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Compile problems with XCMS from BioConductor on Debian testing.
Raw
gistfile1.txt
> source("http://bioconductor.org/biocLite.R")
BiocInstaller version 1.4.9, ?biocLite for help
A newer version of Bioconductor is available for this version of R,
?BiocUpgrade for help
> biocLite("xcms")
BioC_mirror: http://bioconductor.org
Using R version 2.15, BiocInstaller version 1.4.9.
Installing package(s) 'xcms'
also installing the dependency ‘mzR’
trying URL 'http://bioconductor.org/packages/2.10/bioc/src/contrib/mzR_1.2.2.tar.gz'
Content type 'application/x-gzip' length 4893343 bytes (4.7 Mb)
opened URL
==================================================
downloaded 4.7 Mb
trying URL 'http://bioconductor.org/packages/2.10/bioc/src/contrib/xcms_1.32.0.tar.gz'
Content type 'application/x-gzip' length 1320111 bytes (1.3 Mb)
opened URL
==================================================
downloaded 1.3 Mb
* 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
g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I"/home/egonw/R/i486-pc-linux-gnu-library/2.15/Rcpp/include" -fpic -O2 -pipe -g -c cramp.cpp -o cramp.o
g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I"/home/egonw/R/i486-pc-linux-gnu-library/2.15/Rcpp/include" -fpic -O2 -pipe -g -c ramp_base64.cpp -o ramp_base64.o
g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I"/home/egonw/R/i486-pc-linux-gnu-library/2.15/Rcpp/include" -fpic -O2 -pipe -g -c ramp.cpp -o ramp.o
g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I"/home/egonw/R/i486-pc-linux-gnu-library/2.15/Rcpp/include" -fpic -O2 -pipe -g -c RcppRamp.cpp -o RcppRamp.o
g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I"/home/egonw/R/i486-pc-linux-gnu-library/2.15/Rcpp/include" -fpic -O2 -pipe -g -c RcppRampModule.cpp -o RcppRampModule.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I"/home/egonw/R/i486-pc-linux-gnu-library/2.15/Rcpp/include" -fpic -O2 -pipe -g -c rnetCDF.c -o rnetCDF.o
g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I"/home/egonw/R/i486-pc-linux-gnu-library/2.15/Rcpp/include" -fpic -O2 -pipe -g -c boost/system/src/error_code.cpp -o boost/system/src/error_code.o
g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I"/home/egonw/R/i486-pc-linux-gnu-library/2.15/Rcpp/include" -fpic -O2 -pipe -g -c boost/regex/src/posix_api.cpp -o boost/regex/src/posix_api.o
g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I"/home/egonw/R/i486-pc-linux-gnu-library/2.15/Rcpp/include" -fpic -O2 -pipe -g -c boost/regex/src/fileiter.cpp -o boost/regex/src/fileiter.o
g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I"/home/egonw/R/i486-pc-linux-gnu-library/2.15/Rcpp/include" -fpic -O2 -pipe -g -c boost/regex/src/regex_raw_buffer.cpp -o boost/regex/src/regex_raw_buffer.o
g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I"/home/egonw/R/i486-pc-linux-gnu-library/2.15/Rcpp/include" -fpic -O2 -pipe -g -c boost/regex/src/cregex.cpp -o boost/regex/src/cregex.o
g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I"/home/egonw/R/i486-pc-linux-gnu-library/2.15/Rcpp/include" -fpic -O2 -pipe -g -c boost/regex/src/regex_debug.cpp -o boost/regex/src/regex_debug.o
g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I"/home/egonw/R/i486-pc-linux-gnu-library/2.15/Rcpp/include" -fpic -O2 -pipe -g -c boost/regex/src/instances.cpp -o boost/regex/src/instances.o
g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I"/home/egonw/R/i486-pc-linux-gnu-library/2.15/Rcpp/include" -fpic -O2 -pipe -g -c boost/regex/src/icu.cpp -o boost/regex/src/icu.o
g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I"/home/egonw/R/i486-pc-linux-gnu-library/2.15/Rcpp/include" -fpic -O2 -pipe -g -c boost/regex/src/usinstances.cpp -o boost/regex/src/usinstances.o
g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I"/home/egonw/R/i486-pc-linux-gnu-library/2.15/Rcpp/include" -fpic -O2 -pipe -g -c boost/regex/src/regex.cpp -o boost/regex/src/regex.o
g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I"/home/egonw/R/i486-pc-linux-gnu-library/2.15/Rcpp/include" -fpic -O2 -pipe -g -c boost/regex/src/wide_posix_api.cpp -o boost/regex/src/wide_posix_api.o
g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I"/home/egonw/R/i486-pc-linux-gnu-library/2.15/Rcpp/include" -fpic -O2 -pipe -g -c boost/regex/src/regex_traits_defaults.cpp -o boost/regex/src/regex_traits_defaults.o
g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I"/home/egonw/R/i486-pc-linux-gnu-library/2.15/Rcpp/include" -fpic -O2 -pipe -g -c boost/regex/src/winstances.cpp -o boost/regex/src/winstances.o
g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I"/home/egonw/R/i486-pc-linux-gnu-library/2.15/Rcpp/include" -fpic -O2 -pipe -g -c boost/regex/src/wc_regex_traits.cpp -o boost/regex/src/wc_regex_traits.o
g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I"/home/egonw/R/i486-pc-linux-gnu-library/2.15/Rcpp/include" -fpic -O2 -pipe -g -c boost/regex/src/c_regex_traits.cpp -o boost/regex/src/c_regex_traits.o
g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I"/home/egonw/R/i486-pc-linux-gnu-library/2.15/Rcpp/include" -fpic -O2 -pipe -g -c boost/regex/src/cpp_regex_traits.cpp -o boost/regex/src/cpp_regex_traits.o
g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I"/home/egonw/R/i486-pc-linux-gnu-library/2.15/Rcpp/include" -fpic -O2 -pipe -g -c boost/regex/src/static_mutex.cpp -o boost/regex/src/static_mutex.o
g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I"/home/egonw/R/i486-pc-linux-gnu-library/2.15/Rcpp/include" -fpic -O2 -pipe -g -c boost/regex/src/w32_regex_traits.cpp -o boost/regex/src/w32_regex_traits.o
g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I"/home/egonw/R/i486-pc-linux-gnu-library/2.15/Rcpp/include" -fpic -O2 -pipe -g -c pwiz/data/msdata/Version.cpp -o pwiz/data/msdata/Version.o
g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I"/home/egonw/R/i486-pc-linux-gnu-library/2.15/Rcpp/include" -fpic -O2 -pipe -g -c pwiz/utility/minimxml/XMLWriter.cpp -o pwiz/utility/minimxml/XMLWriter.o
g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I"/home/egonw/R/i486-pc-linux-gnu-library/2.15/Rcpp/include" -fpic -O2 -pipe -g -c pwiz/utility/minimxml/SAXParser.cpp -o pwiz/utility/minimxml/SAXParser.o
g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I"/home/egonw/R/i486-pc-linux-gnu-library/2.15/Rcpp/include" -fpic -O2 -pipe -g -c boost/iostreams/src/zlib.cpp -o boost/iostreams/src/zlib.o
g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I"/home/egonw/R/i486-pc-linux-gnu-library/2.15/Rcpp/include" -fpic -O2 -pipe -g -c boost/thread/src/pthread/once.cpp -o boost/thread/src/pthread/once.o
In file included from ./boost/thread/detail/platform.hpp:17:0,
from ./boost/thread/once.hpp:12,
from boost/thread/src/pthread/once.cpp:7:
./boost/config/requires_threads.hpp:29:4: error: #error "Threading support unavaliable: it has been explicitly disabled with BOOST_DISABLE_THREADS"
In file included from ./boost/thread/once.hpp:12:0,
from boost/thread/src/pthread/once.cpp:7:
./boost/thread/detail/platform.hpp:67:9: error: #error "Sorry, no boost threads are available for this platform."
In file included from boost/thread/src/pthread/once.cpp:7:0:
./boost/thread/once.hpp:18:2: error: #error "Boost threads unavailable on this platform"
In file included from boost/thread/src/pthread/once.cpp:7:0:
./boost/thread/once.hpp:25:42: error: variable or field ‘call_once’ declared void
./boost/thread/once.hpp:25:34: error: ‘func’ was not declared in this scope
./boost/thread/once.hpp:25:42: error: ‘once_flag’ was not declared in this scope
./boost/thread/once.hpp:25:53: error: ‘flag’ was not declared in this scope
boost/thread/src/pthread/once.cpp:16:9: error: ‘BOOST_THREAD_DECL’ does not name a type
boost/thread/src/pthread/once.cpp:17:9: error: ‘BOOST_THREAD_DECL’ does not name a type
boost/thread/src/pthread/once.cpp:18:9: error: ‘BOOST_THREAD_DECL’ does not name a type
boost/thread/src/pthread/once.cpp:37:9: error: ‘uintmax_t’ in namespace ‘boost’ does not name a type
make: *** [boost/thread/src/pthread/once.o] Error 1
ERROR: compilation failed for package ‘mzR’
* removing ‘/home/egonw/R/i486-pc-linux-gnu-library/2.15/mzR’
ERROR: dependency ‘mzR’ is not available for package ‘xcms’
* removing ‘/home/egonw/R/i486-pc-linux-gnu-library/2.15/xcms’
The downloaded source packages are in
‘/tmp/RtmpDGasnV/downloaded_packages’
Warning messages:
1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
installation of package ‘mzR’ had non-zero exit status
2: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
installation of package ‘xcms’ had non-zero exit status
3: installed directory not writable, cannot update packages 'boot', 'class',
'cluster', 'foreign', 'lattice', 'MASS', 'Matrix', 'mgcv', 'nlme', 'nnet',
'rpart', 'spatial', 'survival'
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