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### Running command:
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###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL Aerith
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* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘Aerith’ ...
** this is package ‘Aerith’ version ‘0.99.11’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
using C++17
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I. -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I. -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security  -c extractPSMfeatures.cpp -o extractPSMfeatures.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I. -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security  -c filterPSMs.cpp -o filterPSMs.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I. -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security  -c filterPeptides.cpp -o filterPeptides.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I. -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security  -c generateCFG.cpp -o generateCFG.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I. -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security  -c getISOpeak.cpp -o getISOpeak.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I. -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security  -c readScan.cpp -o readScan.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I. -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security  -c readScans.cpp -o readScans.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I. -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security  -c readSips.cpp -o readSips.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I. -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security  -c readSpe2Peps.cpp -o readSpe2Peps.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I. -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security  -c scorePSM.cpp -o scorePSM.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I. -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security  -c writeScans.cpp -o writeScans.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I. -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security  -c lib/PSMfeatureExtractor.cpp -o lib/PSMfeatureExtractor.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I. -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security  -c lib/PSMpeakAnnotator.cpp -o lib/PSMpeakAnnotator.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I. -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security  -c lib/PSMsFiltrator.cpp -o lib/PSMsFiltrator.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I. -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security  -c lib/Spe2PepFileReader.cpp -o lib/Spe2PepFileReader.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I. -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security  -c lib/averagine.cpp -o lib/averagine.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I. -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security  -c lib/cfgParser.cpp -o lib/cfgParser.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I. -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security  -c lib/ftFileReader.cpp -o lib/ftFileReader.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I. -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security  -c lib/ftFileWriter.cpp -o lib/ftFileWriter.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I. -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security  -c lib/isotopologue.cpp -o lib/isotopologue.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I. -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security  -c lib/ms2scan.cpp -o lib/ms2scan.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I. -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security  -c lib/peptide.cpp -o lib/peptide.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I. -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security  -c lib/peptidesFiltrator.cpp -o lib/peptidesFiltrator.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I. -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security  -c lib/proNovoConfig.cpp -o lib/proNovoConfig.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I. -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security  -c lib/sipFileReader.cpp -o lib/sipFileReader.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I. -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security  -c lib/sipGenerator.cpp -o lib/sipGenerator.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I. -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security  -c lib/sipPSM.cpp -o lib/sipPSM.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.23-bioc/R/lib -L/usr/local/lib -o Aerith.so RcppExports.o extractPSMfeatures.o filterPSMs.o filterPeptides.o generateCFG.o getISOpeak.o readScan.o readScans.o readSips.o readSpe2Peps.o scorePSM.o writeScans.o lib/PSMfeatureExtractor.o lib/PSMpeakAnnotator.o lib/PSMsFiltrator.o lib/Spe2PepFileReader.o lib/averagine.o lib/cfgParser.o lib/ftFileReader.o lib/ftFileWriter.o lib/isotopologue.o lib/ms2scan.o lib/peptide.o lib/peptidesFiltrator.o lib/proNovoConfig.o lib/sipFileReader.o lib/sipGenerator.o lib/sipPSM.o -fopenmp -L/home/biocbuild/bbs-3.23-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.23-bioc/R/site-library/00LOCK-Aerith/00new/Aerith/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 (Aerith)