* installing *source* package ‘hibayes’ ...
** using staged installation
** libs
using C++ compiler: ‘Debian clang version 17.0.6 (3)’
clang++-17  -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppProgress/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/BH/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/bigmemory/include' -I'/srv/hornik/tmp/R-d-clang-17/library/Matrix/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -DARMA_64BIT_WORD=1  -fpic  -g -O3 -Wall -pedantic -c Bayes.cpp -o Bayes.o
clang++-17  -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppProgress/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/BH/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/bigmemory/include' -I'/srv/hornik/tmp/R-d-clang-17/library/Matrix/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -DARMA_64BIT_WORD=1  -fpic  -g -O3 -Wall -pedantic -c RcppExports.cpp -o RcppExports.o
clang++-17  -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppProgress/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/BH/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/bigmemory/include' -I'/srv/hornik/tmp/R-d-clang-17/library/Matrix/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -DARMA_64BIT_WORD=1  -fpic  -g -O3 -Wall -pedantic -c SBayesD.cpp -o SBayesD.o
clang++-17  -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppProgress/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/BH/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/bigmemory/include' -I'/srv/hornik/tmp/R-d-clang-17/library/Matrix/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -DARMA_64BIT_WORD=1  -fpic  -g -O3 -Wall -pedantic -c SBayesS.cpp -o SBayesS.o
clang++-17  -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppProgress/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/BH/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/bigmemory/include' -I'/srv/hornik/tmp/R-d-clang-17/library/Matrix/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -DARMA_64BIT_WORD=1  -fpic  -g -O3 -Wall -pedantic -c cg.cpp -o cg.o
clang++-17  -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppProgress/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/BH/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/bigmemory/include' -I'/srv/hornik/tmp/R-d-clang-17/library/Matrix/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -DARMA_64BIT_WORD=1  -fpic  -g -O3 -Wall -pedantic -c cutwind.cpp -o cutwind.o
clang++-17  -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppProgress/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/BH/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/bigmemory/include' -I'/srv/hornik/tmp/R-d-clang-17/library/Matrix/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -DARMA_64BIT_WORD=1  -fpic  -g -O3 -Wall -pedantic -c read_bed.cpp -o read_bed.o
read_bed.cpp:142:2: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result]
  142 |         fread(buffer, 1, 3, fin);
      |         ^~~~~ ~~~~~~~~~~~~~~~~~
read_bed.cpp:150:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result]
  150 |                 fread(buffer, 1, buffer_size, fin);
      |                 ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~
read_bed.cpp:142:2: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result]
  142 |         fread(buffer, 1, 3, fin);
      |         ^~~~~ ~~~~~~~~~~~~~~~~~
read_bed.cpp:240:10: note: in instantiation of function template specialization 'read_bed<char>' requested here
  240 |                 return read_bed<char>(bfile, xpMat, maxLine, NA_CHAR, impt, d, threads);
      |                        ^
read_bed.cpp:150:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result]
  150 |                 fread(buffer, 1, buffer_size, fin);
      |                 ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~
read_bed.cpp:142:2: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result]
  142 |         fread(buffer, 1, 3, fin);
      |         ^~~~~ ~~~~~~~~~~~~~~~~~
read_bed.cpp:242:10: note: in instantiation of function template specialization 'read_bed<short>' requested here
  242 |                 return read_bed<short>(bfile, xpMat, maxLine, NA_SHORT, impt, d, threads);
      |                        ^
read_bed.cpp:150:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result]
  150 |                 fread(buffer, 1, buffer_size, fin);
      |                 ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~
read_bed.cpp:142:2: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result]
  142 |         fread(buffer, 1, 3, fin);
      |         ^~~~~ ~~~~~~~~~~~~~~~~~
read_bed.cpp:244:10: note: in instantiation of function template specialization 'read_bed<int>' requested here
  244 |                 return read_bed<int>(bfile, xpMat, maxLine, NA_INTEGER, impt, d, threads);
      |                        ^
read_bed.cpp:150:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result]
  150 |                 fread(buffer, 1, buffer_size, fin);
      |                 ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~
read_bed.cpp:142:2: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result]
  142 |         fread(buffer, 1, 3, fin);
      |         ^~~~~ ~~~~~~~~~~~~~~~~~
read_bed.cpp:246:10: note: in instantiation of function template specialization 'read_bed<double>' requested here
  246 |                 return read_bed<double>(bfile, xpMat, maxLine, NA_REAL, impt, d, threads);
      |                        ^
read_bed.cpp:150:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result]
  150 |                 fread(buffer, 1, buffer_size, fin);
      |                 ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~
10 warnings generated.
clang++-17  -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppProgress/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/BH/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/bigmemory/include' -I'/srv/hornik/tmp/R-d-clang-17/library/Matrix/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -DARMA_64BIT_WORD=1  -fpic  -g -O3 -Wall -pedantic -c rm.cpp -o rm.o
clang++-17  -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppProgress/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/BH/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/bigmemory/include' -I'/srv/hornik/tmp/R-d-clang-17/library/Matrix/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -DARMA_64BIT_WORD=1  -fpic  -g -O3 -Wall -pedantic -c solver.cpp -o solver.o
clang++-17  -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppProgress/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/BH/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/bigmemory/include' -I'/srv/hornik/tmp/R-d-clang-17/library/Matrix/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -DARMA_64BIT_WORD=1  -fpic  -g -O3 -Wall -pedantic -c stats.cpp -o stats.o
clang++-17  -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppProgress/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/BH/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/bigmemory/include' -I'/srv/hornik/tmp/R-d-clang-17/library/Matrix/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -DARMA_64BIT_WORD=1  -fpic  -g -O3 -Wall -pedantic -c tXXmat.cpp -o tXXmat.o
clang++-17 -std=gnu++17 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -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 -llapack -L/home/hornik/tmp/R/lib -lRblas -L/usr/lib/llvm-17/lib -lFortran_main -lFortranRuntime -lFortranDecimal -lm -L/home/hornik/tmp/R/lib -lR
installing to /srv/hornik/tmp/CRAN/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)