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Package 362/553HostnameOS / ArchBUILDCHECKBUILD BIN
mzR 1.2.2
Bernd Fischer
Snapshot Date: 2012-09-23 17:01:39 -0700 (Sun, 23 Sep 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_10/madman/Rpacks/mzR
Last Changed Rev: 67123 / Revision: 69725
Last Changed Date: 2012-06-28 12:18:23 -0700 (Thu, 28 Jun 2012)
lamb2 Linux (openSUSE 11.4) / x86_64  OK [ OK ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: mzR
Version: 1.2.2
Command: /home/biocbuild/bbs-2.10-bioc/R/bin/R CMD check --no-vignettes --timings mzR_1.2.2.tar.gz
StartedAt: 2012-09-24 02:28:13 -0700 (Mon, 24 Sep 2012)
EndedAt: 2012-09-24 02:33:09 -0700 (Mon, 24 Sep 2012)
EllapsedTime: 296.4 seconds
RetCode: 0
Status:  OK 
CheckDir: mzR.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.10-bioc/meat/mzR.Rcheck’
* using R version 2.15.1 (2012-06-22)
* 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 ‘1.2.2’
* 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 whether package ‘mzR’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 44.8Mb
  sub-directories of 1Mb or more:
    libs  44.3Mb
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 for unstated 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 ... NOTE
File ‘mzR/R/zzz.R’:
  .onLoad calls:
    require("methods", character = TRUE, quietly = TRUE)

Package startup functions should not change the search path.
See section ‘Good practice’ in ?.onAttach.

.onLoad: warning in require("methods", character = TRUE, quietly =
  TRUE): partial argument match of 'character' to 'character.only'
* 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 for portable compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File ‘/loc/home/biocbuild/bbs-2.10-bioc/meat/mzR.Rcheck/mzR/libs/mzR.so’:
  Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++)
    Objects: ‘cramp.o’, ‘./pwiz/utility/misc/sha1calc.o’
  Found ‘_ZSt4cout’, possibly from ‘std::cout’ (C++)
    Objects: ‘ramp.o’, ‘./pwiz/utility/misc/sha1calc.o’
  Found ‘exit’, possibly from ‘exit’ (C)
    Object: ‘ramp.o’
  Found ‘printf’, possibly from ‘printf’ (C)
    Objects: ‘ramp.o’, ‘RcppRamp.o’, ‘rampR.o’
  Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C)
    Objects: ‘ramp.o’, ‘RcppRamp.o’
  Found ‘stderr’, possibly from ‘stderr’ (C)
    Object: ‘ramp.o’

Compiled code should not call functions which might terminate R nor
write to stdout/stderr instead of to the console.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking installed files from ‘inst/doc’ ... NOTE
The following files should probably not be installed:
  ‘Makefile’

Consider the use of a .Rinstignore file: see ‘Writing R Extensions’,
or move the vignette sources from ‘inst/doc’ to ‘vignettes’.
* checking examples ... OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘doRUnit.R’
 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 4 notes.
See
  ‘/loc/home/biocbuild/bbs-2.10-bioc/meat/mzR.Rcheck/00check.log’
for details.

mzR.Rcheck/00install.out:

* 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/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c cramp.cpp -o cramp.o
cramp.cpp:4:1: warning: "/*" within comment
cramp.h: In constructor ‘cRamp::cRamp(const char*, bool)’:
cramp.h:143:9: warning: ‘cRamp::m_declaredScansOnly’ will be initialized after
cramp.h:142:17: warning:   ‘rampRunInfo* cRamp::m_runInfo’
cramp.cpp:59:1: warning:   when initialized here
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c ramp_base64.cpp -o ramp_base64.o
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c ramp.cpp -o ramp.o
ramp.cpp: In function ‘RAMPFILE* rampOpenFile(const char*)’:
ramp.cpp:201:18: warning: unused variable ‘fgot’
ramp.cpp: In function ‘ramp_fileoffset_t getIndexOffset(RAMPFILE*)’:
ramp.cpp:378:11: warning: unused variable ‘nread’
ramp.cpp: In function ‘ramp_fileoffset_t* readIndex(RAMPFILE*, ramp_fileoffset_t, int*)’:
ramp.cpp:555:22: warning: unused variable ‘fgot’
ramp.cpp:591:22: warning: unused variable ‘fgot’
ramp.cpp:627:19: warning: unused variable ‘fgot’
ramp.cpp: In function ‘void readHeader(RAMPFILE*, ramp_fileoffset_t, ScanHeaderStruct*)’:
ramp.cpp:1206:22: warning: unused variable ‘fgot’
ramp.cpp: In function ‘int readMsLevel(RAMPFILE*, ramp_fileoffset_t)’:
ramp.cpp:1284:13: warning: unused variable ‘fgot’
ramp.cpp:1280:10: warning: unused variable ‘fgot’
ramp.cpp: In function ‘char* rampConstructInputPath(char*, int, const char*, const char*)’:
ramp.cpp:1478:24: warning: comparison between signed and unsigned integer expressions
ramp.cpp: In function ‘RAMPREAL* readPeaks(RAMPFILE*, ramp_fileoffset_t)’:
ramp.cpp:1778:23: warning: unused variable ‘nread’
ramp.cpp:1951:21: warning: unused variable ‘fgot’
ramp.cpp:1995:17: warning: unused variable ‘nread’
ramp.cpp:1876:13: warning: unused variable ‘fgot’
ramp.cpp: In function ‘void readMSRun(RAMPFILE*, RunHeaderStruct*)’:
ramp.cpp:2153:13: warning: unused variable ‘fgot’
ramp.cpp:2173:13: warning: unused variable ‘fgot’
ramp.cpp:2149:10: warning: unused variable ‘fgot’
ramp.cpp: In function ‘InstrumentStruct* getInstrumentStruct(RAMPFILE*)’:
ramp.cpp:2315:16: warning: unused variable ‘fgot’
ramp.cpp:2351:15: warning: unused variable ‘fgot’
ramp.cpp:2305:10: warning: unused variable ‘fgot’
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-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’
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
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c RcppRampModule.cpp -o RcppRampModule.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c rnetCDF.c -o rnetCDF.o
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-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-2.10-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-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-2.10-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-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-2.10-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-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-2.10-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-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-2.10-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-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-2.10-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-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-2.10-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-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-2.10-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-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-2.10-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-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-2.10-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-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-2.10-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-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-2.10-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-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-2.10-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-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-2.10-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-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-2.10-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-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-2.10-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-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-2.10-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-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-2.10-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-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-2.10-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c pwiz/utility/minimxml/XMLWriter.cpp -o pwiz/utility/minimxml/XMLWriter.o
pwiz/utility/minimxml/XMLWriter.cpp: In member function ‘void pwiz::minimxml::XMLWriter::Impl::startElement(const std::string&, const pwiz::minimxml::XMLWriter::Attributes&, pwiz::minimxml::XMLWriter::EmptyElementTag)’:
pwiz/utility/minimxml/XMLWriter.cpp:160:59: warning: suggest parentheses around ‘&&’ within ‘||’
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c pwiz/utility/minimxml/SAXParser.cpp -o pwiz/utility/minimxml/SAXParser.o
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-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-2.10-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-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-2.10-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-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-2.10-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-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-2.10-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-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 std::string&, pwiz::cv::CVID, pwiz::cv::CVID)’:
pwiz/data/common/CVTranslator.cpp:134:49: warning: suggest parentheses around ‘&&’ within ‘||’
pwiz/data/common/CVTranslator.cpp:135:49: warning: suggest parentheses around ‘&&’ within ‘||’
pwiz/data/common/CVTranslator.cpp:136:49: warning: suggest parentheses around ‘&&’ within ‘||’
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c pwiz/data/common/cv.cpp -o pwiz/data/common/cv.o
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-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-2.10-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-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-2.10-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-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-2.10-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-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-2.10-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-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-2.10-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-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-2.10-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-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-2.10-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-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-2.10-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-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-2.10-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-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-2.10-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-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-2.10-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-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-2.10-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-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-2.10-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-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-2.10-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c pwiz/data/msdata/BinaryDataEncoder.cpp -o pwiz/data/msdata/BinaryDataEncoder.o
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-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-2.10-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-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-2.10-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-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-2.10-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-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-2.10-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-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 std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)’:
pwiz/data/msdata/IO.cpp:1939:86: warning: suggest parentheses around ‘&&’ within ‘||’
pwiz/data/msdata/IO.cpp: In member function ‘virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::IO::HandlerMSData::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)’:
pwiz/data/msdata/IO.cpp:2644:26: warning: suggest parentheses around ‘&&’ within ‘||’
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-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-2.10-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-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-2.10-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-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-2.10-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-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-2.10-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-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 ‘||’
pwiz/data/msdata/SpectrumIterator.cpp:127:72: warning: suggest parentheses around ‘&&’ within ‘||’
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 ‘||’
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-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-2.10-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-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-2.10-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-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 ‘||’
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-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-2.10-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c pwiz/utility/misc/IterationListener.cpp -o pwiz/utility/misc/IterationListener.o
pwiz/utility/misc/IterationListener.cpp: In member function ‘pwiz::util::IterationListener::Status pwiz::util::IterationListenerRegistry::Impl::broadcastUpdateMessage(const pwiz::util::IterationListener::UpdateMessage&) const’:
pwiz/utility/misc/IterationListener.cpp:76:94: warning: suggest parentheses around ‘&&’ within ‘||’
pwiz/utility/misc/IterationListener.cpp:78:87: warning: suggest parentheses around ‘&&’ within ‘||’
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-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-2.10-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-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-2.10-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-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-2.10-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-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-2.10-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-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-2.10-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-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-2.10-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-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-2.10-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c random_access_gzFile.cpp -o random_access_gzFile.o
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c rampR.cpp -o rampR.o
g++ -shared -L/usr/local/lib64 -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 -L/loc/home/biocbuild/bbs-2.10-bioc/R/library/Rcpp/lib -lRcpp -Wl,-rpath,/loc/home/biocbuild/bbs-2.10-bioc/R/library/Rcpp/lib -lpthread -L/usr/local/lib -lnetcdf -lz -L/home/biocbuild/bbs-2.10-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.10-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
   ‘mzR.Rnw’ 
** testing if installed package can be loaded

* DONE (mzR)

mzR.Rcheck/mzR-Ex.timings:

nameusersystemelapsed
metadata0.3800.0800.511
mzR-class0.2040.0560.257
openMSfile0.2640.0680.336
peaks0.2760.0640.338