##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL rgoslin
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’
* installing *source* package ‘rgoslin’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0’
using C++11
The name of the shared library to be created is: rgoslin.so
make[1]: Entering directory '/home/biocbuild/bbs-3.17-bioc/meat/rgoslin/src/cppgoslin'
rm -f "cppgoslin/parser/KnownGrammars.h"
rm -f "src/domain/LipidClasses.cpp"
rm -f "cppgoslin/domain/ClassesEnum.h"
rm -f cppgoslin/domain/*.o
rm -f cppgoslin/parser/*.o
rm -f cppgoslin/tests/*.o
rm -f libcppGoslin.so
rm -f *Test
rm -f writeGrammarsHeader
rm -f writeLipidEnums
rm -f libcppGoslin.a
make[1]: Leaving directory '/home/biocbuild/bbs-3.17-bioc/meat/rgoslin/src/cppgoslin'
make[1]: Entering directory '/home/biocbuild/bbs-3.17-bioc/meat/rgoslin/src/cppgoslin'
g++ -std=gnu++11 -g -O2  -Wall -I . -o writeGrammarsHeader writeGrammarsHeader.cpp && "./writeGrammarsHeader" "cppgoslin/parser/KnownGrammars.h"
g++ -std=gnu++11 -g -O2  -Wall -I . -o writeLipidEnums writeLipidEnums.cpp src/domain/StringFunctions.cpp src/parser/SumFormulaParserEventHandler.cpp src/parser/ParserClasses.cpp && "./writeLipidEnums" "src/domain/LipidClasses.cpp"
g++ -std=gnu++11 -g -O2  -Wall -I. -fPIC -o src/domain/Adduct.o -c src/domain/Adduct.cpp
g++ -std=gnu++11 -g -O2  -Wall -I. -fPIC -o src/domain/LipidMolecularSpecies.o -c src/domain/LipidMolecularSpecies.cpp
g++ -std=gnu++11 -g -O2  -Wall -I. -fPIC -o src/domain/LipidSnPosition.o -c src/domain/LipidSnPosition.cpp
g++ -std=gnu++11 -g -O2  -Wall -I. -fPIC -o src/domain/LipidStructureDefined.o -c src/domain/LipidStructureDefined.cpp
g++ -std=gnu++11 -g -O2  -Wall -I. -fPIC -o src/domain/FattyAcid.o -c src/domain/FattyAcid.cpp
g++ -std=gnu++11 -g -O2  -Wall -I. -fPIC -o src/domain/LipidAdduct.o -c src/domain/LipidAdduct.cpp
g++ -std=gnu++11 -g -O2  -Wall -I. -fPIC -o src/domain/LipidSpecies.o -c src/domain/LipidSpecies.cpp
g++ -std=gnu++11 -g -O2  -Wall -I. -fPIC -o src/domain/LipidFullStructure.o -c src/domain/LipidFullStructure.cpp
g++ -std=gnu++11 -g -O2  -Wall -I. -fPIC -o src/domain/LipidCompleteStructure.o -c src/domain/LipidCompleteStructure.cpp
g++ -std=gnu++11 -g -O2  -Wall -I. -fPIC -o src/domain/LipidSpeciesInfo.o -c src/domain/LipidSpeciesInfo.cpp
g++ -std=gnu++11 -g -O2  -Wall -I. -fPIC -o src/domain/StringFunctions.o -c src/domain/StringFunctions.cpp
g++ -std=gnu++11 -g -O2  -Wall -I. -fPIC -o src/domain/LipidClasses.o -c src/domain/LipidClasses.cpp
src/domain/LipidClasses.cpp: In constructor ‘goslin::LipidClasses::LipidClasses()’:
src/domain/LipidClasses.cpp:34:1: note: variable tracking size limit exceeded with ‘-fvar-tracking-assignments’, retrying without
   34 | LipidClasses::LipidClasses(){
      | ^~~~~~~~~~~~
g++ -std=gnu++11 -g -O2  -Wall -I. -fPIC -o src/domain/DoubleBonds.o -c src/domain/DoubleBonds.cpp
g++ -std=gnu++11 -g -O2  -Wall -I. -fPIC -o src/domain/FunctionalGroup.o -c src/domain/FunctionalGroup.cpp
g++ -std=gnu++11 -g -O2  -Wall -I. -fPIC -o src/domain/Headgroup.o -c src/domain/Headgroup.cpp
g++ -std=gnu++11 -g -O2  -Wall -I. -fPIC -o src/domain/Cycle.o -c src/domain/Cycle.cpp
g++ -std=gnu++11 -g -O2  -Wall -I. -fPIC -o src/domain/GenericDatastructures.o -c src/domain/GenericDatastructures.cpp
g++ -std=gnu++11 -g -O2  -Wall -I. -fPIC -o src/parser/ParserClasses.o -c src/parser/ParserClasses.cpp
g++ -std=gnu++11 -g -O2  -Wall -I. -fPIC -o src/parser/KnownParsers.o -c src/parser/KnownParsers.cpp
g++ -std=gnu++11 -g -O2  -Wall -I. -fPIC -o src/parser/GoslinParserEventHandler.o -c src/parser/GoslinParserEventHandler.cpp
g++ -std=gnu++11 -g -O2  -Wall -I. -fPIC -o src/parser/LipidMapsParserEventHandler.o -c src/parser/LipidMapsParserEventHandler.cpp
g++ -std=gnu++11 -g -O2  -Wall -I. -fPIC -o src/parser/SwissLipidsParserEventHandler.o -c src/parser/SwissLipidsParserEventHandler.cpp
g++ -std=gnu++11 -g -O2  -Wall -I. -fPIC -o src/parser/HmdbParserEventHandler.o -c src/parser/HmdbParserEventHandler.cpp
g++ -std=gnu++11 -g -O2  -Wall -I. -fPIC -o src/parser/SumFormulaParserEventHandler.o -c src/parser/SumFormulaParserEventHandler.cpp
g++ -std=gnu++11 -g -O2  -Wall -I. -fPIC -o src/parser/SumFormulaParser.o -c src/parser/SumFormulaParser.cpp
g++ -std=gnu++11 -g -O2  -Wall -I. -fPIC -o src/parser/ShorthandParserEventHandler.o -c src/parser/ShorthandParserEventHandler.cpp
g++ -std=gnu++11 -g -O2  -Wall -I. -fPIC -o src/parser/FattyAcidParserEventHandler.o -c src/parser/FattyAcidParserEventHandler.cpp
g++ -std=gnu++11 -g -O2  -Wall -I. -fPIC -o src/parser/LipidBaseParserEventHandler.o -c src/parser/LipidBaseParserEventHandler.cpp
ar rcs libcppGoslin.a src/domain/Adduct.o src/domain/LipidMolecularSpecies.o src/domain/LipidSnPosition.o src/domain/LipidStructureDefined.o src/domain/FattyAcid.o src/domain/LipidAdduct.o src/domain/LipidSpecies.o src/domain/LipidFullStructure.o src/domain/LipidCompleteStructure.o src/domain/LipidSpeciesInfo.o src/domain/StringFunctions.o src/domain/LipidClasses.o src/domain/DoubleBonds.o src/domain/FunctionalGroup.o src/domain/Headgroup.o src/domain/Cycle.o src/domain/GenericDatastructures.o src/parser/ParserClasses.o src/parser/KnownParsers.o src/parser/GoslinParserEventHandler.o src/parser/LipidMapsParserEventHandler.o src/parser/SwissLipidsParserEventHandler.o src/parser/HmdbParserEventHandler.o src/parser/SumFormulaParserEventHandler.o src/parser/SumFormulaParser.o src/parser/ShorthandParserEventHandler.o src/parser/FattyAcidParserEventHandler.o src/parser/LipidBaseParserEventHandler.o
make[1]: Leaving directory '/home/biocbuild/bbs-3.17-bioc/meat/rgoslin/src/cppgoslin'
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"." -I"./cppgoslin" -I"./cppgoslin/cppgoslin" -I"./cppgoslin/cppgoslin/domain" -I"./cppgoslin/cppgoslin/parser" -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"." -I"./cppgoslin" -I"./cppgoslin/cppgoslin" -I"./cppgoslin/cppgoslin/domain" -I"./cppgoslin/cppgoslin/parser" -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c rgoslin.cpp -o rgoslin.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o rgoslin.so RcppExports.o rgoslin.o cppgoslin/libcppGoslin.a -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.17-bioc/R/site-library/00LOCK-rgoslin/00new/rgoslin/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (rgoslin)