Re: [Rd] Using custom R_LIBS with R CMD install
On 08.02.2012 21:05, Hadley Wickham wrote: 2012/2/8 Uwe Liggeslig...@statistik.tu-dortmund.de: On 08.02.2012 19:36, Hadley Wickham wrote: I wonder it works that far. It won't for me on Windows nor Linux, because system2 passes the whole thing shQuoted to the shell. Hence it is highly shell dependent what happens with the ill formed command. Well I was using the env argument to system2, which claims to be cross-platform (at least for R and make). This command: R_LIBS=/Users/hadley/R-dev R CMD INSTALL aL3xa-rapport-08e68ca/ is ok, isn't it? You haven't said you were using the env argument, have you? If so, I missed that part. I assumed you were specifying the above as the command argument. Hmmm, former message not quoted, as we ask in the posting guide. Where is the reproducible example? We seem to be having a bit of a communication breakdown. This is the code that I run from the command line (on mac os x): R_LIBS=/Users/hadley/R-dev R CMD INSTALL aL3xa-rapport-08e68ca/ # Desktop : R_LIBS=/Users/hadley/R-dev R CMD INSTALL aL3xa-rapport-08e68ca/ # * installing to library ‘/Users/hadley/R’ # ERROR: dependency ‘ascii’ is not available for package ‘rapport’ But: ls /Users/hadley/R-dev/ # HandyStuff animation biOps mcmcTools mvbutils quantreg testthat # SparseMascii ggplot2mturkr nstest scales whisker It's hard to provide a reproducible example because it depends on exactly what package you have installed where, but I had hoped that this would at least illustrate my problem - R CMD install doesn't seem to be respecting R_LIBS. I'm trying to understand whether this is a bug, or something I don't understand correctly about R CMD INSTALL. That's right, then you want (under Linux alikes): system2(R, CMD INSTALL package_version.tar.gz, env=R_LIBS=lib) obviously. Under Windows, you have to construct the shell command: set R_LIBS=lib R CMD INSTALL package_version.tar.gz To clarify, system2 doesn't work in windows? It does. The system2 documentation has: On Windows, ‘env’ is currently only supported for commands such as ‘R’ and ‘make’ which accept environment variables on their command line. Yes, but R CMD INSTALL does not accept those variables in the command line. This could perhaps be improved given someone finds some time to do it. Uwe Hadley __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Using custom R_LIBS with R CMD install
To clarify, system2 doesn't work in windows? It does. The system2 documentation has: On Windows, ‘env’ is currently only supported for commands such as ‘R’ and ‘make’ which accept environment variables on their command line. Yes, but R CMD INSTALL does not accept those variables in the command line. This could perhaps be improved given someone finds some time to do it. Ok, so R does, but R CMD INSTALL does not. That was the source of my confusion - thanks for clearing that up! However, is there a reason that system2 doesn't use the more general technique of Sys.setenv? Hadley -- Assistant Professor / Dobelman Family Junior Chair Department of Statistics / Rice University http://had.co.nz/ __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Using custom R_LIBS with R CMD install
On 07.02.2012 19:13, Hadley Wickham wrote: Hi all, Am I using the correct syntax to set a custom R_LIBS when running R CMD INSTALL from the command line? I get: R_LIBS=/Users/hadley/R-dev R CMD INSTALL aL3xa-rapport-08e68ca/ # Desktop : R_LIBS=/Users/hadley/R-dev R CMD INSTALL aL3xa-rapport-08e68ca/ # * installing to library ‘/Users/hadley/R’ # ERROR: dependency ‘ascii’ is not available for package ‘rapport’ I wonder it works that far. It won't for me on Windows nor Linux, because system2 passes the whole thing shQuoted to the shell. Hence it is highly shell dependent what happens with the ill formed command. Whay not specify --library= in R CMD INSTALL if you are calling it programatically from R anyway? Uwe But: ls /Users/hadley/R-dev/ # HandyStuff animation biOps mcmcTools mvbutils quantreg testthat # SparseMascii ggplot2mturkr nstest scales whisker (I'm actually running this from inside R using system2, but I think this is the essence of my misunderstanding) Hadley __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Using custom R_LIBS with R CMD install
I wonder it works that far. It won't for me on Windows nor Linux, because system2 passes the whole thing shQuoted to the shell. Hence it is highly shell dependent what happens with the ill formed command. Well I was using the env argument to system2, which claims to be cross-platform (at least for R and make). This command: R_LIBS=/Users/hadley/R-dev R CMD INSTALL aL3xa-rapport-08e68ca/ is ok, isn't it? Whay not specify --library= in R CMD INSTALL if you are calling it programatically from R anyway? My understanding (from reading R CMD INSTALL --help) was that --library was for specifying the destination library. Here I want to specify the full libpath - i.e. some of the packages that this package depends on may be in library 1, others may be in library 2. Have I misunderstood the documentation? Hadley -- Assistant Professor / Dobelman Family Junior Chair Department of Statistics / Rice University http://had.co.nz/ __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Using custom R_LIBS with R CMD install
On 8 February 2012 at 19:26, Uwe Ligges wrote: | | | On 07.02.2012 19:13, Hadley Wickham wrote: | Hi all, | | Am I using the correct syntax to set a custom R_LIBS when running R | CMD INSTALL from the command line? | | I get: | | R_LIBS=/Users/hadley/R-dev R CMD INSTALL aL3xa-rapport-08e68ca/ | # Desktop : R_LIBS=/Users/hadley/R-dev R CMD INSTALL aL3xa-rapport-08e68ca/ | # * installing to library ‘/Users/hadley/R’ | # ERROR: dependency ‘ascii’ is not available for package ‘rapport’ | | | I wonder it works that far. It won't for me on Windows nor Linux, | because system2 passes the whole thing shQuoted to the shell. Hence it | is highly shell dependent what happens with the ill formed command. | | Whay not specify --library= in R CMD INSTALL if you are calling it | programatically from R anyway? AFAICT Hadley is concerned about a library _source_ directory (for something the package under development needs to run / load) rather than a _destination_. Dirk | Uwe | | But: | | ls /Users/hadley/R-dev/ | # HandyStuff animation biOps mcmcTools mvbutils quantreg testthat | # SparseMascii ggplot2mturkr nstest scales whisker | | (I'm actually running this from inside R using system2, but I think | this is the essence of my misunderstanding) | | Hadley | | | __ | R-devel@r-project.org mailing list | https://stat.ethz.ch/mailman/listinfo/r-devel -- Outside of a dog, a book is a man's best friend. Inside of a dog, it is too dark to read. -- Groucho Marx __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Using custom R_LIBS with R CMD install
On 08.02.2012 19:36, Hadley Wickham wrote: I wonder it works that far. It won't for me on Windows nor Linux, because system2 passes the whole thing shQuoted to the shell. Hence it is highly shell dependent what happens with the ill formed command. Well I was using the env argument to system2, which claims to be cross-platform (at least for R and make). This command: R_LIBS=/Users/hadley/R-dev R CMD INSTALL aL3xa-rapport-08e68ca/ is ok, isn't it? You haven't said you were using the env argument, have you? If so, I missed that part. I assumed you were specifying the above as the command argument. Hmmm, former message not quoted, as we ask in the posting guide. Where is the reproducible example? Anyway, this won't work under a Windows shell, I believe. At least, I do not know how to set an env variable and run RCMD INSTALL in a Windows shell as a one liner - independent of R. Whay not specify --library= in R CMD INSTALL if you are calling it programatically from R anyway? My understanding (from reading R CMD INSTALL --help) was that --library was for specifying the destination library. Here I want to specify the full libpath - i.e. some of the packages that this package depends on may be in library 1, others may be in library 2. Have I misunderstood the documentation? That's right, then you want (under Linux alikes): system2(R, CMD INSTALL package_version.tar.gz, env=R_LIBS=lib) obviously. Under Windows, you have to construct the shell command: set R_LIBS=lib R CMD INSTALL package_version.tar.gz Uwe Hadley __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Using custom R_LIBS with R CMD install
On 8 February 2012 at 20:05, Uwe Ligges wrote: | Anyway, this won't work under a Windows shell, I believe. At least, I do | not know how to set an env variable and run RCMD INSTALL in a Windows | shell as a one liner - independent of R. FWIW this issue was addressed by Oleg years ago in cfunction() in his inline package -- by using Sys.setenv() prior to calling system(). This works in a cross-platform way, avoiding the need for special cases. Dirk -- Outside of a dog, a book is a man's best friend. Inside of a dog, it is too dark to read. -- Groucho Marx __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Using custom R_LIBS with R CMD install
2012/2/8 Uwe Ligges lig...@statistik.tu-dortmund.de: On 08.02.2012 19:36, Hadley Wickham wrote: I wonder it works that far. It won't for me on Windows nor Linux, because system2 passes the whole thing shQuoted to the shell. Hence it is highly shell dependent what happens with the ill formed command. Well I was using the env argument to system2, which claims to be cross-platform (at least for R and make). This command: R_LIBS=/Users/hadley/R-dev R CMD INSTALL aL3xa-rapport-08e68ca/ is ok, isn't it? You haven't said you were using the env argument, have you? If so, I missed that part. I assumed you were specifying the above as the command argument. Hmmm, former message not quoted, as we ask in the posting guide. Where is the reproducible example? We seem to be having a bit of a communication breakdown. This is the code that I run from the command line (on mac os x): R_LIBS=/Users/hadley/R-dev R CMD INSTALL aL3xa-rapport-08e68ca/ # Desktop : R_LIBS=/Users/hadley/R-dev R CMD INSTALL aL3xa-rapport-08e68ca/ # * installing to library ‘/Users/hadley/R’ # ERROR: dependency ‘ascii’ is not available for package ‘rapport’ But: ls /Users/hadley/R-dev/ # HandyStuff animation biOps mcmcTools mvbutils quantreg testthat # SparseMascii ggplot2mturkr nstest scales whisker It's hard to provide a reproducible example because it depends on exactly what package you have installed where, but I had hoped that this would at least illustrate my problem - R CMD install doesn't seem to be respecting R_LIBS. I'm trying to understand whether this is a bug, or something I don't understand correctly about R CMD INSTALL. That's right, then you want (under Linux alikes): system2(R, CMD INSTALL package_version.tar.gz, env=R_LIBS=lib) obviously. Under Windows, you have to construct the shell command: set R_LIBS=lib R CMD INSTALL package_version.tar.gz To clarify, system2 doesn't work in windows? The system2 documentation has: On Windows, ‘env’ is currently only supported for commands such as ‘R’ and ‘make’ which accept environment variables on their command line. Hadley -- Assistant Professor / Dobelman Family Junior Chair Department of Statistics / Rice University http://had.co.nz/ __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Using custom R_LIBS with R CMD install
It's hard to provide a reproducible example because it depends on exactly what package you have installed where, but I had hoped that this would at least illustrate my problem - R CMD install doesn't seem to be respecting R_LIBS. I'm trying to understand whether this is a bug, or something I don't understand correctly about R CMD INSTALL. Ok - found the problem. I had R_LIBS=~/R in my .Renviron which overrides the environment variable. Hadley -- Assistant Professor / Dobelman Family Junior Chair Department of Statistics / Rice University http://had.co.nz/ __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
