gistfile1.txt

$ make clean -f Makefile_STANDALONE_LINUX && make -j8 -f Makefile_STANDALONE_LINUX
rm -rf linux_standalone; rm -f linux_standalone/spectrast linux_standalone/plotspectrast linux_standalone/plotspectrast.cgi linux_standalone/Lib2HTML core* *~
g++  -I/usr/include -Werror -Wformat -Wstrict-aliasing -Wno-deprecated -Wno-char-subscripts -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE  -DSTANDALONE_LINUX   -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -Werror -Wformat -Wstrict-aliasing -Wno-deprecated -Wno-char-subscripts -O2 -c SpectraSTLib.cpp -o linux_standalone/SpectraSTLib.o
g++  -I/usr/include -Werror -Wformat -Wstrict-aliasing -Wno-deprecated -Wno-char-subscripts -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE  -DSTANDALONE_LINUX   -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -Werror -Wformat -Wstrict-aliasing -Wno-deprecated -Wno-char-subscripts -O2 -c SpectraSTLibIndex.cpp -o linux_standalone/SpectraSTLibIndex.o
g++  -I/usr/include -Werror -Wformat -Wstrict-aliasing -Wno-deprecated -Wno-char-subscripts -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE  -DSTANDALONE_LINUX   -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -Werror -Wformat -Wstrict-aliasing -Wno-deprecated -Wno-char-subscripts -O2 -c SpectraSTLibEntry.cpp -o linux_standalone/SpectraSTLibEntry.o
g++  -I/usr/include -Werror -Wformat -Wstrict-aliasing -Wno-deprecated -Wno-char-subscripts -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE  -DSTANDALONE_LINUX   -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -Werror -Wformat -Wstrict-aliasing -Wno-deprecated -Wno-char-subscripts -O2 -c SpectraSTPeakList.cpp -o linux_standalone/SpectraSTPeakList.o
g++  -I/usr/include -Werror -Wformat -Wstrict-aliasing -Wno-deprecated -Wno-char-subscripts -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE  -DSTANDALONE_LINUX   -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -Werror -Wformat -Wstrict-aliasing -Wno-deprecated -Wno-char-subscripts -O2 -c SpectraSTMzLibIndex.cpp -o linux_standalone/SpectraSTMzLibIndex.o
g++  -I/usr/include -Werror -Wformat -Wstrict-aliasing -Wno-deprecated -Wno-char-subscripts -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE  -DSTANDALONE_LINUX   -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -Werror -Wformat -Wstrict-aliasing -Wno-deprecated -Wno-char-subscripts -O2 -c SpectraSTCreateParams.cpp -o linux_standalone/SpectraSTCreateParams.o
g++  -I/usr/include -Werror -Wformat -Wstrict-aliasing -Wno-deprecated -Wno-char-subscripts -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE  -DSTANDALONE_LINUX   -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -Werror -Wformat -Wstrict-aliasing -Wno-deprecated -Wno-char-subscripts -O2 -c SpectraSTLibImporter.cpp -o linux_standalone/SpectraSTLibImporter.o
g++  -I/usr/include -Werror -Wformat -Wstrict-aliasing -Wno-deprecated -Wno-char-subscripts -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE  -DSTANDALONE_LINUX   -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -Werror -Wformat -Wstrict-aliasing -Wno-deprecated -Wno-char-subscripts -O2 -c SpectraSTMspLibImporter.cpp -o linux_standalone/SpectraSTMspLibImporter.o
g++  -I/usr/include -Werror -Wformat -Wstrict-aliasing -Wno-deprecated -Wno-char-subscripts -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE  -DSTANDALONE_LINUX   -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -Werror -Wformat -Wstrict-aliasing -Wno-deprecated -Wno-char-subscripts -O2 -c SpectraSTPepXMLLibImporter.cpp -o linux_standalone/SpectraSTPepXMLLibImporter.o
g++  -I/usr/include -Werror -Wformat -Wstrict-aliasing -Wno-deprecated -Wno-char-subscripts -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE  -DSTANDALONE_LINUX   -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -Werror -Wformat -Wstrict-aliasing -Wno-deprecated -Wno-char-subscripts -O2 -c SpectraSTSpLibImporter.cpp -o linux_standalone/SpectraSTSpLibImporter.o
g++  -I/usr/include -Werror -Wformat -Wstrict-aliasing -Wno-deprecated -Wno-char-subscripts -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE  -DSTANDALONE_LINUX   -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -Werror -Wformat -Wstrict-aliasing -Wno-deprecated -Wno-char-subscripts -O2 -c SpectraSTXHunterLibImporter.cpp -o linux_standalone/SpectraSTXHunterLibImporter.o
g++  -I/usr/include -Werror -Wformat -Wstrict-aliasing -Wno-deprecated -Wno-char-subscripts -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE  -DSTANDALONE_LINUX   -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -Werror -Wformat -Wstrict-aliasing -Wno-deprecated -Wno-char-subscripts -O2 -c SpectraSTTsvLibImporter.cpp -o linux_standalone/SpectraSTTsvLibImporter.o
g++  -I/usr/include -Werror -Wformat -Wstrict-aliasing -Wno-deprecated -Wno-char-subscripts -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE  -DSTANDALONE_LINUX   -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -Werror -Wformat -Wstrict-aliasing -Wno-deprecated -Wno-char-subscripts -O2 -c SpectraSTSearchTask.cpp -o linux_standalone/SpectraSTSearchTask.o
g++  -I/usr/include -Werror -Wformat -Wstrict-aliasing -Wno-deprecated -Wno-char-subscripts -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE  -DSTANDALONE_LINUX   -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -Werror -Wformat -Wstrict-aliasing -Wno-deprecated -Wno-char-subscripts -O2 -c SpectraSTDtaSearchTask.cpp -o linux_standalone/SpectraSTDtaSearchTask.o
g++  -I/usr/include -Werror -Wformat -Wstrict-aliasing -Wno-deprecated -Wno-char-subscripts -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE  -DSTANDALONE_LINUX   -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -Werror -Wformat -Wstrict-aliasing -Wno-deprecated -Wno-char-subscripts -O2 -c SpectraSTMspSearchTask.cpp -o linux_standalone/SpectraSTMspSearchTask.o
g++  -I/usr/include -Werror -Wformat -Wstrict-aliasing -Wno-deprecated -Wno-char-subscripts -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE  -DSTANDALONE_LINUX   -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -Werror -Wformat -Wstrict-aliasing -Wno-deprecated -Wno-char-subscripts -O2 -c SpectraSTMgfSearchTask.cpp -o linux_standalone/SpectraSTMgfSearchTask.o
g++  -I/usr/include -Werror -Wformat -Wstrict-aliasing -Wno-deprecated -Wno-char-subscripts -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE  -DSTANDALONE_LINUX   -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -Werror -Wformat -Wstrict-aliasing -Wno-deprecated -Wno-char-subscripts -O2 -c SpectraSTMzXMLSearchTask.cpp -o linux_standalone/SpectraSTMzXMLSearchTask.o
g++  -I/usr/include -Werror -Wformat -Wstrict-aliasing -Wno-deprecated -Wno-char-subscripts -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE  -DSTANDALONE_LINUX   -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -Werror -Wformat -Wstrict-aliasing -Wno-deprecated -Wno-char-subscripts -O2 -c SpectraSTCandidate.cpp -o linux_standalone/SpectraSTCandidate.o
g++  -I/usr/include -Werror -Wformat -Wstrict-aliasing -Wno-deprecated -Wno-char-subscripts -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE  -DSTANDALONE_LINUX   -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -Werror -Wformat -Wstrict-aliasing -Wno-deprecated -Wno-char-subscripts -O2 -c SpectraSTSearch.cpp -o linux_standalone/SpectraSTSearch.o
g++  -I/usr/include -Werror -Wformat -Wstrict-aliasing -Wno-deprecated -Wno-char-subscripts -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE  -DSTANDALONE_LINUX   -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -Werror -Wformat -Wstrict-aliasing -Wno-deprecated -Wno-char-subscripts -O2 -c SpectraSTReplicates.cpp -o linux_standalone/SpectraSTReplicates.o
g++  -I/usr/include -Werror -Wformat -Wstrict-aliasing -Wno-deprecated -Wno-char-subscripts -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE  -DSTANDALONE_LINUX   -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -Werror -Wformat -Wstrict-aliasing -Wno-deprecated -Wno-char-subscripts -O2 -c SpectraSTSearchOutput.cpp -o linux_standalone/SpectraSTSearchOutput.o
g++  -I/usr/include -Werror -Wformat -Wstrict-aliasing -Wno-deprecated -Wno-char-subscripts -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE  -DSTANDALONE_LINUX   -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -Werror -Wformat -Wstrict-aliasing -Wno-deprecated -Wno-char-subscripts -O2 -c SpectraSTTxtSearchOutput.cpp -o linux_standalone/SpectraSTTxtSearchOutput.o
g++  -I/usr/include -Werror -Wformat -Wstrict-aliasing -Wno-deprecated -Wno-char-subscripts -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE  -DSTANDALONE_LINUX   -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -Werror -Wformat -Wstrict-aliasing -Wno-deprecated -Wno-char-subscripts -O2 -c SpectraSTXlsSearchOutput.cpp -o linux_standalone/SpectraSTXlsSearchOutput.o
g++  -I/usr/include -Werror -Wformat -Wstrict-aliasing -Wno-deprecated -Wno-char-subscripts -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE  -DSTANDALONE_LINUX   -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -Werror -Wformat -Wstrict-aliasing -Wno-deprecated -Wno-char-subscripts -O2 -c SpectraSTPepXMLSearchOutput.cpp -o linux_standalone/SpectraSTPepXMLSearchOutput.o
g++  -I/usr/include -Werror -Wformat -Wstrict-aliasing -Wno-deprecated -Wno-char-subscripts -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE  -DSTANDALONE_LINUX   -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -Werror -Wformat -Wstrict-aliasing -Wno-deprecated -Wno-char-subscripts -O2 -c SpectraSTHtmlSearchOutput.cpp -o linux_standalone/SpectraSTHtmlSearchOutput.o
g++  -I/usr/include -Werror -Wformat -Wstrict-aliasing -Wno-deprecated -Wno-char-subscripts -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE  -DSTANDALONE_LINUX   -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -Werror -Wformat -Wstrict-aliasing -Wno-deprecated -Wno-char-subscripts -O2 -c SpectraSTPeptideLibIndex.cpp -o linux_standalone/SpectraSTPeptideLibIndex.o
g++  -I/usr/include -Werror -Wformat -Wstrict-aliasing -Wno-deprecated -Wno-char-subscripts -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE  -DSTANDALONE_LINUX   -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -Werror -Wformat -Wstrict-aliasing -Wno-deprecated -Wno-char-subscripts -O2 -c SpectraSTSimScores.cpp -o linux_standalone/SpectraSTSimScores.o
g++  -I/usr/include -Werror -Wformat -Wstrict-aliasing -Wno-deprecated -Wno-char-subscripts -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE  -DSTANDALONE_LINUX   -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -Werror -Wformat -Wstrict-aliasing -Wno-deprecated -Wno-char-subscripts -O2 -c SpectraSTSearchParams.cpp -o linux_standalone/SpectraSTSearchParams.o
g++  -I/usr/include -Werror -Wformat -Wstrict-aliasing -Wno-deprecated -Wno-char-subscripts -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE  -DSTANDALONE_LINUX   -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -Werror -Wformat -Wstrict-aliasing -Wno-deprecated -Wno-char-subscripts -O2 -c SpectraSTMain.cpp -o linux_standalone/SpectraSTMain.o
g++  -I/usr/include -Werror -Wformat -Wstrict-aliasing -Wno-deprecated -Wno-char-subscripts -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE  -DSTANDALONE_LINUX   -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -Werror -Wformat -Wstrict-aliasing -Wno-deprecated -Wno-char-subscripts -O2 -c SpectraSTQuery.cpp -o linux_standalone/SpectraSTQuery.o
g++  -I/usr/include -Werror -Wformat -Wstrict-aliasing -Wno-deprecated -Wno-char-subscripts -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE  -DSTANDALONE_LINUX   -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -Werror -Wformat -Wstrict-aliasing -Wno-deprecated -Wno-char-subscripts -O2 -c SpectraSTFileList.cpp -o linux_standalone/SpectraSTFileList.o
g++  -I/usr/include -Werror -Wformat -Wstrict-aliasing -Wno-deprecated -Wno-char-subscripts -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE  -DSTANDALONE_LINUX   -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -Werror -Wformat -Wstrict-aliasing -Wno-deprecated -Wno-char-subscripts -O2 -c SpectraSTLog.cpp -o linux_standalone/SpectraSTLog.o
g++  -I/usr/include -Werror -Wformat -Wstrict-aliasing -Wno-deprecated -Wno-char-subscripts -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE  -DSTANDALONE_LINUX   -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -Werror -Wformat -Wstrict-aliasing -Wno-deprecated -Wno-char-subscripts -O2 -c SpectraSTMs2LibImporter.cpp -o linux_standalone/SpectraSTMs2LibImporter.o
g++  -I/usr/include -Werror -Wformat -Wstrict-aliasing -Wno-deprecated -Wno-char-subscripts -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE  -DSTANDALONE_LINUX   -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -Werror -Wformat -Wstrict-aliasing -Wno-deprecated -Wno-char-subscripts -O2 -c SpectraSTMzXMLLibImporter.cpp -o linux_standalone/SpectraSTMzXMLLibImporter.o
g++  -I/usr/include -Werror -Wformat -Wstrict-aliasing -Wno-deprecated -Wno-char-subscripts -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE  -DSTANDALONE_LINUX   -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -Werror -Wformat -Wstrict-aliasing -Wno-deprecated -Wno-char-subscripts -O2 -c SpectraSTSearchTaskStats.cpp -o linux_standalone/SpectraSTSearchTaskStats.o
g++  -I/usr/include -Werror -Wformat -Wstrict-aliasing -Wno-deprecated -Wno-char-subscripts -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE  -DSTANDALONE_LINUX   -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -Werror -Wformat -Wstrict-aliasing -Wno-deprecated -Wno-char-subscripts -O2 -c SpectraSTFastaFileHandler.cpp -o linux_standalone/SpectraSTFastaFileHandler.o
g++  -I/usr/include -Werror -Wformat -Wstrict-aliasing -Wno-deprecated -Wno-char-subscripts -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE  -DSTANDALONE_LINUX   -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -Werror -Wformat -Wstrict-aliasing -Wno-deprecated -Wno-char-subscripts -O2 -c SpectraSTDenoiser.cpp -o linux_standalone/SpectraSTDenoiser.o
g++  -I/usr/include -Werror -Wformat -Wstrict-aliasing -Wno-deprecated -Wno-char-subscripts -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE  -DSTANDALONE_LINUX   -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -Werror -Wformat -Wstrict-aliasing -Wno-deprecated -Wno-char-subscripts -O2 -c FileUtils.cpp -o linux_standalone/FileUtils.o
g++  -I/usr/include -Werror -Wformat -Wstrict-aliasing -Wno-deprecated -Wno-char-subscripts -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE  -DSTANDALONE_LINUX   -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -Werror -Wformat -Wstrict-aliasing -Wno-deprecated -Wno-char-subscripts -O2 -c Peptide.cpp -o linux_standalone/Peptide.o
In file included from FileUtils.cpp:1:0:
FileUtils.hpp:130:1: error: ‘vector’ does not name a type
 vector<string>* split(string s, const char* delim = " \t\r\n", const char* skipover = " \t\r\n");
 ^
FileUtils.cpp:439:1: error: ‘vector’ does not name a type
 vector<string>* split (string s, const char* delim, const char* skipover) {
 ^
make: *** [linux_standalone/FileUtils.o] Error 1
make: *** Waiting for unfinished jobs....