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.rijlaars...@gmail.com>
To: "bioc-devel" <bioc-devel@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.rijlaars...@gmail.com
Mobile: +31 6 45408508
Telephone (work): +31 10 7033409
Fax +31 10 7044365
Website: http://www.martinrijlaarsdam.nl
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--
Computational Biology / Fred Hutchinson Cancer Research Center
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