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

Fri Mar 14 16:39:52 CET 2014

----- Original Message -----
> From: "Martin Rijlaarsdam" <m.a.rijlaarsdam at gmail.com>
> To: "Dan Tenenbaum" <dtenenba at fhcrc.org>
> Cc: "bioc-devel" <bioc-devel at r-project.org>
> Sent: Friday, March 14, 2014 12:23:36 AM
> Subject: Re: [Bioc-devel] fatal error when installing BioC devel on R devel
> 
> 
> 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?
> 

You should, but unfortunately a binary of R-3.1.0 alpha for windows does not seem to be available on CRAN yet.

biocLite() should work for you again in about 10 minutes.

Dan

> 
> 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.rijlaarsdam at 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 < dtenenba at fhcrc.org >
> 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]]
> > 
> > _______________________________________________
> > Bioc-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > 
> 
> 