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invariantImageSimilarity Rcpp Segfault #119

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cfhammill opened this issue Oct 26, 2016 · 4 comments
Closed

invariantImageSimilarity Rcpp Segfault #119

cfhammill opened this issue Oct 26, 2016 · 4 comments

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@cfhammill
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Hi I've run into a segfault with invariantImageSimilarity. Any thoughts and suggestions would be greatly appreciated.

ANTsR and ITKR were install via devtools::install_github with no customizations,. The system is ubuntu 12.04, system gcc is 4.6.3

GDB backtrace:

> library(ANTsR)
> fi<-antsImageRead( getANTsRData("r16"))
> mi<-antsImageRead( getANTsRData("r64"))
> mival<-invariantImageSimilarity( fi, mi, c(0,10,20) )
terminate called after throwing an instance of 'Rcpp::not_compatible'
  what():  expecting a single value

Program received signal SIGABRT, Aborted.
0x00007ffff71c4035 in __GI_raise (sig=6) at ../nptl/sysdeps/unix/sysv/linux/raise.c:64
64      ../nptl/sysdeps/unix/sysv/linux/raise.c: No such file or directory.
(gdb) 
(gdb) bt
#0  0x00007ffff71c4035 in __GI_raise (sig=6) at ../nptl/sysdeps/unix/sysv/linux/raise.c:64
#1  0x00007ffff71c779b in __GI_abort () at abort.c:91
#2  0x00007ffff37d969d in __gnu_cxx::__verbose_terminate_handler() () from /usr/lib/x86_64-linux-gnu/libstdc++.so.6
#3  0x00007ffff37d7846 in ?? () from /usr/lib/x86_64-linux-gnu/libstdc++.so.6
#4  0x00007ffff37d7873 in std::terminate() () from /usr/lib/x86_64-linux-gnu/libstdc++.so.6
#5  0x00007ffff37d796e in __cxa_throw () from /usr/lib/x86_64-linux-gnu/libstdc++.so.6
#6  0x00007fffefcca16f in Rcpp::internal::primitive_as<unsigned int> (x=<optimized out>) at /axiom2/projects/software/arch/R-versions/R-3.3.1/lib/R/library/Rcpp/include/Rcpp/as.h:32
#7  0x00007ffff056b84a in as<unsigned int> (x=<optimized out>) at /axiom2/projects/software/arch/R-versions/R-3.3.1/lib/R/library/Rcpp/include/Rcpp/as.h:41
#8  as<unsigned int> (x=<optimized out>) at /axiom2/projects/software/arch/R-versions/R-3.3.1/lib/R/library/Rcpp/include/Rcpp/as.h:144
#9  invariantSimilarityHelper<2u, itk::AffineTransform<double, 2u> > (image1=..., image2=..., r_thetas=0x1ec6780, r_thetas2=0x1ec1e40, r_thetas3=0x1ec1f78, r_lsits=<optimized out>, r_WM=0x271b018, r_scale=0x27238b8, r_doreflection=0x2723888, r_txfn=0x2740788)
    at invariantImageSimilarity.cpp:147
#10 0x00007ffff0532bd8 in invariantImageSimilarity (r_in_image1=<optimized out>, r_in_image2=<optimized out>, thetas=0x1ec6780, thetas2=0x1ec1e40, thetas3=0x1ec1f78, localSearchIterations=0x2af23c8, whichMetric=0x271b018, r_scale=0x27238b8, r_doref=0x2723888, 
    txfn=0x2740788, whichTransform=0x2723588) at invariantImageSimilarity.cpp:572
#11 0x00007ffff784704b in R_doDotCall () from /axiom2/projects/software/arch/R-versions/R-3.3.1/lib/R/lib/libR.so
#12 0x00007ffff7855136 in do_dotcall () from /axiom2/projects/software/arch/R-versions/R-3.3.1/lib/R/lib/libR.so
#13 0x00007ffff7890610 in Rf_eval () from /axiom2/projects/software/arch/R-versions/R-3.3.1/lib/R/lib/libR.so
#14 0x00007ffff7894bd7 in do_set () from /axiom2/projects/software/arch/R-versions/R-3.3.1/lib/R/lib/libR.so
#15 0x00007ffff78903fa in Rf_eval () from /axiom2/projects/software/arch/R-versions/R-3.3.1/lib/R/lib/libR.so
#16 0x00007ffff7893bf7 in do_begin () from /axiom2/projects/software/arch/R-versions/R-3.3.1/lib/R/lib/libR.so
#17 0x00007ffff78903fa in Rf_eval () from /axiom2/projects/software/arch/R-versions/R-3.3.1/lib/R/lib/libR.so
#18 0x00007ffff7892bc8 in do_if () from /axiom2/projects/software/arch/R-versions/R-3.3.1/lib/R/lib/libR.so
#19 0x00007ffff78903fa in Rf_eval () from /axiom2/projects/software/arch/R-versions/R-3.3.1/lib/R/lib/libR.so
#20 0x00007ffff7893bf7 in do_begin () from /axiom2/projects/software/arch/R-versions/R-3.3.1/lib/R/lib/libR.so
#21 0x00007ffff78903fa in Rf_eval () from /axiom2/projects/software/arch/R-versions/R-3.3.1/lib/R/lib/libR.so
#22 0x00007ffff78916de in Rf_applyClosure () from /axiom2/projects/software/arch/R-versions/R-3.3.1/lib/R/lib/libR.so
#23 0x00007ffff7890727 in Rf_eval () from /axiom2/projects/software/arch/R-versions/R-3.3.1/lib/R/lib/libR.so
#24 0x00007ffff7894bd7 in do_set () from /axiom2/projects/software/arch/R-versions/R-3.3.1/lib/R/lib/libR.so
#25 0x00007ffff78903fa in Rf_eval () from /axiom2/projects/software/arch/R-versions/R-3.3.1/lib/R/lib/libR.so
#26 0x00007ffff78d038f in Rf_ReplIteration () from /axiom2/projects/software/arch/R-versions/R-3.3.1/lib/R/lib/libR.so
#27 0x00007ffff78d0554 in R_ReplConsole () from /axiom2/projects/software/arch/R-versions/R-3.3.1/lib/R/lib/libR.so
#28 0x00007ffff78d1ebb in run_Rmainloop () from /axiom2/projects/software/arch/R-versions/R-3.3.1/lib/R/lib/libR.so
#29 0x00007ffff78d1ed0 in Rf_mainloop () from /axiom2/projects/software/arch/R-versions/R-3.3.1/lib/R/lib/libR.so
#30 0x0000000000400846 in main ()
#31 0x00007ffff71af7ed in __libc_start_main (main=0x400814 <main>, argc=1, ubp_av=0x7fffffffd418, init=<optimized out>, fini=<optimized out>, rtld_fini=<optimized out>, stack_end=0x7fffffffd408) at libc-start.c:226
#32 0x0000000000400759 in _start ()

valgrind

> library(ANTsR)
==27293== Invalid read of size 8
==27293==    at 0x5750DBD: _wordcopy_fwd_dest_aligned (wordcopy.c:205)
==27293==    by 0x574A9DB: __GI_memmove (memmove.c:76)
==27293==    by 0x5705672: realpath@@GLIBC_2.3 (canonicalize.c:192)
==27293==    by 0xF493C02: itksys::SystemTools::ClassInitialize() (in /axiom2/projects/software/arch/R-versions/R-3.3.1/lib/R/library/ANTsR/libs/ANTsR.so)
==27293==    by 0xE6D9B56: _GLOBAL__sub_I_antsImageHeaderInfo.cpp (SystemTools.hxx:71)
==27293==    by 0x400F2C5: call_init.part.0 (dl-init.c:85)
==27293==    by 0x400F39E: _dl_init (dl-init.c:52)
==27293==    by 0x4013A99: dl_open_worker (dl-open.c:549)
==27293==    by 0x400F135: _dl_catch_error (dl-error.c:178)
==27293==    by 0x40132D9: _dl_open (dl-open.c:639)
==27293==    by 0x6C88F25: dlopen_doit (dlopen.c:67)
==27293==    by 0x400F135: _dl_catch_error (dl-error.c:178)
==27293==  Address 0x7e0cb50 is 96 bytes inside a block of size 99 alloc'd
==27293==    at 0x4C2B1C7: operator new(unsigned long) (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==27293==    by 0xC306A88: std::string::_Rep::_S_create(unsigned long, unsigned long, std::allocator<char> const&) (in /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.16)
==27293==    by 0xC308494: char* std::string::_S_construct<char const*>(char const*, char const*, std::allocator<char> const&, std::forward_iterator_tag) (in /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.16)
==27293==    by 0xC3085E2: std::basic_string<char, std::char_traits<char>, std::allocator<char> >::basic_string(char const*, std::allocator<char> const&) (in /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.16)
==27293==    by 0xF493BDD: itksys::SystemTools::ClassInitialize() (in /axiom2/projects/software/arch/R-versions/R-3.3.1/lib/R/library/ANTsR/libs/ANTsR.so)
==27293==    by 0xE6D9B56: _GLOBAL__sub_I_antsImageHeaderInfo.cpp (SystemTools.hxx:71)
==27293==    by 0x400F2C5: call_init.part.0 (dl-init.c:85)
==27293==    by 0x400F39E: _dl_init (dl-init.c:52)
==27293==    by 0x4013A99: dl_open_worker (dl-open.c:549)
==27293==    by 0x400F135: _dl_catch_error (dl-error.c:178)
==27293==    by 0x40132D9: _dl_open (dl-open.c:639)
==27293==    by 0x6C88F25: dlopen_doit (dlopen.c:67)
==27293==
==27293== Invalid read of size 8
==27293==    at 0x5750DBD: _wordcopy_fwd_dest_aligned (wordcopy.c:205)
==27293==    by 0x574A9DB: __GI_memmove (memmove.c:76)
==27293==    by 0x5705672: realpath@@GLIBC_2.3 (canonicalize.c:192)
==27293==    by 0xF493E02: itksys::SystemTools::ClassInitialize() (in /axiom2/projects/software/arch/R-versions/R-3.3.1/lib/R/library/ANTsR/libs/ANTsR.so)
==27293==    by 0xE6D9B56: _GLOBAL__sub_I_antsImageHeaderInfo.cpp (SystemTools.hxx:71)
==27293==    by 0x400F2C5: call_init.part.0 (dl-init.c:85)
==27293==    by 0x400F39E: _dl_init (dl-init.c:52)
==27293==    by 0x4013A99: dl_open_worker (dl-open.c:549)
==27293==    by 0x400F135: _dl_catch_error (dl-error.c:178)
==27293==    by 0x40132D9: _dl_open (dl-open.c:639)
==27293==    by 0x6C88F25: dlopen_doit (dlopen.c:67)
==27293==    by 0x400F135: _dl_catch_error (dl-error.c:178)
==27293==  Address 0x7e0ceb8 is 88 bytes inside a block of size 93 alloc'd
==27293==    at 0x4C2B1C7: operator new(unsigned long) (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==27293==    by 0xC306A88: std::string::_Rep::_S_create(unsigned long, unsigned long, std::allocator<char> const&) (in /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.16)
==27293==    by 0xC308494: char* std::string::_S_construct<char const*>(char const*, char const*, std::allocator<char> const&, std::forward_iterator_tag) (in /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.16)
==27293==    by 0xC3085E2: std::basic_string<char, std::char_traits<char>, std::allocator<char> >::basic_string(char const*, std::allocator<char> const&) (in /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.16)
==27293==    by 0xF493DE0: itksys::SystemTools::ClassInitialize() (in /axiom2/projects/software/arch/R-versions/R-3.3.1/lib/R/library/ANTsR/libs/ANTsR.so)
==27293==    by 0xE6D9B56: _GLOBAL__sub_I_antsImageHeaderInfo.cpp (SystemTools.hxx:71)
==27293==    by 0x400F2C5: call_init.part.0 (dl-init.c:85)
==27293==    by 0x400F39E: _dl_init (dl-init.c:52)
==27293==    by 0x4013A99: dl_open_worker (dl-open.c:549)
==27293==    by 0x400F135: _dl_catch_error (dl-error.c:178)
==27293==    by 0x40132D9: _dl_open (dl-open.c:639)
==27293==    by 0x6C88F25: dlopen_doit (dlopen.c:67)
==27293==
==27293== Invalid read of size 8
==27293==    at 0x5750D67: _wordcopy_fwd_dest_aligned (wordcopy.c:184)
==27293==    by 0x574A9DB: __GI_memmove (memmove.c:76)
==27293==    by 0x5705672: realpath@@GLIBC_2.3 (canonicalize.c:192)
==27293==    by 0xF493E02: itksys::SystemTools::ClassInitialize() (in /axiom2/projects/software/arch/R-versions/R-3.3.1/lib/R/library/ANTsR/libs/ANTsR.so)
==27293==    by 0xE6D9B56: _GLOBAL__sub_I_antsImageHeaderInfo.cpp (SystemTools.hxx:71)
==27293==    by 0x400F2C5: call_init.part.0 (dl-init.c:85)
==27293==    by 0x400F39E: _dl_init (dl-init.c:52)
==27293==    by 0x4013A99: dl_open_worker (dl-open.c:549)
==27293==    by 0x400F135: _dl_catch_error (dl-error.c:178)
==27293==    by 0x40132D9: _dl_open (dl-open.c:639)
==27293==    by 0x6C88F25: dlopen_doit (dlopen.c:67)
==27293==    by 0x400F135: _dl_catch_error (dl-error.c:178)
==27293==  Address 0x7e0dc90 is 48 bytes inside a block of size 54 alloc'd
==27293==    at 0x4C2B1C7: operator new(unsigned long) (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==27293==    by 0xC306A88: std::string::_Rep::_S_create(unsigned long, unsigned long, std::allocator<char> const&) (in /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.16)
==27293==    by 0xC308494: char* std::string::_S_construct<char const*>(char const*, char const*, std::allocator<char> const&, std::forward_iterator_tag) (in /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.16)
==27293==    by 0xC3085E2: std::basic_string<char, std::char_traits<char>, std::allocator<char> >::basic_string(char const*, std::allocator<char> const&) (in /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.16)
==27293==    by 0xF493DE0: itksys::SystemTools::ClassInitialize() (in /axiom2/projects/software/arch/R-versions/R-3.3.1/lib/R/library/ANTsR/libs/ANTsR.so)
==27293==    by 0xE6D9B56: _GLOBAL__sub_I_antsImageHeaderInfo.cpp (SystemTools.hxx:71)
==27293==    by 0x400F2C5: call_init.part.0 (dl-init.c:85)
==27293==    by 0x400F39E: _dl_init (dl-init.c:52)
==27293==    by 0x4013A99: dl_open_worker (dl-open.c:549)
==27293==    by 0x400F135: _dl_catch_error (dl-error.c:178)
==27293==    by 0x40132D9: _dl_open (dl-open.c:639)
==27293==    by 0x6C88F25: dlopen_doit (dlopen.c:67)
==27293==
> fi<-antsImageRead( getANTsRData("r16"))
> mi<-antsImageRead( getANTsRData("r64"))
> mival<-invariantImageSimilarity( fi, mi, c(0,10,20) )
terminate called after throwing an instance of 'Rcpp::not_compatible'
  what():  expecting a single value
@stnava
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stnava commented Oct 26, 2016

did you install this recently?

anyway, i cant reproduce this error on either osx or centos.

maybe latest Rcpp + antsr would help. no immediate thoughts.

brian

On Wed, Oct 26, 2016 at 5:45 PM, Chris Hammill [email protected]
wrote:

Hi I've run into a segfault with invariantImageSimilarity. Any thoughts
and suggestions would be greatly appreciated.

ANTsR and ITKR were install via devtools::install_github with no
customizations,. The system is ubuntu 12.04, system gcc is 4.6.3

GDB backtrace:

library(ANTsR)
fi<-antsImageRead( getANTsRData("r16"))
mi<-antsImageRead( getANTsRData("r64"))
mival<-invariantImageSimilarity( fi, mi, c(0,10,20) )
terminate called after throwing an instance of 'Rcpp::not_compatible'
what(): expecting a single value

Program received signal SIGABRT, Aborted.
0x00007ffff71c4035 in __GI_raise (sig=6) at ../nptl/sysdeps/unix/sysv/linux/raise.c:64
64 ../nptl/sysdeps/unix/sysv/linux/raise.c: No such file or directory.
(gdb)
(gdb) bt
#0 0x00007ffff71c4035 in __GI_raise (sig=6) at ../nptl/sysdeps/unix/sysv/linux/raise.c:64
#1 0x00007ffff71c779b in __GI_abort () at abort.c:91
#2 0x00007ffff37d969d in __gnu_cxx::__verbose_terminate_handler() () from /usr/lib/x86_64-linux-gnu/libstdc++.so.6
#3 0x00007ffff37d7846 in ?? () from /usr/lib/x86_64-linux-gnu/libstdc++.so.6
#4 0x00007ffff37d7873 in std::terminate() () from /usr/lib/x86_64-linux-gnu/libstdc++.so.6
#5 0x00007ffff37d796e in __cxa_throw () from /usr/lib/x86_64-linux-gnu/libstdc++.so.6
#6 0x00007fffefcca16f in Rcpp::internal::primitive_as (x=) at /axiom2/projects/software/arch/R-versions/R-3.3.1/lib/R/library/Rcpp/include/Rcpp/as.h:32
#7 0x00007ffff056b84a in as (x=) at /axiom2/projects/software/arch/R-versions/R-3.3.1/lib/R/library/Rcpp/include/Rcpp/as.h:41
#8 as (x=) at /axiom2/projects/software/arch/R-versions/R-3.3.1/lib/R/library/Rcpp/include/Rcpp/as.h:144
#9 invariantSimilarityHelper<2u, itk::AffineTransform<double, 2u> > (image1=..., image2=..., r_thetas=0x1ec6780, r_thetas2=0x1ec1e40, r_thetas3=0x1ec1f78, r_lsits=, r_WM=0x271b018, r_scale=0x27238b8, r_doreflection=0x2723888, r_txfn=0x2740788)
at invariantImageSimilarity.cpp:147
#10 0x00007ffff0532bd8 in invariantImageSimilarity (r_in_image1=, r_in_image2=, thetas=0x1ec6780, thetas2=0x1ec1e40, thetas3=0x1ec1f78, localSearchIterations=0x2af23c8, whichMetric=0x271b018, r_scale=0x27238b8, r_doref=0x2723888,
txfn=0x2740788, whichTransform=0x2723588) at invariantImageSimilarity.cpp:572
#11 0x00007ffff784704b in R_doDotCall () from /axiom2/projects/software/arch/R-versions/R-3.3.1/lib/R/lib/libR.so
#12 0x00007ffff7855136 in do_dotcall () from /axiom2/projects/software/arch/R-versions/R-3.3.1/lib/R/lib/libR.so
#13 0x00007ffff7890610 in Rf_eval () from /axiom2/projects/software/arch/R-versions/R-3.3.1/lib/R/lib/libR.so
#14 0x00007ffff7894bd7 in do_set () from /axiom2/projects/software/arch/R-versions/R-3.3.1/lib/R/lib/libR.so
#15 0x00007ffff78903fa in Rf_eval () from /axiom2/projects/software/arch/R-versions/R-3.3.1/lib/R/lib/libR.so
#16 0x00007ffff7893bf7 in do_begin () from /axiom2/projects/software/arch/R-versions/R-3.3.1/lib/R/lib/libR.so
#17 0x00007ffff78903fa in Rf_eval () from /axiom2/projects/software/arch/R-versions/R-3.3.1/lib/R/lib/libR.so
#18 0x00007ffff7892bc8 in do_if () from /axiom2/projects/software/arch/R-versions/R-3.3.1/lib/R/lib/libR.so
#19 0x00007ffff78903fa in Rf_eval () from /axiom2/projects/software/arch/R-versions/R-3.3.1/lib/R/lib/libR.so
#20 0x00007ffff7893bf7 in do_begin () from /axiom2/projects/software/arch/R-versions/R-3.3.1/lib/R/lib/libR.so
#21 0x00007ffff78903fa in Rf_eval () from /axiom2/projects/software/arch/R-versions/R-3.3.1/lib/R/lib/libR.so
#22 0x00007ffff78916de in Rf_applyClosure () from /axiom2/projects/software/arch/R-versions/R-3.3.1/lib/R/lib/libR.so
#23 0x00007ffff7890727 in Rf_eval () from /axiom2/projects/software/arch/R-versions/R-3.3.1/lib/R/lib/libR.so
#24 0x00007ffff7894bd7 in do_set () from /axiom2/projects/software/arch/R-versions/R-3.3.1/lib/R/lib/libR.so
#25 0x00007ffff78903fa in Rf_eval () from /axiom2/projects/software/arch/R-versions/R-3.3.1/lib/R/lib/libR.so
#26 0x00007ffff78d038f in Rf_ReplIteration () from /axiom2/projects/software/arch/R-versions/R-3.3.1/lib/R/lib/libR.so
#27 0x00007ffff78d0554 in R_ReplConsole () from /axiom2/projects/software/arch/R-versions/R-3.3.1/lib/R/lib/libR.so
#28 0x00007ffff78d1ebb in run_Rmainloop () from /axiom2/projects/software/arch/R-versions/R-3.3.1/lib/R/lib/libR.so
#29 0x00007ffff78d1ed0 in Rf_mainloop () from /axiom2/projects/software/arch/R-versions/R-3.3.1/lib/R/lib/libR.so
#30 0x0000000000400846 in main ()
#31 0x00007ffff71af7ed in __libc_start_main (main=0x400814

, argc=1, ubp_av=0x7fffffffd418, init=, fini=, rtld_fini=, stack_end=0x7fffffffd408) at libc-start.c:226
#32 0x0000000000400759 in _start ()

valgrind

library(ANTsR)
==27293== Invalid read of size 8
==27293== at 0x5750DBD: _wordcopy_fwd_dest_aligned (wordcopy.c:205)
==27293== by 0x574A9DB: __GI_memmove (memmove.c:76)
==27293== by 0x5705672: realpath@@GLIBC_2.3 (canonicalize.c:192)
==27293== by 0xF493C02: itksys::SystemTools::ClassInitialize() (in /axiom2/projects/software/arch/R-versions/R-3.3.1/lib/R/library/ANTsR/libs/ANTsR.so)
==27293== by 0xE6D9B56: _GLOBAL__sub_I_antsImageHeaderInfo.cpp (SystemTools.hxx:71)
==27293== by 0x400F2C5: call_init.part.0 (dl-init.c:85)
==27293== by 0x400F39E: _dl_init (dl-init.c:52)
==27293== by 0x4013A99: dl_open_worker (dl-open.c:549)
==27293== by 0x400F135: _dl_catch_error (dl-error.c:178)
==27293== by 0x40132D9: _dl_open (dl-open.c:639)
==27293== by 0x6C88F25: dlopen_doit (dlopen.c:67)
==27293== by 0x400F135: _dl_catch_error (dl-error.c:178)
==27293== Address 0x7e0cb50 is 96 bytes inside a block of size 99 alloc'd
==27293== at 0x4C2B1C7: operator new(unsigned long) (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==27293== by 0xC306A88: std::string::Rep::S_create(unsigned long, unsigned long, std::allocator const&) (in /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.16)
==27293== by 0xC308494: char* std::string::S_construct<char const*>(char const, char const, std::allocator const&, std::forward_iterator_tag) (in /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.16)
==27293== by 0xC3085E2: std::basic_string<char, std::char_traits, std::allocator >::basic_string(char const, std::allocator const&) (in /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.16)
==27293== by 0xF493BDD: itksys::SystemTools::ClassInitialize() (in /axiom2/projects/software/arch/R-versions/R-3.3.1/lib/R/library/ANTsR/libs/ANTsR.so)
==27293== by 0xE6D9B56: _GLOBAL__sub_I_antsImageHeaderInfo.cpp (SystemTools.hxx:71)
==27293== by 0x400F2C5: call_init.part.0 (dl-init.c:85)
==27293== by 0x400F39E: _dl_init (dl-init.c:52)
==27293== by 0x4013A99: dl_open_worker (dl-open.c:549)
==27293== by 0x400F135: _dl_catch_error (dl-error.c:178)
==27293== by 0x40132D9: _dl_open (dl-open.c:639)
==27293== by 0x6C88F25: dlopen_doit (dlopen.c:67)
==27293==
==27293== Invalid read of size 8
==27293== at 0x5750DBD: _wordcopy_fwd_dest_aligned (wordcopy.c:205)
==27293== by 0x574A9DB: __GI_memmove (memmove.c:76)
==27293== by 0x5705672: realpath@@GLIBC_2.3 (canonicalize.c:192)
==27293== by 0xF493E02: itksys::SystemTools::ClassInitialize() (in /axiom2/projects/software/arch/R-versions/R-3.3.1/lib/R/library/ANTsR/libs/ANTsR.so)
==27293== by 0xE6D9B56: _GLOBAL__sub_I_antsImageHeaderInfo.cpp (SystemTools.hxx:71)
==27293== by 0x400F2C5: call_init.part.0 (dl-init.c:85)
==27293== by 0x400F39E: _dl_init (dl-init.c:52)
==27293== by 0x4013A99: dl_open_worker (dl-open.c:549)
==27293== by 0x400F135: _dl_catch_error (dl-error.c:178)
==27293== by 0x40132D9: _dl_open (dl-open.c:639)
==27293== by 0x6C88F25: dlopen_doit (dlopen.c:67)
==27293== by 0x400F135: dl_catch_error (dl-error.c:178)
==27293== Address 0x7e0ceb8 is 88 bytes inside a block of size 93 alloc'd
==27293== at 0x4C2B1C7: operator new(unsigned long) (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==27293== by 0xC306A88: std::string::Rep::S_create(unsigned long, unsigned long, std::allocator const&) (in /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.16)
==27293== by 0xC308494: char std::string::S_construct<char const*>(char const, char const, std::allocator const&, std::forward_iterator_tag) (in /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.16)
==27293== by 0xC3085E2: std::basic_string<char, std::char_traits, std::allocator >::basic_string(char const, std::allocator const&) (in /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.16)
==27293== by 0xF493DE0: itksys::SystemTools::ClassInitialize() (in /axiom2/projects/software/arch/R-versions/R-3.3.1/lib/R/library/ANTsR/libs/ANTsR.so)
==27293== by 0xE6D9B56: _GLOBAL__sub_I_antsImageHeaderInfo.cpp (SystemTools.hxx:71)
==27293== by 0x400F2C5: call_init.part.0 (dl-init.c:85)
==27293== by 0x400F39E: _dl_init (dl-init.c:52)
==27293== by 0x4013A99: dl_open_worker (dl-open.c:549)
==27293== by 0x400F135: _dl_catch_error (dl-error.c:178)
==27293== by 0x40132D9: _dl_open (dl-open.c:639)
==27293== by 0x6C88F25: dlopen_doit (dlopen.c:67)
==27293==
==27293== Invalid read of size 8
==27293== at 0x5750D67: _wordcopy_fwd_dest_aligned (wordcopy.c:184)
==27293== by 0x574A9DB: __GI_memmove (memmove.c:76)
==27293== by 0x5705672: realpath@@GLIBC_2.3 (canonicalize.c:192)
==27293== by 0xF493E02: itksys::SystemTools::ClassInitialize() (in /axiom2/projects/software/arch/R-versions/R-3.3.1/lib/R/library/ANTsR/libs/ANTsR.so)
==27293== by 0xE6D9B56: _GLOBAL__sub_I_antsImageHeaderInfo.cpp (SystemTools.hxx:71)
==27293== by 0x400F2C5: call_init.part.0 (dl-init.c:85)
==27293== by 0x400F39E: _dl_init (dl-init.c:52)
==27293== by 0x4013A99: dl_open_worker (dl-open.c:549)
==27293== by 0x400F135: _dl_catch_error (dl-error.c:178)
==27293== by 0x40132D9: _dl_open (dl-open.c:639)
==27293== by 0x6C88F25: dlopen_doit (dlopen.c:67)
==27293== by 0x400F135: _dl_catch_error (dl-error.c:178)
==27293== Address 0x7e0dc90 is 48 bytes inside a block of size 54 alloc'd
==27293== at 0x4C2B1C7: operator new(unsigned long) (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==27293== by 0xC306A88: std::string::Rep::S_create(unsigned long, unsigned long, std::allocator const&) (in /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.16)
==27293== by 0xC308494: char std::string::S_construct<char const*>(char const, char const, std::allocator const&, std::forward_iterator_tag) (in /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.16)
==27293== by 0xC3085E2: std::basic_string<char, std::char_traits, std::allocator >::basic_string(char const*, std::allocator const&) (in /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.16)
==27293== by 0xF493DE0: itksys::SystemTools::ClassInitialize() (in /axiom2/projects/software/arch/R-versions/R-3.3.1/lib/R/library/ANTsR/libs/ANTsR.so)
==27293== by 0xE6D9B56: _GLOBAL__sub_I_antsImageHeaderInfo.cpp (SystemTools.hxx:71)
==27293== by 0x400F2C5: call_init.part.0 (dl-init.c:85)
==27293== by 0x400F39E: _dl_init (dl-init.c:52)
==27293== by 0x4013A99: dl_open_worker (dl-open.c:549)
==27293== by 0x400F135: _dl_catch_error (dl-error.c:178)
==27293== by 0x40132D9: _dl_open (dl-open.c:639)
==27293== by 0x6C88F25: dlopen_doit (dlopen.c:67)
==27293==
fi<-antsImageRead( getANTsRData("r16"))
mi<-antsImageRead( getANTsRData("r64"))
mival<-invariantImageSimilarity( fi, mi, c(0,10,20) )
terminate called after throwing an instance of 'Rcpp::not_compatible'
what(): expecting a single value

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@cfhammill
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Hmm, I rebuild Rcpp and ANTsR, to no avail, both were already at the latest version anyway.

I'm getting the following message from devtools::install_github("stnava/ANTsR")

Warning message:
GitHub repo contains submodules, may not function as expected!

But I suspect that message is harmless.

@stnava
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stnava commented Oct 27, 2016

probably harmless.

knowing the location of the segfault would be helpful

std::cout in the invariant...cpp file can help there.

brian

On Thu, Oct 27, 2016 at 4:26 PM, Chris Hammill [email protected]
wrote:

Hmm, I rebuild Rcpp and ANTsR, to no avail, both were already at the
latest version anyway.

I'm getting the following message from devtools::install_github("
stnava/ANTsR")

Warning message:
GitHub repo contains submodules, may not function as expected!

But I suspect that message is harmless.

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@cfhammill
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I replicated the build on ubuntu 16.04 and ran into the same issue. I won't be able to debug the c++ code in the near term, but will try to have a look when I get a chance.

@stnava stnava closed this as completed May 14, 2017
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