[Rcpp-devel] Attribute does not compile with 'compileAttributes' but with 'sourceCpp'

Simon Zehnder szehnder at uni-bonn.de
Sat Nov 2 11:12:07 CET 2013 

Thanks Romain,

I’ll come back to this thread when I found out what the reason of this behavior in my environment is.


Best
Simon

On 02 Nov 2013, at 10:46, Romain Francois <romain at r-enthusiasts.com> wrote:

> compileAttributes ends up calling a .Call function that lives inside Rcpp.so. 
> 
> Le 2 nov. 2013 à 10:25, Simon Zehnder <szehnder at uni-bonn.de> a écrit :
> 
>> Thanks Romain,
>> 
>> looks the same here. So the path is the same, but it seems, that the padding is different. I would like to understand what happens when I call compileAttributes. Is there anywhere a linking involved with Rcpp.so or Rcpp.dylib? 
>> 
>> 
>> Best
>> 
>> Simon
>> 
>> 
>> On 02 Nov 2013, at 09:57, Romain Francois <romain at r-enthusiasts.com> wrote:
>> 
>>> Le 02/11/2013 09:35, Simon Zehnder a écrit :
>>>> First, I didn’t. But for getting some output from the functions in attributes.cpp I later compiled the Rcpp package from source. When I compile with the option “-headerpad_max_install_names” the compileAttributes runs without an error. If I compile without this flag, I get the pointer error.
>>>> Problems with header padding is a well-known issue on the Mac (https://svn.boost.org/trac/boost/ticket/1927), usually in frameworks. It is used a relative path in the sections of shared objects (sometimes also in dynamic libs). When the library/shared object has to be included in other libraries, the relative path has to be changed to an absolute path. If then there is not enough space in the header of the Mach-O file, it gives you an exception.
>>>> 
>>>> But my guess is for the compileAttributes function, that no library binding is done, though it takes library paths as arguments when calling ‘.Call’. My perception has been so far, that this function solely creates the RcppExports.cpp and *.R files without any compilation or linking (this is done later, when we compile the package with the attributes). The depends/linkingto names from the DESCRIPTION file are used for headers in the RcppExports.cpp file I have guessed. The point, that I am seemingly the only one, that encounters this error, points me to my compiler (gcc4.8.2). Could be, that under the hood clang uses already a larger header padding.
>>>> 
>>>> Btw: When you are on Mac, could you check what “otool -L Rcpp.so” give you? Is the path relative (Rcpp.so) or absolute (has it something like @exectuable_path in front)?
>>> 
>>> $ otool -L Rcpp.so
>>> Rcpp.so:
>>>   Rcpp.so (compatibility version 0.0.0, current version 0.0.0)
>>>   /Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libR.dylib (compatibility version 3.0.0, current version 3.0.2)
>>>   /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 855.11.0)
>>>   /usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 120.0.0)
>>>   /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1197.1.1)
>>> 
>>> 
>>>> Best
>>>> Simon
>>>> 
>>>> On 02 Nov 2013, at 01:02, Hadley Wickham <h.wickham at gmail.com> wrote:
>>>> 
>>>>> Did you install Rcpp from source? That's what I had to do to solve a similar problem.
>>>>> 
>>>>> Hadley
>>>>> 
>>>>> On Friday, November 1, 2013, Simon Zehnder wrote:
>>>>> Same thing actually on my side: I had a hardware crash lately with 10.8 and made fresh install after formatting my harddrive NSA-style :)
>>>>> 
>>>>> Afterwards I compiled R 3.0.1 and from macports the gcc48 port as well as gettext. Then, Mavericks came and I updated - nothing worked anymore: I reinstalled gcc48 port and deleted R 3.0.1. Then I installed gcc4.8.2 from http://hpc.sourceforge.net, Xcode Command line tools for Mavericks and XQuartz 4.7.2. I work with environment modules, where I can load a certain compiler with its needed environment variables. With gcc 4.8.2 I installed R-3.0.2 and then the packages. Always have to type “module load compilers/gcc-4.8.2 before starting R, but that doesn’t bother me … I still can use openMP to its great extent :)
>>>>> 
>>>>> My problem is linked to the install_name_tool and the way on Mac OS paths are set and replaced in dynamic libraries …  this could of course be caused by “older tools” like the llvm-gcc4.2 “laying” around…. though locate does not find them….
>>>>> 
>>>>> 
>>>>> 
>>>>> On 01 Nov 2013, at 20:33, Dominick Samperi <djsamperi at gmail.com> wrote:
>>>>> 
>>>>>> My original attempt to update to Mavericks failed (unrelated hardware issue), and this
>>>>>> may have actually worked in my favor. It forced me to install Mac OS X 10.8 from
>>>>>> scratch, a "clean" install, that I later upgraded to Mavericks. If you upgraded from
>>>>>> an existing configuration you may have old tools (like llvm-g++-4.2) laying around
>>>>>> that could cause problems.
>>>>>> 
>>>>>> 
>>>>>> On Fri, Nov 1, 2013 at 3:02 PM, Simon Zehnder <szehnder at uni-bonn.de> wrote:
>>>>>> I read through all the thread answers and my variables in the Makeconf are the same alsso I installed the Xcode Command Line Tools for Mavericks. Are there any other apps and libs that have been to be updated? (I do not use brew). What remains is the following:
>>>>>> 
>>>>>> Compiling Rcpp give the pointer exception (when calling compileAttributes), also encountered in the thread you referred to.
>>>>>> 
>>>>>> Compiling Rcpp and adding the flag “-headerpad_max_install_names” lets the compileAttributes function do its work without any exception. My next guess is: possibly the gettext library…
>>>>>> 
>>>>>> Best
>>>>>> 
>>>>>> Simon
>>>>>> 
>>>>>> On 01 Nov 2013, at 19:20, Dominick Samperi <djsamperi at gmail.com> wrote:
>>>>>> 
>>>>>>> In your original post you mention the "pointer being freed was not allocated" error message. I have just tracked this down in another context (Octave
>>>>>>> under Mac OS X). In my case the error occurs on the dlopen() call for
>>>>>>> an R package shared library. The fix was to make sure all apps and libs
>>>>>>> are updated after moving to Mavericks. See the thread in rcppoctave-users
>>>>>>> list for a blow-by-blow description.
>>>>>>> 
>>>>>>> 
>>>>>>> On Fri, Nov 1, 2013 at 1:11 PM, Simon Zehnder <szehnder at uni-bonn.de> wrote:
>>>>>>> You are right, working with apple and C++ is often a mess. Up to now, llvm does not yet support openmp. It is coming but I do not see it fully implemented before next summer. If I want to use openmp I have thus to rely on the gcc which brings a lot of problems with it and from what I read on the R-lists most of the Mac Users suffer. I guess that this time a reinstall of R was unavoidable for most of us. I thought about using the xcrun —find gcc/g++ etc. to get what is needed in a Makevars but this does not give anything so far.
>>>>>>> 
>>>>>>> 
>>>>>>> On 01 Nov 2013, at 17:50, Dominick Samperi <djsamperi at gmail.com> wrote:
>>>>>>> 
>>>>>>>> With Apple moving from gcc/g++ to LLVM/clang++ I guess it makes sense
>>>>>>>> for R/Rcpp to use the LLVM/clang++ tool chain eventuallly, but I don't know
>>>>>>>> if there are plans to do this. Otherwise, the R community would need to
>>>>>>>> support "MACtools" following the model provided by "Rtools" under Windows...
>>>>>>>> 
>>>>>>>> 
>>>>>>>> On Fri, Nov 1, 2013 at 12:12 PM, Simon Zehnder <szehnder at uni-bonn.de> wrote:
>>>>>>>> Hi Dominick,
>>>>>>>> 
>>>>>>>> I did install files from brew but instead used the gcc from http://hpc.sourceforge.net
>>>>>>>> 
>>>>>>>> 
>>>>>>>> On 01 Nov 2013, at 16:55, Dominick Samperi <djsamperi at gmail.com> wrote:
>>>>>>>> 
>>>>>>>>> If you depend on tools installed using brew, you might want to try
>>>>>>>>> removing those that were installed before the Mavericks update,
>>>>>>>>> using:
>>>>>>>>> rm -rf /usr/local/Cellar
>>>>>>>>> brew prune
>>>>>>>>> brew doctor
>>>>>>>>> brew install <what-you-need>
>>>>>>>>> 
>>>>>>>>> 
>>>>>>>>> On Fri, Nov 1, 2013 at 11:19 AM, Simon Zehnder <szehnder at uni-bonn.de> wrote:
>>>>>>>>> Point landing J.J.!
>>>>>>>>> 
>>>>>>>>> I already compiled a new R when Mavericks came out with a newly installed a gcc-4.8.2, that I can load via environment modules. I also installed th
>>>>> 
>>>>> 
>>>>> --
>>>>> Chief Scientist, RStudio
>>>>> http://had.co.nz/
>>>> 
>>>> _______________________________________________
>>>> Rcpp-devel mailing list
>>>> Rcpp-devel at lists.r-forge.r-project.org
>>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel
>>> 
>>> 
>>> -- 
>>> Romain Francois
>>> Professional R Enthusiast
>>> +33(0) 6 28 91 30 30
>>> 
>>> _______________________________________________
>>> Rcpp-devel mailing list
>>> Rcpp-devel at lists.r-forge.r-project.org
>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel
>>

More information about the Rcpp-devel mailing list