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 /bin/R is
> accidentally
> spliced into the CLINK_CPPFLAGS variable at line 606 of /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 /bin/R:
>
> if test -n "${R_HOME}" && \
> test "${R_HOME}" != "${R_HOME_DIR}"; then
> echo "WARNING: ignoring environment value of R_HOME"
> fi
>
> - Here is line 606 of /bin/INSTALL:
>
> CLINK_CPPFLAGS=`echo
> "tools:::.find_cinclude_paths(file='DESCRIPTION')" | \
> "${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" /bin/R calls Rcmd script on line
> 148
> "CMD" /lib/R/bin/Rcmd calls INSTALL script on
> line 45
> "INSTALL" /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 ..."
>
> 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
>
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> and provide commented, minimal, self-contained, reproducible code.
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