sessionInfo() R version 3.0.1 (2013-05-16) Platform: x86_64-w64-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base > source("http://bioconductor.org/biocLite.R") Installing package into ?\\smb.pass.psu.edu/nsa1/My Documents/R/win-library/3.0? (as ?lib? is unspecified) trying URL 'http://www.bioconductor.org/packages/2.12/bioc/bin/windows/contrib/3. 0/BiocInstaller_1.10.4.zip' Content type 'application/zip' length 50486 bytes (49 Kb) opened URL downloaded 49 Kb Warning: cannot remove prior installation of package ?BiocInstaller? The downloaded binary packages are in C:\Users\nsa1\AppData\Local\Temp\RtmpIN7Ew0\downloaded_packages 'biocLite.R' failed to install 'BiocInstaller', use 'install.packages("BiocInstaller", repos="http://www.bioconductor.org/packages/2.12/bioc")' > install.packages("BiocInstaller", + repos="http://www.bioconductor.org/packages/2.12/bioc") Installing package into ?\\smb.pass.psu.edu/nsa1/My Documents/R/win-library/3.0? (as ?lib? is unspecified) trying URL 'http://www.bioconductor.org/packages/2.12/bioc/bin/windows/contrib/3. 0/BiocInstaller_1.10.4.zip' Content type 'application/zip' length 50486 bytes (49 Kb) opened URL downloaded 49 Kb Warning: cannot remove prior installation of package ?BiocInstaller? The downloaded binary packages are in C:\Users\nsa1\AppData\Local\Temp\RtmpIN7Ew0\downloaded_packages >

my conjecture is that this is a privileges mismatch ... to change packages in that installation you'll have to involve (or become) an administrator On Tue, Jan 14, 2014 at 12:18 PM, Naomi Altman <naomi@stat.psu.edu> wrote: > sessionInfo() > R version 3.0.1 (2013-05-16) > Platform: x86_64-w64-mingw32/x64 (64-bit) > > locale: > [1] LC_COLLATE=English_United States.1252 > [2] LC_CTYPE=English_United States.1252 > [3] LC_MONETARY=English_United States.1252 > [4] LC_NUMERIC=C > [5] LC_TIME=English_United States.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > source("http://bioconductor.org/biocLite.R") > Installing package into ‘\\smb.pass.psu.edu/nsa1/MyDocuments/R/win- library/3.0’ > (as ‘lib’ is unspecified) > trying URL 'http://www.bioconductor.org/packages/2.12/bioc/bin/ > windows/contrib/3.0/BiocInstaller_1.10.4.zip' > Content type 'application/zip' length 50486 bytes (49 Kb) > opened URL > downloaded 49 Kb > > Warning: cannot remove prior installation of package ‘BiocInstaller’ > > The downloaded binary packages are in > C:\Users\nsa1\AppData\Local\Temp\RtmpIN7Ew0\downloaded_packages > 'biocLite.R' failed to install 'BiocInstaller', use > 'install.packages("BiocInstaller", > repos="http://www.bioconductor.org/packages/2.12/bioc")' > > install.packages("BiocInstaller", > + repos="http://www.bioconductor.org/packages/2.12/bioc") > Installing package into ‘\\smb.pass.psu.edu/nsa1/MyDocuments/R/win- library/3.0’ > (as ‘lib’ is unspecified) > trying URL 'http://www.bioconductor.org/packages/2.12/bioc/bin/ > windows/contrib/3.0/BiocInstaller_1.10.4.zip' > Content type 'application/zip' length 50486 bytes (49 Kb) > opened URL > downloaded 49 Kb > > Warning: cannot remove prior installation of package ‘BiocInstaller’ > > The downloaded binary packages are in > C:\Users\nsa1\AppData\Local\Temp\RtmpIN7Ew0\downloaded_packages > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane. > science.biology.informatics.conductor > [[alternative HTML version deleted]]

Can you confirm you have write permissions on: ‘\\smb.pass.psu.edu/nsa1/My Documents/R/win-library/3.0’ It all suggests that your previous version of BiocInstaller is installed there and without write permissions the installer cannnot remove it for you to proceed with the upgrade... b 2014/1/14 Naomi Altman <naomi@stat.psu.edu> > sessionInfo() > R version 3.0.1 (2013-05-16) > Platform: x86_64-w64-mingw32/x64 (64-bit) > > locale: > [1] LC_COLLATE=English_United States.1252 > [2] LC_CTYPE=English_United States.1252 > [3] LC_MONETARY=English_United States.1252 > [4] LC_NUMERIC=C > [5] LC_TIME=English_United States.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > source("http://bioconductor.org/biocLite.R") > Installing package into ‘\\smb.pass.psu.edu/nsa1/MyDocuments/R/win- library/3.0’ > (as ‘lib’ is unspecified) > trying URL 'http://www.bioconductor.org/packages/2.12/bioc/bin/ > windows/contrib/3.0/BiocInstaller_1.10.4.zip' > Content type 'application/zip' length 50486 bytes (49 Kb) > opened URL > downloaded 49 Kb > > Warning: cannot remove prior installation of package ‘BiocInstaller’ > > The downloaded binary packages are in > C:\Users\nsa1\AppData\Local\Temp\RtmpIN7Ew0\downloaded_packages > 'biocLite.R' failed to install 'BiocInstaller', use > 'install.packages("BiocInstaller", > repos="http://www.bioconductor.org/packages/2.12/bioc")' > > install.packages("BiocInstaller", > + repos="http://www.bioconductor.org/packages/2.12/bioc") > Installing package into ‘\\smb.pass.psu.edu/nsa1/MyDocuments/R/win- library/3.0’ > (as ‘lib’ is unspecified) > trying URL 'http://www.bioconductor.org/packages/2.12/bioc/bin/ > windows/contrib/3.0/BiocInstaller_1.10.4.zip' > Content type 'application/zip' length 50486 bytes (49 Kb) > opened URL > downloaded 49 Kb > > Warning: cannot remove prior installation of package ‘BiocInstaller’ > > The downloaded binary packages are in > C:\Users\nsa1\AppData\Local\Temp\RtmpIN7Ew0\downloaded_packages > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane. > science.biology.informatics.conductor > [[alternative HTML version deleted]]