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

[Martin Morgan]

Because R is on a yearly release cycle, and Bioconductor is on a six-month 
release cycle, both the Bioconductor 'release' and 'devel' branches after our 
April release will use R version 3.1.*.

R-devel will not be used again until after our October release. Instructions on 
the developer section of the Bioconductor web site will be updated in due course.

Martin

On 03/13/2014 10:13 AM, Dan Tenenbaum wrote:
>
>
> ----- 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]]
>>
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>>
>
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