Installing Bioconductor packages on R 2.14.0 *without* administrator rights / from a script
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Firas Swidan ▴ 50
@firas-swidan-4975
Last seen 10.2 years ago
Hi, I used to be able to install Bioconductor packages from a script *without* having administrator rights (e.g., on Windows) by specifying the library location to where the packages are to be installed. However, with the new R (2.14.0) and Bioconductor releases, the command source("http://bioconductor.org/biocLite.R") would fail without administrator rights, because it tries to install packages to directories that require administrator rights. I checked the file biocLite.R and located the line where this problematic install happens (install.packages("BiocInstaller", repos=a["BioCsoft", "URL"])) Is there a safe way to avoid the requirement for administrator rights? I know that I could modify the above command and add a library location argument, but is that safe? In particular I am wondering why the r-script was modified to require the administrator right? Thanks, Firas. [[alternative HTML version deleted]]
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@vincent-j-carey-jr-4
Last seen 9 weeks ago
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Are you sure this is specific to bioconductor installation? Does install.packages() with a CRAN package selection work for you? If it does not, you should study the R installation and administration guide available at R project manuals, and pose residual questions at r-help. Defining folders where packages can be installed can be accomplished with .libPaths() in the session. Check the value of this, and add a writeable folder and try again once you have done so. If you can make no progress with this advice, send the result of sessionInfo() and the attempted values of .libPaths and perhaps more concrete advice can be given. The details will depend on the specific version of windows you are using along with aspects of the security setup, which may not be readily reproducible outside your site. But in general you should be able to install libraries in personally writeable folders, without administrative privileges, you just have to set the parameters appropriately. These are laid out in some detail in the installation and administration manual. On Thu, Nov 24, 2011 at 9:32 PM, Firas Swidan <firas@biomatters.com> wrote: > Hi, > > I used to be able to install Bioconductor packages from a script *without* > having administrator rights (e.g., on Windows) by specifying the library > location to where the packages are to be installed. > > However, with the new R (2.14.0) and Bioconductor releases, the command > > > > source("http://bioconductor.org/biocLite.R") > > > > would fail without administrator rights, because it tries to install > packages to directories that require administrator rights. > > I checked the file biocLite.R and located the line where this problematic > install happens (install.packages("BiocInstaller", repos=a["BioCsoft", > "URL"])) > > > Is there a safe way to avoid the requirement for administrator rights? I > know that I could modify the above command and add a library location > argument, but is that safe? > > In particular I am wondering why the r-script was modified to require the > administrator right? > > Thanks, > Firas. > > [[alternative HTML version deleted]] > > _______________________________________________ > 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]]
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Dan Tenenbaum ★ 8.2k
@dan-tenenbaum-4256
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Hello, On Thu, Nov 24, 2011 at 6:32 PM, Firas Swidan <firas at="" biomatters.com=""> wrote: > Hi, > > I used to be able to install Bioconductor packages from a script *without* > having administrator rights (e.g., on Windows) by specifying the library > location to where the packages are to be installed. > > However, with the new R (2.14.0) and Bioconductor releases, the command > > > > source("http://bioconductor.org/biocLite.R") > > > > would fail without administrator rights, because it tries to install > packages to directories that require administrator rights. > > I checked the file biocLite.R and located the line where this problematic > install happens (install.packages("BiocInstaller", repos=a["BioCsoft", > "URL"])) > > > Is there a safe way to avoid the requirement for administrator rights? I > know that I could modify the above command and add a library location > argument, but is that safe? > > In particular I am wondering why the r-script was modified to require the > administrator right? > The script was not modified specifically to require administrator rights. I tried to reproduce your situation, as I understand it, but perhaps I don't have enough information. When I (as a Windows user without administrative rights) ran the source() command above, I got a popup asking me if I wanted to create a personal library directory. If I said Yes, BiocInstaller installed itself just fine, and I was then able to install packages with biocLite(). I did get some warnings about packages that cannot be updated because they are installed in directories that are not writeable. However, those are just warnings; if you need to update any of those packages, you can install them yourself with biocLite(). It would be helpful if you could send the complete output of your session, including sessionInfo() and all the commands you tried, plus any errors/warnings. Thanks Dan > Thanks, > Firas. > > ? ? ? ?[[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
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Hi all, thanks for the suggestions - I just got to read them after recovering from a bad flu. I think Dan's experience probably resembles most the one that I had. The problem though gets more troublesome when one tries to automate the process through a script installation. More specifically, imagine that a script needs to install a bioconduct package on different machines (running Windows, and maybe also other OSs) on a fresh R install. Then the 'source' command needs to be run from inside the R script that is executed through 'R CMD BATCH'. In this case there is no pop-up dialog asking to create another user-writable directory, and the command 'install.packages("BiocInstaller", repos=a["BioCsoft", > "URL"])' fails. It would be great in case one could pass an argument specifying the lib.loc to the 'install.packages' command above, but I understand this is not possible through 'sourcing'. The old way of just defining a 'biocLite' function in the biocLite.R script, and then being able to pass the lib.loc argument to it seems to fair better in this use-case model. I do not really have access to the machines where the installation is going to be done, so I cannot change permissions and the like. Also, the installed bioconduct packages need later on to be loaded and used, so I need to specify a specific location for their installation. The saga goes on, as I cannot use the 'R_LIBS_USER' directory because of complications on Windows that diving in would just clutter this post. I am still puzzled why the biocLite.R script had to undergo such a huge change following the new R 2.14 release. Is it safe to fall back to the old behavior under this version, i.e., use the 'else' part in the script: source("http://bioconductor.org/getBioC.R") biocLite <<- function(pkgs, groupName="lite", ...) { if (missing(pkgs)) biocinstall(groupName=groupName, ...) else biocinstall(pkgs=pkgs, groupName=groupName, ...) } Thanks, Firas. On Sun, Nov 27, 2011 at 9:57 AM, Dan Tenenbaum <dtenenba@fhcrc.org> wrote: > Hello, > > On Thu, Nov 24, 2011 at 6:32 PM, Firas Swidan <firas@biomatters.com> > wrote: > > Hi, > > > > I used to be able to install Bioconductor packages from a script > *without* > > having administrator rights (e.g., on Windows) by specifying the library > > location to where the packages are to be installed. > > > > However, with the new R (2.14.0) and Bioconductor releases, the command > > > > > > > > source("http://bioconductor.org/biocLite.R") > > > > > > > > would fail without administrator rights, because it tries to install > > packages to directories that require administrator rights. > > > > I checked the file biocLite.R and located the line where this problematic > > install happens (install.packages("BiocInstaller", repos=a["BioCsoft", > > "URL"])) > > > > > > Is there a safe way to avoid the requirement for administrator rights? I > > know that I could modify the above command and add a library location > > argument, but is that safe? > > > > In particular I am wondering why the r-script was modified to require the > > administrator right? > > > > The script was not modified specifically to require administrator rights. > > I tried to reproduce your situation, as I understand it, but perhaps I > don't have enough information. When I (as a Windows user without > administrative rights) ran the source() command above, I got a popup > asking me if I wanted to create a personal library directory. If I > said Yes, BiocInstaller installed itself just fine, and I was then > able to install packages with biocLite(). I did get some warnings > about packages that cannot be updated because they are installed in > directories that are not writeable. However, those are just warnings; > if you need to update any of those packages, you can install them > yourself with biocLite(). > > It would be helpful if you could send the complete output of your > session, including sessionInfo() and all the commands you tried, plus > any errors/warnings. > > Thanks > Dan > > > > > Thanks, > > Firas. > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > 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 > > > -- Dr Firas Swidan, PhD Computer Science / Computational Biology Bioinformatics Software Engineer Biomatters Ltd firas@biomatters.com [[alternative HTML version deleted]]
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Hi Firas, On Tue, Nov 29, 2011 at 12:49 PM, Firas Swidan <firas at="" biomatters.com=""> wrote: > Hi all, > > thanks for the suggestions - I just got to read them after recovering from a > bad flu. > > I think Dan's experience probably resembles most the one that I had. The > problem though gets more troublesome when one tries to automate the process > through a script installation. More specifically, imagine that a script > needs to install a bioconduct package on different machines (running > Windows, and maybe also other OSs) on a fresh R install. Then the 'source' > command needs to be run from inside the R script that is executed through 'R > CMD BATCH'. In this case there is no pop-up dialog asking to create another > user-writable directory, and the command 'install.packages("BiocInstaller", > repos=a["BioCsoft", >> "URL"])' fails. It would be great in case one could pass an argument >> specifying the lib.loc to the 'install.packages' command above, but I >> understand this is not possible through 'sourcing'. The old way of just >> defining a 'biocLite' function in the biocLite.R script, and then being able >> to pass the lib.loc argument to it seems to fair better in this use-case >> model. Thanks for posting the detailed use case so we can understand the issue better. Please have a look at ?biocLite You'll see that it takes a '...' argument which is passed to install.packages, so you can pass lib (not lib.loc) to install.packages and specify where packages are to be installed. Be sure that any directory you pass here also ends up in .libPaths() so that R will look in it for packages. I don't see a need to use install.packages() directly in the situation you describe. biocLite() should do it, and you won't need to specify the repos argument. > > I do not really have access to the machines where the installation is going > to be done, so I cannot change permissions and the like. Also, the installed > bioconduct packages need later on to be loaded and used, so I need to > specify a specific location for their installation. The saga goes on, as I > cannot use the 'R_LIBS_USER' directory because of complications on Windows > that diving in would just clutter this post. > > I am still puzzled why the biocLite.R script had to undergo such a huge > change following the new R 2.14 release. Is it safe to fall back to the old > behavior under this version, i.e., use the 'else' part in the script: > > source("http://bioconductor.org/getBioC.R") > biocLite <<- > function(pkgs, groupName="lite", ...) > { > if (missing(pkgs)) > biocinstall(groupName=groupName, ...) > else > biocinstall(pkgs=pkgs, groupName=groupName, ...) > } No, it's not safe, but more importantly, it won't work on R >= 2.14. Please let us know if you still are having problems. Thanks Dan > > > Thanks, > > Firas. > > > On Sun, Nov 27, 2011 at 9:57 AM, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> wrote: >> >> Hello, >> >> On Thu, Nov 24, 2011 at 6:32 PM, Firas Swidan <firas at="" biomatters.com=""> >> wrote: >> > Hi, >> > >> > I used to be able to install Bioconductor packages from a script >> > *without* >> > having administrator rights (e.g., on Windows) by specifying the library >> > location to where the packages are to be installed. >> > >> > However, with the new R (2.14.0) and Bioconductor releases, the command >> > >> > >> > >> > source("http://bioconductor.org/biocLite.R") >> > >> > >> > >> > would fail without administrator rights, because it tries to install >> > packages to directories that require administrator rights. >> > >> > I checked the file biocLite.R and located the line where this >> > problematic >> > install happens (install.packages("BiocInstaller", repos=a["BioCsoft", >> > "URL"])) >> > >> > >> > Is there a safe way to avoid the requirement for administrator rights? I >> > know that I could modify the above command and add a library location >> > argument, but is that safe? >> > >> > In particular I am wondering why the r-script was modified to require >> > the >> > administrator right? >> > >> >> The script was not modified specifically to require administrator rights. >> >> I tried to reproduce your situation, as I understand it, but perhaps I >> don't have enough information. When I (as a Windows user without >> administrative rights) ran the source() command above, I got a popup >> asking me if I wanted to create a personal library directory. If I >> said Yes, BiocInstaller installed itself just fine, and I was then >> able to install packages with biocLite(). I did get some warnings >> about packages that cannot be updated because they are installed in >> directories that are not writeable. However, those are just warnings; >> if you need to update any of those packages, you can install them >> yourself with biocLite(). >> >> It would be helpful if you could send the complete output of your >> session, including sessionInfo() and all the commands you tried, plus >> any errors/warnings. >> >> Thanks >> Dan >> >> >> >> > Thanks, >> > Firas. >> > >> > ? ? ? ?[[alternative HTML version deleted]] >> > >> > _______________________________________________ >> > Bioconductor mailing list >> > Bioconductor at r-project.org >> > https://stat.ethz.ch/mailman/listinfo/bioconductor >> > Search the archives: >> > http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > > > > > -- > Dr Firas Swidan, PhD Computer Science / Computational Biology > Bioinformatics Software Engineer > Biomatters Ltd > firas at biomatters.com
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I see there is a misunderstanding regarding the nature of the problem I am trying to describe. To try and eliminate any confusing, the problem that I am describing happens when running this command: 'source("http://bioconductor.org/biocLite.R")' not when trying later on to use the 'biocLite' command. I have been using the lib.loc argument with the biocLite command, and that works great. The problem is that the recent modifications to the " http://bioconductor.org/biocLite.R" script make it install packages without the user having the ability to specify the lib.loc location. Does that help clarifying the problem? On Wed, Nov 30, 2011 at 9:56 AM, Dan Tenenbaum <dtenenba@fhcrc.org> wrote: > Hi Firas, > > On Tue, Nov 29, 2011 at 12:49 PM, Firas Swidan <firas@biomatters.com> > wrote: > > Hi all, > > > > thanks for the suggestions - I just got to read them after recovering > from a > > bad flu. > > > > I think Dan's experience probably resembles most the one that I had. The > > problem though gets more troublesome when one tries to automate the > process > > through a script installation. More specifically, imagine that a script > > needs to install a bioconduct package on different machines (running > > Windows, and maybe also other OSs) on a fresh R install. Then the > 'source' > > command needs to be run from inside the R script that is executed > through 'R > > CMD BATCH'. In this case there is no pop-up dialog asking to create > another > > user-writable directory, and the command > 'install.packages("BiocInstaller", > > repos=a["BioCsoft", > >> "URL"])' fails. It would be great in case one could pass an argument > >> specifying the lib.loc to the 'install.packages' command above, but I > >> understand this is not possible through 'sourcing'. The old way of just > >> defining a 'biocLite' function in the biocLite.R script, and then being > able > >> to pass the lib.loc argument to it seems to fair better in this use-case > >> model. > > Thanks for posting the detailed use case so we can understand the issue > better. > > Please have a look at > ?biocLite > > You'll see that it takes a '...' argument which is passed to > install.packages, so you can pass lib (not lib.loc) to > install.packages and specify where packages are to be installed. Be > sure that any directory you pass here also ends up in .libPaths() so > that R will look in it for packages. > > I don't see a need to use install.packages() directly in the situation > you describe. biocLite() should do it, and you won't need to specify > the repos argument. > > > > > I do not really have access to the machines where the installation is > going > > to be done, so I cannot change permissions and the like. Also, the > installed > > bioconduct packages need later on to be loaded and used, so I need to > > specify a specific location for their installation. The saga goes on, as > I > > cannot use the 'R_LIBS_USER' directory because of complications on > Windows > > that diving in would just clutter this post. > > > > I am still puzzled why the biocLite.R script had to undergo such a huge > > change following the new R 2.14 release. Is it safe to fall back to the > old > > behavior under this version, i.e., use the 'else' part in the script: > > > > source("http://bioconductor.org/getBioC.R") > > biocLite <<- > > function(pkgs, groupName="lite", ...) > > { > > if (missing(pkgs)) > > biocinstall(groupName=groupName, ...) > > else > > biocinstall(pkgs=pkgs, groupName=groupName, ...) > > } > > > > No, it's not safe, but more importantly, it won't work on R >= 2.14. > > Please let us know if you still are having problems. > > Thanks > Dan > > > > > > > > > > Thanks, > > > > Firas. > > > > > > On Sun, Nov 27, 2011 at 9:57 AM, Dan Tenenbaum <dtenenba@fhcrc.org> > wrote: > >> > >> Hello, > >> > >> On Thu, Nov 24, 2011 at 6:32 PM, Firas Swidan <firas@biomatters.com> > >> wrote: > >> > Hi, > >> > > >> > I used to be able to install Bioconductor packages from a script > >> > *without* > >> > having administrator rights (e.g., on Windows) by specifying the > library > >> > location to where the packages are to be installed. > >> > > >> > However, with the new R (2.14.0) and Bioconductor releases, the > command > >> > > >> > > >> > > >> > source("http://bioconductor.org/biocLite.R") > >> > > >> > > >> > > >> > would fail without administrator rights, because it tries to install > >> > packages to directories that require administrator rights. > >> > > >> > I checked the file biocLite.R and located the line where this > >> > problematic > >> > install happens (install.packages("BiocInstaller", repos=a["BioCsoft", > >> > "URL"])) > >> > > >> > > >> > Is there a safe way to avoid the requirement for administrator > rights? I > >> > know that I could modify the above command and add a library location > >> > argument, but is that safe? > >> > > >> > In particular I am wondering why the r-script was modified to require > >> > the > >> > administrator right? > >> > > >> > >> The script was not modified specifically to require administrator > rights. > >> > >> I tried to reproduce your situation, as I understand it, but perhaps I > >> don't have enough information. When I (as a Windows user without > >> administrative rights) ran the source() command above, I got a popup > >> asking me if I wanted to create a personal library directory. If I > >> said Yes, BiocInstaller installed itself just fine, and I was then > >> able to install packages with biocLite(). I did get some warnings > >> about packages that cannot be updated because they are installed in > >> directories that are not writeable. However, those are just warnings; > >> if you need to update any of those packages, you can install them > >> yourself with biocLite(). > >> > >> It would be helpful if you could send the complete output of your > >> session, including sessionInfo() and all the commands you tried, plus > >> any errors/warnings. > >> > >> Thanks > >> Dan > >> > >> > >> > >> > Thanks, > >> > Firas. > >> > > >> > [[alternative HTML version deleted]] > >> > > >> > _______________________________________________ > >> > 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 > >> > > > > > > > > > > > -- > > Dr Firas Swidan, PhD Computer Science / Computational Biology > > Bioinformatics Software Engineer > > Biomatters Ltd > > firas@biomatters.com > -- Dr Firas Swidan, PhD Computer Science / Computational Biology Bioinformatics Software Engineer Biomatters Ltd firas@biomatters.com [[alternative HTML version deleted]]
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Hi Firas, On Tue, Nov 29, 2011 at 1:06 PM, Firas Swidan <firas at="" biomatters.com=""> wrote: > I see there is a misunderstanding regarding the nature of the problem I am > trying to describe. To try and eliminate any confusing, the problem that I > am describing happens when running this command: > > 'source("http://bioconductor.org/biocLite.R")' > > not when trying later on to use the > > 'biocLite' > > command.?I have been using the lib.loc argument with the?biocLite command, > and that works great. > > > The problem is that the recent modifications to > the?"http://bioconductor.org/biocLite.R" script make it install packages > without the user having the ability to specify the lib.loc location. > > > Does that help clarifying the problem? I understand. Have a look at the documentation for ?install.packages Notice that lib defaults to the first element of .libPaths(). If you look at ?.libPaths, you can see how to change that first element, namely something like this: .libPaths(c("c:/a/writeable/directory", .libPaths())) Try doing that prior to your source() line. Thanks Dan > > > On Wed, Nov 30, 2011 at 9:56 AM, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> wrote: >> >> Hi Firas, >> >> On Tue, Nov 29, 2011 at 12:49 PM, Firas Swidan <firas at="" biomatters.com=""> >> wrote: >> > Hi all, >> > >> > thanks for the suggestions - I just got to read them after recovering >> > from a >> > bad flu. >> > >> > I think Dan's experience probably resembles most the one that I had. The >> > problem though gets more troublesome when one tries to automate the >> > process >> > through a script installation. More specifically, imagine that a script >> > needs to install a bioconduct package on different machines (running >> > Windows, and maybe also other OSs) on a fresh R install. Then the >> > 'source' >> > command needs to be run from inside the R script that is executed >> > through 'R >> > CMD BATCH'. In this case there is no pop-up dialog asking to create >> > another >> > user-writable directory, and the command >> > 'install.packages("BiocInstaller", >> > repos=a["BioCsoft", >> >> "URL"])' fails. It would be great in case one could pass an argument >> >> specifying the lib.loc to the 'install.packages' command above, but I >> >> understand this is not possible through 'sourcing'. The old way of just >> >> defining a 'biocLite' function in the biocLite.R script, and then being >> >> able >> >> to pass the lib.loc argument to it seems to fair better in this >> >> use-case >> >> model. >> >> Thanks for posting the detailed use case so we can understand the issue >> better. >> >> Please have a look at >> ?biocLite >> >> You'll see that it takes a '...' argument which is passed to >> install.packages, so you can pass lib (not lib.loc) to >> install.packages and specify where packages are to be installed. Be >> sure that any directory you pass here also ends up in .libPaths() so >> that R will look in it for packages. >> >> I don't see a need to use install.packages() directly in the situation >> you describe. biocLite() should do it, and you won't need to specify >> the repos argument. >> >> > >> > I do not really have access to the machines where the installation is >> > going >> > to be done, so I cannot change permissions and the like. Also, the >> > installed >> > bioconduct packages need later on to be loaded and used, so I need to >> > specify a specific location for their installation. The saga goes on, as >> > I >> > cannot use the 'R_LIBS_USER' directory because of complications on >> > Windows >> > that diving in would just clutter this post. >> > >> > I am still puzzled why the biocLite.R script had to undergo such a huge >> > change following the new R 2.14 release. Is it safe to fall back to the >> > old >> > behavior under this version, i.e., use the 'else' part in the script: >> > >> > ? ? ? ? source("http://bioconductor.org/getBioC.R") >> > ? ? ? ? biocLite <<- >> > ? ? ? ? ? ? function(pkgs, groupName="lite", ...) >> > ? ? ? ? ? ? { >> > ? ? ? ? ? ? ? ? if (missing(pkgs)) >> > ? ? ? ? ? ? ? ? ? ? biocinstall(groupName=groupName, ...) >> > ? ? ? ? ? ? ? ? else >> > ? ? ? ? ? ? ? ? ? ? biocinstall(pkgs=pkgs, groupName=groupName, ...) >> > ? ? ? ? ? ? } >> >> >> >> No, it's not safe, but more importantly, it won't work on R >= 2.14. >> >> Please let us know if you still are having problems. >> >> Thanks >> Dan >> >> >> >> >> > >> > >> > Thanks, >> > >> > Firas. >> > >> > >> > On Sun, Nov 27, 2011 at 9:57 AM, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> >> > wrote: >> >> >> >> Hello, >> >> >> >> On Thu, Nov 24, 2011 at 6:32 PM, Firas Swidan <firas at="" biomatters.com=""> >> >> wrote: >> >> > Hi, >> >> > >> >> > I used to be able to install Bioconductor packages from a script >> >> > *without* >> >> > having administrator rights (e.g., on Windows) by specifying the >> >> > library >> >> > location to where the packages are to be installed. >> >> > >> >> > However, with the new R (2.14.0) and Bioconductor releases, the >> >> > command >> >> > >> >> > >> >> > >> >> > source("http://bioconductor.org/biocLite.R") >> >> > >> >> > >> >> > >> >> > would fail without administrator rights, because it tries to install >> >> > packages to directories that require administrator rights. >> >> > >> >> > I checked the file biocLite.R and located the line where this >> >> > problematic >> >> > install happens (install.packages("BiocInstaller", >> >> > repos=a["BioCsoft", >> >> > "URL"])) >> >> > >> >> > >> >> > Is there a safe way to avoid the requirement for administrator >> >> > rights? I >> >> > know that I could modify the above command and add a library location >> >> > argument, but is that safe? >> >> > >> >> > In particular I am wondering why the r-script was modified to require >> >> > the >> >> > administrator right? >> >> > >> >> >> >> The script was not modified specifically to require administrator >> >> rights. >> >> >> >> I tried to reproduce your situation, as I understand it, but perhaps I >> >> don't have enough information. When I (as a Windows user without >> >> administrative rights) ran the source() command above, I got a popup >> >> asking me if I wanted to create a personal library directory. If I >> >> said Yes, BiocInstaller installed itself just fine, and I was then >> >> able to install packages with biocLite(). I did get some warnings >> >> about packages that cannot be updated because they are installed in >> >> directories that are not writeable. However, those are just warnings; >> >> if you need to update any of those packages, you can install them >> >> yourself with biocLite(). >> >> >> >> It would be helpful if you could send the complete output of your >> >> session, including sessionInfo() and all the commands you tried, plus >> >> any errors/warnings. >> >> >> >> Thanks >> >> Dan >> >> >> >> >> >> >> >> > Thanks, >> >> > Firas. >> >> > >> >> > ? ? ? ?[[alternative HTML version deleted]] >> >> > >> >> > _______________________________________________ >> >> > Bioconductor mailing list >> >> > Bioconductor at r-project.org >> >> > https://stat.ethz.ch/mailman/listinfo/bioconductor >> >> > Search the archives: >> >> > http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> > >> > >> > >> > >> > >> > -- >> > Dr Firas Swidan, PhD Computer Science / Computational Biology >> > Bioinformatics Software Engineer >> > Biomatters Ltd >> > firas at biomatters.com > > > > > -- > Dr Firas Swidan, PhD Computer Science / Computational Biology > Bioinformatics Software Engineer > Biomatters Ltd > firas at biomatters.com
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Thanks. I will give that a try and let you know how it goes. On Wed, Nov 30, 2011 at 10:15 AM, Dan Tenenbaum <dtenenba@fhcrc.org> wrote: > Hi Firas, > > On Tue, Nov 29, 2011 at 1:06 PM, Firas Swidan <firas@biomatters.com> > wrote: > > I see there is a misunderstanding regarding the nature of the problem I > am > > trying to describe. To try and eliminate any confusing, the problem that > I > > am describing happens when running this command: > > > > 'source("http://bioconductor.org/biocLite.R")' > > > > not when trying later on to use the > > > > 'biocLite' > > > > command. I have been using the lib.loc argument with the biocLite > command, > > and that works great. > > > > > > The problem is that the recent modifications to > > the "http://bioconductor.org/biocLite.R" script make it install packages > > without the user having the ability to specify the lib.loc location. > > > > > > Does that help clarifying the problem? > > > I understand. > > Have a look at the documentation for > ?install.packages > > Notice that lib defaults to the first element of .libPaths(). > If you look at ?.libPaths, you can see how to change that first > element, namely something like this: > > .libPaths(c("c:/a/writeable/directory", .libPaths())) > > Try doing that prior to your source() line. > > Thanks > Dan > > > > > > > > On Wed, Nov 30, 2011 at 9:56 AM, Dan Tenenbaum <dtenenba@fhcrc.org> > wrote: > >> > >> Hi Firas, > >> > >> On Tue, Nov 29, 2011 at 12:49 PM, Firas Swidan <firas@biomatters.com> > >> wrote: > >> > Hi all, > >> > > >> > thanks for the suggestions - I just got to read them after recovering > >> > from a > >> > bad flu. > >> > > >> > I think Dan's experience probably resembles most the one that I had. > The > >> > problem though gets more troublesome when one tries to automate the > >> > process > >> > through a script installation. More specifically, imagine that a > script > >> > needs to install a bioconduct package on different machines (running > >> > Windows, and maybe also other OSs) on a fresh R install. Then the > >> > 'source' > >> > command needs to be run from inside the R script that is executed > >> > through 'R > >> > CMD BATCH'. In this case there is no pop-up dialog asking to create > >> > another > >> > user-writable directory, and the command > >> > 'install.packages("BiocInstaller", > >> > repos=a["BioCsoft", > >> >> "URL"])' fails. It would be great in case one could pass an argument > >> >> specifying the lib.loc to the 'install.packages' command above, but I > >> >> understand this is not possible through 'sourcing'. The old way of > just > >> >> defining a 'biocLite' function in the biocLite.R script, and then > being > >> >> able > >> >> to pass the lib.loc argument to it seems to fair better in this > >> >> use-case > >> >> model. > >> > >> Thanks for posting the detailed use case so we can understand the issue > >> better. > >> > >> Please have a look at > >> ?biocLite > >> > >> You'll see that it takes a '...' argument which is passed to > >> install.packages, so you can pass lib (not lib.loc) to > >> install.packages and specify where packages are to be installed. Be > >> sure that any directory you pass here also ends up in .libPaths() so > >> that R will look in it for packages. > >> > >> I don't see a need to use install.packages() directly in the situation > >> you describe. biocLite() should do it, and you won't need to specify > >> the repos argument. > >> > >> > > >> > I do not really have access to the machines where the installation is > >> > going > >> > to be done, so I cannot change permissions and the like. Also, the > >> > installed > >> > bioconduct packages need later on to be loaded and used, so I need to > >> > specify a specific location for their installation. The saga goes on, > as > >> > I > >> > cannot use the 'R_LIBS_USER' directory because of complications on > >> > Windows > >> > that diving in would just clutter this post. > >> > > >> > I am still puzzled why the biocLite.R script had to undergo such a > huge > >> > change following the new R 2.14 release. Is it safe to fall back to > the > >> > old > >> > behavior under this version, i.e., use the 'else' part in the script: > >> > > >> > source("http://bioconductor.org/getBioC.R") > >> > biocLite <<- > >> > function(pkgs, groupName="lite", ...) > >> > { > >> > if (missing(pkgs)) > >> > biocinstall(groupName=groupName, ...) > >> > else > >> > biocinstall(pkgs=pkgs, groupName=groupName, ...) > >> > } > >> > >> > >> > >> No, it's not safe, but more importantly, it won't work on R >= 2.14. > >> > >> Please let us know if you still are having problems. > >> > >> Thanks > >> Dan > >> > >> > >> > >> > >> > > >> > > >> > Thanks, > >> > > >> > Firas. > >> > > >> > > >> > On Sun, Nov 27, 2011 at 9:57 AM, Dan Tenenbaum <dtenenba@fhcrc.org> > >> > wrote: > >> >> > >> >> Hello, > >> >> > >> >> On Thu, Nov 24, 2011 at 6:32 PM, Firas Swidan <firas@biomatters.com> > >> >> wrote: > >> >> > Hi, > >> >> > > >> >> > I used to be able to install Bioconductor packages from a script > >> >> > *without* > >> >> > having administrator rights (e.g., on Windows) by specifying the > >> >> > library > >> >> > location to where the packages are to be installed. > >> >> > > >> >> > However, with the new R (2.14.0) and Bioconductor releases, the > >> >> > command > >> >> > > >> >> > > >> >> > > >> >> > source("http://bioconductor.org/biocLite.R") > >> >> > > >> >> > > >> >> > > >> >> > would fail without administrator rights, because it tries to > install > >> >> > packages to directories that require administrator rights. > >> >> > > >> >> > I checked the file biocLite.R and located the line where this > >> >> > problematic > >> >> > install happens (install.packages("BiocInstaller", > >> >> > repos=a["BioCsoft", > >> >> > "URL"])) > >> >> > > >> >> > > >> >> > Is there a safe way to avoid the requirement for administrator > >> >> > rights? I > >> >> > know that I could modify the above command and add a library > location > >> >> > argument, but is that safe? > >> >> > > >> >> > In particular I am wondering why the r-script was modified to > require > >> >> > the > >> >> > administrator right? > >> >> > > >> >> > >> >> The script was not modified specifically to require administrator > >> >> rights. > >> >> > >> >> I tried to reproduce your situation, as I understand it, but perhaps > I > >> >> don't have enough information. When I (as a Windows user without > >> >> administrative rights) ran the source() command above, I got a popup > >> >> asking me if I wanted to create a personal library directory. If I > >> >> said Yes, BiocInstaller installed itself just fine, and I was then > >> >> able to install packages with biocLite(). I did get some warnings > >> >> about packages that cannot be updated because they are installed in > >> >> directories that are not writeable. However, those are just warnings; > >> >> if you need to update any of those packages, you can install them > >> >> yourself with biocLite(). > >> >> > >> >> It would be helpful if you could send the complete output of your > >> >> session, including sessionInfo() and all the commands you tried, plus > >> >> any errors/warnings. > >> >> > >> >> Thanks > >> >> Dan > >> >> > >> >> > >> >> > >> >> > Thanks, > >> >> > Firas. > >> >> > > >> >> > [[alternative HTML version deleted]] > >> >> > > >> >> > _______________________________________________ > >> >> > 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 > >> >> > > >> > > >> > > >> > > >> > > >> > -- > >> > Dr Firas Swidan, PhD Computer Science / Computational Biology > >> > Bioinformatics Software Engineer > >> > Biomatters Ltd > >> > firas@biomatters.com > > > > > > > > > > -- > > Dr Firas Swidan, PhD Computer Science / Computational Biology > > Bioinformatics Software Engineer > > Biomatters Ltd > > firas@biomatters.com > -- Dr Firas Swidan, PhD Computer Science / Computational Biology Bioinformatics Software Engineer Biomatters Ltd firas@biomatters.com [[alternative HTML version deleted]]
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