Mike Jiang
| Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020) |
| URL: https://git.bioconductor.org/packages/cytolib |
| Branch: master |
| Last Commit: accdeef |
| Last Changed Date: 2019-12-18 13:57:30 -0500 (Wed, 18 Dec 2019) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-01-16 13:48:47 -0500 (Thu, 16 Jan 2020).
| Package 399/1818 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| cytolib 1.9.9 Mike Jiang
| malbec2 | Linux (Ubuntu 18.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | [ OK ] | |
| Package: cytolib |
| Version: 1.9.9 |
| Command: rm -rf cytolib.buildbin-libdir && mkdir cytolib.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh cytolib_1.9.9.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R cytolib.buildbin-libdir |
| StartedAt: 2020-01-16 10:43:57 -0500 (Thu, 16 Jan 2020) |
| EndedAt: 2020-01-16 10:47:49 -0500 (Thu, 16 Jan 2020) |
| EllapsedTime: 232.8 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: cytolib_1.9.9.tgz |
| PackageFileSize: 3.032 MiB |
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###
### Running command:
###
### rm -rf cytolib.buildbin-libdir && mkdir cytolib.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh cytolib_1.9.9.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R cytolib.buildbin-libdir
###
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=cytolib.buildbin-libdir cytolib_1.9.9.tar.gz'
>>>>>>>
* installing *source* package ‘cytolib’ ...
** using staged installation
** preparing to cleanup package 'cytolib' ...
** finished cleanup for package 'cytolib'
** preparing to configure package 'cytolib' ...
*** configured file: 'cytolibConfig.h.in' => 'inst/include/cytolib/cytolibConfig.h'
** finished configure for package 'cytolib'
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -Wno-deprecated-declarations -DBOOST_NO_AUTO_PTR -Wno-unknown-pragmas -Wno-comment -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c CytoFrame.cpp -o CytoFrame.o
CytoFrame.cpp:291:12: warning: unused variable 'chunk_dim' [-Wunused-variable]
hsize_t chunk_dim[] ={1};
^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -Wno-deprecated-declarations -DBOOST_NO_AUTO_PTR -Wno-unknown-pragmas -Wno-comment -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c CytoFrameView.cpp -o CytoFrameView.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -Wno-deprecated-declarations -DBOOST_NO_AUTO_PTR -Wno-unknown-pragmas -Wno-comment -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c GatingHierarchy.cpp -o GatingHierarchy.o
In file included from GatingHierarchy.cpp:4:
../inst/include/cytolib/H5CytoFrame.hpp:47:7: warning: 'cytolib::H5CytoFrame::set_params' hides overloaded virtual function [-Woverloaded-virtual]
void set_params(const vector<cytoParam> & _params)
^
../inst/include/cytolib/CytoFrame.hpp:115:15: note: hidden overloaded virtual function 'cytolib::CytoFrame::set_params' declared here: different number of parameters (2 vs 1)
virtual void set_params(const vector<cytoParam> & _params, bool force = false);
^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -Wno-deprecated-declarations -DBOOST_NO_AUTO_PTR -Wno-unknown-pragmas -Wno-comment -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c GatingSet.cpp -o GatingSet.o
In file included from GatingSet.cpp:4:
../inst/include/cytolib/H5CytoFrame.hpp:47:7: warning: 'cytolib::H5CytoFrame::set_params' hides overloaded virtual function [-Woverloaded-virtual]
void set_params(const vector<cytoParam> & _params)
^
../inst/include/cytolib/CytoFrame.hpp:115:15: note: hidden overloaded virtual function 'cytolib::CytoFrame::set_params' declared here: different number of parameters (2 vs 1)
virtual void set_params(const vector<cytoParam> & _params, bool force = false);
^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -Wno-deprecated-declarations -DBOOST_NO_AUTO_PTR -Wno-unknown-pragmas -Wno-comment -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c GatingSet.pb.cc -o GatingSet.pb.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -Wno-deprecated-declarations -DBOOST_NO_AUTO_PTR -Wno-unknown-pragmas -Wno-comment -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c H5CytoFrame.cpp -o H5CytoFrame.o
In file included from H5CytoFrame.cpp:3:
../inst/include/cytolib/H5CytoFrame.hpp:47:7: warning: 'cytolib::H5CytoFrame::set_params' hides overloaded virtual function [-Woverloaded-virtual]
void set_params(const vector<cytoParam> & _params)
^
../inst/include/cytolib/CytoFrame.hpp:115:15: note: hidden overloaded virtual function 'cytolib::CytoFrame::set_params' declared here: different number of parameters (2 vs 1)
virtual void set_params(const vector<cytoParam> & _params, bool force = false);
^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -Wno-deprecated-declarations -DBOOST_NO_AUTO_PTR -Wno-unknown-pragmas -Wno-comment -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c MemCytoFrame.cpp -o MemCytoFrame.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -Wno-deprecated-declarations -DBOOST_NO_AUTO_PTR -Wno-unknown-pragmas -Wno-comment -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c POPINDICES.cpp -o POPINDICES.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -Wno-deprecated-declarations -DBOOST_NO_AUTO_PTR -Wno-unknown-pragmas -Wno-comment -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c calibrationTable.cpp -o calibrationTable.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -Wno-deprecated-declarations -DBOOST_NO_AUTO_PTR -Wno-unknown-pragmas -Wno-comment -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c compensation.cpp -o compensation.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -Wno-deprecated-declarations -DBOOST_NO_AUTO_PTR -Wno-unknown-pragmas -Wno-comment -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c ellipse2points.cpp -o ellipse2points.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -Wno-deprecated-declarations -DBOOST_NO_AUTO_PTR -Wno-unknown-pragmas -Wno-comment -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c gate.cpp -o gate.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -Wno-deprecated-declarations -DBOOST_NO_AUTO_PTR -Wno-unknown-pragmas -Wno-comment -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c global.cpp -o global.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -Wno-deprecated-declarations -DBOOST_NO_AUTO_PTR -Wno-unknown-pragmas -Wno-comment -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c in_polygon.cpp -o in_polygon.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -Wno-deprecated-declarations -DBOOST_NO_AUTO_PTR -Wno-unknown-pragmas -Wno-comment -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c nodeProperties.cpp -o nodeProperties.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -Wno-deprecated-declarations -DBOOST_NO_AUTO_PTR -Wno-unknown-pragmas -Wno-comment -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c spline.cpp -o spline.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -Wno-deprecated-declarations -DBOOST_NO_AUTO_PTR -Wno-unknown-pragmas -Wno-comment -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c trans_group.cpp -o trans_group.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -Wno-deprecated-declarations -DBOOST_NO_AUTO_PTR -Wno-unknown-pragmas -Wno-comment -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c transformation.cpp -o transformation.o
mkdir -p "/Users/biocbuild/bbs-3.11-bioc/meat/cytolib.buildbin-libdir/00LOCK-cytolib/00new/cytolib/lib"
ar rs "/Users/biocbuild/bbs-3.11-bioc/meat/cytolib.buildbin-libdir/00LOCK-cytolib/00new/cytolib/lib/libboost_fs.a" boost/libs/filesystem/src/codecvt_error_category.o boost/libs/filesystem/src/directory.o boost/libs/filesystem/src/exception.o boost/libs/filesystem/src/operations.o boost/libs/filesystem/src/path.o boost/libs/filesystem/src/path_traits.o boost/libs/filesystem/src/portability.o boost/libs/filesystem/src/unique_path.o boost/libs/filesystem/src/utf8_codecvt_facet.o boost/libs/filesystem/src/windows_file_codecvt.o boost/libs/system/src/error_code.o
ar: creating archive /Users/biocbuild/bbs-3.11-bioc/meat/cytolib.buildbin-libdir/00LOCK-cytolib/00new/cytolib/lib/libboost_fs.a
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Users/biocbuild/bbs-3.11-bioc/meat/cytolib.buildbin-libdir/00LOCK-cytolib/00new/cytolib/lib/libboost_fs.a(windows_file_codecvt.o) has no symbols
clang++ -std=gnu++11 -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 cytolib.so CytoFrame.o CytoFrameView.o GatingHierarchy.o GatingSet.o GatingSet.pb.o H5CytoFrame.o MemCytoFrame.o POPINDICES.o calibrationTable.o compensation.o ellipse2points.o gate.o global.o in_polygon.o nodeProperties.o spline.o trans_group.o transformation.o boost/libs/filesystem/src/codecvt_error_category.o boost/libs/filesystem/src/directory.o boost/libs/filesystem/src/exception.o boost/libs/filesystem/src/operations.o boost/libs/filesystem/src/path.o boost/libs/filesystem/src/path_traits.o boost/libs/filesystem/src/portability.o boost/libs/filesystem/src/unique_path.o boost/libs/filesystem/src/utf8_codecvt_facet.o boost/libs/filesystem/src/windows_file_codecvt.o boost/libs/system/src/error_code.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 /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/lib/libhdf5_cpp.a /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/lib/libhdf5.a /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/lib/libsz.a -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.11-bioc/meat/cytolib.buildbin-libdir/00LOCK-cytolib/00new/cytolib/libs
** R
** 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 (cytolib)
>>>>>>>
>>>>>>> FIXING LINKS FOR cytolib.buildbin-libdir/cytolib/libs//cytolib.so
>>>>>>>
install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libgcc_s.1.dylib" "cytolib.buildbin-libdir/cytolib/libs//cytolib.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libgfortran.3.dylib" "cytolib.buildbin-libdir/cytolib/libs//cytolib.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libreadline.5.2.dylib" "cytolib.buildbin-libdir/cytolib/libs//cytolib.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libreadline.dylib" "cytolib.buildbin-libdir/cytolib/libs//cytolib.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libquadmath.0.dylib" "cytolib.buildbin-libdir/cytolib/libs//cytolib.so"
install_name_tool -change "/usr/local/gfortran/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libgfortran.3.dylib" "cytolib.buildbin-libdir/cytolib/libs//cytolib.so"
install_name_tool -change "/usr/local/gfortran/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libquadmath.0.dylib" "cytolib.buildbin-libdir/cytolib/libs//cytolib.so"