Install log for 'EMC2'

* installing *source* package ‘EMC2’ ...
** this is package ‘EMC2’ version ‘3.5.0’
** package ‘EMC2’ successfully unpacked and MD5 sums checked
** using staged installation
configure: EMC2 build configuration
  PNORM_MODE    : 1
  fast-math     : no
  native        : no
  Accelerate    : no
configure: src/Makevars written
configure: inst/include/build_info.h written
** libs
using C++ compiler: ‘g++ (GCC) 16.1.1 20260515 (Red Hat 16.1.1-2)’
make[1]: Entering directory '/data/localhost/ripley/R/packages/tests-devel/EMC2/src'
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG  -I../inst/include -DPNORM_MODE=1 -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -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 ParamTable.cpp -o ParamTable.o
In file included from ParamTable.cpp:1:
ParamTable.h:462: warning: ignoring ‘#pragma omp simd’ [-Wunknown-pragmas]
  462 | #pragma omp simd
ParamTable.h:487: warning: ignoring ‘#pragma omp simd’ [-Wunknown-pragmas]
  487 |     #pragma omp simd
ParamTable.h:522: warning: ignoring ‘#pragma omp simd’ [-Wunknown-pragmas]
  522 |       #pragma omp simd  // hint for the compiler
ParamTable.h:547: warning: ignoring ‘#pragma omp simd’ [-Wunknown-pragmas]
  547 |       #pragma omp simd  // can be auto-vectorised
ParamTable.cpp:78: warning: ignoring ‘#pragma omp simd’ [-Wunknown-pragmas]
   78 |     #pragma omp simd  // can be vectorised
ParamTable.cpp:96: warning: ignoring ‘#pragma omp simd’ [-Wunknown-pragmas]
   96 |     #pragma omp simd
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG  -I../inst/include -DPNORM_MODE=1 -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -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 RcppExports.cpp -o RcppExports.o
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG  -I../inst/include -DPNORM_MODE=1 -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -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 TrendEngine.cpp -o TrendEngine.o
In file included from TrendEngine.h:7,
                 from TrendEngine.cpp:1:
ParamTable.h:462: warning: ignoring ‘#pragma omp simd’ [-Wunknown-pragmas]
  462 | #pragma omp simd
ParamTable.h:487: warning: ignoring ‘#pragma omp simd’ [-Wunknown-pragmas]
  487 |     #pragma omp simd
ParamTable.h:522: warning: ignoring ‘#pragma omp simd’ [-Wunknown-pragmas]
  522 |       #pragma omp simd  // hint for the compiler
ParamTable.h:547: warning: ignoring ‘#pragma omp simd’ [-Wunknown-pragmas]
  547 |       #pragma omp simd  // can be auto-vectorised
TrendEngine.cpp:987: warning: ignoring ‘#pragma omp simd’ [-Wunknown-pragmas]
  987 | #pragma omp simd
TrendEngine.cpp:1002: warning: ignoring ‘#pragma omp simd’ [-Wunknown-pragmas]
 1002 | #pragma omp simd
TrendEngine.cpp:1027: warning: ignoring ‘#pragma omp simd’ [-Wunknown-pragmas]
 1027 | #pragma omp simd
TrendEngine.cpp:1035: warning: ignoring ‘#pragma omp simd’ [-Wunknown-pragmas]
 1035 | #pragma omp simd
TrendEngine.cpp:1055: warning: ignoring ‘#pragma omp simd’ [-Wunknown-pragmas]
 1055 | #pragma omp simd
TrendEngine.cpp:1073: warning: ignoring ‘#pragma omp simd’ [-Wunknown-pragmas]
 1073 | #pragma omp simd
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG  -I../inst/include -DPNORM_MODE=1 -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -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 build_info.cpp -o build_info.o
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG  -I../inst/include -DPNORM_MODE=1 -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -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 custom_trend_interface.cpp -o custom_trend_interface.o
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG  -I../inst/include -DPNORM_MODE=1 -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -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 fa.cpp -o fa.o
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG  -I../inst/include -DPNORM_MODE=1 -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -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 fncs_seven.cpp -o fncs_seven.o
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG  -I../inst/include -DPNORM_MODE=1 -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -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 group_designs.cpp -o group_designs.o
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG  -I../inst/include -DPNORM_MODE=1 -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -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 hcubature.cpp -o hcubature.o
hcubature.cpp: In function ‘void integrate_GenzMalik(GenzMalik, int, const double*, const double*, one_d&, void*, int (*)(unsigned int, const double*, void*, unsigned int, double*))’:
hcubature.cpp:532:12: warning: ‘c’ may be used uninitialized [-Wmaybe-uninitialized]
  532 |   integrand(n, c, pars, 1, &f1);
      |   ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
hcubature.cpp:532:12: note: by argument 2 of type ‘const double*’ to ‘int(unsigned int, const double*, void*, unsigned int, double*)’
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG  -I../inst/include -DPNORM_MODE=1 -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -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 kernels.cpp -o kernels.o
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG  -I../inst/include -DPNORM_MODE=1 -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -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 math_utils_apple.cpp -o math_utils_apple.o
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG  -I../inst/include -DPNORM_MODE=1 -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -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 math_utils_generic.cpp -o math_utils_generic.o
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG  -I../inst/include -DPNORM_MODE=1 -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -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 model_SS_EXG.cpp -o model_SS_EXG.o
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG  -I../inst/include -DPNORM_MODE=1 -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -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 model_SS_RDEX.cpp -o model_SS_RDEX.o
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG  -I../inst/include -DPNORM_MODE=1 -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -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 mri.cpp -o mri.o
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG  -I../inst/include -DPNORM_MODE=1 -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -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 param_table_interface.cpp -o param_table_interface.o
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG  -I../inst/include -DPNORM_MODE=1 -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -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 particle_ll.cpp -o particle_ll.o
In file included from utility_functions.h:10,
                 from particle_ll.cpp:5:
ParamTable.h:462: warning: ignoring ‘#pragma omp simd’ [-Wunknown-pragmas]
  462 | #pragma omp simd
ParamTable.h:487: warning: ignoring ‘#pragma omp simd’ [-Wunknown-pragmas]
  487 |     #pragma omp simd
ParamTable.h:522: warning: ignoring ‘#pragma omp simd’ [-Wunknown-pragmas]
  522 |       #pragma omp simd  // hint for the compiler
ParamTable.h:547: warning: ignoring ‘#pragma omp simd’ [-Wunknown-pragmas]
  547 |       #pragma omp simd  // can be auto-vectorised
In file included from particle_ll.cpp:12:
model_LBA.h:77: warning: ignoring ‘#pragma omp simd’ [-Wunknown-pragmas]
   77 | #pragma omp simd
model_LBA.h:120: warning: ignoring ‘#pragma omp simd’ [-Wunknown-pragmas]
  120 | #pragma omp simd
In file included from particle_ll.cpp:13:
model_lnr.h:70: warning: ignoring ‘#pragma omp simd’ [-Wunknown-pragmas]
   70 | #pragma omp simd
model_lnr.h:99: warning: ignoring ‘#pragma omp simd’ [-Wunknown-pragmas]
   99 | #pragma omp simd
In file included from particle_ll.cpp:14:
model_RDM.h:355: warning: ignoring ‘#pragma omp simd’ [-Wunknown-pragmas]
  355 | #pragma omp simd
model_RDM.h:365: warning: ignoring ‘#pragma omp simd’ [-Wunknown-pragmas]
  365 | #pragma omp simd
model_RDM.h:425: warning: ignoring ‘#pragma omp simd’ [-Wunknown-pragmas]
  425 | #pragma omp simd
model_RDM.h:435: warning: ignoring ‘#pragma omp simd’ [-Wunknown-pragmas]
  435 | #pragma omp simd
particle_ll.cpp:340: warning: ignoring ‘#pragma omp simd’ [-Wunknown-pragmas]
  340 | #pragma omp simd reduction(+:sum_ll)
particle_ll.cpp:372: warning: ignoring ‘#pragma omp simd’ [-Wunknown-pragmas]
  372 | #pragma omp simd reduction(+:sum_ll)
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG  -I../inst/include -DPNORM_MODE=1 -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -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 pdf_fncs.cpp -o pdf_fncs.o
pdf_fncs.cpp:56: warning: ignoring ‘#pragma omp simd’ [-Wunknown-pragmas]
   56 |     #pragma omp simd reduction(+:sum_plus,sum_minus)
pdf_fncs.cpp:110: warning: ignoring ‘#pragma omp simd’ [-Wunknown-pragmas]
  110 |   #pragma omp simd reduction(+:sum_plus,sum_minus)
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG  -I../inst/include -DPNORM_MODE=1 -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -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 tools.cpp -o tools.o
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG  -I../inst/include -DPNORM_MODE=1 -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -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 transform_utils.cpp -o transform_utils.o
In file included from transform_utils.h:6,
                 from transform_utils.cpp:3:
ParamTable.h:462: warning: ignoring ‘#pragma omp simd’ [-Wunknown-pragmas]
  462 | #pragma omp simd
ParamTable.h:487: warning: ignoring ‘#pragma omp simd’ [-Wunknown-pragmas]
  487 |     #pragma omp simd
ParamTable.h:522: warning: ignoring ‘#pragma omp simd’ [-Wunknown-pragmas]
  522 |       #pragma omp simd  // hint for the compiler
ParamTable.h:547: warning: ignoring ‘#pragma omp simd’ [-Wunknown-pragmas]
  547 |       #pragma omp simd  // can be auto-vectorised
transform_utils.cpp:198: warning: ignoring ‘#pragma omp simd’ [-Wunknown-pragmas]
  198 | #pragma omp simd
g++ -std=gnu++20 -shared -L/usr/local/lib64 -o EMC2.so ParamTable.o RcppExports.o TrendEngine.o build_info.o custom_trend_interface.o fa.o fncs_seven.o group_designs.o hcubature.o kernels.o math_utils_apple.o math_utils_generic.o model_SS_EXG.o model_SS_RDEX.o mri.o param_table_interface.o particle_ll.o pdf_fncs.o tools.o transform_utils.o
make[1]: Leaving directory '/data/localhost/ripley/R/packages/tests-devel/EMC2/src'
make[1]: Entering directory '/data/localhost/ripley/R/packages/tests-devel/EMC2/src'
make[1]: Leaving directory '/data/localhost/ripley/R/packages/tests-devel/EMC2/src'
installing to /data/localhost/ripley/R/packages/tests-devel/EMC2.Rcheck/00LOCK-EMC2/00new/EMC2/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 (EMC2)