* installing *source* package ‘Quartet’ ...
** package ‘Quartet’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/Quartet/src'
clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic -frtti  -c AbstractDistanceCalculator.cpp -o AbstractDistanceCalculator.o
clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic -frtti  -c HDT.cpp -o HDT.o
clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic -frtti  -c HDTCountingCCToC.cpp -o HDTCountingCCToC.o
clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic -frtti  -c HDTCountingCTransform.cpp -o HDTCountingCTransform.o
clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic -frtti  -c HDTCountingG.cpp -o HDTCountingG.o
clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic -frtti  -c HDTCountingIGToC.cpp -o HDTCountingIGToC.o
clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic -frtti  -c HDTCountingLeaf.cpp -o HDTCountingLeaf.o
clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic -frtti  -c HDTFactory.cpp -o HDTFactory.o
clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic -frtti  -c HDTListUtils.cpp -o HDTListUtils.o
clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic -frtti  -c NewickParser.cpp -o NewickParser.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic  -c Quartet-init.c -o Quartet-init.o
clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic -frtti  -c QuartetDistanceCalculator.cpp -o QuartetDistanceCalculator.o
clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang/include   -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' -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic -frtti  -c RootedTree.cpp -o RootedTree.o
NewickParser.cpp:20:63: warning: 'ptr_fun<int, int>' is deprecated [-Wdeprecated-declarations]
    s.erase(std::find_if(s.rbegin(), s.rend(), std::not1(std::ptr_fun<int, int>(std::isspace))).base(), s.end());
                                                              ^
/usr/local/bin/../include/c++/v1/functional:1100:1: note: 'ptr_fun<int, int>' has been explicitly marked deprecated here
_LIBCPP_DEPRECATED_IN_CXX11 inline _LIBCPP_INLINE_VISIBILITY
^
/usr/local/bin/../include/c++/v1/__config:944:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/usr/local/bin/../include/c++/v1/__config:933:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
1 warning generated.
clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic -frtti  -c RootedTreeFactory.cpp -o RootedTreeFactory.o
clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic -frtti  -c TripletDistanceCalculator.cpp -o TripletDistanceCalculator.o
clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic -frtti  -c int_stuff.cpp -o int_stuff.o
clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic -frtti  -c rQuartetDist.cpp -o rQuartetDist.o
clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic -frtti  -c rTripletDist.cpp -o rTripletDist.o
clang++ -std=gnu++11 -shared -L/usr/local/clang/lib64 -L/usr/local/lib64 -o Quartet.so AbstractDistanceCalculator.o HDT.o HDTCountingCCToC.o HDTCountingCTransform.o HDTCountingG.o HDTCountingIGToC.o HDTCountingLeaf.o HDTFactory.o HDTListUtils.o NewickParser.o Quartet-init.o QuartetDistanceCalculator.o RcppExports.o RootedTree.o RootedTreeFactory.o TripletDistanceCalculator.o int_stuff.o rQuartetDist.o rTripletDist.o
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/Quartet/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/Quartet/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/Quartet/src'
installing to /data/gannet/ripley/R/packages/tests-clang/Quartet.Rcheck/00LOCK-Quartet/00new/Quartet/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 (Quartet)