* installing to library ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages’
* installing *source* package ‘aphid’ ...
** package ‘aphid’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-13 (Debian 13.2.0-23) 13.2.0’
using C++11
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpHtQKjc/R.INSTALL1d2f75fe0ff52/aphid/src'
g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c RcppExports.cpp -o RcppExports.o
g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c ViterbiC.cpp -o ViterbiC.o
g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c init.cpp -o init.o
g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c map.cpp -o map.o
map.cpp: In function ‘Rcpp::LogicalVector map(Rcpp::NumericMatrix, Rcpp::LogicalMatrix, Rcpp::List, Rcpp::NumericVector, Rcpp::NumericVector, double)’:
map.cpp:52:25: warning: suggest parentheses around operand of ‘!’ or change ‘&’ to ‘&&’ or ‘!’ to ‘~’ [-Wparentheses]
   52 |         tcounts(_, 0) = !notgaps(_, i) & !notgaps(_, j) & zeroinserts;
      |                         ^~~~~~~~~~~~~~
map.cpp:53:25: warning: suggest parentheses around operand of ‘!’ or change ‘&’ to ‘&&’ or ‘!’ to ‘~’ [-Wparentheses]
   53 |         tcounts(_, 1) = !notgaps(_, i) & notgaps(_, j) & zeroinserts;
      |                         ^~~~~~~~~~~~~~
map.cpp:54:25: warning: suggest parentheses around operand of ‘!’ or change ‘&’ to ‘&&’ or ‘!’ to ‘~’ [-Wparentheses]
   54 |         tcounts(_, 2) = !notgaps(_, i) & !zeroinserts;
      |                         ^~~~~~~~~~~~~~
map.cpp:58:25: warning: suggest parentheses around operand of ‘!’ or change ‘&’ to ‘&&’ or ‘!’ to ‘~’ [-Wparentheses]
   58 |         tcounts(_, 6) = !notgaps(_, j) & !zeroinserts;
      |                         ^~~~~~~~~~~~~~
map.cpp:71:25: warning: suggest parentheses around operand of ‘!’ or change ‘&’ to ‘&&’ or ‘!’ to ‘~’ [-Wparentheses]
   71 |         tcounts(_, 0) = !notgaps(_, i) & !notgaps(_, j); //DD
      |                         ^~~~~~~~~~~~~~
map.cpp:72:25: warning: suggest parentheses around operand of ‘!’ or change ‘&’ to ‘&&’ or ‘!’ to ‘~’ [-Wparentheses]
   72 |         tcounts(_, 1) = !notgaps(_, i) & notgaps(_, j); //DM
      |                         ^~~~~~~~~~~~~~
g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c utils.cpp -o utils.o
g++-13 -std=gnu++11 -shared -L/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib -Wl,-O1 -o aphid.so RcppExports.o ViterbiC.o init.o map.o utils.o -L/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpHtQKjc/R.INSTALL1d2f75fe0ff52/aphid/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpHtQKjc/R.INSTALL1d2f75fe0ff52/aphid/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpHtQKjc/R.INSTALL1d2f75fe0ff52/aphid/src'
installing to /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/00LOCK-aphid/00new/aphid/libs
** R
** data
*** moving datasets to lazyload DB
** 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
* creating tarball
packaged installation of ‘aphid’ as ‘aphid_1.3.5_R_x86_64-pc-linux-gnu.tar.gz’
* DONE (aphid)