networkBMA 1.14.0
Ka Yee Yeung
| Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/networkBMA | | Last Changed Rev: 117079 / Revision: 122332 | | Last Changed Date: 2016-05-03 14:20:18 -0700 (Tue, 03 May 2016) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | WARNINGS | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | ERROR | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | WARNINGS | [ OK ] | |
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### Running command:
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### rm -rf networkBMA.buildbin-libdir && mkdir networkBMA.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh networkBMA_1.14.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R networkBMA.buildbin-libdir
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=networkBMA.buildbin-libdir networkBMA_1.14.0.tar.gz'
>>>>>>>
* installing *source* package ‘networkBMA’ ...
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 how to run the C++ preprocessor... clang++ -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... rm: conftest.dSYM: is a directory
rm: conftest.dSYM: is a directory
yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking unordered_set usability... yes
checking unordered_set presence... yes
checking for unordered_set... yes
checking tr1/unordered_set usability... no
checking tr1/unordered_set presence... no
checking for tr1/unordered_set... no
configure: creating ./config.status
config.status: creating src/config.h
config.status: src/config.h is unchanged
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/RcppEigen/include" -fPIC -Wall -mtune=core2 -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/RcppEigen/include" -fPIC -Wall -mtune=core2 -g -O2 -c ScanBMA_full.cpp -o ScanBMA_full.o
ScanBMA_full.cpp:131:21: warning: 'sort_index' is deprecated [-Wdeprecated-declarations]
arma::uvec pord = sort_index(priorProbs, 1);
^
/Library/Frameworks/R.framework/Versions/3.3/Resources/library/RcppArmadillo/include/armadillo_bits/fn_sort_index.hpp:37:1: note: 'sort_index<arma::Mat<double> >' has been explicitly marked deprecated here
sort_index
^
ScanBMA_full.cpp:322:19: warning: 'sort_index' is deprecated [-Wdeprecated-declarations]
arma::uvec pord = sort_index(priorProbs, 1);
^
/Library/Frameworks/R.framework/Versions/3.3/Resources/library/RcppArmadillo/include/armadillo_bits/fn_sort_index.hpp:37:1: note: 'sort_index<arma::Mat<double> >' has been explicitly marked deprecated here
sort_index
^
ScanBMA_full.cpp:417:21: warning: 'sort_index' is deprecated [-Wdeprecated-declarations]
arma::uvec pord = sort_index(priorProbs, 1);
^
/Library/Frameworks/R.framework/Versions/3.3/Resources/library/RcppArmadillo/include/armadillo_bits/fn_sort_index.hpp:37:1: note: 'sort_index<arma::Mat<double> >' has been explicitly marked deprecated here
sort_index
^
ScanBMA_full.cpp:610:19: warning: 'sort_index' is deprecated [-Wdeprecated-declarations]
arma::uvec pord = sort_index(priorProbs, 1);
^
/Library/Frameworks/R.framework/Versions/3.3/Resources/library/RcppArmadillo/include/armadillo_bits/fn_sort_index.hpp:37:1: note: 'sort_index<arma::Mat<double> >' has been explicitly marked deprecated here
sort_index
^
4 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 networkBMA.so RcppExports.o ScanBMA_full.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2 -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.3-bioc/meat/networkBMA.buildbin-libdir/networkBMA/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (networkBMA)
>>>>>>>
>>>>>>> FIXING LINKS FOR networkBMA.buildbin-libdir/networkBMA/libs//networkBMA.so
>>>>>>>
install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.3/Resources/lib/libgcc_s.1.dylib" "networkBMA.buildbin-libdir/networkBMA/libs//networkBMA.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.3/Resources/lib/libgfortran.3.dylib" "networkBMA.buildbin-libdir/networkBMA/libs//networkBMA.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.3/Resources/lib/libreadline.5.2.dylib" "networkBMA.buildbin-libdir/networkBMA/libs//networkBMA.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.3/Resources/lib/libreadline.dylib" "networkBMA.buildbin-libdir/networkBMA/libs//networkBMA.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.3/Resources/lib/libquadmath.0.dylib" "networkBMA.buildbin-libdir/networkBMA/libs//networkBMA.so"