* installing *source* package 'aphid' ...
** package 'aphid' successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: 'g++.exe (GCC) 13.2.0'
using C++11
make[1]: Entering directory '/d/temp/RtmpWoQlmC/R.INSTALL692426d6d8e/aphid/src'
g++  -std=gnu++11 -I"D:/RCompile/recent/R/include" -DNDEBUG  -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include'   -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c RcppExports.cpp -o RcppExports.o
g++  -std=gnu++11 -I"D:/RCompile/recent/R/include" -DNDEBUG  -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include'   -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c ViterbiC.cpp -o ViterbiC.o
g++  -std=gnu++11 -I"D:/RCompile/recent/R/include" -DNDEBUG  -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include'   -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c init.cpp -o init.o
g++  -std=gnu++11 -I"D:/RCompile/recent/R/include" -DNDEBUG  -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include'   -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -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++  -std=gnu++11 -I"D:/RCompile/recent/R/include" -DNDEBUG  -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include'   -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c utils.cpp -o utils.o
g++ -shared -s -static-libgcc -o aphid.dll tmp.def RcppExports.o ViterbiC.o init.o map.o utils.o -Ld:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -Ld:/rtools44/x86_64-w64-mingw32.static.posix/lib -LD:/RCompile/recent/R/bin/x64 -lR
make[1]: Leaving directory '/d/temp/RtmpWoQlmC/R.INSTALL692426d6d8e/aphid/src'
make[1]: Entering directory '/d/temp/RtmpWoQlmC/R.INSTALL692426d6d8e/aphid/src'
make[1]: Leaving directory '/d/temp/RtmpWoQlmC/R.INSTALL692426d6d8e/aphid/src'
installing to d:/Rcompile/CRANpkg/lib/4.5/00LOCK-aphid/00new/aphid/libs/x64
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* MD5 sums
packaged installation of 'aphid' as aphid_1.3.5.zip
* DONE (aphid)