- using R Under development (unstable) (2025-10-22 r88968)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
clang version 21.1.4
flang version 21.1.4
- running under: Fedora Linux 42 (Workstation Edition)
- using session charset: UTF-8
- using option ‘--no-stop-on-test-error’
- checking for file ‘gkwreg/DESCRIPTION’ ... OK
- this is package ‘gkwreg’ version ‘1.0.10’
- package encoding: UTF-8
- checking package namespace information ... OK
- checking package dependencies ... INFO
Package suggested but not available for checking: ‘simplexreg’
- checking if this is a source package ... OK
- checking if there is a namespace ... OK
- checking for executable files ... OK
- checking for hidden files and directories ... OK
- checking for portable file names ... OK
- checking for sufficient/correct file permissions ... OK
- checking whether package ‘gkwreg’ can be installed ... [16m/25m] OK
See the install log for details.
- used C++ compiler: ‘clang version 21.1.4’
- checking installed package size ... OK
- checking package directory ... OK
- checking DESCRIPTION meta-information ... OK
- checking top-level files ... OK
- checking for left-over files ... OK
- checking index information ... OK
- checking package subdirectories ... OK
- checking code files for non-ASCII characters ... OK
- checking R files for syntax errors ... OK
- checking whether the package can be loaded ... OK
- checking whether the package can be loaded with stated dependencies ... [0m/30m] WARNING
using C++ compiler: ‘clang version 21.1.4’
make[1]: Entering directory '/tmp/RtmpywcjOz/working_dir/RtmpNGwyU6/gkwbetareg_compile_20251025231840'
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I"/data/gannet/ripley/R/test-clang/TMB/include" -I"/data/gannet/ripley/R/test-clang/RcppEigen/include" -DTMB_EIGEN_DISABLE_WARNINGS -DTMB_LIB_INIT=R_init_gkwbetareg -DCPPAD_FRAMEWORK -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 /tmp/RtmpywcjOz/working_dir/RtmpNGwyU6/gkwbetareg_compile_20251025231840/gkwbetareg.cpp -o /tmp/RtmpywcjOz/working_dir/RtmpNGwyU6/gkwbetareg_compile_20251025231840/gkwbetareg.o
In file included from /tmp/RtmpywcjOz/working_dir/RtmpNGwyU6/gkwbetareg_compile_20251025231840/gkwbetareg.cpp:17:
In file included from /data/gannet/ripley/R/test-clang/TMB/include/TMB.hpp:96:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:26:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/SparseCore:61:
/data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable]
273 | Index count = 0;
| ^
In file included from /tmp/RtmpywcjOz/working_dir/RtmpNGwyU6/gkwbetareg_compile_20251025231840/gkwbetareg.cpp:17:
In file included from /data/gannet/ripley/R/test-clang/TMB/include/TMB.hpp:96:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:29:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/SparseLU:35:
/data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable]
78 | Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree
| ^
/data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable]
79 | Index nsuper_et = 0; // Number of relaxed snodes in the original etree
| ^
3 warnings generated.
/usr/local/clang21/bin/clang++ -std=gnu++17 -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 /tmp/RtmpywcjOz/working_dir/RtmpNGwyU6/gkwbetareg_compile_20251025231840/gkwbetareg.so /tmp/RtmpywcjOz/working_dir/RtmpNGwyU6/gkwbetareg_compile_20251025231840/gkwbetareg.o
make[1]: Leaving directory '/tmp/RtmpywcjOz/working_dir/RtmpNGwyU6/gkwbetareg_compile_20251025231840'
make[1]: Entering directory '/tmp/RtmpywcjOz/working_dir/RtmpNGwyU6/gkwbetareg_compile_20251025231840'
make[1]: Leaving directory '/tmp/RtmpywcjOz/working_dir/RtmpNGwyU6/gkwbetareg_compile_20251025231840'
using C++ compiler: ‘clang version 21.1.4’
make[1]: Entering directory '/tmp/RtmpywcjOz/working_dir/RtmpNGwyU6/bkwreg_compile_20251025232341'
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I"/data/gannet/ripley/R/test-clang/TMB/include" -I"/data/gannet/ripley/R/test-clang/RcppEigen/include" -DTMB_EIGEN_DISABLE_WARNINGS -DTMB_LIB_INIT=R_init_bkwreg -DCPPAD_FRAMEWORK -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 /tmp/RtmpywcjOz/working_dir/RtmpNGwyU6/bkwreg_compile_20251025232341/bkwreg.cpp -o /tmp/RtmpywcjOz/working_dir/RtmpNGwyU6/bkwreg_compile_20251025232341/bkwreg.o
In file included from /tmp/RtmpywcjOz/working_dir/RtmpNGwyU6/bkwreg_compile_20251025232341/bkwreg.cpp:13:
In file included from /data/gannet/ripley/R/test-clang/TMB/include/TMB.hpp:96:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:26:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/SparseCore:61:
/data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable]
273 | Index count = 0;
| ^
In file included from /tmp/RtmpywcjOz/working_dir/RtmpNGwyU6/bkwreg_compile_20251025232341/bkwreg.cpp:13:
In file included from /data/gannet/ripley/R/test-clang/TMB/include/TMB.hpp:96:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:29:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/SparseLU:35:
/data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable]
78 | Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree
| ^
/data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable]
79 | Index nsuper_et = 0; // Number of relaxed snodes in the original etree
| ^
3 warnings generated.
/usr/local/clang21/bin/clang++ -std=gnu++17 -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 /tmp/RtmpywcjOz/working_dir/RtmpNGwyU6/bkwreg_compile_20251025232341/bkwreg.so /tmp/RtmpywcjOz/working_dir/RtmpNGwyU6/bkwreg_compile_20251025232341/bkwreg.o
make[1]: Leaving directory '/tmp/RtmpywcjOz/working_dir/RtmpNGwyU6/bkwreg_compile_20251025232341'
make[1]: Entering directory '/tmp/RtmpywcjOz/working_dir/RtmpNGwyU6/bkwreg_compile_20251025232341'
make[1]: Leaving directory '/tmp/RtmpywcjOz/working_dir/RtmpNGwyU6/bkwreg_compile_20251025232341'
using C++ compiler: ‘clang version 21.1.4’
make[1]: Entering directory '/tmp/RtmpywcjOz/working_dir/RtmpNGwyU6/ekwreg_compile_20251025232757'
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I"/data/gannet/ripley/R/test-clang/TMB/include" -I"/data/gannet/ripley/R/test-clang/RcppEigen/include" -DTMB_EIGEN_DISABLE_WARNINGS -DTMB_LIB_INIT=R_init_ekwreg -DCPPAD_FRAMEWORK -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 /tmp/RtmpywcjOz/working_dir/RtmpNGwyU6/ekwreg_compile_20251025232757/ekwreg.cpp -o /tmp/RtmpywcjOz/working_dir/RtmpNGwyU6/ekwreg_compile_20251025232757/ekwreg.o
In file included from /tmp/RtmpywcjOz/working_dir/RtmpNGwyU6/ekwreg_compile_20251025232757/ekwreg.cpp:19:
In file included from /data/gannet/ripley/R/test-clang/TMB/include/TMB.hpp:96:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:26:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/SparseCore:61:
/data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable]
273 | Index count = 0;
| ^
In file included from /tmp/RtmpywcjOz/working_dir/RtmpNGwyU6/ekwreg_compile_20251025232757/ekwreg.cpp:19:
In file included from /data/gannet/ripley/R/test-clang/TMB/include/TMB.hpp:96:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:29:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/SparseLU:35:
/data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable]
78 | Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree
| ^
/data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable]
79 | Index nsuper_et = 0; // Number of relaxed snodes in the original etree
| ^
3 warnings generated.
/usr/local/clang21/bin/clang++ -std=gnu++17 -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 /tmp/RtmpywcjOz/working_dir/RtmpNGwyU6/ekwreg_compile_20251025232757/ekwreg.so /tmp/RtmpywcjOz/working_dir/RtmpNGwyU6/ekwreg_compile_20251025232757/ekwreg.o
make[1]: Leaving directory '/tmp/RtmpywcjOz/working_dir/RtmpNGwyU6/ekwreg_compile_20251025232757'
make[1]: Entering directory '/tmp/RtmpywcjOz/working_dir/RtmpNGwyU6/ekwreg_compile_20251025232757'
make[1]: Leaving directory '/tmp/RtmpywcjOz/working_dir/RtmpNGwyU6/ekwreg_compile_20251025232757'
using C++ compiler: ‘clang version 21.1.4’
make[1]: Entering directory '/tmp/RtmpywcjOz/working_dir/RtmpNGwyU6/gkwmletmb_compile_20251025233223'
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I"/data/gannet/ripley/R/test-clang/TMB/include" -I"/data/gannet/ripley/R/test-clang/RcppEigen/include" -DTMB_EIGEN_DISABLE_WARNINGS -DTMB_LIB_INIT=R_init_gkwmletmb -DCPPAD_FRAMEWORK -isystem /usr/local/clang21/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c /tmp/RtmpywcjOz/working_dir/RtmpNGwyU6/gkwmletmb_compile_20251025233223/gkwmletmb.cpp -o /tmp/RtmpywcjOz/working_dir/RtmpNGwyU6/gkwmletmb_compile_20251025233223/gkwmletmb.o
In file included from /tmp/RtmpywcjOz/working_dir/RtmpNGwyU6/gkwmletmb_compile_20251025233223/gkwmletmb.cpp:1:
In file included from /data/gannet/ripley/R/test-clang/TMB/include/TMB.hpp:96:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:26:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/SparseCore:61:
/data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable]
273 | Index count = 0;
| ^
In file included from /tmp/RtmpywcjOz/working_dir/RtmpNGwyU6/gkwmletmb_compile_20251025233223/gkwmletmb.cpp:1:
In file included from /data/gannet/ripley/R/test-clang/TMB/include/TMB.hpp:96:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:29:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/SparseLU:35:
/data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable]
78 | Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree
| ^
/data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable]
79 | Index nsuper_et = 0; // Number of relaxed snodes in the original etree
| ^
3 warnings generated.
/usr/local/clang21/bin/clang++ -std=gnu++17 -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 /tmp/RtmpywcjOz/working_dir/RtmpNGwyU6/gkwmletmb_compile_20251025233223/gkwmletmb.so /tmp/RtmpywcjOz/working_dir/RtmpNGwyU6/gkwmletmb_compile_20251025233223/gkwmletmb.o -fopenmp
make[1]: Leaving directory '/tmp/RtmpywcjOz/working_dir/RtmpNGwyU6/gkwmletmb_compile_20251025233223'
make[1]: Entering directory '/tmp/RtmpywcjOz/working_dir/RtmpNGwyU6/gkwmletmb_compile_20251025233223'
make[1]: Leaving directory '/tmp/RtmpywcjOz/working_dir/RtmpNGwyU6/gkwmletmb_compile_20251025233223'
using C++ compiler: ‘clang version 21.1.4’
make[1]: Entering directory '/tmp/RtmpywcjOz/working_dir/RtmpNGwyU6/gkwreg_compile_20251025233650'
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I"/data/gannet/ripley/R/test-clang/TMB/include" -I"/data/gannet/ripley/R/test-clang/RcppEigen/include" -DTMB_EIGEN_DISABLE_WARNINGS -DTMB_LIB_INIT=R_init_gkwreg -DCPPAD_FRAMEWORK -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 /tmp/RtmpywcjOz/working_dir/RtmpNGwyU6/gkwreg_compile_20251025233650/gkwreg.cpp -o /tmp/RtmpywcjOz/working_dir/RtmpNGwyU6/gkwreg_compile_20251025233650/gkwreg.o
In file included from /tmp/RtmpywcjOz/working_dir/RtmpNGwyU6/gkwreg_compile_20251025233650/gkwreg.cpp:12:
In file included from /data/gannet/ripley/R/test-clang/TMB/include/TMB.hpp:96:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:26:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/SparseCore:61:
/data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable]
273 | Index count = 0;
| ^
In file included from /tmp/RtmpywcjOz/working_dir/RtmpNGwyU6/gkwreg_compile_20251025233650/gkwreg.cpp:12:
In file included from /data/gannet/ripley/R/test-clang/TMB/include/TMB.hpp:96:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:29:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/SparseLU:35:
/data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable]
78 | Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree
| ^
/data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable]
79 | Index nsuper_et = 0; // Number of relaxed snodes in the original etree
| ^
3 warnings generated.
/usr/local/clang21/bin/clang++ -std=gnu++17 -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 /tmp/RtmpywcjOz/working_dir/RtmpNGwyU6/gkwreg_compile_20251025233650/gkwreg.so /tmp/RtmpywcjOz/working_dir/RtmpNGwyU6/gkwreg_compile_20251025233650/gkwreg.o
make[1]: Leaving directory '/tmp/RtmpywcjOz/working_dir/RtmpNGwyU6/gkwreg_compile_20251025233650'
make[1]: Entering directory '/tmp/RtmpywcjOz/working_dir/RtmpNGwyU6/gkwreg_compile_20251025233650'
make[1]: Leaving directory '/tmp/RtmpywcjOz/working_dir/RtmpNGwyU6/gkwreg_compile_20251025233650'
using C++ compiler: ‘clang version 21.1.4’
make[1]: Entering directory '/tmp/RtmpywcjOz/working_dir/RtmpNGwyU6/kkwreg_compile_20251025234135'
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I"/data/gannet/ripley/R/test-clang/TMB/include" -I"/data/gannet/ripley/R/test-clang/RcppEigen/include" -DTMB_EIGEN_DISABLE_WARNINGS -DTMB_LIB_INIT=R_init_kkwreg -DCPPAD_FRAMEWORK -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 /tmp/RtmpywcjOz/working_dir/RtmpNGwyU6/kkwreg_compile_20251025234135/kkwreg.cpp -o /tmp/RtmpywcjOz/working_dir/RtmpNGwyU6/kkwreg_compile_20251025234135/kkwreg.o
In file included from /tmp/RtmpywcjOz/working_dir/RtmpNGwyU6/kkwreg_compile_20251025234135/kkwreg.cpp:16:
In file included from /data/gannet/ripley/R/test-clang/TMB/include/TMB.hpp:96:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:26:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/SparseCore:61:
/data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable]
273 | Index count = 0;
| ^
In file included from /tmp/RtmpywcjOz/working_dir/RtmpNGwyU6/kkwreg_compile_20251025234135/kkwreg.cpp:16:
In file included from /data/gannet/ripley/R/test-clang/TMB/include/TMB.hpp:96:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:29:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/SparseLU:35:
/data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable]
78 | Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree
| ^
/data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable]
79 | Index nsuper_et = 0; // Number of relaxed snodes in the original etree
| ^
3 warnings generated.
/usr/local/clang21/bin/clang++ -std=gnu++17 -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 /tmp/RtmpywcjOz/working_dir/RtmpNGwyU6/kkwreg_compile_20251025234135/kkwreg.so /tmp/RtmpywcjOz/working_dir/RtmpNGwyU6/kkwreg_compile_20251025234135/kkwreg.o
make[1]: Leaving directory '/tmp/RtmpywcjOz/working_dir/RtmpNGwyU6/kkwreg_compile_20251025234135'
make[1]: Entering directory '/tmp/RtmpywcjOz/working_dir/RtmpNGwyU6/kkwreg_compile_20251025234135'
make[1]: Leaving directory '/tmp/RtmpywcjOz/working_dir/RtmpNGwyU6/kkwreg_compile_20251025234135'
using C++ compiler: ‘clang version 21.1.4’
make[1]: Entering directory '/tmp/RtmpywcjOz/working_dir/RtmpNGwyU6/kwreg_compile_20251025234631'
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I"/data/gannet/ripley/R/test-clang/TMB/include" -I"/data/gannet/ripley/R/test-clang/RcppEigen/include" -DTMB_EIGEN_DISABLE_WARNINGS -DTMB_LIB_INIT=R_init_kwreg -DCPPAD_FRAMEWORK -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 /tmp/RtmpywcjOz/working_dir/RtmpNGwyU6/kwreg_compile_20251025234631/kwreg.cpp -o /tmp/RtmpywcjOz/working_dir/RtmpNGwyU6/kwreg_compile_20251025234631/kwreg.o
In file included from /tmp/RtmpywcjOz/working_dir/RtmpNGwyU6/kwreg_compile_20251025234631/kwreg.cpp:19:
In file included from /data/gannet/ripley/R/test-clang/TMB/include/TMB.hpp:96:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:26:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/SparseCore:61:
/data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable]
273 | Index count = 0;
| ^
In file included from /tmp/RtmpywcjOz/working_dir/RtmpNGwyU6/kwreg_compile_20251025234631/kwreg.cpp:19:
In file included from /data/gannet/ripley/R/test-clang/TMB/include/TMB.hpp:96:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:29:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/SparseLU:35:
/data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable]
78 | Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree
| ^
/data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable]
79 | Index nsuper_et = 0; // Number of relaxed snodes in the original etree
| ^
make[1]: *** wait: No child processes. Stop.
make[1]: *** Waiting for unfinished jobs....
make[1]: *** wait: No child processes. Stop.
using C++ compiler: ‘clang version 21.1.4’
make[1]: Entering directory '/tmp/RtmpywcjOz/working_dir/RtmpNGwyU6/mcreg_compile_20251025234830'
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I"/data/gannet/ripley/R/test-clang/TMB/include" -I"/data/gannet/ripley/R/test-clang/RcppEigen/include" -DTMB_EIGEN_DISABLE_WARNINGS -DTMB_LIB_INIT=R_init_mcreg -DCPPAD_FRAMEWORK -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 /tmp/RtmpywcjOz/working_dir/RtmpNGwyU6/mcreg_compile_20251025234830/mcreg.cpp -o /tmp/RtmpywcjOz/working_dir/RtmpNGwyU6/mcreg_compile_20251025234830/mcreg.o
make[1]: *** [/data/gannet/ripley/R/R-clang/etc/Makeconf:209: /tmp/RtmpywcjOz/working_dir/RtmpNGwyU6/mcreg_compile_20251025234830/mcreg.o] Terminated
It looks like this package (or one of its dependent packages) has an
unstated dependence on a standard package. All dependencies must be
declared in DESCRIPTION.
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
- checking whether the package can be unloaded cleanly ... [222s/599s] OK
- checking whether the namespace can be loaded with stated dependencies ... [3s/13s] OK
- checking whether the namespace can be unloaded cleanly ... [3s/17s] OK
- checking loading without being on the library search path ... [3s/15s] OK
- checking whether startup messages can be suppressed ... [3s/13s] OK
- checking use of S3 registration ... OK
- checking dependencies in R code ... OK
- checking S3 generic/method consistency ... OK
- checking replacement functions ... OK
- checking foreign function calls ... OK
- checking R code for possible problems ... [56s/153s] OK
- checking Rd files ... [3s/11s] OK
- checking Rd metadata ... OK
- checking Rd line widths ... OK
- checking Rd cross-references ... OK
- checking for missing documentation entries ... OK
- checking for code/documentation mismatches ... OK
- checking Rd \usage sections ... OK
- checking Rd contents ... OK
- checking for unstated dependencies in examples ... OK
- checking line endings in C/C++/Fortran sources/headers ... OK
- checking line endings in Makefiles ... OK
- checking compilation flags in Makevars ... OK
- checking for GNU extensions in Makefiles ... OK
- checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
- checking use of PKG_*FLAGS in Makefiles ... OK
- checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
- checking pragmas in C/C++ headers and code ... OK
- checking compilation flags used ... OK
- checking compiled code ... OK
- checking examples ... [4s/15s] OK
- checking PDF version of manual ... [25s/61s] OK
- checking HTML version of manual ... [20s/75s] OK
- checking for non-standard things in the check directory ... OK
- checking for detritus in the temp directory ... OK
- DONE
Status: 1 WARNING