But updating the system R library is not necessary unless you are managing a multi-user system. Just update your personal library. I used to do a two-phase update where I updated my personal libraries and then ran R as administrator just for the purpose of updating the system library. However, many users miss the fact that by never running the install or R explicitly as admin, and enabling a personal library during installation, they can escape that admin addiction entirely. --------------------------------------------------------------------------- Jeff Newmiller The ..... ..... Go Live... DCN:<jdnew...@dcn.davis.ca.us> Basics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/Batteries O.O#. #.O#. with /Software/Embedded Controllers) .OO#. .OO#. rocks...1k --------------------------------------------------------------------------- Sent from my phone. Please excuse my brevity.
Uwe Ligges <lig...@statistik.tu-dortmund.de> wrote: > > >On 09.03.2013 22:06, Jeff Newmiller wrote: >> I have found life to be considerably simpler since I have stopped >using Run-As-Administrator. If you use it at any point with R, various >files throughout your filesystem become accessible only when you use >RAA again... it is like heroin... use begets more use. If you restrict >your use of admin privileges to only the Times when UAC prompts you for >it (installation), and use a User library for all your packages and >package updates, then you avoid tainting those various file permissions >and struggling with the hassles that creates. > > >Right, but if you have R installed with admin priv., then you can only >update in the base library with the same priv., typically. > >Uwe Ligges > >> >--------------------------------------------------------------------------- >> Jeff Newmiller The ..... ..... Go >Live... >> DCN:<jdnew...@dcn.davis.ca.us> Basics: ##.#. ##.#. Live >Go... >> Live: OO#.. Dead: OO#.. >Playing >> Research Engineer (Solar/Batteries O.O#. #.O#. with >> /Software/Embedded Controllers) .OO#. .OO#. >rocks...1k >> >--------------------------------------------------------------------------- >> Sent from my phone. Please excuse my brevity. >> >> Uwe Ligges <lig...@statistik.tu-dortmund.de> wrote: >> >>> >>> >>> 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]] >>>>>> >>>>>> ______________________________________________ >>>>>> 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. >> >> ______________________________________________ >> 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.