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

Valentin Kuznetsov vkuznet at gmail.com
Sat Apr 27 00:38:32 CEST 2013 

Dirk,

having hard-coded path is usually lead to trouble regardless of the OS. Users may have dedicated system with specific compiler/tools in different location. What you need is auto-detection of required components. Since /usr/bin is always in a PATH you don't really need it either. But as I described the different location of gcc/g++ requires appropriate linker and if you enforce in your setup specific linker it leads to the problem. My OS X setup is not unique, many Linux systems may have compiler (or even multiple version of compiler) in different location (I work in High-Energy community and we build our tools ourselves, including compiler and the rest of the OS). What matter is consistency and your setup is not consistent with user environment.

If you don't want to introduce robust configure tool chain you can easily create bash script to test location of required tools. If it is required I can write one.

Regards,
Valentin.

On Apr 26, 2013, at ,Apr 26, 5:54 PM, Dirk Eddelbuettel wrote:

> 
> 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).
> 
> Dirk 
> 
> 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:
> 
>  $(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) $(USERLIB); fi
> 
>  That line, if memory serves, suggested and provided by Simon for the OS X
>  case.  It acts as both a test for OS X (as no other OS has
>  /usr/bin/install_name_tool) as well as a use of the tool.
> 
>  What you suggest (ie remove the leading /usr/bin/) does not seem to
>  work. Witness this:
> 
>  edd at max:~$ 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
>  Found
>  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 
> 
>  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_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
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> 
> -- 
> Dirk Eddelbuettel | edd at debian.org | http://dirk.eddelbuettel.com

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