* installing *source* package ‘cit’ ...
** package ‘cit’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-13 (GCC) 13.2.0’
using C++ compiler: ‘g++-13 (GCC) 13.2.0’
using C++11
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/cit/src'
gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG   -I/usr/local/include   `gsl-config --cflags` -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 cit_init.c -o cit_init.o
g++-13 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG   -I/usr/local/include    -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 citconlog2.cpp -o citconlog2.o
g++-13 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG   -I/usr/local/include    -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 citconlog2cvr.cpp -o citconlog2cvr.o
g++-13 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG   -I/usr/local/include    -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 citconlog3_perm.cpp -o citconlog3_perm.o
citconlog3_perm.cpp: In function 'void citconlog3p(double*, double*, double*, int&, int&, double*, double*, double*, double*, int&, int&, int&, int*)':
citconlog3_perm.cpp:49:22: warning: variable 'cc' set but not used [-Wunused-but-set-variable]
   49 |         bool aa, bb, cc, converged, permute;
      |                      ^~
g++-13 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG   -I/usr/local/include    -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 citconlog3cvr_perm.cpp -o citconlog3cvr_perm.o
citconlog3_perm.cpp:451:17: warning: 'pvalind' may be used uninitialized [-Wmaybe-uninitialized]
  451 |                 if( pvp > pvalind ) npos++;
      |                 ^~
citconlog3_perm.cpp:47:41: note: 'pvalind' was declared here
   47 |         double rss2, rss3, rss5, F, pv, pvalind, pvp, tmp, rhs;
      |                                         ^~~~~~~
g++-13 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG   -I/usr/local/include    -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 logisticfunc.cpp -o logisticfunc.o
citconlog3cvr_perm.cpp: In function 'void citconlog3pcvr(double*, double*, double*, double*, int&, int&, int&, double*, double*, double*, double*, int&, int&, int&, int*)':
citconlog3cvr_perm.cpp:48:22: warning: variable 'cc' set but not used [-Wunused-but-set-variable]
   48 |         bool aa, bb, cc, converged, permute;
      |                      ^~
citconlog3cvr_perm.cpp:482:17: warning: 'pvalind' may be used uninitialized [-Wmaybe-uninitialized]
  482 |                 if( pvp > pvalind ) npos++;
      |                 ^~
citconlog3cvr_perm.cpp:46:41: note: 'pvalind' was declared here
   46 |         double rss2, rss3, rss5, F, pv, pvalind, pvp, tmp, rhs;
      |                                         ^~~~~~~
g++-13 -std=gnu++11 -shared -L/usr/local/gcc13/lib64 -L/usr/local/lib64 -L/usr/local/clang18/lib/x86_64-unknown-linux-gnu -o cit.so cit_init.o citconlog2.o citconlog2cvr.o citconlog3_perm.o citconlog3cvr_perm.o logisticfunc.o -lgsl -lgslcblas -lm
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/cit/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/cit/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/cit/src'
installing to /data/gannet/ripley/R/packages/tests-devel/cit.Rcheck/00LOCK-cit/00new/cit/libs
** R
** 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 (cit)