Install log for 'landsepi'

* installing *source* package ‘landsepi’ ...
** package ‘landsepi’ successfully unpacked and MD5 sums checked
** using staged installation
configure: /data/gannet/ripley/R/R-clang
checking whether to build debug version... no
checking whether to build profiling version... no
configure: /data/gannet/ripley/R/R-clang
checking for Rcpp package... yes
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether /usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 accepts -g... yes
checking for cos in -lm... yes
checking for cblas_dgemm in -lgslcblas... yes
checking for gsl_blas_dgemm in -lgsl... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C++ compiler: ‘clang version 19.1.3’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/landsepi/src'
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/testthat/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include   -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -DR_NO_REMAP -c Basic_patho.cpp -o Basic_patho.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/testthat/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include   -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -DR_NO_REMAP -c Croptype.cpp -o Croptype.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/testthat/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include   -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -DR_NO_REMAP -c Cultivar.cpp -o Cultivar.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/testthat/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include   -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -DR_NO_REMAP -c Gene.cpp -o Gene.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/testthat/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include   -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -DR_NO_REMAP -c Model.cpp -o Model.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/testthat/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include   -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o
Model.cpp:1271:10: warning: unused variable 'duration' [-Wunused-variable]
 1271 |     auto duration = duration_cast<seconds>(stop - start); 
      |          ^~~~~~~~
1 warning generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/testthat/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include   -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -DR_NO_REMAP -c Treatment.cpp -o Treatment.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/testthat/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include   -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -DR_NO_REMAP -c functions.cpp -o functions.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/testthat/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include   -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -DR_NO_REMAP -c gprof.cpp -o gprof.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/testthat/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include   -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -DR_NO_REMAP -c initialisation.cpp -o initialisation.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/testthat/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include   -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -DR_NO_REMAP -c printReadWrite.cpp -o printReadWrite.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -shared -L/usr/local/clang/lib64 -L/usr/local/clang19/lib -L/usr/local/clang19/lib/x86_64-unknown-linux-gnu -L/usr/local/gcc14/lib64 -L/usr/local/lib64 -o landsepi.so Basic_patho.o Croptype.o Cultivar.o Gene.o Model.o RcppExports.o Treatment.o functions.o gprof.o initialisation.o printReadWrite.o -L/usr/local/clang/lib64 -L/usr/local/clang19/lib -L/usr/local/clang19/lib/x86_64-unknown-linux-gnu -L/usr/local/gcc14/lib64 -L/usr/local/lib64 -lgsl -lgslcblas -lm
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/landsepi/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/landsepi/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/landsepi/src'
installing to /data/gannet/ripley/R/packages/tests-clang/landsepi.Rcheck/00LOCK-landsepi/00new/landsepi/libs
** 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
** 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 (landsepi)