* installing *source* package ‘icd’ ...
** package ‘icd’ successfully unpacked and MD5 sums checked
** using staged installation
checking R_HOME already set... /data/gannet/ripley/R/R-clang
checking R CXX11... Setting clang++
checking R CXX11STD... Setting R -std=gnu++11
checking R CXX11FLAGS... Setting R -g -O3 -Wall -pedantic -frtti
'config' variable 'CPP' is deprecated
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++ accepts -g... yes
checking for clang++ option to support OpenMP... -fopenmp
checking OpenMP available, but does it work in a package... OpenMP available and working: yes
icd thinks openmp compilation possible: yes
configure: Not enabling Makevars inclusion
configure: creating ./config.status
config.status: creating src/Makevars
** libs
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/icd/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/RcppEigen/include' -isystem /usr/local/clang/include  -fopenmp -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS -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/RcppEigen/include' -isystem /usr/local/clang/include  -fopenmp -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS -fpic  -g -O3 -Wall -pedantic -frtti  -c appendMinor.cpp -o appendMinor.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/RcppEigen/include' -isystem /usr/local/clang/include  -fopenmp -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS -fpic  -g -O3 -Wall -pedantic -frtti  -c attr.cpp -o attr.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/RcppEigen/include' -isystem /usr/local/clang/include  -fopenmp -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS -fpic  -g -O3 -Wall -pedantic -frtti  -c categorize.cpp -o categorize.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/RcppEigen/include' -isystem /usr/local/clang/include  -fopenmp -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS -fpic  -g -O3 -Wall -pedantic -frtti  -c children.cpp -o children.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/RcppEigen/include' -isystem /usr/local/clang/include  -fopenmp -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS -fpic  -g -O3 -Wall -pedantic -frtti  -c comorbidIcd10.cpp -o comorbidIcd10.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/RcppEigen/include' -isystem /usr/local/clang/include  -fopenmp -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS -fpic  -g -O3 -Wall -pedantic -frtti  -c comorbidMatMul.cpp -o comorbidMatMul.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/RcppEigen/include' -isystem /usr/local/clang/include  -fopenmp -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS -fpic  -g -O3 -Wall -pedantic -frtti  -c convert.cpp -o convert.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/RcppEigen/include' -isystem /usr/local/clang/include  -fopenmp -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS -fpic  -g -O3 -Wall -pedantic -frtti  -c convert10.cpp -o convert10.o
clang -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/RcppEigen/include' -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic  -c cutil.c -o cutil.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/RcppEigen/include' -isystem /usr/local/clang/include  -fopenmp -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS -fpic  -g -O3 -Wall -pedantic -frtti  -c fastIntToString.cpp -o fastIntToString.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/RcppEigen/include' -isystem /usr/local/clang/include  -fopenmp -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS -fpic  -g -O3 -Wall -pedantic -frtti  -c guess.cpp -o guess.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/RcppEigen/include' -isystem /usr/local/clang/include  -fopenmp -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS -fpic  -g -O3 -Wall -pedantic -frtti  -c is.cpp -o is.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/RcppEigen/include' -isystem /usr/local/clang/include  -fopenmp -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS -fpic  -g -O3 -Wall -pedantic -frtti  -c manip.cpp -o manip.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/RcppEigen/include' -isystem /usr/local/clang/include  -fopenmp -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS -fpic  -g -O3 -Wall -pedantic -frtti  -c mapplus.cpp -o mapplus.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/RcppEigen/include' -isystem /usr/local/clang/include  -fopenmp -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS -fpic  -g -O3 -Wall -pedantic -frtti  -c ranges.cpp -o ranges.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/RcppEigen/include' -isystem /usr/local/clang/include  -fopenmp -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS -fpic  -g -O3 -Wall -pedantic -frtti  -c refactor.cpp -o refactor.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/RcppEigen/include' -isystem /usr/local/clang/include  -fopenmp -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS -fpic  -g -O3 -Wall -pedantic -frtti  -c relevant.cpp -o relevant.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/RcppEigen/include' -isystem /usr/local/clang/include  -fopenmp -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS -fpic  -g -O3 -Wall -pedantic -frtti  -c sort.cpp -o sort.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/RcppEigen/include' -isystem /usr/local/clang/include  -fopenmp -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS -fpic  -g -O3 -Wall -pedantic -frtti  -c test-cpp-matmul.cpp -o test-cpp-matmul.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/RcppEigen/include' -isystem /usr/local/clang/include  -fopenmp -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS -fpic  -g -O3 -Wall -pedantic -frtti  -c test-cpp.cpp -o test-cpp.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/RcppEigen/include' -isystem /usr/local/clang/include  -fopenmp -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS -fpic  -g -O3 -Wall -pedantic -frtti  -c test-runner.cpp -o test-runner.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/RcppEigen/include' -isystem /usr/local/clang/include  -fopenmp -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS -fpic  -g -O3 -Wall -pedantic -frtti  -c util.cpp -o util.o
clang++ -std=gnu++11 -shared -L/usr/local/clang/lib64 -L/usr/local/lib64 -o icd.so RcppExports.o appendMinor.o attr.o categorize.o children.o comorbidIcd10.o comorbidMatMul.o convert.o convert10.o cutil.o fastIntToString.o guess.o is.o manip.o mapplus.o ranges.o refactor.o relevant.o sort.o test-cpp-matmul.o test-cpp.o test-runner.o util.o -fopenmp
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/icd/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/icd/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/icd/src'
installing to /data/gannet/ripley/R/packages/tests-clang/icd.Rcheck/00LOCK-icd/00new/icd/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 (icd)