Install log for 'sdmTMB'

* installing to library ‘/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages’
* installing *source* package ‘sdmTMB’ ...
** package ‘sdmTMB’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘Debian clang version 17.0.5 (1)’
make[1]: Entering directory '/tmp/RtmptXkqeR/R.INSTALL31b35b76291934/sdmTMB/src'
clang++-17 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -DTMBAD_FRAMEWORK -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/TMB/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c sdmTMB.cpp -o sdmTMB.o
In file included from sdmTMB.cpp:2:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/TMB/include/TMB.hpp:83:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/Eigen/Dense:1:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/Eigen/Core:540:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:33: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
   14 |     #pragma clang diagnostic pop
      |                                 ^
In file included from sdmTMB.cpp:2:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/TMB/include/TMB.hpp:83:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/Eigen/Dense:2:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/Eigen/LU:47:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:33: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
   14 |     #pragma clang diagnostic pop
      |                                 ^
In file included from sdmTMB.cpp:2:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/TMB/include/TMB.hpp:83:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/Eigen/Dense:3:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/Eigen/Cholesky:12:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/Eigen/Jacobi:29:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:33: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
   14 |     #pragma clang diagnostic pop
      |                                 ^
In file included from sdmTMB.cpp:2:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/TMB/include/TMB.hpp:83:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/Eigen/Dense:3:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/Eigen/Cholesky:43:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:33: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
   14 |     #pragma clang diagnostic pop
      |                                 ^
In file included from sdmTMB.cpp:2:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/TMB/include/TMB.hpp:83:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/Eigen/Dense:4:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/Eigen/QR:15:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/Eigen/Householder:27:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:33: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
   14 |     #pragma clang diagnostic pop
      |                                 ^
In file included from sdmTMB.cpp:2:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/TMB/include/TMB.hpp:83:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/Eigen/Dense:4:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/Eigen/QR:48:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:33: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
   14 |     #pragma clang diagnostic pop
      |                                 ^
In file included from sdmTMB.cpp:2:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/TMB/include/TMB.hpp:83:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/Eigen/Dense:5:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/Eigen/SVD:48:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:33: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
   14 |     #pragma clang diagnostic pop
      |                                 ^
In file included from sdmTMB.cpp:2:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/TMB/include/TMB.hpp:83:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/Eigen/Dense:6:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/Eigen/Geometry:58:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:33: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
   14 |     #pragma clang diagnostic pop
      |                                 ^
In file included from sdmTMB.cpp:2:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/TMB/include/TMB.hpp:83:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/Eigen/Dense:7:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/Eigen/Eigenvalues:58:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:33: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
   14 |     #pragma clang diagnostic pop
      |                                 ^
In file included from sdmTMB.cpp:2:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/TMB/include/TMB.hpp:87:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/Eigen/Sparse:26:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/Eigen/SparseCore:61:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/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 sdmTMB.cpp:2:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/TMB/include/TMB.hpp:87:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/Eigen/Sparse:26:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/Eigen/SparseCore:66:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:33: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
   14 |     #pragma clang diagnostic pop
      |                                 ^
In file included from sdmTMB.cpp:2:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/TMB/include/TMB.hpp:87:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/Eigen/Sparse:27:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/Eigen/OrderingMethods:71:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:33: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
   14 |     #pragma clang diagnostic pop
      |                                 ^
In file included from sdmTMB.cpp:2:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/TMB/include/TMB.hpp:87:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/Eigen/Sparse:29:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/Eigen/SparseCholesky:43:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:33: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
   14 |     #pragma clang diagnostic pop
      |                                 ^
In file included from sdmTMB.cpp:2:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/TMB/include/TMB.hpp:87:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/Eigen/Sparse:31:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/Eigen/SparseLU:33:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/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 
      |         ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/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 
      |         ^
In file included from sdmTMB.cpp:2:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/TMB/include/TMB.hpp:87:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/Eigen/Sparse:32:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/Eigen/SparseQR:34:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:33: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
   14 |     #pragma clang diagnostic pop
      |                                 ^
In file included from sdmTMB.cpp:2:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/TMB/include/TMB.hpp:87:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/Eigen/Sparse:33:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/Eigen/IterativeLinearSolvers:46:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:33: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
   14 |     #pragma clang diagnostic pop
      |                                 ^
sdmTMB.cpp:751:80: warning: unused variable 's1_large' [-Wunused-variable]
  751 |   Type s1, s2, s3, lognzprob, tmp_ll, ll_1, ll_2, p_mix, mix_ratio, tweedie_p, s1_large, s2_large;
      |                                                                                ^~~~~~~~
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/TMB/include/tmb_core.hpp:2031:34: note: in instantiation of member function 'objective_function<double>::operator()' requested here
 2031 |       PROTECT( res = asSEXP( pf->operator()() ) );
      |                                  ^
18 warnings generated.
clang++-17 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -Wl,-O1 -o sdmTMB.so sdmTMB.o -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -lR
make[1]: Leaving directory '/tmp/RtmptXkqeR/R.INSTALL31b35b76291934/sdmTMB/src'
make[1]: Entering directory '/tmp/RtmptXkqeR/R.INSTALL31b35b76291934/sdmTMB/src'
make[1]: Leaving directory '/tmp/RtmptXkqeR/R.INSTALL31b35b76291934/sdmTMB/src'
installing to /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/00LOCK-sdmTMB/00new/sdmTMB/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** 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 (sdmTMB)