* installing *source* package ‘netdiffuseR’ ...
** package ‘netdiffuseR’ successfully unpacked and MD5 sums checked
** using staged installation
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether clang++ -std=gnu++14 accepts -g... yes
checking how to run the C++ preprocessor... clang++ -std=gnu++14 -E
checking for clang++ -std=gnu++14 option to support OpenMP... -fopenmp
configure: creating ./config.status
config.status: creating src/Makevars
** libs
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/netdiffuseR/src'
clang++ -std=gnu++11 -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' -isystem /usr/local/clang/include   -fopenmp -DARMA_64BIT_WORD -DSTRICT_R_HEADERS -fpic  -g -O3 -Wall -pedantic -frtti  -c RcppExports.cpp -o RcppExports.o
clang++ -std=gnu++11 -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' -isystem /usr/local/clang/include   -fopenmp -DARMA_64BIT_WORD -DSTRICT_R_HEADERS -fpic  -g -O3 -Wall -pedantic -frtti  -c adjmat.cpp -o adjmat.o
clang++ -std=gnu++11 -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' -isystem /usr/local/clang/include   -fopenmp -DARMA_64BIT_WORD -DSTRICT_R_HEADERS -fpic  -g -O3 -Wall -pedantic -frtti  -c infection.cpp -o infection.o
clang++ -std=gnu++11 -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' -isystem /usr/local/clang/include   -fopenmp -DARMA_64BIT_WORD -DSTRICT_R_HEADERS -fpic  -g -O3 -Wall -pedantic -frtti  -c netdiffuser_extra.cpp -o netdiffuser_extra.o
clang++ -std=gnu++11 -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' -isystem /usr/local/clang/include   -fopenmp -DARMA_64BIT_WORD -DSTRICT_R_HEADERS -fpic  -g -O3 -Wall -pedantic -frtti  -c plot.cpp -o plot.o
clang++ -std=gnu++11 -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' -isystem /usr/local/clang/include   -fopenmp -DARMA_64BIT_WORD -DSTRICT_R_HEADERS -fpic  -g -O3 -Wall -pedantic -frtti  -c rgraph.cpp -o rgraph.o
netdiffuser_extra.cpp:84:12: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  else if ((funname == "quaddist") | (funname == "^2"))       fun = &st_quaddist;
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                                   ||
netdiffuser_extra.cpp:84:12: note: cast one or both operands to int to silence this warning
netdiffuser_extra.cpp:85:12: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  else if ((funname == "greater") | (funname == ">"))       fun = &st_greater;
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                                  ||
netdiffuser_extra.cpp:85:12: note: cast one or both operands to int to silence this warning
netdiffuser_extra.cpp:86:12: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  else if ((funname == "greaterequal") | (funname == ">=")) fun =  &st_greaterequal;
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                                       ||
netdiffuser_extra.cpp:86:12: note: cast one or both operands to int to silence this warning
netdiffuser_extra.cpp:87:12: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  else if ((funname == "smaller") | (funname == "<"))       fun =  &st_smaller;
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                                  ||
netdiffuser_extra.cpp:87:12: note: cast one or both operands to int to silence this warning
netdiffuser_extra.cpp:88:12: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  else if ((funname == "smallerequal") | (funname == "<=")) fun =  &st_smallerequal;
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                                       ||
netdiffuser_extra.cpp:88:12: note: cast one or both operands to int to silence this warning
netdiffuser_extra.cpp:89:12: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  else if ((funname == "equal") | (funname == "=="))        fun =  &st_equal;
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                                ||
netdiffuser_extra.cpp:89:12: note: cast one or both operands to int to silence this warning
netdiffuser_extra.cpp:90:12: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  else if ((funname == "min") | (funname == "minimum"))        fun =  &st_min;
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                              ||
netdiffuser_extra.cpp:90:12: note: cast one or both operands to int to silence this warning
netdiffuser_extra.cpp:91:12: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  else if ((funname == "max") | (funname == "maximum"))        fun =  &st_max;
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                              ||
netdiffuser_extra.cpp:91:12: note: cast one or both operands to int to silence this warning
netdiffuser_extra.cpp:92:12: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  else if ((funname == "mean") | (funname == "avg"))        fun =  &st_mean;
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                               ||
netdiffuser_extra.cpp:92:12: note: cast one or both operands to int to silence this warning
clang++ -std=gnu++11 -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' -isystem /usr/local/clang/include   -fopenmp -DARMA_64BIT_WORD -DSTRICT_R_HEADERS -fpic  -g -O3 -Wall -pedantic -frtti  -c stats.cpp -o stats.o
clang++ -std=gnu++11 -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' -isystem /usr/local/clang/include   -fopenmp -DARMA_64BIT_WORD -DSTRICT_R_HEADERS -fpic  -g -O3 -Wall -pedantic -frtti  -c struct_test.cpp -o struct_test.o
9 warnings generated.
plot.cpp:70:14: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
        if ( ((x(k) <= xseq(i+1)) & (x(k) > xseq(i))) & ((y(k) <= yseq(j+1)) & (y(k) > yseq(j)))) {
             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                                                      &&
plot.cpp:70:14: note: cast one or both operands to int to silence this warning
plot.cpp:70:58: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
        if ( ((x(k) <= xseq(i+1)) & (x(k) > xseq(i))) & ((y(k) <= yseq(j+1)) & (y(k) > yseq(j)))) {
                                                        ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                                                                             &&
plot.cpp:70:58: note: cast one or both operands to int to silence this warning
plot.cpp:70:15: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
        if ( ((x(k) <= xseq(i+1)) & (x(k) > xseq(i))) & ((y(k) <= yseq(j+1)) & (y(k) > yseq(j)))) {
             ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                                  &&
plot.cpp:70:15: note: cast one or both operands to int to silence this warning
rgraph.cpp:257:7: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
      (newgraph.at(i, newj) != 0) | (newgraph.at(newi, j) != 0);
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                                  ||
rgraph.cpp:257:7: note: cast one or both operands to int to silence this warning
3 warnings generated.
1 warning generated.
clang++ -std=gnu++11 -shared -L/usr/local/clang/lib64 -L/usr/local/lib64 -o netdiffuseR.so RcppExports.o adjmat.o infection.o netdiffuser_extra.o plot.o rgraph.o stats.o struct_test.o -L/data/gannet/ripley/R/R-clang/lib -lRlapack -L/data/gannet/ripley/R/R-clang/lib -lRblas -lgfortran -lm -lquadmath -fopenmp
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/netdiffuseR/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/netdiffuseR/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/netdiffuseR/src'
installing to /data/gannet/ripley/R/packages/tests-clang/netdiffuseR.Rcheck/00LOCK-netdiffuseR/00new/netdiffuseR/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 (netdiffuseR)