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

Dan Tenenbaum dtenenba at fhcrc.org
Sat Mar 15 20:25:40 CET 2014 


----- Original Message -----
> From: "Dan Tenenbaum" <dtenenba at fhcrc.org>
> To: "Martin Rijlaarsdam" <m.a.rijlaarsdam at gmail.com>
> Cc: "bioc-devel" <bioc-devel at r-project.org>
> Sent: Friday, March 14, 2014 8:39:52 AM
> Subject: Re: [Bioc-devel] fatal error when installing BioC devel on R devel
> 
> 
> 
> ----- 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.
> 

R 3.1.0 alpha for windows is now available at
http://cran.r-project.org/bin/windows/base/rtest.html

Dan


> 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
> > > 
> > 
> > 
> 
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