graphics  grDevices utils     datasets  methods   base
>     *
> 
> *other attached packages:*
> *[1] BiocInstaller_1.13.3*
> 
> *loaded via a namespace (and not attached):*
> *[1] tools_3.2.0*
> 
> --
> M.A. (Martin) Rijlaarsdam MSc. MD
> Erasmus MC - University Medical Center Rotterdam
> Department of Pathology
> Room Be-432b
> Shipping adress: P.O. Box 2040, 3000 CA Rotterdam, The Netherlands
> Visiting adress: Dr. Molewaterplein 50, 3015 GE Rotterdam, The
> Netherlands
> 
> Email: m.a.rijlaarsdam at gmail.com
> Mobile: +31 6 45408508
> Telephone (work): +31 10 7033409
> Fax +31 10 7044365
> Website: http://www.martinrijlaarsdam.nl
> 
> 	[[alternative HTML version deleted]]
> 
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>