* installing *source* package ‘missSOM’ ... ** this is package ‘missSOM’ version ‘1.0.1’ ** package ‘missSOM’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++ (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)’ make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/missSOM/src' g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c distance-functions.cpp -o distance-functions.o In file included from /data/gannet/ripley/R/R-devel/include/R.h:73, from distance-functions.h:4, from distance-functions.cpp:7: /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/exceptions/cpp11/exceptions.h: In function ‘void Rcpp::Rf_warning(const char*, Args&& ...) [with Args = {const char*}]’: /data/gannet/ripley/R/R-devel/include/R_ext/Error.h:108:17: warning: infinite recursion detected [-Winfinite-recursion] 108 | #define warning Rf_warning | ^~~~~~~~~~ /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/exceptions/cpp11/exceptions.h:46:13: note: in expansion of macro ‘warning’ 46 | inline void warning(const char* fmt, Args&&... args ) { | ^~~~~~~ In file included from /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/exceptions.h:180, from /data/gannet/ripley/R/test-dev/Rcpp/include/RcppCommon.h:130, from /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp.h:27, from distance-functions.h:5: /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/exceptions/cpp11/exceptions.h:47:15: note: recursive call 47 | Rf_warning("%s", tfm::format(fmt, std::forward<Args>(args)... ).c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c imputeSOM.cpp -o imputeSOM.o imputeSOM.cpp: In function ‘Rcpp::List RcppImputeSOM(Rcpp::NumericMatrix, Rcpp::NumericMatrix, Rcpp::NumericMatrix, Rcpp::ExpressionVector, Rcpp::NumericMatrix, int, Rcpp::NumericVector, Rcpp::NumericVector, int, bool, Rcpp::IntegerVector, Rcpp::IntegerVector)’: imputeSOM.cpp:177:45: warning: ‘threshold’ may be used uninitialized [-Wmaybe-uninitialized] 177 | tmp_bis = neighbourhoodFunctionPtr(pNeighbourhoodDistances[numCodes * nearest + cd], threshold); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ imputeSOM.cpp:63:25: note: ‘threshold’ was declared here 63 | double distance, tmp, threshold, alpha; | ^~~~~~~~~ g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c map.cpp -o map.o g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c neighbourhood-functions.cpp -o neighbourhood-functions.o g++ -std=gnu++17 -shared -L/usr/local/lib64 -o missSOM.so RcppExports.o distance-functions.o imputeSOM.o map.o neighbourhood-functions.o -fopenmp make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/missSOM/src' make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/missSOM/src' make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/missSOM/src' installing to /data/gannet/ripley/R/packages/tests-devel/missSOM.Rcheck/00LOCK-missSOM/00new/missSOM/libs ** R ** data ** 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 (missSOM)