Install log for 'fastTopics'

* installing *source* package ‘fastTopics’ ...
** package ‘fastTopics’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-13 (GCC) 13.2.0’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/fastTopics/src'
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include   -fopenmp -DARMA_DONT_PRINT_ERRORS -DARMA_NO_DEBUG -DARMA_USE_BLAS -DARMA_DONT_USE_OPENMP -DARMA_USE_TBB_ALLOC -DRCPP_PARALLEL_USE_TBB=1 -DARMA_WARN_LEVEL=1 -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
In file included from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/armadillo:26,
                 from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57,
                 from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo.h:29,
                 from RcppExports.cpp:4:
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/armadillo_bits/config.hpp:321:86: note: '#pragma message: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed'
  321 |   #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed")
      |                                                                                      ^
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/armadillo_bits/config.hpp:326:75: note: '#pragma message: INFO: suggest to use ARMA_WARN_LEVEL option instead'
  326 |     #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead")
      |                                                                           ^
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/armadillo_bits/config.hpp:329:61: note: '#pragma message: INFO: see the documentation for details'
  329 |   #pragma message ("INFO: see the documentation for details")
      |                                                             ^
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include   -fopenmp -DARMA_DONT_PRINT_ERRORS -DARMA_NO_DEBUG -DARMA_USE_BLAS -DARMA_DONT_USE_OPENMP -DARMA_USE_TBB_ALLOC -DRCPP_PARALLEL_USE_TBB=1 -DARMA_WARN_LEVEL=1 -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 ccd.cpp -o ccd.o
In file included from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/armadillo:26,
                 from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57,
                 from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo.h:29,
                 from misc.h:4,
                 from ccd.cpp:2:
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/armadillo_bits/config.hpp:321:86: note: '#pragma message: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed'
  321 |   #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed")
      |                                                                                      ^
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/armadillo_bits/config.hpp:326:75: note: '#pragma message: INFO: suggest to use ARMA_WARN_LEVEL option instead'
  326 |     #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead")
      |                                                                           ^
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/armadillo_bits/config.hpp:329:61: note: '#pragma message: INFO: see the documentation for details'
  329 |   #pragma message ("INFO: see the documentation for details")
      |                                                             ^
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include   -fopenmp -DARMA_DONT_PRINT_ERRORS -DARMA_NO_DEBUG -DARMA_USE_BLAS -DARMA_DONT_USE_OPENMP -DARMA_USE_TBB_ALLOC -DRCPP_PARALLEL_USE_TBB=1 -DARMA_WARN_LEVEL=1 -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 cost.cpp -o cost.o
In file included from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/armadillo:26,
                 from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57,
                 from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo.h:29,
                 from misc.h:4,
                 from cost.cpp:1:
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/armadillo_bits/config.hpp:321:86: note: '#pragma message: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed'
  321 |   #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed")
      |                                                                                      ^
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/armadillo_bits/config.hpp:326:75: note: '#pragma message: INFO: suggest to use ARMA_WARN_LEVEL option instead'
  326 |     #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead")
      |                                                                           ^
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/armadillo_bits/config.hpp:329:61: note: '#pragma message: INFO: see the documentation for details'
  329 |   #pragma message ("INFO: see the documentation for details")
      |                                                             ^
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include   -fopenmp -DARMA_DONT_PRINT_ERRORS -DARMA_NO_DEBUG -DARMA_USE_BLAS -DARMA_DONT_USE_OPENMP -DARMA_USE_TBB_ALLOC -DRCPP_PARALLEL_USE_TBB=1 -DARMA_WARN_LEVEL=1 -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 misc.cpp -o misc.o
In file included from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/armadillo:26,
                 from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57,
                 from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo.h:29,
                 from misc.h:4,
                 from misc.cpp:1:
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/armadillo_bits/config.hpp:321:86: note: '#pragma message: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed'
  321 |   #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed")
      |                                                                                      ^
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/armadillo_bits/config.hpp:326:75: note: '#pragma message: INFO: suggest to use ARMA_WARN_LEVEL option instead'
  326 |     #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead")
      |                                                                           ^
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/armadillo_bits/config.hpp:329:61: note: '#pragma message: INFO: see the documentation for details'
  329 |   #pragma message ("INFO: see the documentation for details")
      |                                                             ^
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include   -fopenmp -DARMA_DONT_PRINT_ERRORS -DARMA_NO_DEBUG -DARMA_USE_BLAS -DARMA_DONT_USE_OPENMP -DARMA_USE_TBB_ALLOC -DRCPP_PARALLEL_USE_TBB=1 -DARMA_WARN_LEVEL=1 -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 mixem.cpp -o mixem.o
In file included from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/armadillo:26,
                 from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57,
                 from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo.h:29,
                 from mixem.h:4,
                 from mixem.cpp:1:
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/armadillo_bits/config.hpp:321:86: note: '#pragma message: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed'
  321 |   #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed")
      |                                                                                      ^
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/armadillo_bits/config.hpp:326:75: note: '#pragma message: INFO: suggest to use ARMA_WARN_LEVEL option instead'
  326 |     #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead")
      |                                                                           ^
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/armadillo_bits/config.hpp:329:61: note: '#pragma message: INFO: see the documentation for details'
  329 |   #pragma message ("INFO: see the documentation for details")
      |                                                             ^
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include   -fopenmp -DARMA_DONT_PRINT_ERRORS -DARMA_NO_DEBUG -DARMA_USE_BLAS -DARMA_DONT_USE_OPENMP -DARMA_USE_TBB_ALLOC -DRCPP_PARALLEL_USE_TBB=1 -DARMA_WARN_LEVEL=1 -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 pnmfem.cpp -o pnmfem.o
In file included from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/armadillo:26,
                 from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57,
                 from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo.h:29,
                 from misc.h:4,
                 from pnmfem.cpp:2:
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/armadillo_bits/config.hpp:321:86: note: '#pragma message: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed'
  321 |   #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed")
      |                                                                                      ^
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/armadillo_bits/config.hpp:326:75: note: '#pragma message: INFO: suggest to use ARMA_WARN_LEVEL option instead'
  326 |     #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead")
      |                                                                           ^
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/armadillo_bits/config.hpp:329:61: note: '#pragma message: INFO: see the documentation for details'
  329 |   #pragma message ("INFO: see the documentation for details")
      |                                                             ^
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include   -fopenmp -DARMA_DONT_PRINT_ERRORS -DARMA_NO_DEBUG -DARMA_USE_BLAS -DARMA_DONT_USE_OPENMP -DARMA_USE_TBB_ALLOC -DRCPP_PARALLEL_USE_TBB=1 -DARMA_WARN_LEVEL=1 -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 poismix.cpp -o poismix.o
In file included from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/armadillo:26,
                 from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57,
                 from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo.h:29,
                 from poismix.h:4,
                 from poismix.cpp:1:
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/armadillo_bits/config.hpp:321:86: note: '#pragma message: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed'
  321 |   #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed")
      |                                                                                      ^
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/armadillo_bits/config.hpp:326:75: note: '#pragma message: INFO: suggest to use ARMA_WARN_LEVEL option instead'
  326 |     #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead")
      |                                                                           ^
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/armadillo_bits/config.hpp:329:61: note: '#pragma message: INFO: see the documentation for details'
  329 |   #pragma message ("INFO: see the documentation for details")
      |                                                             ^
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include   -fopenmp -DARMA_DONT_PRINT_ERRORS -DARMA_NO_DEBUG -DARMA_USE_BLAS -DARMA_DONT_USE_OPENMP -DARMA_USE_TBB_ALLOC -DRCPP_PARALLEL_USE_TBB=1 -DARMA_WARN_LEVEL=1 -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 poisson.cpp -o poisson.o
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include   -fopenmp -DARMA_DONT_PRINT_ERRORS -DARMA_NO_DEBUG -DARMA_USE_BLAS -DARMA_DONT_USE_OPENMP -DARMA_USE_TBB_ALLOC -DRCPP_PARALLEL_USE_TBB=1 -DARMA_WARN_LEVEL=1 -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 scd.cpp -o scd.o
In file included from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/armadillo:26,
                 from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57,
                 from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo.h:29,
                 from misc.h:4,
                 from poisson.cpp:1:
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/armadillo_bits/config.hpp:321:86: note: '#pragma message: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed'
  321 |   #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed")
      |                                                                                      ^
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/armadillo_bits/config.hpp:326:75: note: '#pragma message: INFO: suggest to use ARMA_WARN_LEVEL option instead'
  326 |     #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead")
      |                                                                           ^
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/armadillo_bits/config.hpp:329:61: note: '#pragma message: INFO: see the documentation for details'
  329 |   #pragma message ("INFO: see the documentation for details")
      |                                                             ^
In file included from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/armadillo:26,
                 from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57,
                 from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo.h:29,
                 from misc.h:4,
                 from scd.cpp:2:
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/armadillo_bits/config.hpp:321:86: note: '#pragma message: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed'
  321 |   #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed")
      |                                                                                      ^
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/armadillo_bits/config.hpp:326:75: note: '#pragma message: INFO: suggest to use ARMA_WARN_LEVEL option instead'
  326 |     #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead")
      |                                                                           ^
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/armadillo_bits/config.hpp:329:61: note: '#pragma message: INFO: see the documentation for details'
  329 |   #pragma message ("INFO: see the documentation for details")
      |                                                             ^
g++-13 -std=gnu++17 -shared -L/usr/local/gcc13/lib64 -L/usr/local/lib64 -L/usr/local/clang18/lib/x86_64-unknown-linux-gnu -o fastTopics.so RcppExports.o ccd.o cost.o misc.o mixem.o pnmfem.o poismix.o poisson.o scd.o -fopenmp -llapack -L/data/gannet/ripley/R/R-devel/lib -lRblas -lgfortran -lm -lquadmath
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/fastTopics/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/fastTopics/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/fastTopics/src'
installing to /data/gannet/ripley/R/packages/tests-devel/fastTopics.Rcheck/00LOCK-fastTopics/00new/fastTopics/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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 (fastTopics)