Install log for 'hibayes'

* installing *source* package ‘hibayes’ ...
** this is package ‘hibayes’ version ‘3.1.0’
** package ‘hibayes’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘clang version 21.1.0’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/hibayes/src'
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppProgress/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/bigmemory/include' -I'/data/gannet/ripley/R/R-clang/library/Matrix/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include   -DARMA_64BIT_WORD=1 -DARMA_USE_CURRENT -fopenmp -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c Bayes.cpp -o Bayes.o
In file included from Bayes.cpp:1:
In file included from ./hibayes.h:8:
In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo.h:32:
In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57:
In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/current/armadillo:26:
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/current/armadillo_bits/config.hpp:373:11: warning: NOTE: option ARMA_CRIPPLED_LAPACK is not supported [-W#pragma-messages]
  373 |   #pragma message ("NOTE: option ARMA_CRIPPLED_LAPACK is not supported")
      |           ^
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppProgress/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/bigmemory/include' -I'/data/gannet/ripley/R/R-clang/library/Matrix/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include   -DARMA_64BIT_WORD=1 -DARMA_USE_CURRENT -fopenmp -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c RcppExports.cpp -o RcppExports.o
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppProgress/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/bigmemory/include' -I'/data/gannet/ripley/R/R-clang/library/Matrix/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include   -DARMA_64BIT_WORD=1 -DARMA_USE_CURRENT -fopenmp -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c SBayesD.cpp -o SBayesD.o
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppProgress/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/bigmemory/include' -I'/data/gannet/ripley/R/R-clang/library/Matrix/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include   -DARMA_64BIT_WORD=1 -DARMA_USE_CURRENT -fopenmp -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c SBayesS.cpp -o SBayesS.o
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppProgress/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/bigmemory/include' -I'/data/gannet/ripley/R/R-clang/library/Matrix/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include   -DARMA_64BIT_WORD=1 -DARMA_USE_CURRENT -fopenmp -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c cg.cpp -o cg.o
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppProgress/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/bigmemory/include' -I'/data/gannet/ripley/R/R-clang/library/Matrix/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include   -DARMA_64BIT_WORD=1 -DARMA_USE_CURRENT -fopenmp -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c cutwind.cpp -o cutwind.o
In file included from RcppExports.cpp:4:
In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo.h:32:
In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57:
In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/current/armadillo:26:
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/current/armadillo_bits/config.hpp:373:11: warning: NOTE: option ARMA_CRIPPLED_LAPACK is not supported [-W#pragma-messages]
  373 |   #pragma message ("NOTE: option ARMA_CRIPPLED_LAPACK is not supported")
      |           ^
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppProgress/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/bigmemory/include' -I'/data/gannet/ripley/R/R-clang/library/Matrix/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include   -DARMA_64BIT_WORD=1 -DARMA_USE_CURRENT -fopenmp -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c read_bed.cpp -o read_bed.o
In file included from SBayesD.cpp:1:
In file included from ./hibayes.h:8:
In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo.h:32:
In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57:
In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/current/armadillo:26:
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/current/armadillo_bits/config.hpp:373:11: warning: NOTE: option ARMA_CRIPPLED_LAPACK is not supported [-W#pragma-messages]
  373 |   #pragma message ("NOTE: option ARMA_CRIPPLED_LAPACK is not supported")
      |           ^
In file included from cutwind.cpp:5:
In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo.h:32:
In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57:
In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/current/armadillo:26:
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/current/armadillo_bits/config.hpp:373:11: warning: NOTE: option ARMA_CRIPPLED_LAPACK is not supported [-W#pragma-messages]
  373 |   #pragma message ("NOTE: option ARMA_CRIPPLED_LAPACK is not supported")
      |           ^
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppProgress/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/bigmemory/include' -I'/data/gannet/ripley/R/R-clang/library/Matrix/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include   -DARMA_64BIT_WORD=1 -DARMA_USE_CURRENT -fopenmp -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c rm.cpp -o rm.o
In file included from cg.cpp:1:
In file included from ./solver.h:9:
In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo.h:32:
In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57:
In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/current/armadillo:26:
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/current/armadillo_bits/config.hpp:373:11: warning: NOTE: option ARMA_CRIPPLED_LAPACK is not supported [-W#pragma-messages]
  373 |   #pragma message ("NOTE: option ARMA_CRIPPLED_LAPACK is not supported")
      |           ^
In file included from SBayesS.cpp:1:
In file included from ./hibayes.h:8:
In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo.h:32:
In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57:
In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/current/armadillo:26:
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/current/armadillo_bits/config.hpp:373:11: warning: NOTE: option ARMA_CRIPPLED_LAPACK is not supported [-W#pragma-messages]
  373 |   #pragma message ("NOTE: option ARMA_CRIPPLED_LAPACK is not supported")
      |           ^
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppProgress/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/bigmemory/include' -I'/data/gannet/ripley/R/R-clang/library/Matrix/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include   -DARMA_64BIT_WORD=1 -DARMA_USE_CURRENT -fopenmp -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c solver.cpp -o solver.o
read_bed.cpp:142:9: warning: variable 'n_bytes_read' set but not used [-Wunused-but-set-variable]
  142 |         size_t n_bytes_read = static_cast<size_t>(fread(buffer, 1, 3, fin));
      |                ^
In file included from rm.cpp:1:
In file included from ./hibayes.h:8:
In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo.h:32:
In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57:
In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/current/armadillo:26:
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/current/armadillo_bits/config.hpp:373:11: warning: NOTE: option ARMA_CRIPPLED_LAPACK is not supported [-W#pragma-messages]
  373 |   #pragma message ("NOTE: option ARMA_CRIPPLED_LAPACK is not supported")
      |           ^
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppProgress/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/bigmemory/include' -I'/data/gannet/ripley/R/R-clang/library/Matrix/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include   -DARMA_64BIT_WORD=1 -DARMA_USE_CURRENT -fopenmp -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c stats.cpp -o stats.o
In file included from solver.cpp:1:
In file included from ./solver.h:9:
In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo.h:32:
In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57:
In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/current/armadillo:26:
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/current/armadillo_bits/config.hpp:373:11: warning: NOTE: option ARMA_CRIPPLED_LAPACK is not supported [-W#pragma-messages]
  373 |   #pragma message ("NOTE: option ARMA_CRIPPLED_LAPACK is not supported")
      |           ^
In file included from stats.cpp:1:
In file included from ./stats.h:8:
In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo.h:32:
In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57:
In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/current/armadillo:26:
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/current/armadillo_bits/config.hpp:373:11: warning: NOTE: option ARMA_CRIPPLED_LAPACK is not supported [-W#pragma-messages]
  373 |   #pragma message ("NOTE: option ARMA_CRIPPLED_LAPACK is not supported")
      |           ^
1 warning generated.
1 warning generated.
1 warning generated.
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppProgress/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/bigmemory/include' -I'/data/gannet/ripley/R/R-clang/library/Matrix/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include   -DARMA_64BIT_WORD=1 -DARMA_USE_CURRENT -fopenmp -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c tXXmat.cpp -o tXXmat.o
1 warning generated.
1 warning generated.
In file included from tXXmat.cpp:1:
In file included from ./hibayes.h:8:
In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo.h:32:
In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57:
In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/current/armadillo:26:
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/current/armadillo_bits/config.hpp:373:11: warning: NOTE: option ARMA_CRIPPLED_LAPACK is not supported [-W#pragma-messages]
  373 |   #pragma message ("NOTE: option ARMA_CRIPPLED_LAPACK is not supported")
      |           ^
1 warning generated.
1 warning generated.
1 warning generated.
1 warning generated.
1 warning generated.
1 warning generated.
/usr/local/clang21/bin/clang++ -std=gnu++17 -shared -L/usr/local/clang/lib64 -L/usr/local/clang21/lib -L/usr/local/clang21/lib/x86_64-unknown-linux-gnu -L/usr/local/lib64 -L/usr/local/clang21/lib/clang/21/lib/x86_64-unknown-linux-gnu -o hibayes.so Bayes.o RcppExports.o SBayesD.o SBayesS.o cg.o cutwind.o read_bed.o rm.o solver.o stats.o tXXmat.o -fopenmp -L/data/gannet/ripley/R/R-clang/lib -lRlapack -L/data/gannet/ripley/R/R-clang/lib -lRblas -lflang_rt.runtime -lm
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/hibayes/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/hibayes/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/hibayes/src'
installing to /data/gannet/ripley/R/packages/tests-clang/hibayes.Rcheck/00LOCK-hibayes/00new/hibayes/libs
** R
** inst
** 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 (hibayes)