mzR 1.10.8
Bernd Fischer , Steffen Neumann , Laurent Gatto , Qiang Kou
| Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/mzR | | Last Changed Rev: 94710 / Revision: 95116 | | Last Changed Date: 2014-09-30 07:47:22 -0700 (Tue, 30 Sep 2014) |
| zin2 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | OK | [ OK ] | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | ERROR | ERROR | skipped | skipped |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK | OK |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK |
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### Running command:
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### /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings mzR_1.10.8.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/mzR.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘mzR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mzR’ version ‘1.10.8’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘mzR’ can be installed ... [379s/387s] OK
* checking installed package size ... NOTE
installed size is 43.8Mb
sub-directories of 1Mb or more:
libs 43.2Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [2s/2s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running ‘doRUnit.R’ [5s/5s]
[5s/5s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
NOTE: There was 1 note.
See
‘/home/biocbuild/bbs-2.14-bioc/meat/mzR.Rcheck/00check.log’
for details.
* installing *source* package ‘mzR’ ...
** libs
rm -f cramp.o ramp_base64.o pwiz/data/msdata/ramp/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/iostreams/src/file_descriptor.o ./boost/thread/src/pthread/once.o ./boost/thread/src/pthread/thread.o ./boost/filesystem/src/operations.o ./boost/filesystem/src/path.o ./boost/filesystem/src/utf8_codecvt_facet.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/MSNumpress.o ./pwiz/data/msdata/SpectrumListCache.o ./pwiz/data/msdata/Index_mzML.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 R_init_mzR.o
find . -name \*˜ -exec rm {} \; ## from cleanup
find . -name \*.o -exec rm {} \; ## from cleanup
find . -name "#*#" -exec rm {} \; ## from cleanup
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I./boost -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c cramp.cpp -o cramp.o
cramp.h: In constructor ‘cRamp::cRamp(const char*, bool)’:
cramp.h:145:9: warning: ‘cRamp::m_declaredScansOnly’ will be initialized after [-Wreorder]
cramp.h:144:17: warning: ‘rampRunInfo* cRamp::m_runInfo’ [-Wreorder]
cramp.cpp:72:1: warning: when initialized here [-Wreorder]
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I./boost -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c ramp_base64.cpp -o ramp_base64.o
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I./boost -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c pwiz/data/msdata/ramp/ramp.cpp -o pwiz/data/msdata/ramp/ramp.o
pwiz/data/msdata/ramp/ramp.cpp: In function ‘RAMPFILE* rampOpenFile(const char*)’:
pwiz/data/msdata/ramp/ramp.cpp:217:18: warning: unused variable ‘fgot’ [-Wunused-variable]
pwiz/data/msdata/ramp/ramp.cpp: In function ‘ramp_fileoffset_t getIndexOffset(RAMPFILE*)’:
pwiz/data/msdata/ramp/ramp.cpp:394:11: warning: unused variable ‘nread’ [-Wunused-variable]
pwiz/data/msdata/ramp/ramp.cpp: In function ‘ramp_fileoffset_t* readIndex(RAMPFILE*, ramp_fileoffset_t, int*)’:
pwiz/data/msdata/ramp/ramp.cpp:568:22: warning: unused variable ‘fgot’ [-Wunused-variable]
pwiz/data/msdata/ramp/ramp.cpp:604:22: warning: unused variable ‘fgot’ [-Wunused-variable]
pwiz/data/msdata/ramp/ramp.cpp:640:19: warning: unused variable ‘fgot’ [-Wunused-variable]
pwiz/data/msdata/ramp/ramp.cpp: In function ‘void readHeader(RAMPFILE*, ramp_fileoffset_t, ScanHeaderStruct*)’:
pwiz/data/msdata/ramp/ramp.cpp:1153:22: warning: unused variable ‘fgot’ [-Wunused-variable]
pwiz/data/msdata/ramp/ramp.cpp: In function ‘int readMsLevel(RAMPFILE*, ramp_fileoffset_t)’:
pwiz/data/msdata/ramp/ramp.cpp:1231:13: warning: unused variable ‘fgot’ [-Wunused-variable]
pwiz/data/msdata/ramp/ramp.cpp:1227:10: warning: unused variable ‘fgot’ [-Wunused-variable]
pwiz/data/msdata/ramp/ramp.cpp: In function ‘char* rampConstructInputPath(char*, int, const char*, const char*)’:
pwiz/data/msdata/ramp/ramp.cpp:1425:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
pwiz/data/msdata/ramp/ramp.cpp: In function ‘RAMPREAL* readPeaks(RAMPFILE*, ramp_fileoffset_t)’:
pwiz/data/msdata/ramp/ramp.cpp:1725:23: warning: unused variable ‘nread’ [-Wunused-variable]
pwiz/data/msdata/ramp/ramp.cpp:1866:31: warning: variable ‘pEndAttrValue’ set but not used [-Wunused-but-set-variable]
pwiz/data/msdata/ramp/ramp.cpp:1885:31: warning: variable ‘pEndAttrValue’ set but not used [-Wunused-but-set-variable]
pwiz/data/msdata/ramp/ramp.cpp:1898:21: warning: unused variable ‘fgot’ [-Wunused-variable]
pwiz/data/msdata/ramp/ramp.cpp:1942:17: warning: unused variable ‘nread’ [-Wunused-variable]
pwiz/data/msdata/ramp/ramp.cpp:1990:15: warning: variable ‘err’ set but not used [-Wunused-but-set-variable]
pwiz/data/msdata/ramp/ramp.cpp:1823:13: warning: unused variable ‘fgot’ [-Wunused-variable]
pwiz/data/msdata/ramp/ramp.cpp: In function ‘void readMSRun(RAMPFILE*, RunHeaderStruct*)’:
pwiz/data/msdata/ramp/ramp.cpp:2100:13: warning: unused variable ‘fgot’ [-Wunused-variable]
pwiz/data/msdata/ramp/ramp.cpp:2120:13: warning: unused variable ‘fgot’ [-Wunused-variable]
pwiz/data/msdata/ramp/ramp.cpp:2096:10: warning: unused variable ‘fgot’ [-Wunused-variable]
pwiz/data/msdata/ramp/ramp.cpp: In function ‘InstrumentStruct* getInstrumentStruct(RAMPFILE*)’:
pwiz/data/msdata/ramp/ramp.cpp:2262:16: warning: unused variable ‘fgot’ [-Wunused-variable]
pwiz/data/msdata/ramp/ramp.cpp:2298:15: warning: unused variable ‘fgot’ [-Wunused-variable]
pwiz/data/msdata/ramp/ramp.cpp:2252:10: warning: unused variable ‘fgot’ [-Wunused-variable]
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I./boost -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c RcppRamp.cpp -o RcppRamp.o
RcppRamp.cpp: In member function ‘Rcpp::DataFrame RcppRamp::getAllScanHeaderInfo()’:
RcppRamp.cpp:170:21: warning: unused variable ‘info’ [-Wunused-variable]
RcppRamp.cpp: In member function ‘Rcpp::NumericMatrix RcppRamp::get3DMap(std::vector<int>, double, double, double)’:
RcppRamp.cpp:309:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I./boost -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c RcppRampModule.cpp -o RcppRampModule.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I./boost -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c rnetCDF.c -o rnetCDF.o
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I./boost -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c boost/system/src/error_code.cpp -o boost/system/src/error_code.o
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I./boost -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c boost/regex/src/posix_api.cpp -o boost/regex/src/posix_api.o
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I./boost -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c boost/regex/src/fileiter.cpp -o boost/regex/src/fileiter.o
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I./boost -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c boost/regex/src/regex_raw_buffer.cpp -o boost/regex/src/regex_raw_buffer.o
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I./boost -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c boost/regex/src/cregex.cpp -o boost/regex/src/cregex.o
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I./boost -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c boost/regex/src/regex_debug.cpp -o boost/regex/src/regex_debug.o
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I./boost -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c boost/regex/src/instances.cpp -o boost/regex/src/instances.o
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I./boost -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c boost/regex/src/icu.cpp -o boost/regex/src/icu.o
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I./boost -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c boost/regex/src/usinstances.cpp -o boost/regex/src/usinstances.o
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I./boost -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c boost/regex/src/regex.cpp -o boost/regex/src/regex.o
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I./boost -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c boost/regex/src/wide_posix_api.cpp -o boost/regex/src/wide_posix_api.o
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I./boost -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c boost/regex/src/regex_traits_defaults.cpp -o boost/regex/src/regex_traits_defaults.o
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I./boost -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c boost/regex/src/winstances.cpp -o boost/regex/src/winstances.o
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I./boost -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c boost/regex/src/wc_regex_traits.cpp -o boost/regex/src/wc_regex_traits.o
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I./boost -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c boost/regex/src/c_regex_traits.cpp -o boost/regex/src/c_regex_traits.o
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I./boost -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c boost/regex/src/cpp_regex_traits.cpp -o boost/regex/src/cpp_regex_traits.o
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I./boost -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c boost/regex/src/static_mutex.cpp -o boost/regex/src/static_mutex.o
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I./boost -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c boost/regex/src/w32_regex_traits.cpp -o boost/regex/src/w32_regex_traits.o
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I./boost -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c pwiz/data/msdata/Version.cpp -o pwiz/data/msdata/Version.o
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I./boost -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c pwiz/utility/minimxml/XMLWriter.cpp -o pwiz/utility/minimxml/XMLWriter.o
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I./boost -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c pwiz/utility/minimxml/SAXParser.cpp -o pwiz/utility/minimxml/SAXParser.o
pwiz/utility/minimxml/SAXParser.cpp: In function ‘void pwiz::minimxml::SAXParser::parse(std::istream&, pwiz::minimxml::SAXParser::Handler&)’:
pwiz/utility/minimxml/SAXParser.cpp:514:17: warning: ‘inCDATA’ may be used uninitialized in this function [-Wuninitialized]
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I./boost -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c boost/iostreams/src/zlib.cpp -o boost/iostreams/src/zlib.o
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I./boost -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c boost/iostreams/src/file_descriptor.cpp -o boost/iostreams/src/file_descriptor.o
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I./boost -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c boost/thread/src/pthread/once.cpp -o boost/thread/src/pthread/once.o
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I./boost -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c boost/thread/src/pthread/thread.cpp -o boost/thread/src/pthread/thread.o
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I./boost -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c boost/filesystem/src/operations.cpp -o boost/filesystem/src/operations.o
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I./boost -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c boost/filesystem/src/path.cpp -o boost/filesystem/src/path.o
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I./boost -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c boost/filesystem/src/utf8_codecvt_facet.cpp -o boost/filesystem/src/utf8_codecvt_facet.o
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I./boost -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c pwiz/data/common/MemoryIndex.cpp -o pwiz/data/common/MemoryIndex.o
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I./boost -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c pwiz/data/common/CVTranslator.cpp -o pwiz/data/common/CVTranslator.o
pwiz/data/common/CVTranslator.cpp: In function ‘bool pwiz::data::shouldIgnore(const string&, pwiz::cv::CVID, pwiz::cv::CVID)’:
pwiz/data/common/CVTranslator.cpp:134:49: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
pwiz/data/common/CVTranslator.cpp:135:49: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
pwiz/data/common/CVTranslator.cpp:136:49: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I./boost -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c pwiz/data/common/cv.cpp -o pwiz/data/common/cv.o
In file included from pwiz/data/common/cv.cpp:16902:0:
pwiz/data/common/cv.inl: In function ‘const pwiz::cv::CVTermInfo& pwiz::cv::cvTermInfo(const char*)’:
pwiz/data/common/cv.inl:102:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I./boost -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c pwiz/data/common/ParamTypes.cpp -o pwiz/data/common/ParamTypes.o
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I./boost -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c pwiz/data/common/BinaryIndexStream.cpp -o pwiz/data/common/BinaryIndexStream.o
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I./boost -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c pwiz/data/common/diff_std.cpp -o pwiz/data/common/diff_std.o
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I./boost -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c pwiz/data/msdata/SpectrumList_MGF.cpp -o pwiz/data/msdata/SpectrumList_MGF.o
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I./boost -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c pwiz/data/msdata/DefaultReaderList.cpp -o pwiz/data/msdata/DefaultReaderList.o
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I./boost -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c pwiz/data/msdata/ChromatogramList_mzML.cpp -o pwiz/data/msdata/ChromatogramList_mzML.o
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I./boost -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c pwiz/data/msdata/examples.cpp -o pwiz/data/msdata/examples.o
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I./boost -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c pwiz/data/msdata/Serializer_mzML.cpp -o pwiz/data/msdata/Serializer_mzML.o
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I./boost -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c pwiz/data/msdata/Serializer_MSn.cpp -o pwiz/data/msdata/Serializer_MSn.o
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I./boost -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c pwiz/data/msdata/Reader.cpp -o pwiz/data/msdata/Reader.o
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I./boost -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c pwiz/data/msdata/Serializer_MGF.cpp -o pwiz/data/msdata/Serializer_MGF.o
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I./boost -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c pwiz/data/msdata/Serializer_mzXML.cpp -o pwiz/data/msdata/Serializer_mzXML.o
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I./boost -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c pwiz/data/msdata/SpectrumList_mzML.cpp -o pwiz/data/msdata/SpectrumList_mzML.o
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I./boost -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c pwiz/data/msdata/SpectrumList_MSn.cpp -o pwiz/data/msdata/SpectrumList_MSn.o
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I./boost -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c pwiz/data/msdata/BinaryDataEncoder.cpp -o pwiz/data/msdata/BinaryDataEncoder.o
pwiz/data/msdata/BinaryDataEncoder.cpp: In member function ‘void pwiz::msdata::BinaryDataEncoder::Impl::encode(const double*, size_t, std::string&, size_t*)’:
pwiz/data/msdata/BinaryDataEncoder.cpp:284:71: warning: ‘byteCount’ may be used uninitialized in this function [-Wuninitialized]
pwiz/data/msdata/BinaryDataEncoder.cpp:284:71: warning: ‘byteBuffer’ may be used uninitialized in this function [-Wuninitialized]
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I./boost -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c pwiz/data/msdata/Diff.cpp -o pwiz/data/msdata/Diff.o
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I./boost -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c pwiz/data/msdata/MSData.cpp -o pwiz/data/msdata/MSData.o
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I./boost -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c pwiz/data/msdata/References.cpp -o pwiz/data/msdata/References.o
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I./boost -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c pwiz/data/msdata/SpectrumList_mzXML.cpp -o pwiz/data/msdata/SpectrumList_mzXML.o
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I./boost -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c pwiz/data/msdata/IO.cpp -o pwiz/data/msdata/IO.o
pwiz/data/msdata/IO.cpp: In member function ‘virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::IO::HandlerSpectrum::startElement(const string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)’:
pwiz/data/msdata/IO.cpp:2013:90: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
pwiz/data/msdata/IO.cpp: In member function ‘virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::IO::HandlerMSData::startElement(const string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)’:
pwiz/data/msdata/IO.cpp:2723:26: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I./boost -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c pwiz/data/msdata/SpectrumList_BTDX.cpp -o pwiz/data/msdata/SpectrumList_BTDX.o
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I./boost -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c pwiz/data/msdata/SpectrumInfo.cpp -o pwiz/data/msdata/SpectrumInfo.o
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I./boost -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c pwiz/data/msdata/RAMPAdapter.cpp -o pwiz/data/msdata/RAMPAdapter.o
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I./boost -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c pwiz/data/msdata/LegacyAdapter.cpp -o pwiz/data/msdata/LegacyAdapter.o
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I./boost -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c pwiz/data/msdata/SpectrumIterator.cpp -o pwiz/data/msdata/SpectrumIterator.o
pwiz/data/msdata/SpectrumIterator.cpp: In member function ‘bool pwiz::msdata::SpectrumIterator::Impl::equal(const pwiz::msdata::SpectrumIterator::Impl&) const’:
pwiz/data/msdata/SpectrumIterator.cpp:126:58: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
pwiz/data/msdata/SpectrumIterator.cpp:127:72: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
pwiz/data/msdata/SpectrumIterator.cpp: In member function ‘bool pwiz::msdata::SpectrumIterator::Impl::done() const’:
pwiz/data/msdata/SpectrumIterator.cpp:142:48: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I./boost -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c pwiz/data/msdata/MSDataFile.cpp -o pwiz/data/msdata/MSDataFile.o
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I./boost -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c pwiz/data/msdata/MSNumpress.cpp -o pwiz/data/msdata/MSNumpress.o
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I./boost -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c pwiz/data/msdata/SpectrumListCache.cpp -o pwiz/data/msdata/SpectrumListCache.o
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I./boost -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c pwiz/data/msdata/Index_mzML.cpp -o pwiz/data/msdata/Index_mzML.o
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I./boost -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c pwiz/utility/misc/IntegerSet.cpp -o pwiz/utility/misc/IntegerSet.o
pwiz/utility/misc/IntegerSet.cpp: In member function ‘bool pwiz::util::IntegerSet::Iterator::operator==(const pwiz::util::IntegerSet::Iterator&) const’:
pwiz/utility/misc/IntegerSet.cpp:308:49: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I./boost -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c pwiz/utility/misc/Base64.cpp -o pwiz/utility/misc/Base64.o
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I./boost -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c pwiz/utility/misc/IterationListener.cpp -o pwiz/utility/misc/IterationListener.o
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I./boost -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c pwiz/utility/misc/MSIHandler.cpp -o pwiz/utility/misc/MSIHandler.o
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I./boost -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c pwiz/utility/misc/Filesystem.cpp -o pwiz/utility/misc/Filesystem.o
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I./boost -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c pwiz/utility/misc/TabReader.cpp -o pwiz/utility/misc/TabReader.o
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I./boost -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c pwiz/utility/misc/random_access_compressed_ifstream.cpp -o pwiz/utility/misc/random_access_compressed_ifstream.o
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I./boost -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c pwiz/utility/misc/SHA1.cpp -o pwiz/utility/misc/SHA1.o
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I./boost -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c pwiz/utility/misc/SHA1Calculator.cpp -o pwiz/utility/misc/SHA1Calculator.o
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I./boost -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c pwiz/utility/misc/sha1calc.cpp -o pwiz/utility/misc/sha1calc.o
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I./boost -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c random_access_gzFile.cpp -o random_access_gzFile.o
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I./boost -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c rampR.cpp -o rampR.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I./boost -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c R_init_mzR.c -o R_init_mzR.o
/bin/bash: line 1: nc-config: command not found
g++ -shared -L/usr/local/lib -o mzR.so cramp.o ramp_base64.o pwiz/data/msdata/ramp/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/iostreams/src/file_descriptor.o ./boost/thread/src/pthread/once.o ./boost/thread/src/pthread/thread.o ./boost/filesystem/src/operations.o ./boost/filesystem/src/path.o ./boost/filesystem/src/utf8_codecvt_facet.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/MSNumpress.o ./pwiz/data/msdata/SpectrumListCache.o ./pwiz/data/msdata/Index_mzML.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 R_init_mzR.o -lpthread -lnetcdf -lz -L/home/biocbuild/bbs-2.14-bioc/R/lib -lR
/bin/bash: line 2: nc-config: command not found
installing to /home/biocbuild/bbs-2.14-bioc/meat/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
* DONE (mzR)