* installing *source* package ‘nonneg.cg’ ...
** this is package ‘nonneg.cg’ version ‘0.1.6-1’
** package ‘nonneg.cg’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)’
using C++ compiler: ‘g++ (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/nonneg.cg/src'
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FOR_R -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include   -fvisibility=hidden -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 RcppExports.cpp -o RcppExports.o
gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FOR_R -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -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 nonnegcg.c -o nonnegcg.o
nonnegcg.c: In function ‘minimize_nonneg_cg’:
nonnegcg.c:223: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
  223 |                 #pragma omp parallel for schedule(static) firstprivate(x, direction_curr, grad_curr) num_threads(nthreads)
nonnegcg.c:236: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
  236 |                         #pragma omp parallel for schedule(static) firstprivate(x, direction_prev, grad_curr, grad_prev, n_szt) reduction(+:theta, beta) num_threads(nthreads)
nonnegcg.c:247: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
  247 |                         #pragma omp parallel for schedule(static) firstprivate(x, direction_curr, direction_prev, grad_curr, grad_prev, n_szt, theta, beta) num_threads(nthreads)
nonnegcg.c:289: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
  289 |                                 #pragma omp parallel for schedule(static) firstprivate(x, n_szt) num_threads(nthreads)
nonnegcg.c:328: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
  328 |                                 #pragma omp parallel for schedule(static) firstprivate(x, n_szt) num_threads(nthreads)
nonnegcg.c:244:30: warning: ‘grad_prev_norm_sq’ may be used uninitialized [-Wmaybe-uninitialized]
  244 |                         beta /= grad_prev_norm_sq;
      |                         ~~~~~^~~~~~~~~~~~~~~~~~~~
nonnegcg.c:156:16: note: ‘grad_prev_norm_sq’ was declared here
  156 |         double grad_prev_norm_sq;
      |                ^~~~~~~~~~~~~~~~~
nonnegcg.c:240:90: warning: ‘direction_prev’ may be used uninitialized [-Wmaybe-uninitialized]
  240 |                                 theta += ( x[i] <= 0 )? 0 : grad_curr[i] * direction_prev[i];
      |                                                                            ~~~~~~~~~~~~~~^~~
nonnegcg.c:195:26: note: ‘direction_prev’ was declared here
  195 |         double *restrict direction_prev;
      |                          ^~~~~~~~~~~~~~
nonnegcg.c:241:100: warning: ‘grad_prev’ may be used uninitialized [-Wmaybe-uninitialized]
  241 |                                 beta += ( x[i] <= 0 )? 0 : grad_curr[i] * (grad_curr[i] - grad_prev[i]);
      |                                                                                           ~~~~~~~~~^~~
nonnegcg.c:196:26: note: ‘grad_prev’ was declared here
  196 |         double *restrict grad_prev;
      |                          ^~~~~~~~~
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FOR_R -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include   -fvisibility=hidden -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 rwrapper.cpp -o rwrapper.o
g++ -std=gnu++17 -shared -L/usr/local/lib64 -o nonneg.cg.so RcppExports.o nonnegcg.o rwrapper.o -L/data/gannet/ripley/R/R-devel/lib -lRblas -lgfortran -lm -lquadmath
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/nonneg.cg/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/nonneg.cg/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/nonneg.cg/src'
installing to /data/gannet/ripley/R/packages/tests-devel/nonneg.cg.Rcheck/00LOCK-nonneg.cg/00new/nonneg.cg/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 (nonneg.cg)