Re: [R] "ignoring environment value of R_HOME" error when installing packages

From: tub78 <stu.andrews_at_gmail.com>
Date: Wed, 04 Jun 2008 14:40:26 -0700 (PDT)

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 <stu.andr..._at_gmail.com> 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
>
> ______________________________________________
> R-h...@r-project.org 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_at_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. Received on Thu 05 Jun 2008 - 00:11:49 GMT

Archive maintained by Robert King, hosted by the discipline of statistics at the University of Newcastle, Australia.
Archive generated by hypermail 2.2.0, at Thu 05 Jun 2008 - 00:30:47 GMT.

Mailing list information is available at https://stat.ethz.ch/mailman/listinfo/r-help. Please read the posting guide before posting to the list.

list of date sections of archive