Hi Ben, Ok, if I read correctly, it looks like you must have started R in the terminal using 'R --vanilla', based upon the file name below.
In that case, R should bring up help pages in the terminal using the internal text pager, as opposed to externally in a browser with HTML. Start R in the Terminal just using 'R' and see what, if any, differences there are in the output of options() in that case. Grasping at another straw, let's change the default browser in R.app to see if using an external browser, instead of the built-in browser, behaves differently. As it turns out, from discussions some years ago, it is a bit more complex with R.app, as it does not honor the usual options() settings. So, with R.app NOT running, in a terminal, use: defaults write org.R-project.R use.external.help YES and hit enter. Then, start R.app and try to use help again and see what happens. To restore the default use of the internal R.app browser, exit R.app and in a terminal, use: defaults delete org.R-project.R use.external.help and hit enter. See if that does anything. Marc > On Oct 18, 2018, at 10:52 AM, Ben Tupper <btup...@bigelow.org> wrote: > > Hi, > > Thanks for your persistence and kind help. > > (1) Comparing output of options() > > R.app options() includes > > $help_type > [1] "html" > > that terminal R options() does not. Here's the diff of the two... > > ben@gale ~ $ diff R-vanilla-options R-app-options > 81c81 > < <bytecode: 0x7fd3f638b858> > --- > > <bytecode: 0x7fd0b1fcbbc0> > 107a108,110 > > $help_type > > [1] "html" > > > 181,182c184,185 > < CRAN > < "@CRAN@" > --- > > CRAN > > "http://cran.utstat.utoronto.ca"; > 244c247 > < [1] 80 > --- > > [1] 168 > > > (2) Removing ~/Library/Preferences/org.R-project.R.plist > > Starting R.app after removing the plist does not resolve the blank help > window (but did restore R.app's factory-default appearance and settings.) > > > help("help") # brings up blank help page > starting httpd help server ... done > > > > > > > >> On Oct 18, 2018, at 10:36 AM, Marc Schwartz <marc_schwa...@me.com> wrote: >> >> Hi, >> >> Two things: >> >> 1. Can one or both of you guys check locally on your own computers, to see >> if there is any difference between the output of options() in R.app, versus >> the output when R is run from a Terminal session. Many elements will not be >> germane to this issue, but others might, if there are differences. >> >> Just wondering if some option() is altered from the default and/or causing a >> conflict unique to R.app. >> >> >> >> 2. Exit from R.app so that it is not running. >> >> Then look for the file: >> >> ~/Library/Preferences/org.R-project.R.plist >> >> From what I can tell, that is the file that stores the default settings and >> user specific Preferences configurations for R.app. >> >> With R.app NOT running, delete that file, or drag it to the desktop, if >> preferred. >> >> Then start R.app and see what happens with help. The above .plist file, will >> be created new, with the new R.app session, so will return to default >> settings. Perhaps there is something in there screwing things up. >> >> >> Marc >> >> <snip> >> > > Ben Tupper > Bigelow Laboratory for Ocean Sciences > 60 Bigelow Drive, P.O. Box 380 > East Boothbay, Maine 04544 > http://www.bigelow.org > > Ecological Forecasting: https://eco.bigelow.org/ > > > > > _______________________________________________ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
