Install log for 'mets'

* installing *source* package ‘mets’ ...
** this is package ‘mets’ version ‘1.3.9’
** package ‘mets’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘clang version 22.1.1 (https://github.com/llvm/llvm-project fef02d48c08db859ef83f84232ed78bd9d1c323a)’
using Fortran compiler: ‘flang version 22.1.1 (https://github.com/llvm/llvm-project fef02d48c08db859ef83f84232ed78bd9d1c323a)’
using C++ compiler: ‘clang version 22.1.1 (https://github.com/llvm/llvm-project fef02d48c08db859ef83f84232ed78bd9d1c323a)’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/mets/src'
clang++-22 -stdlib=libc++ -std=gnu++20 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/mvtnorm/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include   -fopenmp -I../inst/include -DNDEBUG -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c RcppExports.cpp -o RcppExports.o
clang++-22 -stdlib=libc++ -std=gnu++20 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/mvtnorm/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include   -fopenmp -I../inst/include -DNDEBUG -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c aalenfrailty.cpp -o aalenfrailty.o
clang++-22 -stdlib=libc++ -std=gnu++20 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/mvtnorm/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include   -fopenmp -I../inst/include -DNDEBUG -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c apply.cpp -o apply.o
clang++-22 -stdlib=libc++ -std=gnu++20 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/mvtnorm/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include   -fopenmp -I../inst/include -DNDEBUG -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c binomial-twostage.cpp -o binomial-twostage.o
clang++-22 -stdlib=libc++ -std=gnu++20 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/mvtnorm/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include   -fopenmp -I../inst/include -DNDEBUG -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c biprobit.cpp -o biprobit.o
clang++-22 -stdlib=libc++ -std=gnu++20 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/mvtnorm/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include   -fopenmp -I../inst/include -DNDEBUG -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c claytonoakes.cpp -o claytonoakes.o
clang++-22 -stdlib=libc++ -std=gnu++20 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/mvtnorm/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include   -fopenmp -I../inst/include -DNDEBUG -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c clusterindex.cpp -o clusterindex.o
clang++-22 -stdlib=libc++ -std=gnu++20 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/mvtnorm/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include   -fopenmp -I../inst/include -DNDEBUG -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c cor.cpp -o cor.o
clang++-22 -stdlib=libc++ -std=gnu++20 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/mvtnorm/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include   -fopenmp -I../inst/include -DNDEBUG -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c fastcox.cpp -o fastcox.o
clang++-22 -stdlib=libc++ -std=gnu++20 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/mvtnorm/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include   -fopenmp -I../inst/include -DNDEBUG -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c mvn.cpp -o mvn.o
clang++-22 -stdlib=libc++ -std=gnu++20 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/mvtnorm/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include   -fopenmp -I../inst/include -DNDEBUG -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c pch.cpp -o pch.o
clang++-22 -stdlib=libc++ -std=gnu++20 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/mvtnorm/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include   -fopenmp -I../inst/include -DNDEBUG -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c prop-odd.cpp -o prop-odd.o
clang-22 -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/mvtnorm/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c randomF77.c -o randomF77.o
clang++-22 -stdlib=libc++ -std=gnu++20 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/mvtnorm/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include   -fopenmp -I../inst/include -DNDEBUG -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c sim-tools.cpp -o sim-tools.o
clang++-22 -stdlib=libc++ -std=gnu++20 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/mvtnorm/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include   -fopenmp -I../inst/include -DNDEBUG -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c survival-twostage.cpp -o survival-twostage.o
clang++-22 -stdlib=libc++ -std=gnu++20 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/mvtnorm/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include   -fopenmp -I../inst/include -DNDEBUG -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c tools.cpp -o tools.o
flang-22  -fpic  -O2 -pedantic  -c tvpack.f -o tvpack.o
./tvpack.f:293:24: warning: Value of uninitialized local variable 'wg' is used but never defined [-Wused-undefined-variable]
        DOUBLE PRECISION WG(0:(N+1)/2), WGK(0:N), XGK(0:N) 
                         ^^
./tvpack.f:293:39: warning: Value of uninitialized local variable 'wgk' is used but never defined [-Wused-undefined-variable]
        DOUBLE PRECISION WG(0:(N+1)/2), WGK(0:N), XGK(0:N) 
                                        ^^^
./tvpack.f:293:49: warning: Value of uninitialized local variable 'xgk' is used but never defined [-Wused-undefined-variable]
        DOUBLE PRECISION WG(0:(N+1)/2), WGK(0:N), XGK(0:N) 
                                                  ^^^
./tvpack.f:575:24: warning: Value of uninitialized local variable 'x' is used but never defined [-Wused-undefined-variable]
        DOUBLE PRECISION X(10,3), W(10,3), AS, A, B, C, D, RS, XS, BVN 
                         ^
./tvpack.f:575:33: warning: Value of uninitialized local variable 'w' is used but never defined [-Wused-undefined-variable]
        DOUBLE PRECISION X(10,3), W(10,3), AS, A, B, C, D, RS, XS, BVN 
                                  ^
survival-twostage.cpp:2077:57: warning: variable 'sdj' set but not used [-Wunused-but-set-variable]
 2077 |  double dl1,dl2,ll1,ll2,ll=1,Li,Lk,diff=0,loglikecont=0,sdj=0;
      |                                                         ^
survival-twostage.cpp:2762:21: warning: variable 'thetak' set but not used [-Wunused-but-set-variable]
 2762 |  double llt=1,ssf=0,thetak=0; 
      |                     ^
clang++-22 -stdlib=libc++ -std=gnu++20 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/mvtnorm/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include   -fopenmp -I../inst/include -DNDEBUG -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c weibull.cpp -o weibull.o
2 warnings generated.
clang++-22 -stdlib=libc++ -std=gnu++20 -shared -L/usr/local/clang/lib64 -L/usr/local/clang22/lib -L/usr/local/clang22/lib/x86_64-unknown-linux-gnu -L/usr/local/lib64 -L/usr/local/clang21/lib/clang/22/lib/x86_64-unknown-linux-gnu -o mets.so RcppExports.o aalenfrailty.o apply.o binomial-twostage.o biprobit.o claytonoakes.o clusterindex.o cor.o fastcox.o mvn.o pch.o prop-odd.o randomF77.o sim-tools.o survival-twostage.o tools.o tvpack.o weibull.o -fopenmp -L/data/gannet/ripley/R/R-clang/lib -lRlapack -L/data/gannet/ripley/R/R-clang/lib -lRblas -lflang_rt.runtime -lm -lflang_rt.runtime -lm
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/mets/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/mets/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/mets/src'
installing to /data/gannet/ripley/R/packages/tests-clang/mets.Rcheck/00LOCK-mets/00new/mets/libs
** R
** data
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (mets)