Notice that we have a similar, but unresolved, bug report a month old. https://bugs.r-project.org/bugzilla/show_bug.cgi?id=15940
I assume that the obvious things like a .Rprofile in the current directory has been checked? Running R under a debugger, single-stepping through the startup code would likely isolate the trouble, but it's a bit of work to set up, and of course it needs to be on the machine that actually displays the problem. -pd On 20 Sep 2014, at 21:27 , David Winsemius <[email protected]> wrote: > > > On Sep 19, 2014, at 2:01 PM, Gang Chen wrote: > >> When R starts in GUI on my Mac OS X 10.7.5, the startup configuration in >> .Rprofile works fine. However, when R starts through command line interface >> (CLI) on the terminal , it does not work at all. >> >> The GUI R on my Mac is aliased on the terminal to >> /Applications/R.app/Contents/MacOS/R while the CLI R (/usr/bin/R) is linked >> to /Library/Frameworks/R.framework/Resources/bin/R. There is only one >> .Rprofile, which resides in my home directory ~/. >> >>> sessionInfo() >> R version 3.1.0 (2014-04-10) >> Platform: x86_64-apple-darwin10.8.0 (64-bit) >> >> What could be the cause for the failure with CLI? > > Caveat: I'm not the best person to answer this. I'm not a skilled user of > Unix and I'm not one of the Mac development team. But those guys are often > not reading the mailing list on weekends so I thought I'd throw some ideas > out that you could investigate. > > > #----- Idea # 1 --------- > Running 3.1.1 this is what I see among the environment variables that are > different in a CLI session of R from those in a GUI session. In particular I > am wondering if your PWD variable points to your User/username/ directory: > >> Sys.getenv()[grep('Users', Sys.getenv())] > HOME PWD > "/Users/davidwinsemius" "/Users/davidwinsemius" > XDG_CACHE_HOME XDG_CONFIG_HOME > "/Users/davidwinsemius/.cache" "/Users/davidwinsemius/.config" > XDG_DATA_HOME > "/Users/davidwinsemius/.local/share" > > I haven't been able to find exactly what PWD is pointing to. It's not listed > in the "environment variables" link from ?Sys.getenv. I think it's related > tot eh Unix cli command `pwd` which prints the working directory. I don't > know how to give you a direct link to the page with a listing of environment > variables, since that page is one the doesn't conform to the convention of > having a ?NameOfPage lookup. Its page name is "EnvVar" but ?EnvVar gives a > "No documentation for ‘EnvVar’ ..." message. I also do not find "PWD" in a > search of the Install/Admin document. > > I tried changing PWD in a session an quitting, but it didn't seem to "stick". > >> Sys.getenv()["PWD"] > PWD > "/Users/davidwinsemius" >> sessionInfo() > R version 3.1.1 (2014-07-10) > Platform: x86_64-apple-darwin10.8.0 (64-bit) > > locale: > [1] en_US.utf-8/en_US.utf-8/en_US.utf-8/C/en_US.utf-8/en_US.utf-8 > > attached base packages: > [1] grDevices datasets splines graphics utils stats grid > [8] methods base > > other attached packages: > [1] rms_4.2-1 SparseM_1.03 Hmisc_3.14-4 Formula_1.1-1 > [5] survival_2.37-7 sos_1.3-8 brew_1.0-6 lattice_0.20-29 > > loaded via a namespace (and not attached): > [1] cluster_1.15.2 latticeExtra_0.6-26 multcomp_1.3-1 > [4] mvtnorm_0.9-9999 nlme_3.1-117 polspline_1.1.9 > [7] quantreg_5.05 RColorBrewer_1.0-5 rpart_4.1-8 > [10] sandwich_2.3-0 zoo_1.7-11 > > #---------- Idea # 2 -------- > > Another possibility is implied by this portion of the ?Startup page that (I > already suggested you read): > > "If you want ‘~/.Renviron’ or ‘~/.Rprofile’ to be ignored by child R > processes (such as those run by R CMD check and R CMD build), set the > appropriate environment variable R_ENVIRON_USER or R_PROFILE_USER to (if > possible, which it is not on Windows) "" or to the name of a non-existent > file." > > > #------ Suggestion ------------- > So you need to check whether any of those are different than what you expect. > Failing illumination after poking around in your setup, I suspect you may > need to post the output of ALL of sessionInfo() AND the results of > dput(Sys.getenv()) . > > -- > David. > >> >> Thanks, >> Gang >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> R-SIG-Mac mailing list >> [email protected] >> https://stat.ethz.ch/mailman/listinfo/r-sig-mac > > David Winsemius > Alameda, CA, USA > > _______________________________________________ > R-SIG-Mac mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/r-sig-mac -- Peter Dalgaard, Professor, Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: [email protected] Priv: [email protected] _______________________________________________ R-SIG-Mac mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-mac
