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### Running command:
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###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL FLAMES
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* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘FLAMES’ ...
** this is package ‘FLAMES’ version ‘2.1.4’
** using non-staged installation via StagedInstall field
** 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-3.21-bioc/R/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -DR_NO_REMAP -c RcppFunctions.cpp -o RcppFunctions.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -DR_NO_REMAP -c classes/BamRecord.cpp -o classes/BamRecord.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -DR_NO_REMAP -c classes/GFFRecord.cpp -o classes/GFFRecord.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -DR_NO_REMAP -c classes/GeneAnnotationParser.cpp -o classes/GeneAnnotationParser.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -DR_NO_REMAP -c classes/Isoforms.cpp -o classes/Isoforms.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -DR_NO_REMAP -c classes/junctions.cpp -o classes/junctions.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -DR_NO_REMAP -c main-functions/find_isoform.cpp -o main-functions/find_isoform.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -DR_NO_REMAP -c main-functions/flexiplex.cpp -o main-functions/flexiplex.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -DR_NO_REMAP -c main-functions/get_transcript_seq.cpp -o main-functions/get_transcript_seq.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -DR_NO_REMAP -c main-functions/group_bam2isoform.cpp -o main-functions/group_bam2isoform.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -DR_NO_REMAP -c main-functions/pileup_readid.cpp -o main-functions/pileup_readid.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -DR_NO_REMAP -c tests/test-junctions.cpp -o tests/test-junctions.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -DR_NO_REMAP -c tests/test-parsing.cpp -o tests/test-parsing.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -DR_NO_REMAP -c utility/cigars.cpp -o utility/cigars.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -DR_NO_REMAP -c utility/edlib-1.2.7/edlib.cpp -o utility/edlib-1.2.7/edlib.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -c utility/bam.c -o utility/bam.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.21-bioc/R/lib -L/usr/local/lib -o FLAMES.so RcppExports.o RcppFunctions.o classes/BamRecord.o classes/GFFRecord.o classes/GeneAnnotationParser.o classes/Isoforms.o classes/junctions.o main-functions/find_isoform.o main-functions/flexiplex.o main-functions/get_transcript_seq.o main-functions/group_bam2isoform.o main-functions/pileup_readid.o tests/test-junctions.o tests/test-parsing.o utility/cigars.o utility/edlib-1.2.7/edlib.o utility/bam.o -pthread -lz /home/biocbuild/bbs-3.21-bioc/R/site-library/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -L/home/biocbuild/bbs-3.21-bioc/R/lib -lR
if test -e "/usr/bin/strip" & test -e "/bin/uname" & [[ `uname` == "Linux" ]] ; then /usr/bin/strip --strip-debug FLAMES.so; fi
installing to /home/biocbuild/bbs-3.21-bioc/R/site-library/FLAMES/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (FLAMES)