Hi It is unlikely not to have the required permissions as I was working on my own pc as administrator. 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]] >> >> ______________________________________________ >> 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. > > ______________________________________________ > 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. > ______________________________________________ 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.