[Rcpp-devel] Rcpp.package.skeleton(module=TRUE) fails to load

[Florian Oswald]

Thanks Davor.
I have exactly the same computer as you have, and my compiler calls
are identical as well. upgraded to Xcode 4.4 just to make sure. I get
the same error:

R(420) malloc: *** error for object 0x7fff7247f860: pointer being
freed was not allocated
*** set a breakpoint in malloc_error_break to debug
sh: line 1:   420 Abort trap: 6
'/Library/Frameworks/R.framework/Resources/bin/R' --no-save --slave <
/var/folders/bd/xhwzz96x2xl6b02bwt4myhy00000gn/T//RtmpuUhAG7/file17642ce6044


I think this means process id 420, R, is making a memory mistake.
I googled around and people get this error when developing iPhone
apps. They then actually find a bug in their code, fix it and that's
it. I guess I can exclude the bug in this case. Very weird.
Thanks anyway.
Florian

On 15 August 2012 17:49, Davor Cubranic <cubranic at stat.ubc.ca> wrote:
> Works fine for me:
>
>> bash-3.2$ R CMD INSTALL mypack --no-multiarch
>> * installing to library '/Library/Frameworks/R.framework/Versions/2.15/Resources/library'
>> * installing *source* package 'mypack' ...
>> ** libs
>> *** arch - x86_64
>> g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rcpp/include"   -fPIC  -g -O2  -c Num.cpp -o Num.o
>> g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rcpp/include"   -fPIC  -g -O2  -c rcpp_hello_world.cpp -o rcpp_hello_world.o
>> g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rcpp/include"   -fPIC  -g -O2  -c rcpp_module.cpp -o rcpp_module.o
>> g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rcpp/include"   -fPIC  -g -O2  -c stdVector.cpp -o stdVector.o
>> g++ -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o mypack.so Num.o rcpp_hello_world.o rcpp_module.o stdVector.o /Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rcpp/lib/x86_64/libRcpp.a -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
>> ld: warning: directory not found for option '-L/usr/local/lib'
>> installing to /Library/Frameworks/R.framework/Versions/2.15/Resources/library/mypack/libs/x86_64
>> ** R
>> ** preparing package for lazy loading
>> ** help
>> Warning: /private/tmp/mypack/man/mypack-package.Rd:31: All text must be in a section
>> Warning: /private/tmp/mypack/man/mypack-package.Rd:32: All text must be in a section
>> *** installing help indices
>> ** building package indices
>> ** testing if installed package can be loaded
>>
>> * DONE (mypack)
>
> sessionInfo:
>> > sessionInfo()
>> R version 2.15.1 (2012-06-22)
>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>>
>> locale:
>> [1] C
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>> loaded via a namespace (and not attached):
>> [1] tools_2.15.1
>
> This is on 10.7.4 (Lion), using Xcode 4.4.
>
> Davor
>
>
> On 2012-08-15, at 7:32 AM, Dirk Eddelbuettel wrote:
>
>>
>> On 15 August 2012 at 14:56, Florian Oswald wrote:
>> | I tried out your RcppBDT package and I could build it without any
>> | problem, and it works in R. It's quite strange. I've used Rcpp many
>> | times before without problem, most of the time with inline tough. I'm
>> | using the apple default compiler llvm-g++-4.2.
>> |
>> | Thanks for any other suggestions. I'll try to reverse engineer RcppBDT
>> | and see how far I get.
>>
>> Weird.  I spent quite some time in March/April going over Rcpp modules and
>> the loading code as John had made changes -- we were then forced to wait for
>> R 2.15.1 to come out to use them.
>>
>> The Rcpp modules vignette is mostly right. There are sort of two ways to do
>> it, and you have to follow things closely.  But that is what the skeleton
>> does so I am unsure what goes haywire here.
>>
>> Maybe someone else with an OS X box and R 2.15.1 can help?
>>
>> Dirk
>>
>> | Florian
>> |
>> | On 15 August 2012 14:14, Dirk Eddelbuettel <edd at debian.org> wrote:
>> | >
>> | > Florian,
>> | >
>> | > I cannot reproduce that on Linux -- just did a quick test from the
>> | > command-line:
>> | >
>> | > edd at max:~$ cd /tmp/
>> | > edd at max:/tmp$ r -lRcpp -e'Rcpp.package.skeleton("mypack",module=TRUE)'
>> | >
>> | > Attaching package: ‘utils’
>> | >
>> | > The following object(s) are masked from ‘package:Rcpp’:
>> | >
>> | >     .DollarNames, prompt
>> | >
>> | > Creating directories ...
>> | > Creating DESCRIPTION ...
>> | > Creating NAMESPACE ...
>> | > Creating Read-and-delete-me ...
>> | > Saving functions and data ...
>> | > Making help files ...
>> | > Done.
>> | > Further steps are described in './mypack/Read-and-delete-me'.
>> | >
>> | > Adding Rcpp settings
>> | >  >> added RcppModules: yada
>> | >  >> added Depends: Rcpp
>> | >  >> added LinkingTo: Rcpp
>> | >  >> added useDynLib directive to NAMESPACE
>> | >  >> added Makevars file with Rcpp settings
>> | >  >> added Makevars.win file with Rcpp settings
>> | >  >> added example header file using Rcpp classes
>> | >  >> added example src file using Rcpp classes
>> | >  >> added example R file calling the C++ example
>> | >  >> added Rd file for rcpp_hello_world
>> | >  >> copied the example module file
>> | > edd at max:/tmp$ R CMD INSTALL mypack
>> | > * installing to library ‘/usr/local/lib/R/site-library’
>> | > * installing *source* package ‘mypack’ ...
>> | > ** libs
>> | > ccache g++-4.6 -I/usr/share/R/include -DNDEBUG   -I"/usr/local/lib/R/site-library/Rcpp/include"   -fpic  -g0 -O3 -Wall -pipe -Wno-variadic-macros -pedantic -c Num.cpp -o Num.o
>> | > ccache g++-4.6 -I/usr/share/R/include -DNDEBUG   -I"/usr/local/lib/R/site-library/Rcpp/include"   -fpic  -g0 -O3 -Wall -pipe -Wno-variadic-macros -pedantic -c rcpp_hello_world.cpp -o rcpp_hello_world.o
>> | > ccache g++-4.6 -I/usr/share/R/include -DNDEBUG   -I"/usr/local/lib/R/site-library/Rcpp/include"   -fpic  -g0 -O3 -Wall -pipe -Wno-variadic-macros -pedantic -c rcpp_module.cpp -o rcpp_module.o
>> | > ccache g++-4.6 -I/usr/share/R/include -DNDEBUG   -I"/usr/local/lib/R/site-library/Rcpp/include"   -fpic  -g0 -O3 -Wall -pipe -Wno-variadic-macros -pedantic -c stdVector.cpp -o stdVector.o
>> | > g++-4.6 -shared -o mypack.so Num.o rcpp_hello_world.o rcpp_module.o stdVector.o -L/usr/local/lib/R/site-library/Rcpp/lib -lRcpp -Wl,-rpath,/usr/local/lib/R/site-library/Rcpp/lib -L/usr/lib/R/lib -lR
>> | > installing to /usr/local/lib/R/site-library/mypack/libs
>> | > ** R
>> | > ** preparing package for lazy loading
>> | > ** help
>> | > Warning: /tmp/mypack/man/mypack-package.Rd:31: All text must be in a section
>> | > Warning: /tmp/mypack/man/mypack-package.Rd:32: All text must be in a section
>> | > *** installing help indices
>> | > ** building package indices
>> | > ** testing if installed package can be loaded
>> | >
>> | > * DONE (mypack)
>> | > edd at max:/tmp$ r -lmypack -e'cat("Hello, world\n")'
>> | > Hello, world
>> | > edd at max:/tmp$
>> | >
>> | > and dito in an R session I had open:
>> | >
>> | > R> library(mypack)
>> | > R> mypack::foo()
>> | > [1] 1
>> | > R>
>> | >
>> | > Also note that these package.skeleton tests are part of the normal unit
>> | > tests.
>> | >
>> | > With Romain taking it a little easier these days, there is no committed
>> | > developer access to OS X so I am afraid you (or someone else) will have to
>> | > debug this.
>> | >
>> | > One last thing: you could try my package RcppBDT and RcppCNPy which both use
>> | > Modules.  They are pretty small, see if you can get them built and loaded.
>> | >
>> | > Dirk
>> | >
>> | > --
>> | > Dirk Eddelbuettel | edd at debian.org | http://dirk.eddelbuettel.com
>>
>> --
>> Dirk Eddelbuettel | edd at debian.org | http://dirk.eddelbuettel.com
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