Package: slalom

Version: 1.0.0

Command: rm -rf slalom.buildbin-libdir && mkdir slalom.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh slalom_1.0.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R slalom.buildbin-libdir

StartedAt: 2018-04-12 12:16:25 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 12:17:04 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 39.3 seconds

RetCode: 0

Status:  OK

PackageFile: slalom_1.0.0.tgz

PackageFileSize: 19.94 MiB

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### Running command:
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###   rm -rf slalom.buildbin-libdir && mkdir slalom.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh slalom_1.0.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R slalom.buildbin-libdir
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=slalom.buildbin-libdir slalom_1.0.0.tar.gz'
>>>>>>> 

* installing *source* package ‘slalom’ ...
** libs
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c slalom-classes.cpp -o slalom-classes.o
In file included from slalom-classes.cpp:20:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/math/special_functions/digamma.hpp:20:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/math/constants/constants.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/math/tools/convert_from_string.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/lexical_cast.hpp:32:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/lexical_cast/try_lexical_convert.hpp:42:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/lexical_cast/detail/converter_lexical.hpp:52:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/container/container_fwd.hpp:61:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/container/detail/std_fwd.hpp:27:1: warning: inline namespaces are a C++11 feature [-Wc++11-inline-namespace]
BOOST_MOVE_STD_NS_BEG
^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/move/detail/std_ns_begin.hpp:18:34: note: expanded from macro 'BOOST_MOVE_STD_NS_BEG'
   #define BOOST_MOVE_STD_NS_BEG _LIBCPP_BEGIN_NAMESPACE_STD
                                 ^
/usr/local/clang4/bin/../include/c++/v1/__config:388:52: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD'
#define _LIBCPP_BEGIN_NAMESPACE_STD namespace std {inline namespace _LIBCPP_NAMESPACE {
                                                   ^
slalom-classes.cpp:128:9: warning: field 'Y' will be initialized after field 'Pi_E1' [-Wreorder]
        Y(Y_init), Pi_E1(pi_init), I(pi_init), W_gamma0(pi_init), X_E1(X_init),
        ^
slalom-classes.cpp:128:20: warning: field 'Pi_E1' will be initialized after field 'I' [-Wreorder]
        Y(Y_init), Pi_E1(pi_init), I(pi_init), W_gamma0(pi_init), X_E1(X_init),
                   ^
slalom-classes.cpp:128:36: warning: field 'I' will be initialized after field 'W_gamma0' [-Wreorder]
        Y(Y_init), Pi_E1(pi_init), I(pi_init), W_gamma0(pi_init), X_E1(X_init),
                                   ^
slalom-classes.cpp:128:48: warning: field 'W_gamma0' will be initialized after field 'X_E1' [-Wreorder]
        Y(Y_init), Pi_E1(pi_init), I(pi_init), W_gamma0(pi_init), X_E1(X_init),
                                               ^
slalom-classes.cpp:221:20: warning: unused variable 'meanerr' [-Wunused-variable]
            double meanerr = arma::mean(error);
                   ^
slalom-classes.cpp:200:12: warning: unused variable 'meanerr' [-Wunused-variable]
    double meanerr = arma::mean(error);
           ^
7 warnings generated.
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o slalom.so RcppExports.o slalom-classes.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.6-bioc/meat/slalom.buildbin-libdir/slalom/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (slalom)


>>>>>>> 
>>>>>>> FIXING LINKS FOR slalom.buildbin-libdir/slalom/libs//slalom.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libgcc_s.1.dylib" "slalom.buildbin-libdir/slalom/libs//slalom.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libgfortran.3.dylib" "slalom.buildbin-libdir/slalom/libs//slalom.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libreadline.5.2.dylib" "slalom.buildbin-libdir/slalom/libs//slalom.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libreadline.dylib" "slalom.buildbin-libdir/slalom/libs//slalom.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libquadmath.0.dylib" "slalom.buildbin-libdir/slalom/libs//slalom.so"
install_name_tool -change "/usr/local/gfortran/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libgfortran.3.dylib" "slalom.buildbin-libdir/slalom/libs//slalom.so"
install_name_tool -change "/usr/local/gfortran/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libquadmath.0.dylib" "slalom.buildbin-libdir/slalom/libs//slalom.so"