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

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?

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

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