[Rcpp-devel] Remove hard-coded path to /usr/bin in Makevars

Dirk Eddelbuettel edd at debian.org
Fri Apr 26 23:54:17 CEST 2013

Hi Valentin,

Thanks for subscribing.

On 26 April 2013 at 17:08, Valentin Kuznetsov wrote:
| Hi,
| this is re-post from
| https://r-forge.r-project.org/tracker/?func=detail&atid=637&aid=2743&group_id=155
| as been advised by Dirk.

Now that you are here, let me repost what I wrote earlier. I'll intend it all
by two spaces.

I still think that what you suggested is not all that appealing as a general
solution; you have a very particular local setup and maybe you will just have
to diver /usr/bin/install_name_tool.  I don't want to break the general OS X
setup for which this is part (and was added/suggested by Simon a while back).


Quoted earlier message below

  From: Dirk Eddelbuettel <edd at debian.org>
  To: rcpp-bugs at r-forge.r-project.org
  Cc: simon.urbanek at r-project.org, rcpp-devel <rcpp-devel at r-forge.wu-wien.ac.at>
  Subject: Re: [Rcpp-devel] [rcpp-Bugs][2743] Remove hard-coded path to
  	/usr/bin in Makevars
  Date: Fri, 26 Apr 2013 14:21:56 -0500
  On 26 April 2013 at 20:56, rcpp-bugs at r-forge.r-project.org 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_nam
  |  e_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:
  		@if test -e "/usr/bin/install_name_tool"; then /usr/bin/install_name_tool -id $(R_PACKAGE_DIR)/lib$(R_ARCH)/$(USERLIB) $(USERLIB); fi
  That line, if memory serves, suggested and provided by Simon for the OS X
  case.  It acts as both a test for OS X (as no other OS has
  /usr/bin/install_name_tool) as well as a use of the tool.
  What you suggest (ie remove the leading /usr/bin/) does not seem to
  work. Witness this:
  edd at max:~$ 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 at max:~$ test -e install && echo "Found"                   # yet 'test -e' fails
  edd at max:~$ test -e /usr/bin/install && echo "Found"          # only full path works
  edd at 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 
  | 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_modul
     e -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 | edd at debian.org | http://dirk.eddelbuettel.com
  Rcpp-devel mailing list
  Rcpp-devel at lists.r-forge.r-project.org

Dirk Eddelbuettel | edd at debian.org | http://dirk.eddelbuettel.com

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