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mzR 1.3.6 compilation error (R 2.15.0 / gcc 4.7.0)

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May 11th, 2012
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  1. > biocLite("mzR")
  2. BioC_mirror: http://bioconductor.org
  3. Using R version 2.15, BiocInstaller version 1.5.7.
  4. Installing package(s) 'mzR'
  5. trying URL 'http://bioconductor.org/packages/2.11/bioc/src/contrib/mzR_1.3.6.tar.gz'
  6. Content type 'application/x-gzip' length 4887384 bytes (4.7 Mb)
  7. opened URL
  8. ==================================================
  9. downloaded 4.7 Mb
  10.  
  11. * installing *source* package ‘mzR’ ...
  12. ** libs
  13. 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
  14. g++ -I/opt/R/R-2.15.0/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/opt/R/R-2.15.0/library/Rcpp/include" -fpic -g -O2 -c cramp.cpp -o cramp.o
  15. g++ -I/opt/R/R-2.15.0/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/opt/R/R-2.15.0/library/Rcpp/include" -fpic -g -O2 -c ramp_base64.cpp -o ramp_base64.o
  16. g++ -I/opt/R/R-2.15.0/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/opt/R/R-2.15.0/library/Rcpp/include" -fpic -g -O2 -c ramp.cpp -o ramp.o
  17. g++ -I/opt/R/R-2.15.0/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/opt/R/R-2.15.0/library/Rcpp/include" -fpic -g -O2 -c RcppRamp.cpp -o RcppRamp.o
  18. g++ -I/opt/R/R-2.15.0/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/opt/R/R-2.15.0/library/Rcpp/include" -fpic -g -O2 -c RcppRampModule.cpp -o RcppRampModule.o
  19. gcc -std=gnu99 -I/opt/R/R-2.15.0/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/opt/R/R-2.15.0/library/Rcpp/include" -fpic -g -O2 -c rnetCDF.c -o rnetCDF.o
  20. g++ -I/opt/R/R-2.15.0/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/opt/R/R-2.15.0/library/Rcpp/include" -fpic -g -O2 -c boost/system/src/error_code.cpp -o boost/system/src/error_code.o
  21. g++ -I/opt/R/R-2.15.0/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/opt/R/R-2.15.0/library/Rcpp/include" -fpic -g -O2 -c boost/regex/src/posix_api.cpp -o boost/regex/src/posix_api.o
  22. g++ -I/opt/R/R-2.15.0/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/opt/R/R-2.15.0/library/Rcpp/include" -fpic -g -O2 -c boost/regex/src/fileiter.cpp -o boost/regex/src/fileiter.o
  23. g++ -I/opt/R/R-2.15.0/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/opt/R/R-2.15.0/library/Rcpp/include" -fpic -g -O2 -c boost/regex/src/regex_raw_buffer.cpp -o boost/regex/src/regex_raw_buffer.o
  24. g++ -I/opt/R/R-2.15.0/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/opt/R/R-2.15.0/library/Rcpp/include" -fpic -g -O2 -c boost/regex/src/cregex.cpp -o boost/regex/src/cregex.o
  25. g++ -I/opt/R/R-2.15.0/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/opt/R/R-2.15.0/library/Rcpp/include" -fpic -g -O2 -c boost/regex/src/regex_debug.cpp -o boost/regex/src/regex_debug.o
  26. g++ -I/opt/R/R-2.15.0/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/opt/R/R-2.15.0/library/Rcpp/include" -fpic -g -O2 -c boost/regex/src/instances.cpp -o boost/regex/src/instances.o
  27. g++ -I/opt/R/R-2.15.0/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/opt/R/R-2.15.0/library/Rcpp/include" -fpic -g -O2 -c boost/regex/src/icu.cpp -o boost/regex/src/icu.o
  28. g++ -I/opt/R/R-2.15.0/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/opt/R/R-2.15.0/library/Rcpp/include" -fpic -g -O2 -c boost/regex/src/usinstances.cpp -o boost/regex/src/usinstances.o
  29. g++ -I/opt/R/R-2.15.0/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/opt/R/R-2.15.0/library/Rcpp/include" -fpic -g -O2 -c boost/regex/src/regex.cpp -o boost/regex/src/regex.o
  30. g++ -I/opt/R/R-2.15.0/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/opt/R/R-2.15.0/library/Rcpp/include" -fpic -g -O2 -c boost/regex/src/wide_posix_api.cpp -o boost/regex/src/wide_posix_api.o
  31. g++ -I/opt/R/R-2.15.0/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/opt/R/R-2.15.0/library/Rcpp/include" -fpic -g -O2 -c boost/regex/src/regex_traits_defaults.cpp -o boost/regex/src/regex_traits_defaults.o
  32. g++ -I/opt/R/R-2.15.0/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/opt/R/R-2.15.0/library/Rcpp/include" -fpic -g -O2 -c boost/regex/src/winstances.cpp -o boost/regex/src/winstances.o
  33. g++ -I/opt/R/R-2.15.0/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/opt/R/R-2.15.0/library/Rcpp/include" -fpic -g -O2 -c boost/regex/src/wc_regex_traits.cpp -o boost/regex/src/wc_regex_traits.o
  34. g++ -I/opt/R/R-2.15.0/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/opt/R/R-2.15.0/library/Rcpp/include" -fpic -g -O2 -c boost/regex/src/c_regex_traits.cpp -o boost/regex/src/c_regex_traits.o
  35. g++ -I/opt/R/R-2.15.0/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/opt/R/R-2.15.0/library/Rcpp/include" -fpic -g -O2 -c boost/regex/src/cpp_regex_traits.cpp -o boost/regex/src/cpp_regex_traits.o
  36. g++ -I/opt/R/R-2.15.0/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/opt/R/R-2.15.0/library/Rcpp/include" -fpic -g -O2 -c boost/regex/src/static_mutex.cpp -o boost/regex/src/static_mutex.o
  37. g++ -I/opt/R/R-2.15.0/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/opt/R/R-2.15.0/library/Rcpp/include" -fpic -g -O2 -c boost/regex/src/w32_regex_traits.cpp -o boost/regex/src/w32_regex_traits.o
  38. g++ -I/opt/R/R-2.15.0/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/opt/R/R-2.15.0/library/Rcpp/include" -fpic -g -O2 -c pwiz/data/msdata/Version.cpp -o pwiz/data/msdata/Version.o
  39. g++ -I/opt/R/R-2.15.0/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/opt/R/R-2.15.0/library/Rcpp/include" -fpic -g -O2 -c pwiz/utility/minimxml/XMLWriter.cpp -o pwiz/utility/minimxml/XMLWriter.o
  40. g++ -I/opt/R/R-2.15.0/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/opt/R/R-2.15.0/library/Rcpp/include" -fpic -g -O2 -c pwiz/utility/minimxml/SAXParser.cpp -o pwiz/utility/minimxml/SAXParser.o
  41. g++ -I/opt/R/R-2.15.0/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/opt/R/R-2.15.0/library/Rcpp/include" -fpic -g -O2 -c boost/iostreams/src/zlib.cpp -o boost/iostreams/src/zlib.o
  42. g++ -I/opt/R/R-2.15.0/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/opt/R/R-2.15.0/library/Rcpp/include" -fpic -g -O2 -c boost/thread/src/pthread/once.cpp -o boost/thread/src/pthread/once.o
  43. In file included from ./boost/thread/detail/platform.hpp:17:0,
  44. from ./boost/thread/once.hpp:12,
  45. from boost/thread/src/pthread/once.cpp:7:
  46. ./boost/config/requires_threads.hpp:29:4: error: #error "Threading support unavaliable: it has been explicitly disabled with BOOST_DISABLE_THREADS"
  47. In file included from ./boost/thread/once.hpp:12:0,
  48. from boost/thread/src/pthread/once.cpp:7:
  49. ./boost/thread/detail/platform.hpp:67:9: error: #error "Sorry, no boost threads are available for this platform."
  50. In file included from boost/thread/src/pthread/once.cpp:7:0:
  51. ./boost/thread/once.hpp:18:2: error: #error "Boost threads unavailable on this platform"
  52. In file included from boost/thread/src/pthread/once.cpp:7:0:
  53. ./boost/thread/once.hpp:25:42: error: variable or field ‘call_once’ declared void
  54. ./boost/thread/once.hpp:25:34: error: ‘func’ was not declared in this scope
  55. ./boost/thread/once.hpp:25:42: error: ‘once_flag’ was not declared in this scope
  56. ./boost/thread/once.hpp:25:53: error: ‘flag’ was not declared in this scope
  57. boost/thread/src/pthread/once.cpp:16:9: error: ‘BOOST_THREAD_DECL’ does not name a type
  58. boost/thread/src/pthread/once.cpp:17:9: error: ‘BOOST_THREAD_DECL’ does not name a type
  59. boost/thread/src/pthread/once.cpp:18:9: error: ‘BOOST_THREAD_DECL’ does not name a type
  60. boost/thread/src/pthread/once.cpp:37:9: error: ‘uintmax_t’ in namespace ‘boost’ does not name a type
  61. make: *** [boost/thread/src/pthread/once.o] Error 1
  62. ERROR: compilation failed for package ‘mzR’
  63. * removing ‘/opt/R/R-lib-dev/mzR’
  64.  
  65. The downloaded source packages are in
  66. ‘/tmp/RtmpuW1dQK/downloaded_packages’
  67. Warning message:
  68. In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
  69. installation of package ‘mzR’ had non-zero exit status
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