[Rcpp-devel] no matching function for call in mzR on Mac afterRcpp 0.11.0 updatee
Kevin Ushey
kevinushey at gmail.com
Thu May 15 06:44:03 CEST 2014
Hi Laurent, Jack,
Can I ask that you take this to bioc-devel? This is not an Rcpp issue,
and you will get more heads looking at the problem.
Thanks,
Kevin
On Wed, May 14, 2014 at 8:41 PM, Jack Howarth
<howarth.mailing.lists at gmail.com> wrote:
> This new failure isn't libc++ dependent as I also see it with
> -stdlib=libstdc++ passed to clang++ on 10.9.
>
>
>
>
> On Wed, May 14, 2014 at 10:03 PM, Jack Howarth
> <howarth.mailing.lists at gmail.com> wrote:
>>
>> This fails differently now on Mac OS X 10.9 against Xcode 5.1.1 clang
>> compilers…
>>
>> $BIN_R --verbose CMD build --no-build-vignettes mzR
>> * checking for file 'mzR/DESCRIPTION' ... OK
>> * preparing 'mzR':
>> * checking DESCRIPTION meta-information ... OK
>> * cleaning src
>> * running 'cleanup'
>> * checking for LF line-endings in source and make files
>> * checking for empty or unneeded directories
>> * building 'mzR_1.11.1.tar.gz'
>>
>> phase test: passed
>> /bin/rm -rf /sw/src/fink.build/root-bioconductor-mzr-r31-1.11.1-1
>> /bin/mkdir -p /sw/src/fink.build/root-bioconductor-mzr-r31-1.11.1-1/sw
>> /bin/mkdir -p /sw/src/fink.build/root-bioconductor-mzr-r31-1.11.1-1/DEBIAN
>> /usr/sbin/chown -R fink-bld:fink-bld
>> /sw/src/fink.build/root-bioconductor-mzr-r31-1.11.1-1
>> sudo -u fink-bld [ENV] sh -c /tmp/fink.L88Ao
>> /tmp/fink.jkQ9d
>> #!/bin/sh -ev
>> BIN_R=/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/bin/R
>>
>> mkdir -p
>> /sw/src/fink.build/root-bioconductor-mzr-r31-1.11.1-1/sw/lib/R/3.1/site-library
>> pushd /sw/src/fink.build/bioconductor-mzr-r31-1.11.1-1/mzR/.. && $BIN_R
>> --verbose CMD install
>> --library=/sw/src/fink.build/root-bioconductor-mzr-r31-1.11.1-1/sw/lib/R/3.1/site-library
>> mzR
>> /sw/src/fink.build/bioconductor-mzr-r31-1.11.1-1
>> /sw/src/fink.build/bioconductor-mzr-r31-1.11.1-1/mzR
>> * installing *source* package 'mzR' ...
>> ** libs
>> rm -f cramp.o ramp_base64.o ramp.o RcppRamp.o RcppRampModule.o
>> rnetCDF.o ./boost/system/src/error_code.o ./boost/regex/src/posix_api.o
>> ./boost/regex/src/fileiter.o ./boost/regex/src/regex_raw_buffer.o
>> ./boost/regex/src/cregex.o ./boost/regex/src/regex_debug.o
>> ./boost/regex/src/instances.o ./boost/regex/src/icu.o
>> ./boost/regex/src/usinstances.o ./boost/regex/src/regex.o
>> ./boost/regex/src/wide_posix_api.o ./boost/regex/src/regex_traits_defaults.o
>> ./boost/regex/src/winstances.o ./boost/regex/src/wc_regex_traits.o
>> ./boost/regex/src/c_regex_traits.o ./boost/regex/src/cpp_regex_traits.o
>> ./boost/regex/src/static_mutex.o ./boost/regex/src/w32_regex_traits.o
>> ./pwiz/data/msdata/Version.o ./pwiz/utility/minimxml/XMLWriter.o
>> ./pwiz/utility/minimxml/SAXParser.o ./boost/iostreams/src/zlib.o
>> ./boost/thread/src/pthread/once.o ./boost/filesystem/src/operations.o
>> ./pwiz/data/common/MemoryIndex.o ./pwiz/data/common/CVTranslator.o
>> ./pwiz/data/common/cv.o ./pwiz/data/common/ParamTypes.o
>> ./pwiz/data/common/BinaryIndexStream.o ./pwiz/data/common/diff_std.o
>> ./pwiz/data/msdata/SpectrumList_MGF.o ./pwiz/data/msdata/DefaultReaderList.o
>> ./pwiz/data/msdata/ChromatogramList_mzML.o ./pwiz/data/msdata/examples.o
>> ./pwiz/data/msdata/Serializer_mzML.o ./pwiz/data/msdata/Serializer_MSn.o
>> ./pwiz/data/msdata/Reader.o ./pwiz/data/msdata/Serializer_MGF.o
>> ./pwiz/data/msdata/Serializer_mzXML.o ./pwiz/data/msdata/SpectrumList_mzML.o
>> ./pwiz/data/msdata/SpectrumList_MSn.o ./pwiz/data/msdata/BinaryDataEncoder.o
>> ./pwiz/data/msdata/Diff.o ./pwiz/data/msdata/MSData.o
>> ./pwiz/data/msdata/References.o ./pwiz/data/msdata/SpectrumList_mzXML.o
>> ./pwiz/data/msdata/IO.o ./pwiz/data/msdata/SpectrumList_BTDX.o
>> ./pwiz/data/msdata/SpectrumInfo.o ./pwiz/data/msdata/RAMPAdapter.o
>> ./pwiz/data/msdata/LegacyAdapter.o ./pwiz/data/msdata/SpectrumIterator.o
>> ./pwiz/data/msdata/MSDataFile.o ./pwiz/data/msdata/SpectrumListCache.o
>> ./pwiz/utility/misc/IntegerSet.o ./pwiz/utility/misc/Base64.o
>> ./pwiz/utility/misc/IterationListener.o ./pwiz/utility/misc/MSIHandler.o
>> ./pwiz/utility/misc/Filesystem.o ./pwiz/utility/misc/TabReader.o
>> ./pwiz/utility/misc/random_access_compressed_ifstream.o
>> ./pwiz/utility/misc/SHA1.o ./pwiz/utility/misc/SHA1Calculator.o
>> ./pwiz/utility/misc/sha1calc.o ./random_access_gzFile.o rampR.o
>> find . -name \*~ -exec rm {} \; ## from cleanup
>> find . -name \*.o -exec rm {} \; ## from cleanup
>> find . -name "#*#" -exec rm {} \; ## from cleanup
>> flag-sort -r g++
>> -I/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/include -DNDEBUG
>> -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG
>> -I/sw/include -I"/sw/lib/R/3.1/site-library/Rcpp/include" -fPIC -g -O3
>> -c cramp.cpp -o cramp.o
>> cramp.cpp:4:1: warning: '/*' within block comment [-Wcomment]
>>
>> /***************************************************************************
>> ^
>> In file included from cramp.cpp:40:
>> ./cramp.h:236:15: warning: destination for this 'memmove' call is a
>> pointer to dynamic class 'rampScanInfo'; vtable pointer will be overwritten
>> [-Wdynamic-class-memaccess]
>> memmove(this,&rhs,sizeof(rhs));
>> ~~~~~~~ ^
>> ./cramp.h:236:15: note: explicitly cast the pointer to silence this
>> warning
>> memmove(this,&rhs,sizeof(rhs));
>> ^
>> (void*)
>> ./cramp.h:283:15: warning: destination for this 'memmove' call is a
>> pointer to dynamic class 'rampRunInfo'; vtable pointer will be overwritten
>> [-Wdynamic-class-memaccess]
>> memmove(this,&rhs,sizeof(rhs));
>> ~~~~~~~ ^
>> ./cramp.h:283:15: note: explicitly cast the pointer to silence this
>> warning
>> memmove(this,&rhs,sizeof(rhs));
>> ^
>> (void*)
>> cramp.cpp:288:95: warning: while loop has empty body [-Wempty-body]
>> while (++m_currentScan <= m_cramp.getLastScan() &&
>> m_cramp.getScanOffset(m_currentScan) <= 0);
>>
>> ^
>> cramp.cpp:288:95: note: put the semicolon on a separate line to silence
>> this warning
>> 4 warnings generated.
>> flag-sort -r g++
>> -I/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/include -DNDEBUG
>> -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG
>> -I/sw/include -I"/sw/lib/R/3.1/site-library/Rcpp/include" -fPIC -g -O3
>> -c ramp_base64.cpp -o ramp_base64.o
>> flag-sort -r g++
>> -I/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/include -DNDEBUG
>> -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG
>> -I/sw/include -I"/sw/lib/R/3.1/site-library/Rcpp/include" -fPIC -g -O3
>> -c ramp.cpp -o ramp.o
>> ramp.cpp:1858:36: warning: expression which evaluates to zero treated as a
>> null pointer constant of type 'const char *' [-Wnon-literal-null-conversion]
>> pEndAttrValue = '\0';
>> ^~~~
>> ramp.cpp:1877:35: warning: expression which evaluates to zero treated as a
>> null pointer constant of type 'const char *' [-Wnon-literal-null-conversion]
>> pEndAttrValue = '\0';
>> ^~~~
>> 2 warnings generated.
>> flag-sort -r g++
>> -I/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/include -DNDEBUG
>> -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG
>> -I/sw/include -I"/sw/lib/R/3.1/site-library/Rcpp/include" -fPIC -g -O3
>> -c RcppRamp.cpp -o RcppRamp.o
>> In file included from RcppRamp.cpp:1:
>> In file included from ./RcppRamp.h:4:
>> ./cramp.h:236:15: warning: destination for this 'memmove' call is a
>> pointer to dynamic class 'rampScanInfo'; vtable pointer will be overwritten
>> [-Wdynamic-class-memaccess]
>> memmove(this,&rhs,sizeof(rhs));
>> ~~~~~~~ ^
>> ./cramp.h:236:15: note: explicitly cast the pointer to silence this
>> warning
>> memmove(this,&rhs,sizeof(rhs));
>> ^
>> (void*)
>> ./cramp.h:283:15: warning: destination for this 'memmove' call is a
>> pointer to dynamic class 'rampRunInfo'; vtable pointer will be overwritten
>> [-Wdynamic-class-memaccess]
>> memmove(this,&rhs,sizeof(rhs));
>> ~~~~~~~ ^
>> ./cramp.h:283:15: note: explicitly cast the pointer to silence this
>> warning
>> memmove(this,&rhs,sizeof(rhs));
>> ^
>> (void*)
>> 2 warnings generated.
>> flag-sort -r g++
>> -I/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/include -DNDEBUG
>> -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG
>> -I/sw/include -I"/sw/lib/R/3.1/site-library/Rcpp/include" -fPIC -g -O3
>> -c RcppRampModule.cpp -o RcppRampModule.o
>> In file included from RcppRampModule.cpp:2:
>> In file included from ./RcppRamp.h:4:
>> ./cramp.h:236:15: warning: destination for this 'memmove' call is a
>> pointer to dynamic class 'rampScanInfo'; vtable pointer will be overwritten
>> [-Wdynamic-class-memaccess]
>> memmove(this,&rhs,sizeof(rhs));
>> ~~~~~~~ ^
>> ./cramp.h:236:15: note: explicitly cast the pointer to silence this
>> warning
>> memmove(this,&rhs,sizeof(rhs));
>> ^
>> (void*)
>> ./cramp.h:283:15: warning: destination for this 'memmove' call is a
>> pointer to dynamic class 'rampRunInfo'; vtable pointer will be overwritten
>> [-Wdynamic-class-memaccess]
>> memmove(this,&rhs,sizeof(rhs));
>> ~~~~~~~ ^
>> ./cramp.h:283:15: note: explicitly cast the pointer to silence this
>> warning
>> memmove(this,&rhs,sizeof(rhs));
>> ^
>> (void*)
>> 2 warnings generated.
>> flag-sort -r gcc -ffor-scope
>> -I/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/include -DNDEBUG
>> -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG
>> -I/sw/include -I"/sw/lib/R/3.1/site-library/Rcpp/include" -fPIC -g -O3
>> -c rnetCDF.c -o rnetCDF.o
>> flag-sort -r g++
>> -I/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/include -DNDEBUG
>> -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG
>> -I/sw/include -I"/sw/lib/R/3.1/site-library/Rcpp/include" -fPIC -g -O3
>> -c boost/system/src/error_code.cpp -o boost/system/src/error_code.o
>> flag-sort -r g++
>> -I/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/include -DNDEBUG
>> -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG
>> -I/sw/include -I"/sw/lib/R/3.1/site-library/Rcpp/include" -fPIC -g -O3
>> -c boost/regex/src/posix_api.cpp -o boost/regex/src/posix_api.o
>> flag-sort -r g++
>> -I/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/include -DNDEBUG
>> -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG
>> -I/sw/include -I"/sw/lib/R/3.1/site-library/Rcpp/include" -fPIC -g -O3
>> -c boost/regex/src/fileiter.cpp -o boost/regex/src/fileiter.o
>> flag-sort -r g++
>> -I/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/include -DNDEBUG
>> -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG
>> -I/sw/include -I"/sw/lib/R/3.1/site-library/Rcpp/include" -fPIC -g -O3
>> -c boost/regex/src/regex_raw_buffer.cpp -o
>> boost/regex/src/regex_raw_buffer.o
>> flag-sort -r g++
>> -I/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/include -DNDEBUG
>> -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG
>> -I/sw/include -I"/sw/lib/R/3.1/site-library/Rcpp/include" -fPIC -g -O3
>> -c boost/regex/src/cregex.cpp -o boost/regex/src/cregex.o
>> flag-sort -r g++
>> -I/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/include -DNDEBUG
>> -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG
>> -I/sw/include -I"/sw/lib/R/3.1/site-library/Rcpp/include" -fPIC -g -O3
>> -c boost/regex/src/regex_debug.cpp -o boost/regex/src/regex_debug.o
>> flag-sort -r g++
>> -I/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/include -DNDEBUG
>> -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG
>> -I/sw/include -I"/sw/lib/R/3.1/site-library/Rcpp/include" -fPIC -g -O3
>> -c boost/regex/src/instances.cpp -o boost/regex/src/instances.o
>> flag-sort -r g++
>> -I/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/include -DNDEBUG
>> -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG
>> -I/sw/include -I"/sw/lib/R/3.1/site-library/Rcpp/include" -fPIC -g -O3
>> -c boost/regex/src/icu.cpp -o boost/regex/src/icu.o
>> flag-sort -r g++
>> -I/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/include -DNDEBUG
>> -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG
>> -I/sw/include -I"/sw/lib/R/3.1/site-library/Rcpp/include" -fPIC -g -O3
>> -c boost/regex/src/usinstances.cpp -o boost/regex/src/usinstances.o
>> flag-sort -r g++
>> -I/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/include -DNDEBUG
>> -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG
>> -I/sw/include -I"/sw/lib/R/3.1/site-library/Rcpp/include" -fPIC -g -O3
>> -c boost/regex/src/regex.cpp -o boost/regex/src/regex.o
>> flag-sort -r g++
>> -I/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/include -DNDEBUG
>> -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG
>> -I/sw/include -I"/sw/lib/R/3.1/site-library/Rcpp/include" -fPIC -g -O3
>> -c boost/regex/src/wide_posix_api.cpp -o boost/regex/src/wide_posix_api.o
>> flag-sort -r g++
>> -I/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/include -DNDEBUG
>> -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG
>> -I/sw/include -I"/sw/lib/R/3.1/site-library/Rcpp/include" -fPIC -g -O3
>> -c boost/regex/src/regex_traits_defaults.cpp -o
>> boost/regex/src/regex_traits_defaults.o
>> flag-sort -r g++
>> -I/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/include -DNDEBUG
>> -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG
>> -I/sw/include -I"/sw/lib/R/3.1/site-library/Rcpp/include" -fPIC -g -O3
>> -c boost/regex/src/winstances.cpp -o boost/regex/src/winstances.o
>> flag-sort -r g++
>> -I/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/include -DNDEBUG
>> -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG
>> -I/sw/include -I"/sw/lib/R/3.1/site-library/Rcpp/include" -fPIC -g -O3
>> -c boost/regex/src/wc_regex_traits.cpp -o boost/regex/src/wc_regex_traits.o
>> flag-sort -r g++
>> -I/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/include -DNDEBUG
>> -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG
>> -I/sw/include -I"/sw/lib/R/3.1/site-library/Rcpp/include" -fPIC -g -O3
>> -c boost/regex/src/c_regex_traits.cpp -o boost/regex/src/c_regex_traits.o
>> flag-sort -r g++
>> -I/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/include -DNDEBUG
>> -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG
>> -I/sw/include -I"/sw/lib/R/3.1/site-library/Rcpp/include" -fPIC -g -O3
>> -c boost/regex/src/cpp_regex_traits.cpp -o
>> boost/regex/src/cpp_regex_traits.o
>> flag-sort -r g++
>> -I/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/include -DNDEBUG
>> -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG
>> -I/sw/include -I"/sw/lib/R/3.1/site-library/Rcpp/include" -fPIC -g -O3
>> -c boost/regex/src/static_mutex.cpp -o boost/regex/src/static_mutex.o
>> flag-sort -r g++
>> -I/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/include -DNDEBUG
>> -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG
>> -I/sw/include -I"/sw/lib/R/3.1/site-library/Rcpp/include" -fPIC -g -O3
>> -c boost/regex/src/w32_regex_traits.cpp -o
>> boost/regex/src/w32_regex_traits.o
>> flag-sort -r g++
>> -I/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/include -DNDEBUG
>> -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG
>> -I/sw/include -I"/sw/lib/R/3.1/site-library/Rcpp/include" -fPIC -g -O3
>> -c pwiz/data/msdata/Version.cpp -o pwiz/data/msdata/Version.o
>> flag-sort -r g++
>> -I/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/include -DNDEBUG
>> -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG
>> -I/sw/include -I"/sw/lib/R/3.1/site-library/Rcpp/include" -fPIC -g -O3
>> -c pwiz/utility/minimxml/XMLWriter.cpp -o pwiz/utility/minimxml/XMLWriter.o
>> In file included from pwiz/utility/minimxml/XMLWriter.cpp:25:
>> In file included from pwiz/utility/minimxml/XMLWriter.hpp:29:
>> In file included from ./pwiz/utility/misc/optimized_lexical_cast.hpp:36:
>> In file included from ./pwiz/utility/misc/Singleton.hpp:26:
>> ./boost_aux/boost/utility/singleton.hpp:83:11: error: visibility does not
>> match previous declaration
>> class BOOST_UTILITY_SINGLETON_API
>> singleton<Derived,DisposalSlot,SubsystemTag>::instance_proxy
>> ^
>> ./boost_aux/boost/utility/singleton.hpp:26:58: note: expanded from macro
>> 'BOOST_UTILITY_SINGLETON_API'
>> # define BOOST_UTILITY_SINGLETON_API __attribute__
>> ((visibility("default")))
>> ^
>> ./boost_aux/boost/utility/singleton.hpp:27:18: note: previous attribute is
>> here
>> # pragma GCC visibility push(hidden)
>> ^
>> ./boost_aux/boost/utility/singleton.hpp:154:11: error: visibility does not
>> match previous declaration
>> class BOOST_UTILITY_SINGLETON_API
>> singleton<Derived,DisposalSlot,SubsystemTag>::lease
>> ^
>> ./boost_aux/boost/utility/singleton.hpp:26:58: note: expanded from macro
>> 'BOOST_UTILITY_SINGLETON_API'
>> # define BOOST_UTILITY_SINGLETON_API __attribute__
>> ((visibility("default")))
>> ^
>> ./boost_aux/boost/utility/singleton.hpp:27:18: note: previous attribute is
>> here
>> # pragma GCC visibility push(hidden)
>> ^
>> 2 errors generated.
>> make: *** [pwiz/utility/minimxml/XMLWriter.o] Error 1
>> ERROR: compilation failed for package 'mzR'
>> * removing
>> '/sw/src/fink.build/root-bioconductor-mzr-r31-1.11.1-1/sw/lib/R/3.1/site-library/mzR'
>> ### execution of /tmp/fink.jkQ9d failed, exit code 1
>> ### execution of /tmp/fink.L88Ao failed, exit code 1
>>
>>
>> Also, once this error is fixed, you might also consider adding the missing
>> (void*) casts on the 'this' parameter to the memmove calls as recommended by
>> the warnings from the clang++ compiler. It will remove some noise off the
>> build.
>> Jack
>>
>>
>> On Wed, May 14, 2014 at 6:11 PM, Laurent Gatto <lg390 at cam.ac.uk> wrote:
>>>
>>>
>>> Updated to boost 1_54 and latest pwiz - see
>>> https://github.com/sneumann/mzR/tree/test for details.
>>>
>>> [...]
>>> g++ -shared -L/usr/local/lib -o mzR.so cramp.o ramp_base64.o ramp.o
>>> RcppRamp.o RcppRampModule.o rnetCDF.o ./boost/system/src/error_code.o
>>> ./boost/regex/src/posix_api.o ./boost/regex/src/fileiter.o
>>> ./boost/regex/src/regex_raw_buffer.o ./boost/regex/src/cregex.o
>>> ./boost/regex/src/regex_debug.o ./boost/regex/src/instances.o
>>> ./boost/regex/src/icu.o ./boost/regex/src/usinstances.o
>>> ./boost/regex/src/regex.o ./boost/regex/src/wide_posix_api.o
>>> ./boost/regex/src/regex_traits_defaults.o ./boost/regex/src/winstances.o
>>> ./boost/regex/src/wc_regex_traits.o ./boost/regex/src/c_regex_traits.o
>>> ./boost/regex/src/cpp_regex_traits.o ./boost/regex/src/static_mutex.o
>>> ./boost/regex/src/w32_regex_traits.o ./pwiz/data/msdata/Version.o
>>> ./pwiz/utility/minimxml/XMLWriter.o ./pwiz/utility/minimxml/SAXParser.o
>>> ./boost/iostreams/src/zlib.o ./boost/thread/src/pthread/once.o
>>> ./boost/filesystem/src/operations.o ./pwiz/data/common/MemoryIndex.o
>>> ./pwiz/data/common/CVTranslator.o ./pwiz/data/common/cv.o
>>> ./pwiz/data/common/ParamTypes.o ./pwiz/data/common/BinaryIndexStream.o
>>> ./pwiz/data/common/diff_std.o ./pwiz/data/msdata/SpectrumList_MGF.o
>>> ./pwiz/data/msdata/DefaultReaderList.o
>>> ./pwiz/data/msdata/ChromatogramList_mzML.o ./pwiz/data/msdata/examples.o
>>> ./pwiz/data/msdata/Serializer_mzML.o ./pwiz/data/msdata/Serializer_MSn.o
>>> ./pwiz/data/msdata/Reader.o ./pwiz/data/msdata/Serializer_MGF.o
>>> ./pwiz/data/msdata/Serializer_mzXML.o ./pwiz/data/msdata/SpectrumList_mzML.o
>>> ./pwiz/data/msdata/SpectrumList_MSn.o ./pwiz/data/msdata/BinaryDataEncoder.o
>>> ./pwiz/data/msdata/Diff.o ./pwiz/data/msdata/MSData.o
>>> ./pwiz/data/msdata/References.o ./pwiz/data/msdata/SpectrumList_mzXML.o
>>> ./pwiz/data/msdata/IO.o ./pwiz/data/msdata/SpectrumList_BTDX.o
>>> ./pwiz/data/msdata/SpectrumInfo.o ./pwiz/data/msdata/RAMPAdapter.o
>>> ./pwiz/data/msdata/LegacyAdapter.o ./pwiz/data/msdata/SpectrumIterator.o
>>> ./pwiz/data/msdata/MSDataFile.o ./pwiz/data/msdata/SpectrumListCache.o
>>> ./pwiz/utility/misc/IntegerSet.o ./pwiz/utility/misc/Base64.o
>>> ./pwiz/utility/misc/IterationListener.o ./pwiz/utility/misc/MSIHandler.o
>>> ./pwiz/utility/misc/Filesystem.o ./pwiz/utility/misc/TabReader.o
>>> ./pwiz/utility/misc/random_access_compressed_ifstream.o
>>> ./pwiz/utility/misc/SHA1.o ./pwiz/utility/misc/SHA1Calculator.o
>>> ./pwiz/utility/misc/sha1calc.o ./random_access_gzFile.o rampR.o -lpthread
>>> -lnetcdf -lhdf5 -lz -L/usr/local/lib/R/lib -lR
>>> /bin/bash: line 2: nc-config: command not found
>>> make[1]: Leaving directory
>>> `/home/lgatto/dev/00_github/mzR.Rcheck/00_pkg_src/mzR/src'
>>> make[1]: Entering directory
>>> `/home/lgatto/dev/00_github/mzR.Rcheck/00_pkg_src/mzR/src'
>>> make[1]: Leaving directory
>>> `/home/lgatto/dev/00_github/mzR.Rcheck/00_pkg_src/mzR/src'
>>> installing to /home/lgatto/dev/00_github/mzR.Rcheck/mzR/libs
>>> ** R
>>> ** inst
>>> ** preparing package for lazy loading
>>> Creating a generic function for ‘close’ from package ‘base’ in package
>>> ‘mzR’
>>> ** help
>>> *** installing help indices
>>> ** building package indices
>>> ** installing vignettes
>>> ** testing if installed package can be loaded
>>> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>>> unable to load shared object
>>> '/home/lgatto/dev/00_github/mzR.Rcheck/mzR/libs/mzR.so':
>>> /home/lgatto/dev/00_github/mzR.Rcheck/mzR/libs/mzR.so: undefined
>>> symbol: _ZTIN5boost6detail16thread_data_baseE
>>> Error: loading failed
>>> Execution halted
>>> ERROR: loading failed
>>> * removing ‘/home/lgatto/dev/00_github/mzR.Rcheck/mzR’
>>>
>>> with
>>>
>>> echo _ZTIN5boost6detail16thread_data_baseE | c++filt
>>> typeinfo for boost::detail::thread_data_base
>>>
>>> Any suggestions welcome.
>>>
>>> Laurent
>>>
>>>
>>> On 14 May 2014 09:07, Laurent Gatto <lg390 at cam.ac.uk> wrote:
>>>
>>> > We hope to be able to provide a fix soon - will get back to you later
>>> > today. Apologies for the inconvenience.
>>> >
>>> > Laurent
>>> >
>>> >
>>> > On 14 May 2014 05:49, Kevin Ushey <kevinushey at gmail.com> wrote:
>>> >
>>> >> Hi Jack,
>>> >>
>>> >> I've already brought this up with the package maintainer. It's because
>>> >> they bundle an old, broken version of boost. I asked them to fix it; I
>>> >> guess they haven't (the BioC build reports also show it failing on
>>> >> Mavericks) I've appended a copy of my e-mail at the end of this just
>>> >> so you know what's up (and maybe others having problems will stumble
>>> >> upon it).
>>> >>
>>> >> A local fix would involve removing the (broken, illegal) forward
>>> >> declarations.
>>> >>
>>> >> The error you saw before, re reference classes, was something separate
>>> >> -- that was indeed our bug, and is fixed in the current version of
>>> >> Rcpp on CRAN.
>>> >>
>>> >> Thanks,
>>> >> Kevin
>>> >>
>>> >> ---
>>> >>
>>> >> Hi Bernd, Nicolas,
>>> >>
>>> >> I'm unable to install mzR from source. Here's the script I use:
>>> >>
>>> >> #!/usr/bin/env sh
>>> >>
>>> >> cd ~
>>> >> mkdir .mzR
>>> >> cd .mzR
>>> >> wget
>>> >> http://www.bioconductor.org/packages/devel/bioc/src/contrib/mzR_1.9.8.tar.gz
>>> >> R CMD INSTALL mzR_1.9.8.tar.gz
>>> >>
>>> >> This gives me the same error as Nicolas sees:
>>> >>
>>> >> In file included from pwiz/data/msdata/DefaultReaderList.cpp:40:
>>> >>
>>> >> In file included from ./boost/regex.hpp:31:
>>> >> In file included from ./boost/regex/v4/regex.hpp:67:
>>> >> ./boost/regex/v4/basic_regex.hpp:149:9: error: too few template
>>> >> arguments for class
>>> >> template 'vector'
>>> >> std::vector<name> m_sub_names;
>>> >> ^
>>> >> ./boost/detail/container_fwd.hpp:82:47: note: template is declared
>>> >> here
>>> >> template <class T, class Allocator> class vector;
>>> >> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^
>>> >>
>>> >> This is actually a case of boost doing something it shouldn't -- it's
>>> >> trying to forward-declare std::vector, but one cannot assume the
>>> >> template structure of a vector is of <class T, class Allocator> -- in
>>> >> particular this breaks on clang with libc++. See e.g.
>>> >>
>>> >> http://stackoverflow.com/questions/307343/forward-declare-an-stl-container
>>> >>
>>> >> One can work around this by forcing the following Makevars flags:
>>> >>
>>> >> PKG_CXXFLAGS=-std=gnu++11 -stdlib=libstdc++
>>> >>
>>> >> However, this will only work if both Rcpp and mzR are built with the
>>> >> same flags, and using libstdc++ kind of defeats the purpose of using
>>> >> clang...
>>> >>
>>> >> I'm sure you'll get some mail from Dan Tenenbaum when he tries to
>>> >> build the package on the new Mavericks machines, so I think you will
>>> >> have to either update the version of boost packaged with mzR, or fix
>>> >> the forward declarations that it tries to use.
>>> >>
>>> >> Cheers,
>>> >> Kevin
>>> >>
>>> >> On Tue, May 13, 2014 at 8:52 PM, Jack Howarth
>>> >> <howarth.mailing.lists at gmail.com> wrote:
>>> >>> After updating the bioconductor packages to the Bioc 2.14 release, I
>>> >>> ran in
>>> >>> to this failure on Mac OS X 10.9 with the clang compilers from Xcode
>>> >>> 5.1.1.
>>> >>> Interestingly, this failure doesn't occur on Mac OS X 10.8 with the
>>> >>> clang
>>> >>> compilers from Xcode 5.1.1 which suggests it somehow libc++ related.
>>> >>> The
>>> >>> error below is suppressed on 10.9 f I append -stdlib=libstdc++ to the
>>> >>> compile line so it is definitely libc++ specific.
>>> >>> Jack
>>> >>> ps The error I see in mzR using Rcpp 0.11.1 is…
>>> >>>
>>> >>> clang++
>>> >>> -I/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/include
>>> >>> -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB
>>> >>> -D_NODEBUG -I/sw/include -I"/sw/lib/R/3.1/site-library/Rcpp/include"
>>> >>> -fPIC
>>> >>> -g -O3 -c boost/regex/src/posix_api.cpp -o
>>> >>> boost/regex/src/posix_api.o
>>> >>> In file included from boost/regex/src/posix_api.cpp:22:
>>> >>> In file included from ./boost/regex.hpp:31:
>>> >>> In file included from ./boost/regex/v4/regex.hpp:67:
>>> >>> ./boost/regex/v4/basic_regex.hpp:149:9: error: too few template
>>> >>> arguments
>>> >>> for class template 'vector'
>>> >>> std::vector<name> m_sub_names;
>>> >>> ^
>>> >>> ./boost/detail/container_fwd.hpp:82:47: note: template is declared
>>> >>> here
>>> >>> template <class T, class Allocator> class vector;
>>> >>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^
>>> >>> In file included from boost/regex/src/posix_api.cpp:22:
>>> >>> In file included from ./boost/regex.hpp:31:
>>> >>> In file included from ./boost/regex/v4/regex.hpp:67:
>>> >>> ./boost/regex/v4/basic_regex.hpp:131:21: error: too few template
>>> >>> arguments
>>> >>> for class template 'vector'
>>> >>> typename std::vector<name>::const_iterator pos =
>>> >>> std::lower_bound(m_sub_names.begin(), m_sub_names.end(), t);
>>> >>> ^
>>> >>> ./boost/detail/container_fwd.hpp:82:47: note: template is declared
>>> >>> here
>>> >>> template <class T, class Allocator> class vector;
>>> >>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^
>>> >>> In file included from boost/regex/src/posix_api.cpp:22:
>>> >>> In file included from ./boost/regex.hpp:31:
>>> >>> In file included from ./boost/regex/v4/regex.hpp:67:
>>> >>> ./boost/regex/v4/basic_regex.hpp:131:35: error: expected a qualified
>>> >>> name
>>> >>> after 'typename'
>>> >>> typename std::vector<name>::const_iterator pos =
>>> >>> std::lower_bound(m_sub_names.begin(), m_sub_names.end(), t);
>>> >>> ^
>>> >>> ./boost/regex/v4/basic_regex.hpp:131:35: error: unknown type name
>>> >>> 'const_iterator'
>>> >>> ./boost/regex/v4/basic_regex.hpp:141:21: error: too few template
>>> >>> arguments
>>> >>> for class template 'vector'
>>> >>> typename std::vector<name>::const_iterator pos =
>>> >>> std::lower_bound(m_sub_names.begin(), m_sub_names.end(), t);
>>> >>> ^
>>> >>> ./boost/detail/container_fwd.hpp:82:47: note: template is declared
>>> >>> here
>>> >>> template <class T, class Allocator> class vector;
>>> >>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^
>>> >>> In file included from boost/regex/src/posix_api.cpp:22:
>>> >>> In file included from ./boost/regex.hpp:31:
>>> >>> In file included from ./boost/regex/v4/regex.hpp:67:
>>> >>> ./boost/regex/v4/basic_regex.hpp:141:35: error: expected a qualified
>>> >>> name
>>> >>> after 'typename'
>>> >>> typename std::vector<name>::const_iterator pos =
>>> >>> std::lower_bound(m_sub_names.begin(), m_sub_names.end(), t);
>>> >>> ^
>>> >>> ./boost/regex/v4/basic_regex.hpp:141:35: error: unknown type name
>>> >>> 'const_iterator'
>>> >>> ./boost/regex/v4/basic_regex.hpp:163:12: error: too few template
>>> >>> arguments
>>> >>> for class template 'vector'
>>> >>> std::vector<Other> v;
>>> >>> ^
>>> >>> ./boost/detail/container_fwd.hpp:82:47: note: template is declared
>>> >>> here
>>> >>> template <class T, class Allocator> class vector;
>>> >>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^
>>> >>> In file included from boost/regex/src/posix_api.cpp:22:
>>> >>> In file included from ./boost/regex.hpp:31:
>>> >>> In file included from ./boost/regex/v4/regex.hpp:67:
>>> >>> ./boost/regex/v4/basic_regex.hpp:228:9: error: too few template
>>> >>> arguments
>>> >>> for class template 'vector'
>>> >>> std::vector<
>>> >>> ^
>>> >>> ./boost/detail/container_fwd.hpp:82:47: note: template is declared
>>> >>> here
>>> >>> template <class T, class Allocator> class vector;
>>> >>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^
>>> >>> In file included from boost/regex/src/posix_api.cpp:22:
>>> >>> In file included from ./boost/regex.hpp:31:
>>> >>> In file included from ./boost/regex/v4/regex.hpp:67:
>>> >>> ./boost/regex/v4/basic_regex.hpp:269:9: error: too few template
>>> >>> arguments
>>> >>> for class template 'basic_string'
>>> >>> std::basic_string<charT> BOOST_REGEX_CALL str()const
>>> >>> ^
>>> >>> ./boost/detail/container_fwd.hpp:63:65: note: template is declared
>>> >>> here
>>> >>> template <class charT, class traits, class Allocator> class
>>> >>> basic_string;
>>> >>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^
>>> >>> In file included from boost/regex/src/posix_api.cpp:22:
>>> >>> In file included from ./boost/regex.hpp:31:
>>> >>> In file included from ./boost/regex/v4/regex.hpp:67:
>>> >>> ./boost/regex/v4/basic_regex.hpp:271:12: error: too few template
>>> >>> arguments
>>> >>> for class template 'basic_string'
>>> >>> std::basic_string<charT> result;
>>> >>> ^
>>> >>> ./boost/detail/container_fwd.hpp:63:65: note: template is declared
>>> >>> here
>>> >>> template <class charT, class traits, class Allocator> class
>>> >>> basic_string;
>>> >>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^
>>> >>> In file included from boost/regex/src/posix_api.cpp:22:
>>> >>> In file included from ./boost/regex.hpp:31:
>>> >>> In file included from ./boost/regex/v4/regex.hpp:67:
>>> >>> ./boost/regex/v4/basic_regex.hpp:273:24: error: too few template
>>> >>> arguments
>>> >>> for class template 'basic_string'
>>> >>> result = std::basic_string<charT>(this->m_expression,
>>> >>> this->m_expression_len);
>>> >>> ^
>>> >>> ./boost/detail/container_fwd.hpp:63:65: note: template is declared
>>> >>> here
>>> >>> template <class charT, class traits, class Allocator> class
>>> >>> basic_string;
>>> >>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^
>>> >>> In file included from boost/regex/src/posix_api.cpp:22:
>>> >>> In file included from ./boost/regex.hpp:31:
>>> >>> In file included from ./boost/regex/v4/regex.hpp:67:
>>> >>> ./boost/regex/v4/basic_regex.hpp:285:68: error: implicit
>>> >>> instantiation of
>>> >>> undefined template 'std::pair<unsigned long, unsigned long>'
>>> >>> std::pair<const_iterator, const_iterator> p(expression() +
>>> >>> pi.first,
>>> >>> expression() + pi.second);
>>> >>> ^
>>> >>> ./boost/detail/container_fwd.hpp:92:42: note: template is declared
>>> >>> here
>>> >>> template <class T1, class T2> struct pair;
>>> >>> ^
>>> >>> In file included from boost/regex/src/posix_api.cpp:22:
>>> >>> In file included from ./boost/regex.hpp:31:
>>> >>> In file included from ./boost/regex/v4/regex.hpp:67:
>>> >>> ./boost/regex/v4/basic_regex.hpp:527:9: error: too few template
>>> >>> arguments
>>> >>> for class template 'basic_string'
>>> >>> std::basic_string<charT> BOOST_REGEX_CALL str()const
>>> >>> ^
>>> >>> ./boost/detail/container_fwd.hpp:63:65: note: template is declared
>>> >>> here
>>> >>> template <class charT, class traits, class Allocator> class
>>> >>> basic_string;
>>> >>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^
>>> >>> In file included from boost/regex/src/posix_api.cpp:22:
>>> >>> In file included from ./boost/regex.hpp:31:
>>> >>> In file included from ./boost/regex/v4/regex.hpp:67:
>>> >>> ./boost/regex/v4/basic_regex.hpp:529:52: error: too few template
>>> >>> arguments
>>> >>> for class template 'basic_string'
>>> >>> return m_pimpl.get() ? m_pimpl->str() :
>>> >>> std::basic_string<charT>();
>>> >>> ^
>>> >>> ./boost/detail/container_fwd.hpp:63:65: note: template is declared
>>> >>> here
>>> >>> template <class charT, class traits, class Allocator> class
>>> >>> basic_string;
>>> >>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^
>>> >>> In file included from boost/regex/src/posix_api.cpp:22:
>>> >>> In file included from ./boost/regex.hpp:31:
>>> >>> In file included from ./boost/regex/v4/regex.hpp:70:
>>> >>> ./boost/regex/v4/basic_regex_creator.hpp:140:26: error: too few
>>> >>> template
>>> >>> arguments for class template 'vector'
>>> >>> typedef typename std::vector<digraph_type>::const_iterator
>>> >>> list_iterator;
>>> >>> ^
>>> >>> ./boost/detail/container_fwd.hpp:82:47: note: template is declared
>>> >>> here
>>> >>> template <class T, class Allocator> class vector;
>>> >>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^
>>> >>> In file included from boost/regex/src/posix_api.cpp:22:
>>> >>> In file included from ./boost/regex.hpp:31:
>>> >>> In file included from ./boost/regex/v4/regex.hpp:70:
>>> >>> ./boost/regex/v4/basic_regex_creator.hpp:140:48: error: expected a
>>> >>> qualified
>>> >>> name after 'typename'
>>> >>> typedef typename std::vector<digraph_type>::const_iterator
>>> >>> list_iterator;
>>> >>> ^
>>> >>> ./boost/regex/v4/basic_regex_creator.hpp:140:62: error: expected ';'
>>> >>> at end
>>> >>> of declaration list
>>> >>> typedef typename std::vector<digraph_type>::const_iterator
>>> >>> list_iterator;
>>> >>> ^
>>> >>> ;
>>> >>> ./boost/regex/v4/basic_regex_creator.hpp:141:4: error: unknown type
>>> >>> name
>>> >>> 'list_iterator'
>>> >>> list_iterator singles_begin()const
>>> >>> ^
>>> >>> fatal error: too many errors emitted, stopping now [-ferror-limit=]
>>> >>> 20 errors generated.
>>> >>>
>>> >>>
>>> >>> _______________________________________________
>>> >>> 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
>>> >> _______________________________________________
>>> >> 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
>>> >
>>> > _______________________________________________
>>> > 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
>>>
>>
>
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