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=gstq=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
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