* installing *source* package ‘perms’ ...
** this is package ‘perms’ version ‘1.14’
** package ‘perms’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (GCC) 16.1.1 20260515 (Red Hat 16.1.1-2)’
make[1]: Entering directory '/data/localhost/ripley/R/packages/tests-devel/perms/src'
gcc -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c C_get_log_permanent.c -o C_get_log_permanent.o
gcc -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c get_alphabetagamma.c -o get_alphabetagamma.o
gcc -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c get_log_ML.c -o get_log_ML.o
get_log_ML.c: In function ‘C_get_log_ML’:
get_log_ML.c:12:13: warning: unused variable ‘debug’ [-Wunused-variable]
12 | int debug = *(INTEGER(debugSEXP));
| ^~~~~
get_log_ML.c: In function ‘C_get_log_ML_bioassay’:
get_log_ML.c:74:13: warning: unused variable ‘debug’ [-Wunused-variable]
74 | int debug = *(INTEGER(debugSEXP));
| ^~~~~
gcc -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c help_functions.c -o help_functions.o
help_functions.c: In function ‘update_dict’:
help_functions.c:70:13: warning: variable ‘collcount’ set but not used [-Wunused-but-set-variable=]
70 | int collcount = 0;
| ^~~~~~~~~
gcc -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c init.c -o init.o
gcc -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c methods.c -o methods.o
methods.c: In function ‘reduction’:
methods.c:588:13: warning: variable ‘cc’ set but not used [-Wunused-but-set-variable=]
588 | int cc = 0;
| ^~
methods.c: In function ‘reverse_reduction’:
methods.c:843:13: warning: variable ‘num_nonzeros’ set but not used [-Wunused-but-set-variable=]
843 | int num_nonzeros = 0;
| ^~~~~~~~~~~~
gcc -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c methods_sparse.c -o methods_sparse.o
gcc -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c xxhash.c -o xxhash.o
gcc -shared -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -L/usr/local/lib64 -o perms.so C_get_log_permanent.o get_alphabetagamma.o get_log_ML.o help_functions.o init.o methods.o methods_sparse.o xxhash.o
make[1]: Leaving directory '/data/localhost/ripley/R/packages/tests-devel/perms/src'
make[1]: Entering directory '/data/localhost/ripley/R/packages/tests-devel/perms/src'
make[1]: Leaving directory '/data/localhost/ripley/R/packages/tests-devel/perms/src'
installing to /data/localhost/ripley/R/packages/tests-devel/perms.Rcheck/00LOCK-perms/00new/perms/libs
** R
** 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 (perms)