* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘aphid’ ...
** this is package ‘aphid’ version ‘1.3.5’
** package ‘aphid’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-14 (Debian 14.3.0-10) 14.3.0’
using C++11
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpawTVfI/R.INSTALL101371201b5960/aphid/src'
g++-14 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-patched-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++-14 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-patched-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++-14 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-patched-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++-14 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-patched-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++-14 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-patched-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++-14 -std=gnu++11 -shared -L/home/hornik/tmp/R.check/r-patched-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-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpawTVfI/R.INSTALL101371201b5960/aphid/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpawTVfI/R.INSTALL101371201b5960/aphid/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpawTVfI/R.INSTALL101371201b5960/aphid/src'
installing to /home/hornik/tmp/R.check/r-patched-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
  converting help for package ‘aphid’
    finding HTML links ... done
    Viterbi                                 html  
    align                                   html  
    aphid                                   html  
    backward                                html  
    casino                                  html  
    deriveHMM                               html  
    derivePHMM                              html  
    forward                                 html  
    generate                                html  
    globins                                 html  
    logsum                                  html  
    map                                     html  
    plot.HMM                                html  
    plot.PHMM                               html  
    posterior                               html  
    print                                   html  
    readPHMM                                html  
    substitution                            html  
    train                                   html  
    unalign                                 html  
    weight                                  html  
    writePHMM                               html  
** 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 (aphid)