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Question: unable to install biocLite or BiocInstaller
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gravatar for Naomi Altman
3.8 years ago by
Naomi Altman6.0k
Naomi Altman6.0k 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/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 >
ADD COMMENTlink modified 2.1 years ago by av0 • written 3.8 years ago by Naomi Altman6.0k
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gravatar for Vincent J. Carey, Jr.
3.8 years ago by
United States
Vincent J. Carey, Jr.6.2k wrote:
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]]
ADD COMMENTlink written 3.8 years ago by Vincent J. Carey, Jr.6.2k
Hi, On Tue, Jan 14, 2014 at 10:04 AM, Vincent Carey <stvjc at="" channing.harvard.edu=""> wrote: > my conjecture is that this is a privileges mismatch ... to change packages > in that installation you'll have to involve (or become) an administrator Or one could set an R_LIBS_USER environment variable to point to a directory writable by the user, and install the new stuff directly there. The OP would need to be careful to ensure that a complete installation of all new packages are then (re)-installed into the R_LIBS_USER directory so you don't get any weirdness from loading mismatched versions of packages. HTH, -steve -- Steve Lianoglou Computational Biologist Genentech
ADD REPLYlink written 3.8 years ago by Steve Lianoglou12k
Thanks everyone. You are undoubtedly correct as I did not have problems with installation on my personal laptop. I will talk with the local IT folks about the set-up at work. --Naomi > Hi, > > On Tue, Jan 14, 2014 at 10:04 AM, Vincent Carey > <stvjc at="" channing.harvard.edu=""> wrote: >> my conjecture is that this is a privileges mismatch ... to change >> packages >> in that installation you'll have to involve (or become) an administrator > > Or one could set an R_LIBS_USER environment variable to point to a > directory writable by the user, and install the new stuff directly > there. > > The OP would need to be careful to ensure that a complete installation > of all new packages are then (re)-installed into the R_LIBS_USER > directory so you don't get any weirdness from loading mismatched > versions of packages. > > HTH, > -steve > > -- > Steve Lianoglou > Computational Biologist > Genentech >
ADD REPLYlink written 3.8 years ago by Naomi Altman6.0k
0
gravatar for Benilton Carvalho
3.8 years ago by
Brazil/Campinas/UNICAMP
Benilton Carvalho4.2k wrote:
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]]
ADD COMMENTlink written 3.8 years ago by Benilton Carvalho4.2k
0
gravatar for av
2.1 years ago by
av0
Norway
av0 wrote:

I have the same problem:

Error: cannot remove prior installation of package ‘BiocInstaller’

 

but I have administrator rights and sudo password. How can I fix it?

ADD COMMENTlink written 2.1 years ago by av0
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