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### Running command:
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###   /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL pqsfinder
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* installing to library ‘/home/biocbuild/R/R-4.3.1/site-library’
* installing *source* package ‘pqsfinder’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 10.3.1’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/BH/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/BH/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c pqsfinder.cpp -o pqsfinder.o
pqsfinder.cpp: In function ‘void find_all_runs(SEXP, int, std::__cxx11::basic_string<char>::const_iterator, std::__cxx11::basic_string<char>::const_iterator, run_match*, const regex&, const opts_t&, const scoring&, const const_iterator&, size_t, storage&, int&, results&, bool, std::chrono::_V2::system_clock::time_point, int, int, int, int&, bool)’:
pqsfinder.cpp:582:22: warning: ‘loop_len’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  582 |         find_all_runs(
      |         ~~~~~~~~~~~~~^
  583 |           subject, i+1, e, end, m, run_re_c, opts, sc, ref, len,
      |           ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  584 |           pqs_storage, int_cnt, res, (loop_len == 0 ? true : zero_loop),
      |           ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  585 |           s_time, next_tetrad_count, next_defect_count, next_loop_sum, fn_call_count, show_progress
      |           ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  586 |         );
      |         ~             
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/BH/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c boost_regex/posix_api.cpp -o boost_regex/posix_api.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/BH/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c boost_regex/regex.cpp -o boost_regex/regex.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/BH/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c boost_regex/regex_debug.cpp -o boost_regex/regex_debug.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/BH/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c boost_regex/static_mutex.cpp -o boost_regex/static_mutex.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/BH/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c boost_regex/wide_posix_api.cpp -o boost_regex/wide_posix_api.o
mkdir -p "/home/biocbuild/R/R-4.3.1/site-library/00LOCK-pqsfinder/00new/pqsfinder/lib"
ar rs "/home/biocbuild/R/R-4.3.1/site-library/00LOCK-pqsfinder/00new/pqsfinder/lib/libboost_regex.a" boost_regex/posix_api.o boost_regex/regex.o boost_regex/regex_debug.o boost_regex/static_mutex.o boost_regex/wide_posix_api.o
ar: creating /home/biocbuild/R/R-4.3.1/site-library/00LOCK-pqsfinder/00new/pqsfinder/lib/libboost_regex.a
g++ -std=gnu++11 -shared -L/home/biocbuild/R/R-4.3.1/lib -L/usr/local/lib -o pqsfinder.so RcppExports.o pqsfinder.o /home/biocbuild/R/R-4.3.1/site-library/00LOCK-pqsfinder/00new/pqsfinder/lib/libboost_regex.a -L/home/biocbuild/R/R-4.3.1/lib -lR
installing to /home/biocbuild/R/R-4.3.1/site-library/00LOCK-pqsfinder/00new/pqsfinder/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 (pqsfinder)