Dear Dan,
Thanks for your reply. Unfortunately, the errors remain the same:
> source("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 '403 Forbidden'
Warning in install.packages :
cannot open: HTTP status was '403 Forbidden'
Warning in install.packages :
unable to access index for repository
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";)'
> biocLite()
Error: could not find function "biocLite"
Should I switch to R 3.1 for beta testing as Martin suggested?
BW,
Martin
--
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
On Thu, Mar 13, 2014 at 6:13 PM, Dan Tenenbaum <dtene...@fhcrc.org> 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
> >
> > [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>
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