* installing *source* package ‘rtk’ ...
** this is package ‘rtk’ version ‘0.2.6.1’
** package ‘rtk’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘clang version 21.1.4’
using C++ compiler: ‘clang version 21.1.4’
using C++11
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/rtk/src'
/usr/local/clang21/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/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c ClStr2Mat.cpp -o ClStr2Mat.o
/usr/local/clang21/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/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c IO.cpp -o IO.o
/usr/local/clang21/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/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c Math.cpp -o Math.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;
| ^
/usr/local/clang21/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/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c Matrix.cpp -o Matrix.o
1 warning generated.
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;
| ^
/usr/local/clang21/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/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c RRare.cpp -o RRare.o
/usr/local/clang21/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/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c RcppExports.cpp -o RcppExports.o
RRare.cpp:307:7: warning: unused variable 'writeFiles' [-Wunused-variable]
307 | bool writeFiles = false;
| ^~~~~~~~~~
/usr/local/clang21/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/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c Rwrapper.cpp -o Rwrapper.o
6 warnings generated.
/usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c register.c -o register.o
1 warning generated.
/usr/local/clang21/bin/clang++ -std=gnu++11 -shared -L/usr/local/clang/lib64 -L/usr/local/clang21/lib -L/usr/local/clang21/lib/x86_64-unknown-linux-gnu -L/usr/local/lib64 -L/usr/local/clang21/lib/clang/21/lib/x86_64-unknown-linux-gnu -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)