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BUILD BIN report for flowType on merida2

This page was generated on 2018-10-17 08:49:21 -0400 (Wed, 17 Oct 2018).

Package 521/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowType 2.18.0
Nima Aghaeepour
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/flowType
Branch: RELEASE_3_7
Last Commit: 19b54b8
Last Changed Date: 2018-04-30 10:35:19 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: flowType
Version: 2.18.0
Command: rm -rf flowType.buildbin-libdir && mkdir flowType.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh flowType_2.18.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R flowType.buildbin-libdir
StartedAt: 2018-10-17 01:20:38 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 01:21:31 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 52.9 seconds
RetCode: 0
Status:  OK 
PackageFile: flowType_2.18.0.tgz
PackageFileSize: 1.23 MiB

Command output

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###
### Running command:
###
###   rm -rf flowType.buildbin-libdir && mkdir flowType.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh flowType_2.18.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R flowType.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=flowType.buildbin-libdir flowType_2.18.0.tar.gz'
>>>>>>> 

* installing *source* package ‘flowType’ ...
** libs
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c countsAndMeans.cpp -o countsAndMeans.o
In file included from countsAndMeans.cpp:5:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/dynamic_bitset.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/dynamic_bitset/dynamic_bitset.hpp:44:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/move/move.hpp:30:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/move/iterator.hpp:27:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/move/detail/iterator_traits.hpp:29:1: warning: inline namespaces are a C++11 feature [-Wc++11-inline-namespace]
BOOST_MOVE_STD_NS_BEG
^
/Library/Frameworks/R.framework/Versions/3.5/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 {
                                                   ^
1 warning generated.
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c flowType.cpp -o flowType.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c numberGenerator.cpp -o numberGenerator.o
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 flowType.so countsAndMeans.o flowType.o numberGenerator.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.7-bioc/meat/flowType.buildbin-libdir/flowType/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
* DONE (flowType)


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

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libgcc_s.1.dylib" "flowType.buildbin-libdir/flowType/libs//flowType.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libgfortran.3.dylib" "flowType.buildbin-libdir/flowType/libs//flowType.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libreadline.5.2.dylib" "flowType.buildbin-libdir/flowType/libs//flowType.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libreadline.dylib" "flowType.buildbin-libdir/flowType/libs//flowType.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libquadmath.0.dylib" "flowType.buildbin-libdir/flowType/libs//flowType.so"