mzR 1.2.0
Bernd Fischer
| Snapshot Date: 2012-03-31 17:01:49 -0700 (Sat, 31 Mar 2012) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_10/madman/Rpacks/mzR | | Last Changed Rev: 64678 / Revision: 64719 | | Last Changed Date: 2012-03-30 15:05:02 -0700 (Fri, 30 Mar 2012) |
| lamb2 | Linux (openSUSE 11.4) / x86_64 | OK | OK | |
| puck5 | Linux (Ubuntu 12.04) / 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 |
* using log directory '/loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/mzR.Rcheck'
* using R version 2.15.0 RC (2012-03-22 r58802)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'mzR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'mzR' version '1.2.0'
* 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 34.8Mb
sub-directories of 1Mb or more:
libs 34.3Mb
* 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/hpages/test-puck5/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 '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/hpages/test-puck5/bbs-2.10-bioc/meat/mzR.Rcheck/00check.log'
for details.
* 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/hpages/test-puck5/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/hpages/test-puck5/bbs-2.10-bioc/R/library/Rcpp/include" -fpic -g -O2 -c cramp.cpp -o cramp.o
g++ -I/home/hpages/test-puck5/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/hpages/test-puck5/bbs-2.10-bioc/R/library/Rcpp/include" -fpic -g -O2 -c ramp_base64.cpp -o ramp_base64.o
g++ -I/home/hpages/test-puck5/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/hpages/test-puck5/bbs-2.10-bioc/R/library/Rcpp/include" -fpic -g -O2 -c ramp.cpp -o ramp.o
g++ -I/home/hpages/test-puck5/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/hpages/test-puck5/bbs-2.10-bioc/R/library/Rcpp/include" -fpic -g -O2 -c RcppRamp.cpp -o RcppRamp.o
g++ -I/home/hpages/test-puck5/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/hpages/test-puck5/bbs-2.10-bioc/R/library/Rcpp/include" -fpic -g -O2 -c RcppRampModule.cpp -o RcppRampModule.o
gcc -std=gnu99 -I/home/hpages/test-puck5/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/hpages/test-puck5/bbs-2.10-bioc/R/library/Rcpp/include" -fpic -g -O2 -c rnetCDF.c -o rnetCDF.o
g++ -I/home/hpages/test-puck5/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/hpages/test-puck5/bbs-2.10-bioc/R/library/Rcpp/include" -fpic -g -O2 -c boost/system/src/error_code.cpp -o boost/system/src/error_code.o
g++ -I/home/hpages/test-puck5/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/hpages/test-puck5/bbs-2.10-bioc/R/library/Rcpp/include" -fpic -g -O2 -c boost/regex/src/posix_api.cpp -o boost/regex/src/posix_api.o
g++ -I/home/hpages/test-puck5/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/hpages/test-puck5/bbs-2.10-bioc/R/library/Rcpp/include" -fpic -g -O2 -c boost/regex/src/fileiter.cpp -o boost/regex/src/fileiter.o
g++ -I/home/hpages/test-puck5/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/hpages/test-puck5/bbs-2.10-bioc/R/library/Rcpp/include" -fpic -g -O2 -c boost/regex/src/regex_raw_buffer.cpp -o boost/regex/src/regex_raw_buffer.o
g++ -I/home/hpages/test-puck5/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/hpages/test-puck5/bbs-2.10-bioc/R/library/Rcpp/include" -fpic -g -O2 -c boost/regex/src/cregex.cpp -o boost/regex/src/cregex.o
g++ -I/home/hpages/test-puck5/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/hpages/test-puck5/bbs-2.10-bioc/R/library/Rcpp/include" -fpic -g -O2 -c boost/regex/src/regex_debug.cpp -o boost/regex/src/regex_debug.o
g++ -I/home/hpages/test-puck5/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/hpages/test-puck5/bbs-2.10-bioc/R/library/Rcpp/include" -fpic -g -O2 -c boost/regex/src/instances.cpp -o boost/regex/src/instances.o
g++ -I/home/hpages/test-puck5/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/hpages/test-puck5/bbs-2.10-bioc/R/library/Rcpp/include" -fpic -g -O2 -c boost/regex/src/icu.cpp -o boost/regex/src/icu.o
g++ -I/home/hpages/test-puck5/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/hpages/test-puck5/bbs-2.10-bioc/R/library/Rcpp/include" -fpic -g -O2 -c boost/regex/src/usinstances.cpp -o boost/regex/src/usinstances.o
g++ -I/home/hpages/test-puck5/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/hpages/test-puck5/bbs-2.10-bioc/R/library/Rcpp/include" -fpic -g -O2 -c boost/regex/src/regex.cpp -o boost/regex/src/regex.o
g++ -I/home/hpages/test-puck5/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/hpages/test-puck5/bbs-2.10-bioc/R/library/Rcpp/include" -fpic -g -O2 -c boost/regex/src/wide_posix_api.cpp -o boost/regex/src/wide_posix_api.o
g++ -I/home/hpages/test-puck5/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/hpages/test-puck5/bbs-2.10-bioc/R/library/Rcpp/include" -fpic -g -O2 -c boost/regex/src/regex_traits_defaults.cpp -o boost/regex/src/regex_traits_defaults.o
g++ -I/home/hpages/test-puck5/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/hpages/test-puck5/bbs-2.10-bioc/R/library/Rcpp/include" -fpic -g -O2 -c boost/regex/src/winstances.cpp -o boost/regex/src/winstances.o
g++ -I/home/hpages/test-puck5/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/hpages/test-puck5/bbs-2.10-bioc/R/library/Rcpp/include" -fpic -g -O2 -c boost/regex/src/wc_regex_traits.cpp -o boost/regex/src/wc_regex_traits.o
g++ -I/home/hpages/test-puck5/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/hpages/test-puck5/bbs-2.10-bioc/R/library/Rcpp/include" -fpic -g -O2 -c boost/regex/src/c_regex_traits.cpp -o boost/regex/src/c_regex_traits.o
g++ -I/home/hpages/test-puck5/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/hpages/test-puck5/bbs-2.10-bioc/R/library/Rcpp/include" -fpic -g -O2 -c boost/regex/src/cpp_regex_traits.cpp -o boost/regex/src/cpp_regex_traits.o
g++ -I/home/hpages/test-puck5/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/hpages/test-puck5/bbs-2.10-bioc/R/library/Rcpp/include" -fpic -g -O2 -c boost/regex/src/static_mutex.cpp -o boost/regex/src/static_mutex.o
g++ -I/home/hpages/test-puck5/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/hpages/test-puck5/bbs-2.10-bioc/R/library/Rcpp/include" -fpic -g -O2 -c boost/regex/src/w32_regex_traits.cpp -o boost/regex/src/w32_regex_traits.o
g++ -I/home/hpages/test-puck5/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/hpages/test-puck5/bbs-2.10-bioc/R/library/Rcpp/include" -fpic -g -O2 -c pwiz/data/msdata/Version.cpp -o pwiz/data/msdata/Version.o
g++ -I/home/hpages/test-puck5/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/hpages/test-puck5/bbs-2.10-bioc/R/library/Rcpp/include" -fpic -g -O2 -c pwiz/utility/minimxml/XMLWriter.cpp -o pwiz/utility/minimxml/XMLWriter.o
g++ -I/home/hpages/test-puck5/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/hpages/test-puck5/bbs-2.10-bioc/R/library/Rcpp/include" -fpic -g -O2 -c pwiz/utility/minimxml/SAXParser.cpp -o pwiz/utility/minimxml/SAXParser.o
g++ -I/home/hpages/test-puck5/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/hpages/test-puck5/bbs-2.10-bioc/R/library/Rcpp/include" -fpic -g -O2 -c boost/iostreams/src/zlib.cpp -o boost/iostreams/src/zlib.o
g++ -I/home/hpages/test-puck5/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/hpages/test-puck5/bbs-2.10-bioc/R/library/Rcpp/include" -fpic -g -O2 -c boost/thread/src/pthread/once.cpp -o boost/thread/src/pthread/once.o
g++ -I/home/hpages/test-puck5/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/hpages/test-puck5/bbs-2.10-bioc/R/library/Rcpp/include" -fpic -g -O2 -c boost/filesystem/src/operations.cpp -o boost/filesystem/src/operations.o
g++ -I/home/hpages/test-puck5/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/hpages/test-puck5/bbs-2.10-bioc/R/library/Rcpp/include" -fpic -g -O2 -c pwiz/data/common/MemoryIndex.cpp -o pwiz/data/common/MemoryIndex.o
g++ -I/home/hpages/test-puck5/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/hpages/test-puck5/bbs-2.10-bioc/R/library/Rcpp/include" -fpic -g -O2 -c pwiz/data/common/CVTranslator.cpp -o pwiz/data/common/CVTranslator.o
g++ -I/home/hpages/test-puck5/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/hpages/test-puck5/bbs-2.10-bioc/R/library/Rcpp/include" -fpic -g -O2 -c pwiz/data/common/cv.cpp -o pwiz/data/common/cv.o
g++ -I/home/hpages/test-puck5/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/hpages/test-puck5/bbs-2.10-bioc/R/library/Rcpp/include" -fpic -g -O2 -c pwiz/data/common/ParamTypes.cpp -o pwiz/data/common/ParamTypes.o
g++ -I/home/hpages/test-puck5/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/hpages/test-puck5/bbs-2.10-bioc/R/library/Rcpp/include" -fpic -g -O2 -c pwiz/data/common/BinaryIndexStream.cpp -o pwiz/data/common/BinaryIndexStream.o
g++ -I/home/hpages/test-puck5/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/hpages/test-puck5/bbs-2.10-bioc/R/library/Rcpp/include" -fpic -g -O2 -c pwiz/data/common/diff_std.cpp -o pwiz/data/common/diff_std.o
g++ -I/home/hpages/test-puck5/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/hpages/test-puck5/bbs-2.10-bioc/R/library/Rcpp/include" -fpic -g -O2 -c pwiz/data/msdata/SpectrumList_MGF.cpp -o pwiz/data/msdata/SpectrumList_MGF.o
g++ -I/home/hpages/test-puck5/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/hpages/test-puck5/bbs-2.10-bioc/R/library/Rcpp/include" -fpic -g -O2 -c pwiz/data/msdata/DefaultReaderList.cpp -o pwiz/data/msdata/DefaultReaderList.o
g++ -I/home/hpages/test-puck5/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/hpages/test-puck5/bbs-2.10-bioc/R/library/Rcpp/include" -fpic -g -O2 -c pwiz/data/msdata/ChromatogramList_mzML.cpp -o pwiz/data/msdata/ChromatogramList_mzML.o
g++ -I/home/hpages/test-puck5/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/hpages/test-puck5/bbs-2.10-bioc/R/library/Rcpp/include" -fpic -g -O2 -c pwiz/data/msdata/examples.cpp -o pwiz/data/msdata/examples.o
g++ -I/home/hpages/test-puck5/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/hpages/test-puck5/bbs-2.10-bioc/R/library/Rcpp/include" -fpic -g -O2 -c pwiz/data/msdata/Serializer_mzML.cpp -o pwiz/data/msdata/Serializer_mzML.o
g++ -I/home/hpages/test-puck5/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/hpages/test-puck5/bbs-2.10-bioc/R/library/Rcpp/include" -fpic -g -O2 -c pwiz/data/msdata/Serializer_MSn.cpp -o pwiz/data/msdata/Serializer_MSn.o
g++ -I/home/hpages/test-puck5/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/hpages/test-puck5/bbs-2.10-bioc/R/library/Rcpp/include" -fpic -g -O2 -c pwiz/data/msdata/Reader.cpp -o pwiz/data/msdata/Reader.o
g++ -I/home/hpages/test-puck5/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/hpages/test-puck5/bbs-2.10-bioc/R/library/Rcpp/include" -fpic -g -O2 -c pwiz/data/msdata/Serializer_MGF.cpp -o pwiz/data/msdata/Serializer_MGF.o
g++ -I/home/hpages/test-puck5/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/hpages/test-puck5/bbs-2.10-bioc/R/library/Rcpp/include" -fpic -g -O2 -c pwiz/data/msdata/Serializer_mzXML.cpp -o pwiz/data/msdata/Serializer_mzXML.o
g++ -I/home/hpages/test-puck5/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/hpages/test-puck5/bbs-2.10-bioc/R/library/Rcpp/include" -fpic -g -O2 -c pwiz/data/msdata/SpectrumList_mzML.cpp -o pwiz/data/msdata/SpectrumList_mzML.o
g++ -I/home/hpages/test-puck5/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/hpages/test-puck5/bbs-2.10-bioc/R/library/Rcpp/include" -fpic -g -O2 -c pwiz/data/msdata/SpectrumList_MSn.cpp -o pwiz/data/msdata/SpectrumList_MSn.o
g++ -I/home/hpages/test-puck5/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/hpages/test-puck5/bbs-2.10-bioc/R/library/Rcpp/include" -fpic -g -O2 -c pwiz/data/msdata/BinaryDataEncoder.cpp -o pwiz/data/msdata/BinaryDataEncoder.o
g++ -I/home/hpages/test-puck5/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/hpages/test-puck5/bbs-2.10-bioc/R/library/Rcpp/include" -fpic -g -O2 -c pwiz/data/msdata/Diff.cpp -o pwiz/data/msdata/Diff.o
g++ -I/home/hpages/test-puck5/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/hpages/test-puck5/bbs-2.10-bioc/R/library/Rcpp/include" -fpic -g -O2 -c pwiz/data/msdata/MSData.cpp -o pwiz/data/msdata/MSData.o
g++ -I/home/hpages/test-puck5/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/hpages/test-puck5/bbs-2.10-bioc/R/library/Rcpp/include" -fpic -g -O2 -c pwiz/data/msdata/References.cpp -o pwiz/data/msdata/References.o
g++ -I/home/hpages/test-puck5/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/hpages/test-puck5/bbs-2.10-bioc/R/library/Rcpp/include" -fpic -g -O2 -c pwiz/data/msdata/SpectrumList_mzXML.cpp -o pwiz/data/msdata/SpectrumList_mzXML.o
g++ -I/home/hpages/test-puck5/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/hpages/test-puck5/bbs-2.10-bioc/R/library/Rcpp/include" -fpic -g -O2 -c pwiz/data/msdata/IO.cpp -o pwiz/data/msdata/IO.o
g++ -I/home/hpages/test-puck5/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/hpages/test-puck5/bbs-2.10-bioc/R/library/Rcpp/include" -fpic -g -O2 -c pwiz/data/msdata/SpectrumList_BTDX.cpp -o pwiz/data/msdata/SpectrumList_BTDX.o
g++ -I/home/hpages/test-puck5/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/hpages/test-puck5/bbs-2.10-bioc/R/library/Rcpp/include" -fpic -g -O2 -c pwiz/data/msdata/SpectrumInfo.cpp -o pwiz/data/msdata/SpectrumInfo.o
g++ -I/home/hpages/test-puck5/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/hpages/test-puck5/bbs-2.10-bioc/R/library/Rcpp/include" -fpic -g -O2 -c pwiz/data/msdata/RAMPAdapter.cpp -o pwiz/data/msdata/RAMPAdapter.o
g++ -I/home/hpages/test-puck5/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/hpages/test-puck5/bbs-2.10-bioc/R/library/Rcpp/include" -fpic -g -O2 -c pwiz/data/msdata/LegacyAdapter.cpp -o pwiz/data/msdata/LegacyAdapter.o
g++ -I/home/hpages/test-puck5/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/hpages/test-puck5/bbs-2.10-bioc/R/library/Rcpp/include" -fpic -g -O2 -c pwiz/data/msdata/SpectrumIterator.cpp -o pwiz/data/msdata/SpectrumIterator.o
g++ -I/home/hpages/test-puck5/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/hpages/test-puck5/bbs-2.10-bioc/R/library/Rcpp/include" -fpic -g -O2 -c pwiz/data/msdata/MSDataFile.cpp -o pwiz/data/msdata/MSDataFile.o
g++ -I/home/hpages/test-puck5/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/hpages/test-puck5/bbs-2.10-bioc/R/library/Rcpp/include" -fpic -g -O2 -c pwiz/data/msdata/SpectrumListCache.cpp -o pwiz/data/msdata/SpectrumListCache.o
g++ -I/home/hpages/test-puck5/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/hpages/test-puck5/bbs-2.10-bioc/R/library/Rcpp/include" -fpic -g -O2 -c pwiz/utility/misc/IntegerSet.cpp -o pwiz/utility/misc/IntegerSet.o
g++ -I/home/hpages/test-puck5/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/hpages/test-puck5/bbs-2.10-bioc/R/library/Rcpp/include" -fpic -g -O2 -c pwiz/utility/misc/Base64.cpp -o pwiz/utility/misc/Base64.o
g++ -I/home/hpages/test-puck5/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/hpages/test-puck5/bbs-2.10-bioc/R/library/Rcpp/include" -fpic -g -O2 -c pwiz/utility/misc/IterationListener.cpp -o pwiz/utility/misc/IterationListener.o
g++ -I/home/hpages/test-puck5/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/hpages/test-puck5/bbs-2.10-bioc/R/library/Rcpp/include" -fpic -g -O2 -c pwiz/utility/misc/MSIHandler.cpp -o pwiz/utility/misc/MSIHandler.o
g++ -I/home/hpages/test-puck5/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/hpages/test-puck5/bbs-2.10-bioc/R/library/Rcpp/include" -fpic -g -O2 -c pwiz/utility/misc/Filesystem.cpp -o pwiz/utility/misc/Filesystem.o
g++ -I/home/hpages/test-puck5/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/hpages/test-puck5/bbs-2.10-bioc/R/library/Rcpp/include" -fpic -g -O2 -c pwiz/utility/misc/TabReader.cpp -o pwiz/utility/misc/TabReader.o
g++ -I/home/hpages/test-puck5/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/hpages/test-puck5/bbs-2.10-bioc/R/library/Rcpp/include" -fpic -g -O2 -c pwiz/utility/misc/random_access_compressed_ifstream.cpp -o pwiz/utility/misc/random_access_compressed_ifstream.o
g++ -I/home/hpages/test-puck5/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/hpages/test-puck5/bbs-2.10-bioc/R/library/Rcpp/include" -fpic -g -O2 -c pwiz/utility/misc/SHA1.cpp -o pwiz/utility/misc/SHA1.o
g++ -I/home/hpages/test-puck5/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/hpages/test-puck5/bbs-2.10-bioc/R/library/Rcpp/include" -fpic -g -O2 -c pwiz/utility/misc/SHA1Calculator.cpp -o pwiz/utility/misc/SHA1Calculator.o
g++ -I/home/hpages/test-puck5/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/hpages/test-puck5/bbs-2.10-bioc/R/library/Rcpp/include" -fpic -g -O2 -c pwiz/utility/misc/sha1calc.cpp -o pwiz/utility/misc/sha1calc.o
g++ -I/home/hpages/test-puck5/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/hpages/test-puck5/bbs-2.10-bioc/R/library/Rcpp/include" -fpic -g -O2 -c random_access_gzFile.cpp -o random_access_gzFile.o
g++ -I/home/hpages/test-puck5/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/hpages/test-puck5/bbs-2.10-bioc/R/library/Rcpp/include" -fpic -g -O2 -c rampR.cpp -o rampR.o
/bin/bash: line 1: nc-config: command not found
g++ -shared -L/usr/local/lib -o mzR.so cramp.o ramp_base64.o ramp.o RcppRamp.o RcppRampModule.o rnetCDF.o ./boost/system/src/error_code.o ./boost/regex/src/posix_api.o ./boost/regex/src/fileiter.o ./boost/regex/src/regex_raw_buffer.o ./boost/regex/src/cregex.o ./boost/regex/src/regex_debug.o ./boost/regex/src/instances.o ./boost/regex/src/icu.o ./boost/regex/src/usinstances.o ./boost/regex/src/regex.o ./boost/regex/src/wide_posix_api.o ./boost/regex/src/regex_traits_defaults.o ./boost/regex/src/winstances.o ./boost/regex/src/wc_regex_traits.o ./boost/regex/src/c_regex_traits.o ./boost/regex/src/cpp_regex_traits.o ./boost/regex/src/static_mutex.o ./boost/regex/src/w32_regex_traits.o ./pwiz/data/msdata/Version.o ./pwiz/utility/minimxml/XMLWriter.o ./pwiz/utility/minimxml/SAXParser.o ./boost/iostreams/src/zlib.o ./boost/thread/src/pthread/once.o ./boost/filesystem/src/operations.o ./pwiz/data/common/MemoryIndex.o ./pwiz/data/common/CVTranslator.o ./pwiz/data/common/cv.o ./pwiz/data/common/ParamTypes.o ./pwiz/data/common/BinaryIndexStream.o ./pwiz/data/common/diff_std.o ./pwiz/data/msdata/SpectrumList_MGF.o ./pwiz/data/msdata/DefaultReaderList.o ./pwiz/data/msdata/ChromatogramList_mzML.o ./pwiz/data/msdata/examples.o ./pwiz/data/msdata/Serializer_mzML.o ./pwiz/data/msdata/Serializer_MSn.o ./pwiz/data/msdata/Reader.o ./pwiz/data/msdata/Serializer_MGF.o ./pwiz/data/msdata/Serializer_mzXML.o ./pwiz/data/msdata/SpectrumList_mzML.o ./pwiz/data/msdata/SpectrumList_MSn.o ./pwiz/data/msdata/BinaryDataEncoder.o ./pwiz/data/msdata/Diff.o ./pwiz/data/msdata/MSData.o ./pwiz/data/msdata/References.o ./pwiz/data/msdata/SpectrumList_mzXML.o ./pwiz/data/msdata/IO.o ./pwiz/data/msdata/SpectrumList_BTDX.o ./pwiz/data/msdata/SpectrumInfo.o ./pwiz/data/msdata/RAMPAdapter.o ./pwiz/data/msdata/LegacyAdapter.o ./pwiz/data/msdata/SpectrumIterator.o ./pwiz/data/msdata/MSDataFile.o ./pwiz/data/msdata/SpectrumListCache.o ./pwiz/utility/misc/IntegerSet.o ./pwiz/utility/misc/Base64.o ./pwiz/utility/misc/IterationListener.o ./pwiz/utility/misc/MSIHandler.o ./pwiz/utility/misc/Filesystem.o ./pwiz/utility/misc/TabReader.o ./pwiz/utility/misc/random_access_compressed_ifstream.o ./pwiz/utility/misc/SHA1.o ./pwiz/utility/misc/SHA1Calculator.o ./pwiz/utility/misc/sha1calc.o ./random_access_gzFile.o rampR.o -L/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/Rcpp/lib -lRcpp -Wl,-rpath,/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/Rcpp/lib -lpthread -lnetcdf -lz -L/home/hpages/test-puck5/bbs-2.10-bioc/R/lib -lR
/bin/bash: line 2: nc-config: command not found
installing to /loc/home/hpages/test-puck5/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)