* installing *source* package ‘BatchMap’ ...
** package ‘BatchMap’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
make[2]: Entering directory '/data/gannet/ripley/R/packages/tests-LTO/BatchMap/src'
g++ -std=gnu++11 -I"/data/gannet/ripley/R/LTO9/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-3.7/Rcpp/include' -I'/data/gannet/ripley/R/test-3.7/RcppArmadillo/include' -I/usr/local/include   -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-deprecated-declarations -Wno-parentheses -flto -c GET_RF.cpp -o GET_RF.o
g++ -std=gnu++11 -I"/data/gannet/ripley/R/LTO9/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-3.7/Rcpp/include' -I'/data/gannet/ripley/R/test-3.7/RcppArmadillo/include' -I/usr/local/include   -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-deprecated-declarations -Wno-parentheses -flto -c READ_OUTCROSS.cpp -o READ_OUTCROSS.o
In file included from READ_OUTCROSS.cpp:9:
progressBar.h: In constructor ‘progressBar::progressBar(short unsigned int, long unsigned int, bool)’:
progressBar.h:21:7: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
   21 |       if(_type == 1)
      |       ^~
progressBar.h:25:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
   25 |         Rcpp::Rcout << "[";
      |         ^~~~
g++ -std=gnu++11 -I"/data/gannet/ripley/R/LTO9/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-3.7/Rcpp/include' -I'/data/gannet/ripley/R/test-3.7/RcppArmadillo/include' -I/usr/local/include   -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-deprecated-declarations -Wno-parentheses -flto -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/data/gannet/ripley/R/LTO9/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-3.7/Rcpp/include' -I'/data/gannet/ripley/R/test-3.7/RcppArmadillo/include' -I/usr/local/include   -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-deprecated-declarations -Wno-parentheses -flto -c find_bins.cpp -o find_bins.o
find_bins.cpp: In function ‘int check_occurrence(std::vector<int>&, int)’:
find_bins.cpp:124:3: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
  124 |   for(unsigned int i = 0; i < v.size(); i++)
      |   ^~~
find_bins.cpp:127:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
  127 |     return(-1);
      |     ^~~~~~
g++ -std=gnu++11 -I"/data/gannet/ripley/R/LTO9/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-3.7/Rcpp/include' -I'/data/gannet/ripley/R/test-3.7/RcppArmadillo/include' -I/usr/local/include   -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-deprecated-declarations -Wno-parentheses -flto -c hmm_out.cpp -o hmm_out.o
g++ -std=gnu++11 -I"/data/gannet/ripley/R/LTO9/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-3.7/Rcpp/include' -I'/data/gannet/ripley/R/test-3.7/RcppArmadillo/include' -I/usr/local/include   -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-deprecated-declarations -Wno-parentheses -flto -c out_est.cpp -o out_est.o
g++ -std=gnu++11 -I"/data/gannet/ripley/R/LTO9/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-3.7/Rcpp/include' -I'/data/gannet/ripley/R/test-3.7/RcppArmadillo/include' -I/usr/local/include   -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-deprecated-declarations -Wno-parentheses -flto -c record.cpp -o record.o
g++ -std=gnu++11 -I"/data/gannet/ripley/R/LTO9/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-3.7/Rcpp/include' -I'/data/gannet/ripley/R/test-3.7/RcppArmadillo/include' -I/usr/local/include   -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-deprecated-declarations -Wno-parentheses -flto -c twopts_out.cpp -o twopts_out.o
In file included from twopts_out.cpp:38:
progressBar.h: In constructor ‘progressBar::progressBar(short unsigned int, long unsigned int, bool)’:
progressBar.h:21:7: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
   21 |       if(_type == 1)
      |       ^~
progressBar.h:25:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
   25 |         Rcpp::Rcout << "[";
      |         ^~~~
g++ -std=gnu++11 -I"/data/gannet/ripley/R/LTO9/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-3.7/Rcpp/include' -I'/data/gannet/ripley/R/test-3.7/RcppArmadillo/include' -I/usr/local/include   -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-deprecated-declarations -Wno-parentheses -flto -c utils.cpp -o utils.o
g++ -std=gnu++11 -shared -L/usr/local/lib64 -o BatchMap.so GET_RF.o READ_OUTCROSS.o RcppExports.o find_bins.o hmm_out.o out_est.o record.o twopts_out.o utils.o
RcppExports.cpp:53:17: warning: ‘get_bins’ violates the C++ One Definition Rule [-Wodr]
   53 | RcppExport SEXP get_bins(SEXP, SEXP, SEXP);
      |                 ^
find_bins.cpp:48:17: note: type mismatch in parameter 3
   48 | RcppExport SEXP get_bins(SEXP geno_R, SEXP exact_R)
      |                 ^
find_bins.cpp:48:17: note: type ‘void’ should match type ‘struct SEXPREC *’
find_bins.cpp:48:17: note: ‘get_bins’ was previously declared here
make[2]: Leaving directory '/data/gannet/ripley/R/packages/tests-LTO/BatchMap/src'
installing to /data/gannet/ripley/R/packages/tests-LTO/Libs/BatchMap-lib/00LOCK-BatchMap/00new/BatchMap/libs
** R
** data
** 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 (BatchMap)
Time 8:12.46, 128.24 + 7.50