On 26 April 2013 at 20:56, [email protected] wrote:
| Bugs item #2743, was opened at 2013-04-26 18:56 by Valentin Kuznetsov
| You can respond by visiting:
|
https://r-forge.r-project.org/tracker/?func=detail&atid=637&aid=2743&group_id=155
|
| Status: Open
| Priority: 3
| Submitted By: Valentin Kuznetsov (vkuznet)
| Assigned to: Nobody (None)
| Summary: Remove hard-coded path to /usr/bin in Makevars
| Hardware: Macintosh
| Product: None
| Operating System: MacOS X
| Component: None
| Version: None
| Severity: None
| Resolution: None
| URL:
|
|
| Initial Comment:
| I was unable to build Rcpp due to the fact that on my system I use another
compiler (it is installed from MacPorts in /opt/local/bin area). The
Rcpp/src/Makevars uses hard-coded path to /usr/bin/install_name_tool. This
cause the linker to pick-up wrong install_name_tool which in my case should
come from location of my compiler (i.e. /opt/local/bin). The error I got was
the following:
|
It would appear that you are referring to the last line of this section:
$(USERLIB): $(OBJECTS)
$(SHLIB_CXXLD) -o $(USERLIB) $(OBJECTS) $(SHLIB_CXXLDFLAGS)
$(ALL_LIBS)
@if test -e "/usr/bin/install_name_tool"; then
/usr/bin/install_name_tool -id $(R_PACKAGE_DIR)/lib$(R_ARCH)/$(USERLIB)
$(USERLIB); fi
That line, if memory serves, suggested and provided by Simon for the OS X
case. It acts as both a test for OS X (as no other OS has
/usr/bin/install_name_tool) as well as a use of the tool.
What you suggest (ie remove the leading /usr/bin/) does not seem to
work. Witness this:
edd@max:~$ ls -l /usr/bin/install # I know I have
thos
-rwxr-xr-x 1 root root 113864 Nov 19 16:20 /usr/bin/install
edd@max:~$ test -e install && echo "Found" # yet 'test -e'
fails
edd@max:~$ test -e /usr/bin/install && echo "Found" # only full path
works
Found
edd@max:~$
With that I think your bug report is way too local. I am sorry that your
particular case is not covered by our installation, but I have not intention
of breaking lots of working systems only to accomodate you.
There may be other ways, and I am open to suggestions. Maybe Simon can help
once more.
One idea would be
@if test -e "/usr/bin/install_name_tool"; then
install_name_tool -id $(R_PACKAGE_DIR)/lib$(R_ARCH)/$(USERLIB) $(USERLIB); fi
which still has the explicit test with a path, but then calls without a
path. Or is that too fragile?
Any help from OS X users appreciated
Dirk
|
| R CMD INSTALL /Users/vk/Work/Languages/R/Rcpp_0.10.3.tar.gz
|
| Loading required package: utils
|
| * installing to library ‘/Users/vk/Library/R/3.0/library’
|
| * installing *source* package ‘Rcpp’ ...
|
| ** package ‘Rcpp’ successfully unpacked and MD5 sums checked
|
| ** libs
|
| /opt/local/bin/g++-mp-4.7
-I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG
-I../inst/include/ -I/opt/local/include -fPIC -O2 -m64 -c Date.cpp -o
Date.o
|
| /opt/local/bin/g++-mp-4.7
-I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG
-I../inst/include/ -I/opt/local/include -fPIC -O2 -m64 -c Module.cpp -o
Module.o
|
| /opt/local/bin/gcc-mp-4.7 -std=gnu99
-I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG
-I../inst/include/ -I/opt/local/include -fPIC -O2 -DOS_OBJECT_USE_OBJC=0
-m64 -c Rcpp_init.c -o Rcpp_init.o
|
| /opt/local/bin/g++-mp-4.7
-I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG
-I../inst/include/ -I/opt/local/include -fPIC -O2 -m64 -c Timer.cpp -o
Timer.o
|
| /opt/local/bin/g++-mp-4.7
-I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG
-I../inst/include/ -I/opt/local/include -fPIC -O2 -m64 -c api.cpp -o api.o
|
| /opt/local/bin/g++-mp-4.7
-I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG
-I../inst/include/ -I/opt/local/include -fPIC -O2 -m64 -c attributes.cpp
-o attributes.o
|
| /opt/local/bin/g++-mp-4.7
-I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG
-I../inst/include/ -I/opt/local/include -fPIC -O2 -m64 -c barrier.cpp -o
barrier.o
|
| /opt/local/bin/g++-mp-4.7
-I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG
-I../inst/include/ -I/opt/local/include -fPIC -O2 -m64 -c exceptions.cpp
-o exceptions.o
|
| /opt/local/bin/g++-mp-4.7 -dynamiclib -Wl,-headerpad_max_install_names
-undefined dynamic_lookup -single_module -multiply_defined suppress
-L/opt/local/lib -o Rcpp.so Date.o Module.o Rcpp_init.o Timer.o api.o
attributes.o barrier.o exceptions.o
-F/opt/local/Library/Frameworks/R.framework/.. -framework R -Wl,-framework
-Wl,CoreFoundation
|
| /opt/local/bin/g++-mp-4.7 -o libRcpp.dylib Date.o Module.o Rcpp_init.o
Timer.o api.o attributes.o barrier.o exceptions.o -dynamiclib
-Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module
-multiply_defined suppress -F/opt/local/Library/Frameworks/R.framework/..
-framework R -Wl,-framework -Wl,CoreFoundation
|
| /usr/bin/install_name_tool: object: libRcpp.dylib malformed object (unknown
load command 15)
|
| make: *** [libRcpp] Error 1
|
| ERROR: compilation failed for package ‘Rcpp’
|
|
|
| To fix the problem I untar the source code, modified Rcpp/src/Makevars,
replaced the path to install_name_tool, tar the package again and manually
install it. Please review your test in Makevars and remove hard-coded path to
install_name_tool. It should be picked up from the environment.
|
| Thanks,
|
| Valentin.
|
| ----------------------------------------------------------------------
|
| You can respond by visiting:
|
https://r-forge.r-project.org/tracker/?func=detail&atid=637&aid=2743&group_id=155
--
Dirk Eddelbuettel | [email protected] | http://dirk.eddelbuettel.com
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