* installing *source* package ‘rtk’ ...
** package ‘rtk’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘clang version 18.1.4’
using C++ compiler: ‘clang version 18.1.4’
using C++11
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/rtk/src'
/usr/local/clang18/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3   -c ClStr2Mat.cpp -o ClStr2Mat.o
/usr/local/clang18/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3   -c IO.cpp -o IO.o
In file included from IO.cpp:1:
./IO.h:147:6: warning: private field 'num_threads' is not used [-Wunused-private-field]
  147 |         int num_threads;
      |             ^
1 warning generated.
/usr/local/clang18/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3   -c Math.cpp -o Math.o
/usr/local/clang18/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3   -c Matrix.cpp -o Matrix.o
/usr/local/clang18/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3   -c RRare.cpp -o RRare.o
Matrix.cpp:439:7: warning: variable 'writeCnt' set but not used [-Wunused-but-set-variable]
  439 |         uint writeCnt(0);
      |              ^
Matrix.cpp:672:6: warning: unused variable 'ini_ColPerRow' [-Wunused-variable]
  672 |         int ini_ColPerRow = iniCols(in);
      |             ^~~~~~~~~~~~~
Matrix.cpp:686:6: warning: variable 'cnt' set but not used [-Wunused-but-set-variable]
  686 |         int cnt(-1), geneCnt(0);
      |             ^
Matrix.cpp:686:15: warning: variable 'geneCnt' set but not used [-Wunused-but-set-variable]
  686 |         int cnt(-1), geneCnt(0);
      |                      ^
Matrix.cpp:820:6: warning: variable 'geneCnt' set but not used [-Wunused-but-set-variable]
  820 |         int geneCnt(0);
      |             ^
Matrix.cpp:1399:6: warning: variable 'cnt' set but not used [-Wunused-but-set-variable]
 1399 |         int cnt = 0;
      |             ^
RRare.cpp:307:7: warning: unused variable 'writeFiles' [-Wunused-variable]
  307 |         bool writeFiles = false;
      |              ^~~~~~~~~~
/usr/local/clang18/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3   -c RcppExports.cpp -o RcppExports.o
/usr/local/clang18/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3   -c Rwrapper.cpp -o Rwrapper.o
1 warning generated.
6 warnings generated.
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c register.c -o register.o
/usr/local/clang18/bin/clang++ -std=gnu++11 -shared -L/usr/local/clang/lib64 -L/usr/local/clang18/lib -L/usr/local/clang18/lib/x86_64-unknown-linux-gnu -L/usr/local/gcc13/lib64 -L/usr/local/lib64 -o rtk.so ClStr2Mat.o IO.o Math.o Matrix.o RRare.o RcppExports.o Rwrapper.o register.o
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/rtk/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/rtk/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/rtk/src'
installing to /data/gannet/ripley/R/packages/tests-clang/rtk.Rcheck/00LOCK-rtk/00new/rtk/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** 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 (rtk)