* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘cit’ ...
** package ‘cit’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-14 (Debian 14.2.0-8) 14.2.0’
using C++ compiler: ‘g++-14 (Debian 14.2.0-8) 14.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmppCHuCR/R.INSTALL14116942b0f02/cit/src'
gcc-14 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3  `gsl-config --cflags` -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c cit_init.c -o cit_init.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c citconlog2.cpp -o citconlog2.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c citconlog2cvr.cpp -o citconlog2cvr.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -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:50:22: warning: variable ‘cc’ set but not used [-Wunused-but-set-variable]
   50 |         bool aa, bb, cc, converged, permute;
      |                      ^~
citconlog3_perm.cpp:453:17: warning: ‘pvalind’ may be used uninitialized [-Wmaybe-uninitialized]
  453 |                 if( pvp > pvalind ) npos++;
      |                 ^~
citconlog3_perm.cpp:48:41: note: ‘pvalind’ was declared here
   48 |         double rss2, rss3, rss5, F, pv, pvalind, pvp, tmp, rhs;
      |                                         ^~~~~~~
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c citconlog3cvr_perm.cpp -o citconlog3cvr_perm.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:49:22: warning: variable ‘cc’ set but not used [-Wunused-but-set-variable]
   49 |         bool aa, bb, cc, converged, permute;
      |                      ^~
citconlog3cvr_perm.cpp:484:17: warning: ‘pvalind’ may be used uninitialized [-Wmaybe-uninitialized]
  484 |                 if( pvp > pvalind ) npos++;
      |                 ^~
citconlog3cvr_perm.cpp:47:41: note: ‘pvalind’ was declared here
   47 |         double rss2, rss3, rss5, F, pv, pvalind, pvp, tmp, rhs;
      |                                         ^~~~~~~
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c logisticfunc.cpp -o logisticfunc.o
g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o cit.so cit_init.o citconlog2.o citconlog2cvr.o citconlog3_perm.o citconlog3cvr_perm.o logisticfunc.o -L/usr/lib/x86_64-linux-gnu -lgsl -lgslcblas -lm -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmppCHuCR/R.INSTALL14116942b0f02/cit/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmppCHuCR/R.INSTALL14116942b0f02/cit/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmppCHuCR/R.INSTALL14116942b0f02/cit/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-cit/00new/cit/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package ‘cit’
    finding HTML links ... done
    cit-package                             html  
    cit.bp                                  html  
    cit.cp                                  html  
    fdr.cit                                 html  
    fdr.od                                  html  
    fdr.q.para                              html  
    fdr.q.perm                              html  
    iuq                                     html  
    linreg                                  html  
** 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)