On 09.03.2013 18:22, lefelit wrote:
Hi
It is unlikely not to have the required permissions as I was working
on my
own pc as administrator.
Fine, so start R by right-click and "Run as Administrator" or so, and
it
will work (unless the packages are already loaded before you start).
Uwe Ligges
The packages " kernSmooth" and "survival" are
loaded with the R software in the library folder. This is the
sequence of
the installation process
source("http://bioconductor.org/biocLite.R";)
Warning in install.packages("BiocInstaller", repos = a["BioCsoft",
"URL"]) :
'lib = "C:/Program Files/R/R-2.15.3/library"' is not writable
trying URL
'http://www.bioconductor.org/packages/2.11/bioc/bin/windows/contrib/2.15/Bio
cInstaller_1.8.3.zip'
Content type 'application/zip' length 43242 bytes (42 Kb)
opened URL
downloaded 42 Kb
package 'BiocInstaller' successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\Philippos\AppData\Local\Temp\RtmpW2o83w\downloaded_packages
Bioconductor version 2.11 (BiocInstaller 1.8.3), ?biocLite for help
biocLite("xcms", dep=T)
BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version
2.15.
Installing package(s) 'xcms'
also installing the dependencies 'BiocGenerics', 'Rcpp', 'Biobase',
'waveslim', 'mzR', 'faahKO', 'msdata', 'ncdf', 'multtest', 'rgl',
'MassSpecWavelet', 'RANN', 'snow', 'RUnit'
trying URL
'http://bioconductor.org/packages/2.11/bioc/bin/windows/contrib/2.15/BiocGen
erics_0.4.0.zip'
Content type 'application/zip' length 246934 bytes (241 Kb)
opened URL
downloaded 241 Kb
trying URL
'http://cran.fhcrc.org/bin/windows/contrib/2.15/Rcpp_0.10.2.zip'
Content type 'application/zip' length 3882722 bytes (3.7 Mb)
opened URL
downloaded 3.7 Mb
trying URL
'http://bioconductor.org/packages/2.11/bioc/bin/windows/contrib/2.15/Biobase
_2.18.0.zip'
Content type 'application/zip' length 2346708 bytes (2.2 Mb)
opened URL
downloaded 2.2 Mb
trying URL
'http://cran.fhcrc.org/bin/windows/contrib/2.15/waveslim_1.7.1.zip'
Content type 'application/zip' length 927137 bytes (905 Kb)
opened URL
downloaded 905 Kb
trying URL
'http://bioconductor.org/packages/2.11/bioc/bin/windows/contrib/2.15/mzR_1.4
.6.zip'
Content type 'application/zip' length 3256167 bytes (3.1 Mb)
opened URL
downloaded 3.1 Mb
trying URL
'http://bioconductor.org/packages/2.11/data/experiment/bin/windows/contrib/2
.15/faahKO_1.2.12.zip'
Content type 'application/zip' length 16590820 bytes (15.8 Mb)
opened URL
downloaded 15.8 Mb
trying URL
'http://bioconductor.org/packages/2.11/data/experiment/bin/windows/contrib/2
.15/msdata_0.1.12.zip'
Content type 'application/zip' length 13742308 bytes (13.1 Mb)
opened URL
downloaded 13.1 Mb
trying URL
'http://cran.fhcrc.org/bin/windows/contrib/2.15/ncdf_1.6.6.zip'
Content type 'application/zip' length 331657 bytes (323 Kb)
opened URL
downloaded 323 Kb
trying URL
'http://bioconductor.org/packages/2.11/bioc/bin/windows/contrib/2.15/multtes
t_2.14.0.zip'
Content type 'application/zip' length 1512257 bytes (1.4 Mb)
opened URL
downloaded 1.4 Mb
trying URL
'http://cran.fhcrc.org/bin/windows/contrib/2.15/rgl_0.93.928.zip'
Content type 'application/zip' length 1978923 bytes (1.9 Mb)
opened URL
downloaded 1.9 Mb
trying URL
'http://bioconductor.org/packages/2.11/bioc/bin/windows/contrib/2.15/MassSpe
cWavelet_1.24.0.zip'
Content type 'application/zip' length 1190983 bytes (1.1 Mb)
opened URL
downloaded 1.1 Mb
trying URL
'http://cran.fhcrc.org/bin/windows/contrib/2.15/RANN_2.2.1.zip'
Content type 'application/zip' length 445857 bytes (435 Kb)
opened URL
downloaded 435 Kb
trying URL
'http://cran.fhcrc.org/bin/windows/contrib/2.15/snow_0.3-10.zip'
Content type 'application/zip' length 65961 bytes (64 Kb)
opened URL
downloaded 64 Kb
trying URL
'http://cran.fhcrc.org/bin/windows/contrib/2.15/RUnit_0.4.26.zip'
Content type 'application/zip' length 195724 bytes (191 Kb)
opened URL
downloaded 191 Kb
trying URL
'http://bioconductor.org/packages/2.11/bioc/bin/windows/contrib/2.15/xcms_1.
34.0.zip'
Content type 'application/zip' length 1871439 bytes (1.8 Mb)
opened URL
downloaded 1.8 Mb
package 'BiocGenerics' successfully unpacked and MD5 sums checked
package 'Rcpp' successfully unpacked and MD5 sums checked
package 'Biobase' successfully unpacked and MD5 sums checked
package 'waveslim' successfully unpacked and MD5 sums checked
package 'mzR' successfully unpacked and MD5 sums checked
package 'faahKO' successfully unpacked and MD5 sums checked
package 'msdata' successfully unpacked and MD5 sums checked
package 'ncdf' successfully unpacked and MD5 sums checked
package 'multtest' successfully unpacked and MD5 sums checked
package 'rgl' successfully unpacked and MD5 sums checked
package 'MassSpecWavelet' successfully unpacked and MD5 sums checked
package 'RANN' successfully unpacked and MD5 sums checked
package 'snow' successfully unpacked and MD5 sums checked
package 'RUnit' successfully unpacked and MD5 sums checked
package 'xcms' successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\Philippos\AppData\Local\Temp\RtmpW2o83w\downloaded_packages
Warning message:
installed directory not writable, cannot update packages
'KernSmooth',
'survival'
Apologies if I was doing any silly mistakes
Filippos
-----Original Message-----
From: Uwe Ligges [mailto:lig...@statistik.tu-dortmund.de]
Sent: 09 March 2013 15:14
To: lefelit
Cc: 'PIKAL Petr'; r-help@r-project.org
Subject: Re: [R] R GUI frond has stopped working
On 09.03.2013 00:53, lefelit wrote:
Hi
I found the source of the problem. The R would not let me update the
"survival" and "KernSmooth" package at the R/library folder. I
manually delete them and then download the latest version of them to
proceed with the xcms installation. I work on a window 7 computer
and
R 2.15.3/2/1 (all version gave the same error).
Hope this provides more information about the problem
"Not let me update" means either you have not had the required
permissions
for the file access or you had the packages already loaded, so R
could not
remove them.
Uwe Ligges
Regards
Filippos
-----Original Message-----
From: PIKAL Petr [mailto:petr.pi...@precheza.cz]
Sent: 08 March 2013 15:18
To: lefelit; r-help@r-project.org
Subject: RE: [R] R GUI frond has stopped working
Hi
Some issues:
1 do not use HTML mail
2 what OS
3 which R version
4 when and how it stopped working - exact error message (if any)
5 did you ask xcms maintainer for help? (it is not in standard CRAN
packages)
6 try to send reproducible example for others to enable them to test
the problem
Regards
Petr
-----Original Message-----
From: r-help-boun...@r-project.org [mailto:r-help-bounces@r-
project.org] On Behalf Of lefelit
Sent: Friday, March 08, 2013 10:58 AM
To: r-help@r-project.org
Subject: [R] R GUI frond has stopped working
Hi
I have sent couple of days ago an email describing an issue in
regards to R software when I use the xcms package. I haven't got
any
response whether my post has been made public to receive any help
for
other users. Is my email again treated as spam or considered as
inappropriate to be published?
Kind regards
Filippos
[[alternative HTML version deleted]]
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______________________________________________
R-help@r-project.org mailing list
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PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
______________________________________________
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
