This bug has been resolved, after our administrator updated the path of R_HOME in our scripts. I believe that the cause of trouble was the parallel nature of the installation, as mentioned in the following thread:
http://groups.google.com/group/r-help-archive/browse_thread/thread/632175125a7c4 16f/6a5220b73d3ac682?lnk=gst&q=R_HOME# regards - S. On Jun 4, 12:35 am, tub78 <[EMAIL PROTECTED]> wrote: > I am troubled by what appears to be a glitch in the current > distribution, or in > its installation on our system. I've traced it, and found a work- > around. Is > this normal? Is there a cleaner solution? > > The problem: > > During a package installation, the warning message "WARNING: ignoring > environment value of R_HOME" from line 31 of <R_HOME>/bin/R is > accidentally > spliced into the CLINK_CPPFLAGS variable at line 606 of <R_HOME>/bin/ > INSTALL. > This prevents the compilation C files. Please note that I have not > set the R_HOME > environment variable; it is undefined in my shell. > > - Here are lines 29-32 from <R_HOME>/bin/R: > > if test -n "${R_HOME}" && \ > test "${R_HOME}" != "${R_HOME_DIR}"; then > echo "WARNING: ignoring environment value of R_HOME" > fi > > - Here is line 606 of <R_HOME>/bin/INSTALL: > > CLINK_CPPFLAGS=`echo > "tools:::.find_cinclude_paths(file='DESCRIPTION')" | \ > "${R_EXE}" --vanilla --slave` > > The work-around: > > First some background. The command sequence "R CMD INSTALL" sets in > motion a sequence of scripts that collectively manage the installation > process. > > "R" <R_HOME>/bin/R calls Rcmd script on line > 148 > "CMD" <R_HOME>/lib/R/bin/Rcmd calls INSTALL script on > line 45 > "INSTALL" <R_HOME>/lib/R/bin/INSTALL encounters the error on > line 606 > > Now, if you are the owner of you installation, then you can probably > just edit > the INSTALL file directly. > > Otherwise, if you specify the full path of an executable in place of > the word > "INSTALL" on the command line, the Rcmd script will detect this and > call your > script instead of the normal INSTALL script (see Rcmd line 37). > > e.g. "R CMD <path.to.alternate.install.script> ..." > > One can just copy the INSTALL script, changing line 606 to > CLINK_CPPFLAGS = "" > and hope for the best. If the package you are compiling specifies its > own C > include files, then you will have to modify the variable accordingly, > or else > use the ~/.R/Makevars mechanism. > > But, the question remains, is there an nicer solution? > > Thanks, > - Stu > > ______________________________________________ > [EMAIL PROTECTED] mailing listhttps://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guidehttp://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
