[Omega-remote] Installing RSPython with R 1.3.0
Hi Greg.
What you are seeing is probably a result of using R embedded within another
application/system (Python in this case) but having R originally compiled
without support for R as a shared library. If you were to build R in the default
manner, i.e.
configure
make
and then re-configure to build as a shared library
configure --enable-R-shlib
make
the shared objects that make up the modules and package libraries
will not be rebuilt. Perhaps they should, but that is not currently
what happens.
If you were to start afresh (e.g. make distclean)
and then configure with shared library support
(
configure --enable-R-shlib
make
)
all should be well and all the .so's that R attempts to load will
also be linked against libR.so and so the symbols within R on which
they depend will be located.
Hope this is the correct diagnosis of the problem.
D.
Gregory R. Warnes wrote:
To get RSPython installed on my debian test box, I had to make a couple
of changes not listed in
ftp://www.omegahat.org/pub/Omega/RSPython/FAQ.html
1) I had to change $R_HOME/src/modules/X11 :
$(R_X11_la): $(R_X11_la_OBJECTS) $(R_X11_la_DEPENDENCIES)
$(SHLIB_LINK) -o $@ $(R_X11_la_LDFLAGS) $(R_X11_la_OBJECTS)
$(R_X11_la_LIBADD) $(LIBS)
to
$(R_X11_la): $(R_X11_la_OBJECTS) $(R_X11_la_DEPENDENCIES)
$(SHLIB_LINK) -o $@ $(R_X11_la_LDFLAGS) $(R_X11_la_OBJECTS)
$(R_X11_la_LIBADD) $(LIBS) -L$(R_HOME)/bin -lR
2) I had the same link problem with ctest, so I changed
PKG_LIBS = -lg2c -lm -L/usr/lib/gcc-lib/i386-linux/2.95.4 -lm
to
PKG_LIBS = -lg2c -lm -L/usr/lib/gcc-lib/i386-linux/2.95.4 -lm
-L$(R_HOME)/bin -lR
3) Will all libraries that get loaded into R inside of python require
this?
If I try to load other 'recommended' packages that include C code I get
dyn.load erros, EG:
RS.call("library","splines")
Error in dyn.load(x, as.logical(local), as.logical(now)) :
unable to load shared library
"/usr/local/lib/R/library/splines/libs/splines.so":
/usr/local/lib/R/library/splines/libs/splines.so: undefined symbol:
R_NaN
Error in function (package, help, lib.loc = .lib.loc, character.only =
FALSE, :
.First.lib failed
In the local error handler
In the local error handler
Error in if (!is.numeric(name) || name != (pos <- as.integer(name))) { :
missing value where logical needed
In the local error handler
In the local error handler
Error in pos.to.env(pos) : invalid argument
In the local error handler
In the local error handler
Error in objects(lib.pos) : invalid envir= argument
In the local error handler
['RSPython', 'ctest', 'base']
-Greg
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