Installation error in macOS

RGLab / cytolib

c++ library for representing and interacting the gated cytometry data structure

GNU Affero General Public License v3.0

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> remotes::install_github("RGLab/cytolib") Downloading GitHub repo RGLab/cytolib@HEAD Skipping 2 packages ahead of CRAN: Rhdf5lib, RProtoBufLib ✓ checking for file ‘/private/var/folders/0l/27166dcs57z48cjmt6y57r540000gp/T/Rtmpx27kuL/remotes1867d162102bb/RGLab-cytolib-b3931f3/DESCRIPTION’ ... ─ preparing ‘cytolib’: (363ms) ✓ checking DESCRIPTION meta-information ─ cleaning src ─ running ‘cleanup’ ─ checking for LF line-endings in source and make files and shell scripts (495ms) ─ checking for empty or unneeded directories ─ building ‘cytolib_2.1.18.tar.gz’ Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: ‘cytolib/thirdparty/protobuf/win/include/google/protobuf/stubs/atomicops_internals_atomicword_compat.h’ * installing *source* package ‘cytolib’ ... ** using staged installation checking for a sed that does not truncate output... /usr/bin/sed checking for g++... g++ 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 g++ accepts -g... yes checking how to run the C++ preprocessor... g++ -E checking whether we are using the GNU C++ compiler... (cached) yes checking whether g++ accepts -g... (cached) yes checking for pkg-config... /usr/local/bin/pkg-config checking pkg-config knows TileDB... no 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 no 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 tiledb/tiledb.h usability... no checking tiledb/tiledb.h presence... no checking for tiledb/tiledb.h... no configure: No tiledb is found, build without tiledb... configure: Parsing cytolib version info ... configure: CYTOLIB_VERSION=2.1.18 configure: creating ./config.status config.status: creating inst/include/cytolib/cytolibConfig.h config.status: creating src/Makevars ** libs /usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -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' -I/usr/local/include -fPIC -Wall -g -O2 -c CytoFrame.cpp -o CytoFrame.o In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/arg.hpp:25, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/placeholders.hpp:24, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_categories.hpp:16, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_facade.hpp:13, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range_core.hpp:27, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range.hpp:13, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/as_literal.hpp:22, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string/trim.hpp:19, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string.hpp:19, from ../inst/include/cytolib/transformation.hpp:18, from ../inst/include/cytolib/compensation.hpp:15, from ../inst/include/cytolib/CytoFrame.hpp:16, from CytoFrame.cpp:3: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_<Pred>::************ ^ In file included from ../inst/include/cytolib/CytoFrame.hpp:16, from CytoFrame.cpp:3: ../inst/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)': ../inst/include/cytolib/compensation.hpp:50:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if(valVec.size() != 1+n+n*n){ ~~~~~~~~~~~~~~^~~~~~~~~~ ../inst/include/cytolib/compensation.hpp:54:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if(valVec.size() == 1+n+2*n*n){ ~~~~~~~~~~~~~~^~~~~~~~~~~~ ../inst/include/cytolib/compensation.hpp:60:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2) ~~^~~~~~~~~~~~~~~~~~~~~ /usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -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' -I/usr/local/include -fPIC -Wall -g -O2 -c CytoFrameView.cpp -o CytoFrameView.o In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/arg.hpp:25, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/placeholders.hpp:24, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_categories.hpp:16, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_facade.hpp:13, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range_core.hpp:27, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range.hpp:13, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/as_literal.hpp:22, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string/trim.hpp:19, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string.hpp:19, from ../inst/include/cytolib/transformation.hpp:18, from ../inst/include/cytolib/compensation.hpp:15, from ../inst/include/cytolib/CytoFrame.hpp:16, from ../inst/include/cytolib/MemCytoFrame.hpp:12, from ../inst/include/cytolib/CytoFrameView.hpp:12, from CytoFrameView.cpp:3: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_<Pred>::************ ^ In file included from ../inst/include/cytolib/CytoFrame.hpp:16, from ../inst/include/cytolib/MemCytoFrame.hpp:12, from ../inst/include/cytolib/CytoFrameView.hpp:12, from CytoFrameView.cpp:3: ../inst/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)': ../inst/include/cytolib/compensation.hpp:50:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if(valVec.size() != 1+n+n*n){ ~~~~~~~~~~~~~~^~~~~~~~~~ ../inst/include/cytolib/compensation.hpp:54:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if(valVec.size() == 1+n+2*n*n){ ~~~~~~~~~~~~~~^~~~~~~~~~~~ ../inst/include/cytolib/compensation.hpp:60:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2) ~~^~~~~~~~~~~~~~~~~~~~~ /usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -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' -I/usr/local/include -fPIC -Wall -g -O2 -c CytoVFS.cpp -o CytoVFS.o In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/arg.hpp:25, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/placeholders.hpp:24, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_categories.hpp:16, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_facade.hpp:13, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/filesystem/path.hpp:29, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/filesystem.hpp:16, from ../inst/include/cytolib/CytoVFS.hpp:16, from CytoVFS.cpp:8: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_<Pred>::************ ^ /usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -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' -I/usr/local/include -fPIC -Wall -g -O2 -c GatingHierarchy.cpp -o GatingHierarchy.o In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/arg.hpp:25, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/placeholders.hpp:24, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_categories.hpp:16, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_facade.hpp:13, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range_core.hpp:27, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range.hpp:13, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/as_literal.hpp:22, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string/trim.hpp:19, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string.hpp:19, from ../inst/include/cytolib/transformation.hpp:18, from ../inst/include/cytolib/compensation.hpp:15, from ../inst/include/cytolib/CytoFrame.hpp:16, from ../inst/include/cytolib/MemCytoFrame.hpp:12, from ../inst/include/cytolib/gate.hpp:12, from ../inst/include/cytolib/POPINDICES.hpp:14, from ../inst/include/cytolib/nodeProperties.hpp:13, from ../inst/include/cytolib/populationTree.hpp:13, from ../inst/include/cytolib/GatingHierarchy.hpp:17, from GatingHierarchy.cpp:3: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_<Pred>::************ ^ In file included from ../inst/include/cytolib/CytoFrame.hpp:16, from ../inst/include/cytolib/MemCytoFrame.hpp:12, from ../inst/include/cytolib/gate.hpp:12, from ../inst/include/cytolib/POPINDICES.hpp:14, from ../inst/include/cytolib/nodeProperties.hpp:13, from ../inst/include/cytolib/populationTree.hpp:13, from ../inst/include/cytolib/GatingHierarchy.hpp:17, from GatingHierarchy.cpp:3: ../inst/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)': ../inst/include/cytolib/compensation.hpp:50:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if(valVec.size() != 1+n+n*n){ ~~~~~~~~~~~~~~^~~~~~~~~~ ../inst/include/cytolib/compensation.hpp:54:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if(valVec.size() == 1+n+2*n*n){ ~~~~~~~~~~~~~~^~~~~~~~~~~~ ../inst/include/cytolib/compensation.hpp:60:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2) ~~^~~~~~~~~~~~~~~~~~~~~ /usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -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' -I/usr/local/include -fPIC -Wall -g -O2 -c GatingSet.cpp -o GatingSet.o In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/arg.hpp:25, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/placeholders.hpp:24, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_categories.hpp:16, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_facade.hpp:13, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range_core.hpp:27, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range.hpp:13, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/as_literal.hpp:22, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string/trim.hpp:19, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string.hpp:19, from ../inst/include/cytolib/transformation.hpp:18, from ../inst/include/cytolib/compensation.hpp:15, from ../inst/include/cytolib/CytoFrame.hpp:16, from ../inst/include/cytolib/MemCytoFrame.hpp:12, from ../inst/include/cytolib/gate.hpp:12, from ../inst/include/cytolib/POPINDICES.hpp:14, from ../inst/include/cytolib/nodeProperties.hpp:13, from ../inst/include/cytolib/populationTree.hpp:13, from ../inst/include/cytolib/GatingHierarchy.hpp:17, from ../inst/include/cytolib/GatingSet.hpp:14, from GatingSet.cpp:3: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_<Pred>::************ ^ In file included from ../inst/include/cytolib/CytoFrame.hpp:16, from ../inst/include/cytolib/MemCytoFrame.hpp:12, from ../inst/include/cytolib/gate.hpp:12, from ../inst/include/cytolib/POPINDICES.hpp:14, from ../inst/include/cytolib/nodeProperties.hpp:13, from ../inst/include/cytolib/populationTree.hpp:13, from ../inst/include/cytolib/GatingHierarchy.hpp:17, from ../inst/include/cytolib/GatingSet.hpp:14, from GatingSet.cpp:3: ../inst/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)': ../inst/include/cytolib/compensation.hpp:50:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if(valVec.size() != 1+n+n*n){ ~~~~~~~~~~~~~~^~~~~~~~~~ ../inst/include/cytolib/compensation.hpp:54:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if(valVec.size() == 1+n+2*n*n){ ~~~~~~~~~~~~~~^~~~~~~~~~~~ ../inst/include/cytolib/compensation.hpp:60:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2) ~~^~~~~~~~~~~~~~~~~~~~~ In file included from ../inst/include/cytolib/compensation.hpp:19, from ../inst/include/cytolib/CytoFrame.hpp:16, from ../inst/include/cytolib/MemCytoFrame.hpp:12, from ../inst/include/cytolib/gate.hpp:12, from ../inst/include/cytolib/POPINDICES.hpp:14, from ../inst/include/cytolib/nodeProperties.hpp:13, from ../inst/include/cytolib/populationTree.hpp:13, from ../inst/include/cytolib/GatingHierarchy.hpp:17, from ../inst/include/cytolib/GatingSet.hpp:14, from GatingSet.cpp:3: ../inst/include/cytolib/global.hpp: In constructor 'cytolib::GatingSet::GatingSet(std::__cxx11::string, bool, bool, std::vector<std::__cxx11::basic_string<char> >, bool, cytolib::CytoCtx)': ../inst/include/cytolib/global.hpp:29:3: warning: 'fmt' may be used uninitialized in this function [-Wmaybe-uninitialized] switch(fmt) ^~~~~~ GatingSet.cpp:30:14: note: 'fmt' was declared here FileFormat fmt; ^~~ /usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -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' -I/usr/local/include -fPIC -Wall -g -O2 -c GatingSet.pb.cc -o GatingSet.pb.o /usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -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' -I/usr/local/include -fPIC -Wall -g -O2 -c H5CytoFrame.cpp -o H5CytoFrame.o In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/arg.hpp:25, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/placeholders.hpp:24, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_categories.hpp:16, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_facade.hpp:13, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range_core.hpp:27, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range.hpp:13, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/as_literal.hpp:22, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string/trim.hpp:19, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string.hpp:19, from ../inst/include/cytolib/transformation.hpp:18, from ../inst/include/cytolib/compensation.hpp:15, from ../inst/include/cytolib/CytoFrame.hpp:16, from ../inst/include/cytolib/MemCytoFrame.hpp:12, from ../inst/include/cytolib/H5CytoFrame.hpp:12, from H5CytoFrame.cpp:3: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_<Pred>::************ ^ In file included from ../inst/include/cytolib/CytoFrame.hpp:16, from ../inst/include/cytolib/MemCytoFrame.hpp:12, from ../inst/include/cytolib/H5CytoFrame.hpp:12, from H5CytoFrame.cpp:3: ../inst/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)': ../inst/include/cytolib/compensation.hpp:50:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if(valVec.size() != 1+n+n*n){ ~~~~~~~~~~~~~~^~~~~~~~~~ ../inst/include/cytolib/compensation.hpp:54:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if(valVec.size() == 1+n+2*n*n){ ~~~~~~~~~~~~~~^~~~~~~~~~~~ ../inst/include/cytolib/compensation.hpp:60:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2) ~~^~~~~~~~~~~~~~~~~~~~~ /usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -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' -I/usr/local/include -fPIC -Wall -g -O2 -c MemCytoFrame.cpp -o MemCytoFrame.o MemCytoFrame.cpp:551: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/arg.hpp:25, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/placeholders.hpp:24, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_categories.hpp:16, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_facade.hpp:13, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range_core.hpp:27, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range.hpp:13, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/as_literal.hpp:22, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string/trim.hpp:19, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string.hpp:19, from ../inst/include/cytolib/transformation.hpp:18, from ../inst/include/cytolib/compensation.hpp:15, from ../inst/include/cytolib/CytoFrame.hpp:16, from ../inst/include/cytolib/MemCytoFrame.hpp:12, from MemCytoFrame.cpp:3: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_<Pred>::************ ^ In file included from ../inst/include/cytolib/CytoFrame.hpp:16, from ../inst/include/cytolib/MemCytoFrame.hpp:12, from MemCytoFrame.cpp:3: ../inst/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)': ../inst/include/cytolib/compensation.hpp:50:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if(valVec.size() != 1+n+n*n){ ~~~~~~~~~~~~~~^~~~~~~~~~ ../inst/include/cytolib/compensation.hpp:54:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if(valVec.size() == 1+n+2*n*n){ ~~~~~~~~~~~~~~^~~~~~~~~~~~ ../inst/include/cytolib/compensation.hpp:60:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2) ~~^~~~~~~~~~~~~~~~~~~~~ /usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -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' -I/usr/local/include -fPIC -Wall -g -O2 -c POPINDICES.cpp -o POPINDICES.o In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/arg.hpp:25, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/placeholders.hpp:24, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_categories.hpp:16, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_facade.hpp:13, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range_core.hpp:27, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range.hpp:13, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/as_literal.hpp:22, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string/trim.hpp:19, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string.hpp:19, from ../inst/include/cytolib/transformation.hpp:18, from ../inst/include/cytolib/compensation.hpp:15, from ../inst/include/cytolib/CytoFrame.hpp:16, from ../inst/include/cytolib/MemCytoFrame.hpp:12, from ../inst/include/cytolib/gate.hpp:12, from ../inst/include/cytolib/POPINDICES.hpp:14, from POPINDICES.cpp:3: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_<Pred>::************ ^ In file included from ../inst/include/cytolib/CytoFrame.hpp:16, from ../inst/include/cytolib/MemCytoFrame.hpp:12, from ../inst/include/cytolib/gate.hpp:12, from ../inst/include/cytolib/POPINDICES.hpp:14, from POPINDICES.cpp:3: ../inst/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)': ../inst/include/cytolib/compensation.hpp:50:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if(valVec.size() != 1+n+n*n){ ~~~~~~~~~~~~~~^~~~~~~~~~ ../inst/include/cytolib/compensation.hpp:54:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if(valVec.size() == 1+n+2*n*n){ ~~~~~~~~~~~~~~^~~~~~~~~~~~ ../inst/include/cytolib/compensation.hpp:60:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2) ~~^~~~~~~~~~~~~~~~~~~~~ /usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -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' -I/usr/local/include -fPIC -Wall -g -O2 -c calibrationTable.cpp -o calibrationTable.o In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/foreach.hpp:76, from calibrationTable.cpp:5: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_<Pred>::************ ^ /usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -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' -I/usr/local/include -fPIC -Wall -g -O2 -c compensation.cpp -o compensation.o In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/arg.hpp:25, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/placeholders.hpp:24, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_categories.hpp:16, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_facade.hpp:13, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range_core.hpp:27, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range.hpp:13, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/as_literal.hpp:22, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string/trim.hpp:19, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string.hpp:19, from ../inst/include/cytolib/transformation.hpp:18, from ../inst/include/cytolib/compensation.hpp:15, from compensation.cpp:3: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_<Pred>::************ ^ In file included from compensation.cpp:3: ../inst/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)': ../inst/include/cytolib/compensation.hpp:50:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if(valVec.size() != 1+n+n*n){ ~~~~~~~~~~~~~~^~~~~~~~~~ ../inst/include/cytolib/compensation.hpp:54:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if(valVec.size() == 1+n+2*n*n){ ~~~~~~~~~~~~~~^~~~~~~~~~~~ ../inst/include/cytolib/compensation.hpp:60:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2) ~~^~~~~~~~~~~~~~~~~~~~~ /usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -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' -I/usr/local/include -fPIC -Wall -g -O2 -c dummy.cpp -o dummy.o /usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -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' -I/usr/local/include -fPIC -Wall -g -O2 -c ellipse2points.cpp -o ellipse2points.o /usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -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' -I/usr/local/include -fPIC -Wall -g -O2 -c gate.cpp -o gate.o In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/arg.hpp:25, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/placeholders.hpp:24, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_categories.hpp:16, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_facade.hpp:13, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range_core.hpp:27, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range.hpp:13, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/as_literal.hpp:22, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string/trim.hpp:19, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string.hpp:19, from ../inst/include/cytolib/transformation.hpp:18, from ../inst/include/cytolib/compensation.hpp:15, from ../inst/include/cytolib/CytoFrame.hpp:16, from ../inst/include/cytolib/MemCytoFrame.hpp:12, from ../inst/include/cytolib/gate.hpp:12, from gate.cpp:3: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_<Pred>::************ ^ In file included from ../inst/include/cytolib/CytoFrame.hpp:16, from ../inst/include/cytolib/MemCytoFrame.hpp:12, from ../inst/include/cytolib/gate.hpp:12, from gate.cpp:3: ../inst/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)': ../inst/include/cytolib/compensation.hpp:50:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if(valVec.size() != 1+n+n*n){ ~~~~~~~~~~~~~~^~~~~~~~~~ ../inst/include/cytolib/compensation.hpp:54:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if(valVec.size() == 1+n+2*n*n){ ~~~~~~~~~~~~~~^~~~~~~~~~~~ ../inst/include/cytolib/compensation.hpp:60:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2) ~~^~~~~~~~~~~~~~~~~~~~~ /usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -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' -I/usr/local/include -fPIC -Wall -g -O2 -c global.cpp -o global.o In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/arg.hpp:25, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/placeholders.hpp:24, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_categories.hpp:16, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_facade.hpp:13, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/filesystem/path.hpp:29, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/filesystem.hpp:16, from ../inst/include/cytolib/CytoVFS.hpp:16, from ../inst/include/cytolib/global.hpp:21, from global.cpp:3: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_<Pred>::************ ^ global.cpp: In function 'std::__cxx11::string cytolib::s3_to_http(std::__cxx11::string)': global.cpp:46:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for(int i = 1; i < tokens.size(); i++) ~~^~~~~~~~~~~~~~~ /usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -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' -I/usr/local/include -fPIC -Wall -g -O2 -c in_polygon.cpp -o in_polygon.o /usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -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' -I/usr/local/include -fPIC -Wall -g -O2 -c nodeProperties.cpp -o nodeProperties.o In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/arg.hpp:25, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/placeholders.hpp:24, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_categories.hpp:16, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_facade.hpp:13, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range_core.hpp:27, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range.hpp:13, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/as_literal.hpp:22, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string/trim.hpp:19, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string.hpp:19, from ../inst/include/cytolib/transformation.hpp:18, from ../inst/include/cytolib/compensation.hpp:15, from ../inst/include/cytolib/CytoFrame.hpp:16, from ../inst/include/cytolib/MemCytoFrame.hpp:12, from ../inst/include/cytolib/gate.hpp:12, from ../inst/include/cytolib/POPINDICES.hpp:14, from ../inst/include/cytolib/nodeProperties.hpp:13, from nodeProperties.cpp:3: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_<Pred>::************ ^ In file included from ../inst/include/cytolib/CytoFrame.hpp:16, from ../inst/include/cytolib/MemCytoFrame.hpp:12, from ../inst/include/cytolib/gate.hpp:12, from ../inst/include/cytolib/POPINDICES.hpp:14, from ../inst/include/cytolib/nodeProperties.hpp:13, from nodeProperties.cpp:3: ../inst/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)': ../inst/include/cytolib/compensation.hpp:50:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if(valVec.size() != 1+n+n*n){ ~~~~~~~~~~~~~~^~~~~~~~~~ ../inst/include/cytolib/compensation.hpp:54:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if(valVec.size() == 1+n+2*n*n){ ~~~~~~~~~~~~~~^~~~~~~~~~~~ ../inst/include/cytolib/compensation.hpp:60:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2) ~~^~~~~~~~~~~~~~~~~~~~~ /usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -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' -I/usr/local/include -fPIC -Wall -g -O2 -c spline.cpp -o spline.o /usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -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' -I/usr/local/include -fPIC -Wall -g -O2 -c trans_group.cpp -o trans_group.o In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/arg.hpp:25, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/placeholders.hpp:24, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_categories.hpp:16, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_facade.hpp:13, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range_core.hpp:27, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range.hpp:13, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/as_literal.hpp:22, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string/trim.hpp:19, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string.hpp:19, from ../inst/include/cytolib/transformation.hpp:18, from ../inst/include/cytolib/trans_group.hpp:13, from trans_group.cpp:3: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_<Pred>::************ ^ /usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -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' -I/usr/local/include -fPIC -Wall -g -O2 -c transformation.cpp -o transformation.o In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/arg.hpp:25, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/placeholders.hpp:24, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_categories.hpp:16, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_facade.hpp:13, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range_core.hpp:27, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range.hpp:13, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/as_literal.hpp:22, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string/trim.hpp:19, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string.hpp:19, from ../inst/include/cytolib/transformation.hpp:18, from transformation.cpp:3: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_<Pred>::************ ^ /usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -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' -I/usr/local/include -fPIC -Wall -g -O2 -c boost/libs/system/src/error_code.cpp -o boost/libs/system/src/error_code.o /usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -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' -I/usr/local/include -fPIC -Wall -g -O2 -c boost/libs/filesystem/src/codecvt_error_category.cpp -o boost/libs/filesystem/src/codecvt_error_category.o /usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -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' -I/usr/local/include -fPIC -Wall -g -O2 -c boost/libs/filesystem/src/directory.cpp -o boost/libs/filesystem/src/directory.o In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/arg.hpp:25, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/placeholders.hpp:24, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_categories.hpp:16, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_facade.hpp:13, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/filesystem/path.hpp:29, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/filesystem/directory.hpp:26, from boost/libs/filesystem/src/directory.cpp:28: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_<Pred>::************ ^ /usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -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' -I/usr/local/include -fPIC -Wall -g -O2 -c boost/libs/filesystem/src/exception.cpp -o boost/libs/filesystem/src/exception.o In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/arg.hpp:25, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/placeholders.hpp:24, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_categories.hpp:16, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_facade.hpp:13, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/filesystem/path.hpp:29, from boost/libs/filesystem/src/exception.cpp:13: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_<Pred>::************ ^ /usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -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' -I/usr/local/include -fPIC -Wall -g -O2 -c boost/libs/filesystem/src/operations.cpp -o boost/libs/filesystem/src/operations.o In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/arg.hpp:25, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/placeholders.hpp:24, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_categories.hpp:16, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_facade.hpp:13, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/filesystem/path.hpp:29, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/filesystem/operations.hpp:25, from boost/libs/filesystem/src/operations.cpp:71: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_<Pred>::************ ^ /usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -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' -I/usr/local/include -fPIC -Wall -g -O2 -c boost/libs/filesystem/src/path.cpp -o boost/libs/filesystem/src/path.o In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/arg.hpp:25, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/placeholders.hpp:24, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_categories.hpp:16, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_facade.hpp:13, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/filesystem/path.hpp:29, from boost/libs/filesystem/src/path.cpp:28: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_<Pred>::************ ^ /usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -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' -I/usr/local/include -fPIC -Wall -g -O2 -c boost/libs/filesystem/src/path_traits.cpp -o boost/libs/filesystem/src/path_traits.o /usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -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' -I/usr/local/include -fPIC -Wall -g -O2 -c boost/libs/filesystem/src/portability.cpp -o boost/libs/filesystem/src/portability.o In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/arg.hpp:25, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/placeholders.hpp:24, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_categories.hpp:16, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_facade.hpp:13, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/filesystem/path.hpp:29, from boost/libs/filesystem/src/portability.cpp:17: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_<Pred>::************ ^ /usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -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' -I/usr/local/include -fPIC -Wall -g -O2 -c boost/libs/filesystem/src/unique_path.cpp -o boost/libs/filesystem/src/unique_path.o In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/arg.hpp:25, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/placeholders.hpp:24, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_categories.hpp:16, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_facade.hpp:13, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/filesystem/path.hpp:29, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/filesystem/operations.hpp:25, from boost/libs/filesystem/src/unique_path.cpp:16: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_<Pred>::************ ^ /usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -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' -I/usr/local/include -fPIC -Wall -g -O2 -c boost/libs/filesystem/src/utf8_codecvt_facet.cpp -o boost/libs/filesystem/src/utf8_codecvt_facet.o /usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -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' -I/usr/local/include -fPIC -Wall -g -O2 -c boost/libs/filesystem/src/windows_file_codecvt.cpp -o boost/libs/filesystem/src/windows_file_codecvt.o /usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -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/Cellar/gcc@8/8.4.0_1/lib -o cytolib.so CytoFrame.o CytoFrameView.o CytoVFS.o GatingHierarchy.o GatingSet.o GatingSet.pb.o H5CytoFrame.o MemCytoFrame.o POPINDICES.o calibrationTable.o compensation.o dummy.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-darwin18/8.2.0 -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 ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0' ld: warning: directory not found for option '-L/usr/local/gfortran/lib' ld: warning: text-based stub file /System/Library/Frameworks//CoreFoundation.framework/CoreFoundation.tbd and library file /System/Library/Frameworks//CoreFoundation.framework/CoreFoundation are out of sync. Falling back to library file for linking. installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/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 Error: package or namespace load failed for ‘cytolib’: .onLoad failed in loadNamespace() for 'cytolib', details: call: dyn.load(cytolib, local = FALSE, now = TRUE) error: unable to load shared object '/Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-cytolib/00new/cytolib/libs/cytolib.so': dlopen(/Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-cytolib/00new/cytolib/libs/cytolib.so, 10): Symbol not found: __ZN6google8protobuf8internal26fixed_address_empty_stringB5cxx11E Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-cytolib/00new/cytolib/libs/cytolib.so Expected in: flat namespace in /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-cytolib/00new/cytolib/libs/cytolib.so Error: loading failed Execution halted ERROR: loading failed * removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib’ * restoring previous ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib’ Error: Failed to install 'cytolib' from GitHub: (converted from warning) installation of package ‘/var/folders/0l/27166dcs57z48cjmt6y57r540000gp/T//Rtmpx27kuL/file1867d3e878b3/cytolib_2.1.18.tar.gz’ had non-zero exit status **To Reproduce** sessionInfo R version 4.0.2 (2020-06-22) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS High Sierra 10.13.6 Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] prettyunits_1.1.1 ps_1.3.4 fansi_0.4.1 withr_2.2.0 rprojroot_1.3-2 crayon_1.3.4 assertthat_0.2.1 [8] R6_2.4.1 backports_1.1.9 cli_2.0.2 curl_4.3 remotes_2.2.0 rstudioapi_0.11 callr_3.4.3 [15] tools_4.0.2 glue_1.4.2 tinytex_0.25 xfun_0.16 compiler_4.0.2 processx_3.4.3 pkgbuild_1.1.0

>install_github("RGLab/cytolib") Using github PAT from envvar GITHUB_PAT Downloading GitHub repo RGLab/cytolib@HEAD ✓ checking for file ‘/private/var/folders/2w/156qfrbn4tg52hxt7pmq38qr0000gn/T/Rtmp2DbJPZ/remotes414a767703ae/RGLab-cytolib-5afbec8/DESCRIPTION’ (376ms) ─ preparing ‘cytolib’: (462ms) ✓ checking DESCRIPTION meta-information ... ─ cleaning src ─ running ‘cleanup’ ─ checking for LF line-endings in source and make files and shell scripts (627ms) ─ checking for empty or unneeded directories ─ building ‘cytolib_2.1.18.tar.gz’ Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: ‘cytolib/thirdparty/protobuf/win/include/google/protobuf/stubs/atomicops_internals_atomicword_compat.h’ * installing *source* package ‘cytolib’ ... ** using staged installation checking for a sed that does not truncate output... /usr/bin/sed checking for g++... g++ 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 g++ accepts -g... yes checking how to run the C++ preprocessor... g++ -E checking whether we are using the GNU C++ compiler... (cached) yes checking whether g++ accepts -g... (cached) yes checking for pkg-config... no 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 no 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 tiledb/tiledb.h usability... no checking tiledb/tiledb.h presence... no checking for tiledb/tiledb.h... no configure: No tiledb is found, build without tiledb... configure: Parsing cytolib version info ... configure: CYTOLIB_VERSION=2.1.18 configure: creating ./config.status config.status: creating inst/include/cytolib/cytolibConfig.h config.status: creating src/Makevars ** libs clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -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' -I/usr/local/include -fPIC -Wall -g -O2 -c CytoFrame.cpp -o CytoFrame.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -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' -I/usr/local/include -fPIC -Wall -g -O2 -c CytoFrameView.cpp -o CytoFrameView.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -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' -I/usr/local/include -fPIC -Wall -g -O2 -c CytoVFS.cpp -o CytoVFS.o In file included from CytoVFS.cpp:8: ../inst/include/cytolib/CytoVFS.hpp:31:7: warning: private field 'num_threads_' is not used [-Wunused-private-field] int num_threads_; ^ 1 warning generated. clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -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' -I/usr/local/include -fPIC -Wall -g -O2 -c GatingHierarchy.cpp -o GatingHierarchy.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -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' -I/usr/local/include -fPIC -Wall -g -O2 -c GatingSet.cpp -o GatingSet.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -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' -I/usr/local/include -fPIC -Wall -g -O2 -c GatingSet.pb.cc -o GatingSet.pb.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -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' -I/usr/local/include -fPIC -Wall -g -O2 -c H5CytoFrame.cpp -o H5CytoFrame.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -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' -I/usr/local/include -fPIC -Wall -g -O2 -c MemCytoFrame.cpp -o MemCytoFrame.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -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' -I/usr/local/include -fPIC -Wall -g -O2 -c POPINDICES.cpp -o POPINDICES.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -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' -I/usr/local/include -fPIC -Wall -g -O2 -c calibrationTable.cpp -o calibrationTable.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -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' -I/usr/local/include -fPIC -Wall -g -O2 -c compensation.cpp -o compensation.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -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' -I/usr/local/include -fPIC -Wall -g -O2 -c dummy.cpp -o dummy.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -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' -I/usr/local/include -fPIC -Wall -g -O2 -c ellipse2points.cpp -o ellipse2points.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -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' -I/usr/local/include -fPIC -Wall -g -O2 -c gate.cpp -o gate.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -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' -I/usr/local/include -fPIC -Wall -g -O2 -c global.cpp -o global.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -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' -I/usr/local/include -fPIC -Wall -g -O2 -c in_polygon.cpp -o in_polygon.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -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' -I/usr/local/include -fPIC -Wall -g -O2 -c nodeProperties.cpp -o nodeProperties.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -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' -I/usr/local/include -fPIC -Wall -g -O2 -c spline.cpp -o spline.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -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' -I/usr/local/include -fPIC -Wall -g -O2 -c trans_group.cpp -o trans_group.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -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' -I/usr/local/include -fPIC -Wall -g -O2 -c transformation.cpp -o transformation.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -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' -I/usr/local/include -fPIC -Wall -g -O2 -c boost/libs/system/src/error_code.cpp -o boost/libs/system/src/error_code.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -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' -I/usr/local/include -fPIC -Wall -g -O2 -c boost/libs/filesystem/src/codecvt_error_category.cpp -o boost/libs/filesystem/src/codecvt_error_category.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -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' -I/usr/local/include -fPIC -Wall -g -O2 -c boost/libs/filesystem/src/directory.cpp -o boost/libs/filesystem/src/directory.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -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' -I/usr/local/include -fPIC -Wall -g -O2 -c boost/libs/filesystem/src/exception.cpp -o boost/libs/filesystem/src/exception.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -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' -I/usr/local/include -fPIC -Wall -g -O2 -c boost/libs/filesystem/src/operations.cpp -o boost/libs/filesystem/src/operations.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -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' -I/usr/local/include -fPIC -Wall -g -O2 -c boost/libs/filesystem/src/path.cpp -o boost/libs/filesystem/src/path.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -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' -I/usr/local/include -fPIC -Wall -g -O2 -c boost/libs/filesystem/src/path_traits.cpp -o boost/libs/filesystem/src/path_traits.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -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' -I/usr/local/include -fPIC -Wall -g -O2 -c boost/libs/filesystem/src/portability.cpp -o boost/libs/filesystem/src/portability.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -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' -I/usr/local/include -fPIC -Wall -g -O2 -c boost/libs/filesystem/src/unique_path.cpp -o boost/libs/filesystem/src/unique_path.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -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' -I/usr/local/include -fPIC -Wall -g -O2 -c boost/libs/filesystem/src/utf8_codecvt_facet.cpp -o boost/libs/filesystem/src/utf8_codecvt_facet.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -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' -I/usr/local/include -fPIC -Wall -g -O2 -c boost/libs/filesystem/src/windows_file_codecvt.cpp -o boost/libs/filesystem/src/windows_file_codecvt.o clang++ -mmacosx-version-min=10.13 -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 CytoVFS.o GatingHierarchy.o GatingSet.o GatingSet.pb.o H5CytoFrame.o MemCytoFrame.o POPINDICES.o calibrationTable.o compensation.o dummy.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 /Users/juancamilosanchezarcila/gfortran/usr/local/lib /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 /Library/Frameworks/R.framework/Versions/4.0/Resources/library/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 Error: package or namespace load failed for ‘cytolib’: .onLoad failed in loadNamespace() for 'cytolib', details: call: dyn.load(cytolib, local = FALSE, now = TRUE) error: unable to load shared object '/Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-cytolib/00new/cytolib/libs/cytolib.so': dlopen(/Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-cytolib/00new/cytolib/libs/cytolib.so, 10): Symbol not found: __ZN6google8protobuf16RepeatedPtrFieldINSt3__112basic_stringIcNS2_11char_traitsIcEENS2_9allocatorIcEEEEE3AddEv Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-cytolib/00new/cytolib/libs/cytolib.so Expected in: flat namespace in /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-cytolib/00new/cytolib/libs/cytolib.so Error: loading failed Execution halted ERROR: loading failed * removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib’ * restoring previous ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib’ Error: Failed to install 'cytolib' from GitHub: (converted from warning) installation of package ‘/var/folders/2w/156qfrbn4tg52hxt7pmq38qr0000gn/T//Rtmp2DbJPZ/file414a7f92d144/cytolib_2.1.18.tar.gz’ had non-zero exit status ##### The sessionInfo ### ─ Session info ────────────────────────────────────────────────────────────────── setting value version R version 4.0.2 (2020-06-22) os macOS High Sierra 10.13.6 system x86_64, darwin17.0 ui RStudio language (EN) collate en_US.UTF-8 ctype en_US.UTF-8 tz America/Los_Angeles date 2020-09-09 ─ Packages ────────────────────────────────────────────────────────────────────── package * version date lib source assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.0.2) backports 1.1.9 2020-08-24 [1] CRAN (R 4.0.2) bit 4.0.4 2020-08-04 [1] CRAN (R 4.0.2) bit64 4.0.5 2020-08-30 [1] CRAN (R 4.0.2) callr 3.4.4 2020-09-07 [1] CRAN (R 4.0.2) cli 2.0.2 2020-02-28 [1] CRAN (R 4.0.2) crayon 1.3.4 2017-09-16 [1] CRAN (R 4.0.2) curl 4.3 2019-12-02 [1] CRAN (R 4.0.1) desc 1.2.0 2018-05-01 [1] CRAN (R 4.0.2) devtools * 2.3.1 2020-07-21 [1] CRAN (R 4.0.2) digest 0.6.25 2020-02-23 [1] CRAN (R 4.0.2) ellipsis 0.3.1 2020-05-15 [1] CRAN (R 4.0.2) fansi 0.4.1 2020-01-08 [1] CRAN (R 4.0.2) fs 1.5.0 2020-07-31 [1] CRAN (R 4.0.2) glue 1.4.2 2020-08-27 [1] CRAN (R 4.0.2) lattice 0.20-41 2020-04-02 [1] CRAN (R 4.0.2) magrittr 1.5 2014-11-22 [1] CRAN (R 4.0.2) memoise 1.1.0 2017-04-21 [1] CRAN (R 4.0.2) nanotime 0.3.2 2020-09-04 [1] CRAN (R 4.0.2) pkgbuild 1.1.0 2020-07-13 [1] CRAN (R 4.0.2) pkgload 1.1.0 2020-05-29 [1] CRAN (R 4.0.2) prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.0.2) processx 3.4.4 2020-09-03 [1] CRAN (R 4.0.2) ps 1.3.4 2020-08-11 [1] CRAN (R 4.0.2) R6 2.4.1 2019-11-12 [1] CRAN (R 4.0.2) Rcpp 1.0.5 2020-07-06 [1] CRAN (R 4.0.2) RcppCCTZ 0.2.9 2020-08-30 [1] CRAN (R 4.0.2) remotes 2.2.0 2020-07-21 [1] CRAN (R 4.0.2) rlang 0.4.7 2020-07-09 [1] CRAN (R 4.0.2) rprojroot 1.3-2 2018-01-03 [1] CRAN (R 4.0.2) rstudioapi 0.11 2020-02-07 [1] CRAN (R 4.0.2) sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 4.0.2) testthat 2.3.2 2020-03-02 [1] CRAN (R 4.0.2) tiledb * 0.8.0 2020-09-03 [1] CRAN (R 4.0.2) usethis * 1.6.1 2020-04-29 [1] CRAN (R 4.0.2) withr 2.2.0 2020-04-20 [1] CRAN (R 4.0.2) zoo 1.8-8 2020-05-02 [1] CRAN (R 4.0.2) [1] /Library/Frameworks/R.framework/Versions/4.0/Resources/library

I was able to install the RProtoBufLib, but I still didn't have the luck for the cytolib. Here's my output. Hope you can resolve this mystery. Or, for the time being, could you consider compiling the package and push it to the bioconductor dev branch? (same for the flowWorkspace)? Thank you for your help!


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
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Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

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> devtools::install_github("RGLab/cytolib", force = TRUE)
Downloading GitHub repo RGLab/cytolib@HEAD
These packages have more recent versions available.
It is recommended to update all of them.
Which would you like to update?

1: All                                             
2: CRAN packages only                              
3: None                                            
4: RcppArmad... (0.9.900.2.0 -> 0.9.900.3.0) [CRAN]

Enter one or more numbers, or an empty line to skip updates:3
✓  checking for file ‘/private/var/folders/0l/27166dcs57z48cjmt6y57r540000gp/T/RtmpmgcZaY/remotes14c7749f64993/RGLab-cytolib-94f2683/DESCRIPTION’ ...
─  preparing ‘cytolib’:
✓  checking DESCRIPTION meta-information ...
─  cleaning src
─  running ‘cleanup’
─  checking for LF line-endings in source and make files and shell scripts (455ms)
─  checking for empty or unneeded directories
─  building ‘cytolib_2.1.18.tar.gz’
   Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
     storing paths of more than 100 bytes is not portable:
     ‘cytolib/thirdparty/protobuf/win/include/google/protobuf/stubs/atomicops_internals_atomicword_compat.h’

* installing *source* package ‘cytolib’ ...
** using staged installation
checking for a sed that does not truncate output... /usr/bin/sed
checking for g++... g++
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 g++ accepts -g... yes
checking how to run the C++ preprocessor... g++ -E
checking whether we are using the GNU C++ compiler... (cached) yes
checking whether g++ accepts -g... (cached) yes
checking for pkg-config... /usr/local/bin/pkg-config
checking pkg-config knows TileDB... no
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
no
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 tiledb/tiledb.h usability... no
checking tiledb/tiledb.h presence... no
checking for tiledb/tiledb.h... no
configure: No tiledb is found, build without tiledb...
configure: Parsing cytolib version info ...
configure: CYTOLIB_VERSION=2.1.18
configure: creating ./config.status
config.status: creating inst/include/cytolib/cytolibConfig.h
config.status: creating src/Makevars
** libs
/usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -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' -I/usr/local/include   -fPIC  -Wall -g -O2  -c CytoFrame.cpp -o CytoFrame.o
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/arg.hpp:25,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range.hpp:13,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/as_literal.hpp:22,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string/trim.hpp:19,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string.hpp:19,
                 from ../inst/include/cytolib/transformation.hpp:18,
                 from ../inst/include/cytolib/compensation.hpp:15,
                 from ../inst/include/cytolib/CytoFrame.hpp:16,
                 from CytoFrame.cpp:3:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ../inst/include/cytolib/CytoFrame.hpp:16,
                 from CytoFrame.cpp:3:
../inst/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
../inst/include/cytolib/compensation.hpp:50:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
   if(valVec.size() != 1+n+n*n){
      ~~~~~~~~~~~~~~^~~~~~~~~~
../inst/include/cytolib/compensation.hpp:54:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
    if(valVec.size() == 1+n+2*n*n){
       ~~~~~~~~~~~~~~^~~~~~~~~~~~
../inst/include/cytolib/compensation.hpp:60:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
                               ~~^~~~~~~~~~~~~~~~~~~~~
/usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -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' -I/usr/local/include   -fPIC  -Wall -g -O2  -c CytoFrameView.cpp -o CytoFrameView.o
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/arg.hpp:25,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range.hpp:13,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/as_literal.hpp:22,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string/trim.hpp:19,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string.hpp:19,
                 from ../inst/include/cytolib/transformation.hpp:18,
                 from ../inst/include/cytolib/compensation.hpp:15,
                 from ../inst/include/cytolib/CytoFrame.hpp:16,
                 from ../inst/include/cytolib/MemCytoFrame.hpp:12,
                 from ../inst/include/cytolib/CytoFrameView.hpp:12,
                 from CytoFrameView.cpp:3:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ../inst/include/cytolib/CytoFrame.hpp:16,
                 from ../inst/include/cytolib/MemCytoFrame.hpp:12,
                 from ../inst/include/cytolib/CytoFrameView.hpp:12,
                 from CytoFrameView.cpp:3:
../inst/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
../inst/include/cytolib/compensation.hpp:50:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
   if(valVec.size() != 1+n+n*n){
      ~~~~~~~~~~~~~~^~~~~~~~~~
../inst/include/cytolib/compensation.hpp:54:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
    if(valVec.size() == 1+n+2*n*n){
       ~~~~~~~~~~~~~~^~~~~~~~~~~~
../inst/include/cytolib/compensation.hpp:60:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
                               ~~^~~~~~~~~~~~~~~~~~~~~
/usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -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' -I/usr/local/include   -fPIC  -Wall -g -O2  -c CytoVFS.cpp -o CytoVFS.o
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/arg.hpp:25,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/filesystem/path.hpp:29,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/filesystem.hpp:16,
                 from ../inst/include/cytolib/CytoVFS.hpp:16,
                 from CytoVFS.cpp:8:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
/usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -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' -I/usr/local/include   -fPIC  -Wall -g -O2  -c GatingHierarchy.cpp -o GatingHierarchy.o
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/arg.hpp:25,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range.hpp:13,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/as_literal.hpp:22,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string/trim.hpp:19,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string.hpp:19,
                 from ../inst/include/cytolib/transformation.hpp:18,
                 from ../inst/include/cytolib/compensation.hpp:15,
                 from ../inst/include/cytolib/CytoFrame.hpp:16,
                 from ../inst/include/cytolib/MemCytoFrame.hpp:12,
                 from ../inst/include/cytolib/gate.hpp:12,
                 from ../inst/include/cytolib/POPINDICES.hpp:14,
                 from ../inst/include/cytolib/nodeProperties.hpp:13,
                 from ../inst/include/cytolib/populationTree.hpp:13,
                 from ../inst/include/cytolib/GatingHierarchy.hpp:17,
                 from GatingHierarchy.cpp:3:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ../inst/include/cytolib/CytoFrame.hpp:16,
                 from ../inst/include/cytolib/MemCytoFrame.hpp:12,
                 from ../inst/include/cytolib/gate.hpp:12,
                 from ../inst/include/cytolib/POPINDICES.hpp:14,
                 from ../inst/include/cytolib/nodeProperties.hpp:13,
                 from ../inst/include/cytolib/populationTree.hpp:13,
                 from ../inst/include/cytolib/GatingHierarchy.hpp:17,
                 from GatingHierarchy.cpp:3:
../inst/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
../inst/include/cytolib/compensation.hpp:50:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
   if(valVec.size() != 1+n+n*n){
      ~~~~~~~~~~~~~~^~~~~~~~~~
../inst/include/cytolib/compensation.hpp:54:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
    if(valVec.size() == 1+n+2*n*n){
       ~~~~~~~~~~~~~~^~~~~~~~~~~~
../inst/include/cytolib/compensation.hpp:60:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
                               ~~^~~~~~~~~~~~~~~~~~~~~
/usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -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' -I/usr/local/include   -fPIC  -Wall -g -O2  -c GatingSet.cpp -o GatingSet.o
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/arg.hpp:25,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range.hpp:13,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/as_literal.hpp:22,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string/trim.hpp:19,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string.hpp:19,
                 from ../inst/include/cytolib/transformation.hpp:18,
                 from ../inst/include/cytolib/compensation.hpp:15,
                 from ../inst/include/cytolib/CytoFrame.hpp:16,
                 from ../inst/include/cytolib/MemCytoFrame.hpp:12,
                 from ../inst/include/cytolib/gate.hpp:12,
                 from ../inst/include/cytolib/POPINDICES.hpp:14,
                 from ../inst/include/cytolib/nodeProperties.hpp:13,
                 from ../inst/include/cytolib/populationTree.hpp:13,
                 from ../inst/include/cytolib/GatingHierarchy.hpp:17,
                 from ../inst/include/cytolib/GatingSet.hpp:14,
                 from GatingSet.cpp:3:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ../inst/include/cytolib/CytoFrame.hpp:16,
                 from ../inst/include/cytolib/MemCytoFrame.hpp:12,
                 from ../inst/include/cytolib/gate.hpp:12,
                 from ../inst/include/cytolib/POPINDICES.hpp:14,
                 from ../inst/include/cytolib/nodeProperties.hpp:13,
                 from ../inst/include/cytolib/populationTree.hpp:13,
                 from ../inst/include/cytolib/GatingHierarchy.hpp:17,
                 from ../inst/include/cytolib/GatingSet.hpp:14,
                 from GatingSet.cpp:3:
../inst/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
../inst/include/cytolib/compensation.hpp:50:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
   if(valVec.size() != 1+n+n*n){
      ~~~~~~~~~~~~~~^~~~~~~~~~
../inst/include/cytolib/compensation.hpp:54:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
    if(valVec.size() == 1+n+2*n*n){
       ~~~~~~~~~~~~~~^~~~~~~~~~~~
../inst/include/cytolib/compensation.hpp:60:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
                               ~~^~~~~~~~~~~~~~~~~~~~~
In file included from ../inst/include/cytolib/compensation.hpp:19,
                 from ../inst/include/cytolib/CytoFrame.hpp:16,
                 from ../inst/include/cytolib/MemCytoFrame.hpp:12,
                 from ../inst/include/cytolib/gate.hpp:12,
                 from ../inst/include/cytolib/POPINDICES.hpp:14,
                 from ../inst/include/cytolib/nodeProperties.hpp:13,
                 from ../inst/include/cytolib/populationTree.hpp:13,
                 from ../inst/include/cytolib/GatingHierarchy.hpp:17,
                 from ../inst/include/cytolib/GatingSet.hpp:14,
                 from GatingSet.cpp:3:
../inst/include/cytolib/global.hpp: In constructor 'cytolib::GatingSet::GatingSet(std::__cxx11::string, bool, bool, std::vector<std::__cxx11::basic_string<char> >, bool, cytolib::CytoCtx)':
../inst/include/cytolib/global.hpp:29:3: warning: 'fmt' may be used uninitialized in this function [-Wmaybe-uninitialized]
   switch(fmt)
   ^~~~~~
GatingSet.cpp:30:14: note: 'fmt' was declared here
   FileFormat fmt;
              ^~~
/usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -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' -I/usr/local/include   -fPIC  -Wall -g -O2  -c GatingSet.pb.cc -o GatingSet.pb.o
/usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -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' -I/usr/local/include   -fPIC  -Wall -g -O2  -c H5CytoFrame.cpp -o H5CytoFrame.o
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/arg.hpp:25,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range.hpp:13,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/as_literal.hpp:22,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string/trim.hpp:19,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string.hpp:19,
                 from ../inst/include/cytolib/transformation.hpp:18,
                 from ../inst/include/cytolib/compensation.hpp:15,
                 from ../inst/include/cytolib/CytoFrame.hpp:16,
                 from ../inst/include/cytolib/MemCytoFrame.hpp:12,
                 from ../inst/include/cytolib/H5CytoFrame.hpp:12,
                 from H5CytoFrame.cpp:3:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ../inst/include/cytolib/CytoFrame.hpp:16,
                 from ../inst/include/cytolib/MemCytoFrame.hpp:12,
                 from ../inst/include/cytolib/H5CytoFrame.hpp:12,
                 from H5CytoFrame.cpp:3:
../inst/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
../inst/include/cytolib/compensation.hpp:50:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
   if(valVec.size() != 1+n+n*n){
      ~~~~~~~~~~~~~~^~~~~~~~~~
../inst/include/cytolib/compensation.hpp:54:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
    if(valVec.size() == 1+n+2*n*n){
       ~~~~~~~~~~~~~~^~~~~~~~~~~~
../inst/include/cytolib/compensation.hpp:60:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
                               ~~^~~~~~~~~~~~~~~~~~~~~
/usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -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' -I/usr/local/include   -fPIC  -Wall -g -O2  -c MemCytoFrame.cpp -o MemCytoFrame.o
MemCytoFrame.cpp:551: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
      #pragma omp parallel for

In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/arg.hpp:25,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range.hpp:13,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/as_literal.hpp:22,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string/trim.hpp:19,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string.hpp:19,
                 from ../inst/include/cytolib/transformation.hpp:18,
                 from ../inst/include/cytolib/compensation.hpp:15,
                 from ../inst/include/cytolib/CytoFrame.hpp:16,
                 from ../inst/include/cytolib/MemCytoFrame.hpp:12,
                 from MemCytoFrame.cpp:3:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ../inst/include/cytolib/CytoFrame.hpp:16,
                 from ../inst/include/cytolib/MemCytoFrame.hpp:12,
                 from MemCytoFrame.cpp:3:
../inst/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
../inst/include/cytolib/compensation.hpp:50:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
   if(valVec.size() != 1+n+n*n){
      ~~~~~~~~~~~~~~^~~~~~~~~~
../inst/include/cytolib/compensation.hpp:54:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
    if(valVec.size() == 1+n+2*n*n){
       ~~~~~~~~~~~~~~^~~~~~~~~~~~
../inst/include/cytolib/compensation.hpp:60:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
                               ~~^~~~~~~~~~~~~~~~~~~~~
/usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -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' -I/usr/local/include   -fPIC  -Wall -g -O2  -c POPINDICES.cpp -o POPINDICES.o
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/arg.hpp:25,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range.hpp:13,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/as_literal.hpp:22,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string/trim.hpp:19,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string.hpp:19,
                 from ../inst/include/cytolib/transformation.hpp:18,
                 from ../inst/include/cytolib/compensation.hpp:15,
                 from ../inst/include/cytolib/CytoFrame.hpp:16,
                 from ../inst/include/cytolib/MemCytoFrame.hpp:12,
                 from ../inst/include/cytolib/gate.hpp:12,
                 from ../inst/include/cytolib/POPINDICES.hpp:14,
                 from POPINDICES.cpp:3:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ../inst/include/cytolib/CytoFrame.hpp:16,
                 from ../inst/include/cytolib/MemCytoFrame.hpp:12,
                 from ../inst/include/cytolib/gate.hpp:12,
                 from ../inst/include/cytolib/POPINDICES.hpp:14,
                 from POPINDICES.cpp:3:
../inst/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
../inst/include/cytolib/compensation.hpp:50:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
   if(valVec.size() != 1+n+n*n){
      ~~~~~~~~~~~~~~^~~~~~~~~~
../inst/include/cytolib/compensation.hpp:54:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
    if(valVec.size() == 1+n+2*n*n){
       ~~~~~~~~~~~~~~^~~~~~~~~~~~
../inst/include/cytolib/compensation.hpp:60:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
                               ~~^~~~~~~~~~~~~~~~~~~~~
/usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -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' -I/usr/local/include   -fPIC  -Wall -g -O2  -c calibrationTable.cpp -o calibrationTable.o
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/foreach.hpp:76,
                 from calibrationTable.cpp:5:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
/usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -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' -I/usr/local/include   -fPIC  -Wall -g -O2  -c compensation.cpp -o compensation.o
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/arg.hpp:25,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range.hpp:13,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/as_literal.hpp:22,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string/trim.hpp:19,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string.hpp:19,
                 from ../inst/include/cytolib/transformation.hpp:18,
                 from ../inst/include/cytolib/compensation.hpp:15,
                 from compensation.cpp:3:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from compensation.cpp:3:
../inst/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
../inst/include/cytolib/compensation.hpp:50:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
   if(valVec.size() != 1+n+n*n){
      ~~~~~~~~~~~~~~^~~~~~~~~~
../inst/include/cytolib/compensation.hpp:54:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
    if(valVec.size() == 1+n+2*n*n){
       ~~~~~~~~~~~~~~^~~~~~~~~~~~
../inst/include/cytolib/compensation.hpp:60:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
                               ~~^~~~~~~~~~~~~~~~~~~~~
/usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -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' -I/usr/local/include   -fPIC  -Wall -g -O2  -c dummy.cpp -o dummy.o
/usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -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' -I/usr/local/include   -fPIC  -Wall -g -O2  -c ellipse2points.cpp -o ellipse2points.o
/usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -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' -I/usr/local/include   -fPIC  -Wall -g -O2  -c gate.cpp -o gate.o
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/arg.hpp:25,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range.hpp:13,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/as_literal.hpp:22,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string/trim.hpp:19,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string.hpp:19,
                 from ../inst/include/cytolib/transformation.hpp:18,
                 from ../inst/include/cytolib/compensation.hpp:15,
                 from ../inst/include/cytolib/CytoFrame.hpp:16,
                 from ../inst/include/cytolib/MemCytoFrame.hpp:12,
                 from ../inst/include/cytolib/gate.hpp:12,
                 from gate.cpp:3:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ../inst/include/cytolib/CytoFrame.hpp:16,
                 from ../inst/include/cytolib/MemCytoFrame.hpp:12,
                 from ../inst/include/cytolib/gate.hpp:12,
                 from gate.cpp:3:
../inst/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
../inst/include/cytolib/compensation.hpp:50:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
   if(valVec.size() != 1+n+n*n){
      ~~~~~~~~~~~~~~^~~~~~~~~~
../inst/include/cytolib/compensation.hpp:54:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
    if(valVec.size() == 1+n+2*n*n){
       ~~~~~~~~~~~~~~^~~~~~~~~~~~
../inst/include/cytolib/compensation.hpp:60:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
                               ~~^~~~~~~~~~~~~~~~~~~~~
/usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -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' -I/usr/local/include   -fPIC  -Wall -g -O2  -c global.cpp -o global.o
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/arg.hpp:25,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/filesystem/path.hpp:29,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/filesystem.hpp:16,
                 from ../inst/include/cytolib/CytoVFS.hpp:16,
                 from ../inst/include/cytolib/global.hpp:21,
                 from global.cpp:3:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
global.cpp: In function 'std::__cxx11::string cytolib::s3_to_http(std::__cxx11::string)':
global.cpp:46:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   for(int i = 1; i < tokens.size(); i++)
                  ~~^~~~~~~~~~~~~~~
/usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -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' -I/usr/local/include   -fPIC  -Wall -g -O2  -c in_polygon.cpp -o in_polygon.o
/usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -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' -I/usr/local/include   -fPIC  -Wall -g -O2  -c nodeProperties.cpp -o nodeProperties.o
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/arg.hpp:25,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range.hpp:13,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/as_literal.hpp:22,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string/trim.hpp:19,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string.hpp:19,
                 from ../inst/include/cytolib/transformation.hpp:18,
                 from ../inst/include/cytolib/compensation.hpp:15,
                 from ../inst/include/cytolib/CytoFrame.hpp:16,
                 from ../inst/include/cytolib/MemCytoFrame.hpp:12,
                 from ../inst/include/cytolib/gate.hpp:12,
                 from ../inst/include/cytolib/POPINDICES.hpp:14,
                 from ../inst/include/cytolib/nodeProperties.hpp:13,
                 from nodeProperties.cpp:3:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from ../inst/include/cytolib/CytoFrame.hpp:16,
                 from ../inst/include/cytolib/MemCytoFrame.hpp:12,
                 from ../inst/include/cytolib/gate.hpp:12,
                 from ../inst/include/cytolib/POPINDICES.hpp:14,
                 from ../inst/include/cytolib/nodeProperties.hpp:13,
                 from nodeProperties.cpp:3:
../inst/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
../inst/include/cytolib/compensation.hpp:50:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
   if(valVec.size() != 1+n+n*n){
      ~~~~~~~~~~~~~~^~~~~~~~~~
../inst/include/cytolib/compensation.hpp:54:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
    if(valVec.size() == 1+n+2*n*n){
       ~~~~~~~~~~~~~~^~~~~~~~~~~~
../inst/include/cytolib/compensation.hpp:60:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
                               ~~^~~~~~~~~~~~~~~~~~~~~
/usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -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' -I/usr/local/include   -fPIC  -Wall -g -O2  -c spline.cpp -o spline.o
/usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -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' -I/usr/local/include   -fPIC  -Wall -g -O2  -c trans_group.cpp -o trans_group.o
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/arg.hpp:25,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range.hpp:13,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/as_literal.hpp:22,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string/trim.hpp:19,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string.hpp:19,
                 from ../inst/include/cytolib/transformation.hpp:18,
                 from ../inst/include/cytolib/trans_group.hpp:13,
                 from trans_group.cpp:3:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
/usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -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' -I/usr/local/include   -fPIC  -Wall -g -O2  -c transformation.cpp -o transformation.o
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/arg.hpp:25,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range.hpp:13,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/as_literal.hpp:22,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string/trim.hpp:19,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string.hpp:19,
                 from ../inst/include/cytolib/transformation.hpp:18,
                 from transformation.cpp:3:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
/usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -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' -I/usr/local/include   -fPIC  -Wall -g -O2  -c boost/libs/system/src/error_code.cpp -o boost/libs/system/src/error_code.o
/usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -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' -I/usr/local/include   -fPIC  -Wall -g -O2  -c boost/libs/filesystem/src/codecvt_error_category.cpp -o boost/libs/filesystem/src/codecvt_error_category.o
/usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -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' -I/usr/local/include   -fPIC  -Wall -g -O2  -c boost/libs/filesystem/src/directory.cpp -o boost/libs/filesystem/src/directory.o
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/arg.hpp:25,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/filesystem/path.hpp:29,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/filesystem/directory.hpp:26,
                 from boost/libs/filesystem/src/directory.cpp:28:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
/usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -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' -I/usr/local/include   -fPIC  -Wall -g -O2  -c boost/libs/filesystem/src/exception.cpp -o boost/libs/filesystem/src/exception.o
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/arg.hpp:25,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/filesystem/path.hpp:29,
                 from boost/libs/filesystem/src/exception.cpp:13:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
/usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -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' -I/usr/local/include   -fPIC  -Wall -g -O2  -c boost/libs/filesystem/src/operations.cpp -o boost/libs/filesystem/src/operations.o
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/arg.hpp:25,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/filesystem/path.hpp:29,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/filesystem/operations.hpp:25,
                 from boost/libs/filesystem/src/operations.cpp:71:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
/usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -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' -I/usr/local/include   -fPIC  -Wall -g -O2  -c boost/libs/filesystem/src/path.cpp -o boost/libs/filesystem/src/path.o
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/arg.hpp:25,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/filesystem/path.hpp:29,
                 from boost/libs/filesystem/src/path.cpp:28:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
/usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -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' -I/usr/local/include   -fPIC  -Wall -g -O2  -c boost/libs/filesystem/src/path_traits.cpp -o boost/libs/filesystem/src/path_traits.o
/usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -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' -I/usr/local/include   -fPIC  -Wall -g -O2  -c boost/libs/filesystem/src/portability.cpp -o boost/libs/filesystem/src/portability.o
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/arg.hpp:25,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/filesystem/path.hpp:29,
                 from boost/libs/filesystem/src/portability.cpp:17:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
/usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -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' -I/usr/local/include   -fPIC  -Wall -g -O2  -c boost/libs/filesystem/src/unique_path.cpp -o boost/libs/filesystem/src/unique_path.o
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/arg.hpp:25,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/filesystem/path.hpp:29,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/filesystem/operations.hpp:25,
                 from boost/libs/filesystem/src/unique_path.cpp:16:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
/usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -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' -I/usr/local/include   -fPIC  -Wall -g -O2  -c boost/libs/filesystem/src/utf8_codecvt_facet.cpp -o boost/libs/filesystem/src/utf8_codecvt_facet.o
/usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -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' -I/usr/local/include   -fPIC  -Wall -g -O2  -c boost/libs/filesystem/src/windows_file_codecvt.cpp -o boost/libs/filesystem/src/windows_file_codecvt.o
/usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -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/Cellar/gcc@8/8.4.0_1/lib -o cytolib.so CytoFrame.o CytoFrameView.o CytoVFS.o GatingHierarchy.o GatingSet.o GatingSet.pb.o H5CytoFrame.o MemCytoFrame.o POPINDICES.o calibrationTable.o compensation.o dummy.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/Cellar/gcc@8/8.4.0_1/lib/gcc/8 /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
ld: warning: text-based stub file /System/Library/Frameworks//CoreFoundation.framework/CoreFoundation.tbd and library file /System/Library/Frameworks//CoreFoundation.framework/CoreFoundation are out of sync. Falling back to library file for linking.
installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/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
Error: package or namespace load failed for ‘cytolib’:
 .onLoad failed in loadNamespace() for 'cytolib', details:
  call: dyn.load(cytolib, local = FALSE, now = TRUE)
  error: unable to load shared object '/Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-cytolib/00new/cytolib/libs/cytolib.so':
  dlopen(/Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-cytolib/00new/cytolib/libs/cytolib.so, 10): Symbol not found: __ZN2H56H5FileC1ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEjRKNS_17FileCreatPropListERKNS_15FileAccPropListE
  Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-cytolib/00new/cytolib/libs/cytolib.so
  Expected in: flat namespace
 in /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-cytolib/00new/cytolib/libs/cytolib.so
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib’
Error: Failed to install 'cytolib' from GitHub:
  (converted from warning) installation of package ‘/var/folders/0l/27166dcs57z48cjmt6y57r540000gp/T//RtmpmgcZaY/file14c771b2afac7/cytolib_2.1.18.tar.gz’ had non-zero exit status

[root@ip-172-31-79-152 library]# R R version 4.0.2 (2020-06-22) -- "Taking Off Again" Copyright (C) 2020 The R Foundation for Statistical Computing Platform: x86_64-koji-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > remotes::install_github("RGLab/cytolib", force = TRUE) Downloading GitHub repo RGLab/cytolib@HEAD checking for file ‘/tmp/Rtmpzj3ruz/remotes49485fd3080c/RGLab-cytolib-b884a31/✔ checking for file ‘/tmp/Rtmpzj3ruz/remotes49485fd3080c/RGLab-cytolib-b884a31/DESCRIPTION’ ─ preparing ‘cytolib’: ✔ checking DESCRIPTION meta-information ... ─ cleaning src ─ running ‘cleanup’ ─ checking for LF line-endings in source and make files and shell scripts ─ checking for empty or unneeded directories ─ building ‘cytolib_2.3.2.tar.gz’ Installing package into ‘/usr/lib64/R/library’ (as ‘lib’ is unspecified) * installing *source* package ‘cytolib’ ... ** using staged installation checking for a sed that does not truncate output... /usr/bin/sed checking for g++... g++ 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 g++ accepts -g... yes checking how to run the C++ preprocessor... g++ -E checking whether we are using the GNU C++ compiler... (cached) yes checking whether g++ accepts -g... (cached) yes configure: Parsing cytolib version info ... configure: CYTOLIB_VERSION=2.3.2 configure: creating ./config.status config.status: creating inst/include/cytolib/cytolibConfig.h config.status: creating src/Makevars ** libs g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/usr/lib64/R/library/Rcpp/include' -I'/usr/lib64/R/library/BH/include' -I'/usr/lib64/R/library/RProtoBufLib/include' -I'/usr/lib64/R/library/Rhdf5lib/include' -I'/usr/lib64/R/library/RcppArmadillo/include' -I'/usr/lib64/R/library/RcppParallel/include' -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c CytoFrame.cpp -o CytoFrame.o In file included from ../inst/include/cytolib/CytoFrame.hpp:16:0, from CytoFrame.cpp:3: ../inst/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’: ../inst/include/cytolib/compensation.hpp:50:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(valVec.size() != 1+n+n*n){ ~~~~~~~~~~~~~~^~~~~~~~~~ ../inst/include/cytolib/compensation.hpp:54:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(valVec.size() == 1+n+2*n*n){ ~~~~~~~~~~~~~~^~~~~~~~~~~~ ../inst/include/cytolib/compensation.hpp:60:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2) ~~^~~~~~~~~~~~~~~~~~~~~ g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/usr/lib64/R/library/Rcpp/include' -I'/usr/lib64/R/library/BH/include' -I'/usr/lib64/R/library/RProtoBufLib/include' -I'/usr/lib64/R/library/Rhdf5lib/include' -I'/usr/lib64/R/library/RcppArmadillo/include' -I'/usr/lib64/R/library/RcppParallel/include' -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c CytoFrameView.cpp -o CytoFrameView.o In file included from ../inst/include/cytolib/CytoFrame.hpp:16:0, from ../inst/include/cytolib/MemCytoFrame.hpp:12, from ../inst/include/cytolib/CytoFrameView.hpp:12, from CytoFrameView.cpp:3: ../inst/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’: ../inst/include/cytolib/compensation.hpp:50:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(valVec.size() != 1+n+n*n){ ~~~~~~~~~~~~~~^~~~~~~~~~ ../inst/include/cytolib/compensation.hpp:54:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(valVec.size() == 1+n+2*n*n){ ~~~~~~~~~~~~~~^~~~~~~~~~~~ ../inst/include/cytolib/compensation.hpp:60:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2) ~~^~~~~~~~~~~~~~~~~~~~~ g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/usr/lib64/R/library/Rcpp/include' -I'/usr/lib64/R/library/BH/include' -I'/usr/lib64/R/library/RProtoBufLib/include' -I'/usr/lib64/R/library/Rhdf5lib/include' -I'/usr/lib64/R/library/RcppArmadillo/include' -I'/usr/lib64/R/library/RcppParallel/include' -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c CytoVFS.cpp -o CytoVFS.o g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/usr/lib64/R/library/Rcpp/include' -I'/usr/lib64/R/library/BH/include' -I'/usr/lib64/R/library/RProtoBufLib/include' -I'/usr/lib64/R/library/Rhdf5lib/include' -I'/usr/lib64/R/library/RcppArmadillo/include' -I'/usr/lib64/R/library/RcppParallel/include' -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c GatingHierarchy.cpp -o GatingHierarchy.o In file included from ../inst/include/cytolib/CytoFrame.hpp:16:0, from ../inst/include/cytolib/MemCytoFrame.hpp:12, from ../inst/include/cytolib/gate.hpp:12, from ../inst/include/cytolib/POPINDICES.hpp:14, from ../inst/include/cytolib/nodeProperties.hpp:13, from ../inst/include/cytolib/populationTree.hpp:13, from ../inst/include/cytolib/GatingHierarchy.hpp:17, from GatingHierarchy.cpp:3: ../inst/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’: ../inst/include/cytolib/compensation.hpp:50:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(valVec.size() != 1+n+n*n){ ~~~~~~~~~~~~~~^~~~~~~~~~ ../inst/include/cytolib/compensation.hpp:54:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(valVec.size() == 1+n+2*n*n){ ~~~~~~~~~~~~~~^~~~~~~~~~~~ ../inst/include/cytolib/compensation.hpp:60:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2) ~~^~~~~~~~~~~~~~~~~~~~~ In file included from /usr/lib64/R/library/BH/include/boost/graph/adjacency_iterator.hpp:13:0, from /usr/lib64/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:37, from /usr/lib64/R/library/BH/include/boost/graph/adjacency_list.hpp:255, from ../inst/include/cytolib/populationTree.hpp:14, from ../inst/include/cytolib/GatingHierarchy.hpp:17, from GatingHierarchy.cpp:3: /usr/lib64/R/library/BH/include/boost/detail/iterator.hpp: At global scope: /usr/lib64/R/library/BH/include/boost/detail/iterator.hpp:13:37: note: #pragma message: This header is deprecated. Use <iterator> instead. BOOST_HEADER_DEPRECATED("<iterator>") ^ g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/usr/lib64/R/library/Rcpp/include' -I'/usr/lib64/R/library/BH/include' -I'/usr/lib64/R/library/RProtoBufLib/include' -I'/usr/lib64/R/library/Rhdf5lib/include' -I'/usr/lib64/R/library/RcppArmadillo/include' -I'/usr/lib64/R/library/RcppParallel/include' -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c GatingSet.cpp -o GatingSet.o In file included from ../inst/include/cytolib/CytoFrame.hpp:16:0, from ../inst/include/cytolib/MemCytoFrame.hpp:12, from ../inst/include/cytolib/gate.hpp:12, from ../inst/include/cytolib/POPINDICES.hpp:14, from ../inst/include/cytolib/nodeProperties.hpp:13, from ../inst/include/cytolib/populationTree.hpp:13, from ../inst/include/cytolib/GatingHierarchy.hpp:17, from ../inst/include/cytolib/GatingSet.hpp:14, from GatingSet.cpp:3: ../inst/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’: ../inst/include/cytolib/compensation.hpp:50:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(valVec.size() != 1+n+n*n){ ~~~~~~~~~~~~~~^~~~~~~~~~ ../inst/include/cytolib/compensation.hpp:54:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(valVec.size() == 1+n+2*n*n){ ~~~~~~~~~~~~~~^~~~~~~~~~~~ ../inst/include/cytolib/compensation.hpp:60:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2) ~~^~~~~~~~~~~~~~~~~~~~~ In file included from /usr/lib64/R/library/BH/include/boost/graph/adjacency_iterator.hpp:13:0, from /usr/lib64/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:37, from /usr/lib64/R/library/BH/include/boost/graph/adjacency_list.hpp:255, from ../inst/include/cytolib/populationTree.hpp:14, from ../inst/include/cytolib/GatingHierarchy.hpp:17, from ../inst/include/cytolib/GatingSet.hpp:14, from GatingSet.cpp:3: /usr/lib64/R/library/BH/include/boost/detail/iterator.hpp: At global scope: /usr/lib64/R/library/BH/include/boost/detail/iterator.hpp:13:37: note: #pragma message: This header is deprecated. Use <iterator> instead. BOOST_HEADER_DEPRECATED("<iterator>") ^ In file included from ../inst/include/cytolib/compensation.hpp:19:0, from ../inst/include/cytolib/CytoFrame.hpp:16, from ../inst/include/cytolib/MemCytoFrame.hpp:12, from ../inst/include/cytolib/gate.hpp:12, from ../inst/include/cytolib/POPINDICES.hpp:14, from ../inst/include/cytolib/nodeProperties.hpp:13, from ../inst/include/cytolib/populationTree.hpp:13, from ../inst/include/cytolib/GatingHierarchy.hpp:17, from ../inst/include/cytolib/GatingSet.hpp:14, from GatingSet.cpp:3: ../inst/include/cytolib/global.hpp: In constructor ‘cytolib::GatingSet::GatingSet(std::__cxx11::string, bool, bool, std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >, bool, cytolib::CytoCtx)’: ../inst/include/cytolib/global.hpp:29:3: warning: ‘fmt’ may be used uninitialized in this function [-Wmaybe-uninitialized] switch(fmt) ^~~~~~ GatingSet.cpp:30:14: note: ‘fmt’ was declared here FileFormat fmt; ^~~ g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/usr/lib64/R/library/Rcpp/include' -I'/usr/lib64/R/library/BH/include' -I'/usr/lib64/R/library/RProtoBufLib/include' -I'/usr/lib64/R/library/Rhdf5lib/include' -I'/usr/lib64/R/library/RcppArmadillo/include' -I'/usr/lib64/R/library/RcppParallel/include' -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c GatingSet.pb.cc -o GatingSet.pb.o g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/usr/lib64/R/library/Rcpp/include' -I'/usr/lib64/R/library/BH/include' -I'/usr/lib64/R/library/RProtoBufLib/include' -I'/usr/lib64/R/library/Rhdf5lib/include' -I'/usr/lib64/R/library/RcppArmadillo/include' -I'/usr/lib64/R/library/RcppParallel/include' -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c H5CytoFrame.cpp -o H5CytoFrame.o In file included from ../inst/include/cytolib/CytoFrame.hpp:16:0, from ../inst/include/cytolib/MemCytoFrame.hpp:12, from ../inst/include/cytolib/H5CytoFrame.hpp:12, from H5CytoFrame.cpp:3: ../inst/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’: ../inst/include/cytolib/compensation.hpp:50:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(valVec.size() != 1+n+n*n){ ~~~~~~~~~~~~~~^~~~~~~~~~ ../inst/include/cytolib/compensation.hpp:54:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(valVec.size() == 1+n+2*n*n){ ~~~~~~~~~~~~~~^~~~~~~~~~~~ ../inst/include/cytolib/compensation.hpp:60:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2) ~~^~~~~~~~~~~~~~~~~~~~~ g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/usr/lib64/R/library/Rcpp/include' -I'/usr/lib64/R/library/BH/include' -I'/usr/lib64/R/library/RProtoBufLib/include' -I'/usr/lib64/R/library/Rhdf5lib/include' -I'/usr/lib64/R/library/RcppArmadillo/include' -I'/usr/lib64/R/library/RcppParallel/include' -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c MemCytoFrame.cpp -o MemCytoFrame.o MemCytoFrame.cpp:538:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for In file included from ../inst/include/cytolib/CytoFrame.hpp:16:0, from ../inst/include/cytolib/MemCytoFrame.hpp:12, from MemCytoFrame.cpp:3: ../inst/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’: ../inst/include/cytolib/compensation.hpp:50:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(valVec.size() != 1+n+n*n){ ~~~~~~~~~~~~~~^~~~~~~~~~ ../inst/include/cytolib/compensation.hpp:54:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(valVec.size() == 1+n+2*n*n){ ~~~~~~~~~~~~~~^~~~~~~~~~~~ ../inst/include/cytolib/compensation.hpp:60:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2) ~~^~~~~~~~~~~~~~~~~~~~~ g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/usr/lib64/R/library/Rcpp/include' -I'/usr/lib64/R/library/BH/include' -I'/usr/lib64/R/library/RProtoBufLib/include' -I'/usr/lib64/R/library/Rhdf5lib/include' -I'/usr/lib64/R/library/RcppArmadillo/include' -I'/usr/lib64/R/library/RcppParallel/include' -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c POPINDICES.cpp -o POPINDICES.o In file included from ../inst/include/cytolib/CytoFrame.hpp:16:0, from ../inst/include/cytolib/MemCytoFrame.hpp:12, from ../inst/include/cytolib/gate.hpp:12, from ../inst/include/cytolib/POPINDICES.hpp:14, from POPINDICES.cpp:3: ../inst/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’: ../inst/include/cytolib/compensation.hpp:50:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(valVec.size() != 1+n+n*n){ ~~~~~~~~~~~~~~^~~~~~~~~~ ../inst/include/cytolib/compensation.hpp:54:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(valVec.size() == 1+n+2*n*n){ ~~~~~~~~~~~~~~^~~~~~~~~~~~ ../inst/include/cytolib/compensation.hpp:60:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2) ~~^~~~~~~~~~~~~~~~~~~~~ g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/usr/lib64/R/library/Rcpp/include' -I'/usr/lib64/R/library/BH/include' -I'/usr/lib64/R/library/RProtoBufLib/include' -I'/usr/lib64/R/library/Rhdf5lib/include' -I'/usr/lib64/R/library/RcppArmadillo/include' -I'/usr/lib64/R/library/RcppParallel/include' -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c calibrationTable.cpp -o calibrationTable.o g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/usr/lib64/R/library/Rcpp/include' -I'/usr/lib64/R/library/BH/include' -I'/usr/lib64/R/library/RProtoBufLib/include' -I'/usr/lib64/R/library/Rhdf5lib/include' -I'/usr/lib64/R/library/RcppArmadillo/include' -I'/usr/lib64/R/library/RcppParallel/include' -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c compensation.cpp -o compensation.o In file included from compensation.cpp:3:0: ../inst/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’: ../inst/include/cytolib/compensation.hpp:50:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(valVec.size() != 1+n+n*n){ ~~~~~~~~~~~~~~^~~~~~~~~~ ../inst/include/cytolib/compensation.hpp:54:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(valVec.size() == 1+n+2*n*n){ ~~~~~~~~~~~~~~^~~~~~~~~~~~ ../inst/include/cytolib/compensation.hpp:60:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2) ~~^~~~~~~~~~~~~~~~~~~~~ g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/usr/lib64/R/library/Rcpp/include' -I'/usr/lib64/R/library/BH/include' -I'/usr/lib64/R/library/RProtoBufLib/include' -I'/usr/lib64/R/library/Rhdf5lib/include' -I'/usr/lib64/R/library/RcppArmadillo/include' -I'/usr/lib64/R/library/RcppParallel/include' -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c dummy.cpp -o dummy.o g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/usr/lib64/R/library/Rcpp/include' -I'/usr/lib64/R/library/BH/include' -I'/usr/lib64/R/library/RProtoBufLib/include' -I'/usr/lib64/R/library/Rhdf5lib/include' -I'/usr/lib64/R/library/RcppArmadillo/include' -I'/usr/lib64/R/library/RcppParallel/include' -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c ellipse2points.cpp -o ellipse2points.o g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/usr/lib64/R/library/Rcpp/include' -I'/usr/lib64/R/library/BH/include' -I'/usr/lib64/R/library/RProtoBufLib/include' -I'/usr/lib64/R/library/Rhdf5lib/include' -I'/usr/lib64/R/library/RcppArmadillo/include' -I'/usr/lib64/R/library/RcppParallel/include' -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c gate.cpp -o gate.o In file included from ../inst/include/cytolib/CytoFrame.hpp:16:0, from ../inst/include/cytolib/MemCytoFrame.hpp:12, from ../inst/include/cytolib/gate.hpp:12, from gate.cpp:3: ../inst/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’: ../inst/include/cytolib/compensation.hpp:50:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(valVec.size() != 1+n+n*n){ ~~~~~~~~~~~~~~^~~~~~~~~~ ../inst/include/cytolib/compensation.hpp:54:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(valVec.size() == 1+n+2*n*n){ ~~~~~~~~~~~~~~^~~~~~~~~~~~ ../inst/include/cytolib/compensation.hpp:60:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2) ~~^~~~~~~~~~~~~~~~~~~~~ g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/usr/lib64/R/library/Rcpp/include' -I'/usr/lib64/R/library/BH/include' -I'/usr/lib64/R/library/RProtoBufLib/include' -I'/usr/lib64/R/library/Rhdf5lib/include' -I'/usr/lib64/R/library/RcppArmadillo/include' -I'/usr/lib64/R/library/RcppParallel/include' -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c global.cpp -o global.o global.cpp: In function ‘std::__cxx11::string cytolib::s3_to_http(std::__cxx11::string)’: global.cpp:46:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int i = 1; i < tokens.size(); i++) ~~^~~~~~~~~~~~~~~ g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/usr/lib64/R/library/Rcpp/include' -I'/usr/lib64/R/library/BH/include' -I'/usr/lib64/R/library/RProtoBufLib/include' -I'/usr/lib64/R/library/Rhdf5lib/include' -I'/usr/lib64/R/library/RcppArmadillo/include' -I'/usr/lib64/R/library/RcppParallel/include' -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c in_polygon.cpp -o in_polygon.o g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/usr/lib64/R/library/Rcpp/include' -I'/usr/lib64/R/library/BH/include' -I'/usr/lib64/R/library/RProtoBufLib/include' -I'/usr/lib64/R/library/Rhdf5lib/include' -I'/usr/lib64/R/library/RcppArmadillo/include' -I'/usr/lib64/R/library/RcppParallel/include' -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c nodeProperties.cpp -o nodeProperties.o In file included from ../inst/include/cytolib/CytoFrame.hpp:16:0, from ../inst/include/cytolib/MemCytoFrame.hpp:12, from ../inst/include/cytolib/gate.hpp:12, from ../inst/include/cytolib/POPINDICES.hpp:14, from ../inst/include/cytolib/nodeProperties.hpp:13, from nodeProperties.cpp:3: ../inst/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’: ../inst/include/cytolib/compensation.hpp:50:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(valVec.size() != 1+n+n*n){ ~~~~~~~~~~~~~~^~~~~~~~~~ ../inst/include/cytolib/compensation.hpp:54:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(valVec.size() == 1+n+2*n*n){ ~~~~~~~~~~~~~~^~~~~~~~~~~~ ../inst/include/cytolib/compensation.hpp:60:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2) ~~^~~~~~~~~~~~~~~~~~~~~ g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/usr/lib64/R/library/Rcpp/include' -I'/usr/lib64/R/library/BH/include' -I'/usr/lib64/R/library/RProtoBufLib/include' -I'/usr/lib64/R/library/Rhdf5lib/include' -I'/usr/lib64/R/library/RcppArmadillo/include' -I'/usr/lib64/R/library/RcppParallel/include' -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c spline.cpp -o spline.o g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/usr/lib64/R/library/Rcpp/include' -I'/usr/lib64/R/library/BH/include' -I'/usr/lib64/R/library/RProtoBufLib/include' -I'/usr/lib64/R/library/Rhdf5lib/include' -I'/usr/lib64/R/library/RcppArmadillo/include' -I'/usr/lib64/R/library/RcppParallel/include' -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c trans_group.cpp -o trans_group.o g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/usr/lib64/R/library/Rcpp/include' -I'/usr/lib64/R/library/BH/include' -I'/usr/lib64/R/library/RProtoBufLib/include' -I'/usr/lib64/R/library/Rhdf5lib/include' -I'/usr/lib64/R/library/RcppArmadillo/include' -I'/usr/lib64/R/library/RcppParallel/include' -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c transformation.cpp -o transformation.o g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/usr/lib64/R/library/Rcpp/include' -I'/usr/lib64/R/library/BH/include' -I'/usr/lib64/R/library/RProtoBufLib/include' -I'/usr/lib64/R/library/Rhdf5lib/include' -I'/usr/lib64/R/library/RcppArmadillo/include' -I'/usr/lib64/R/library/RcppParallel/include' -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c boost/libs/system/src/error_code.cpp -o boost/libs/system/src/error_code.o g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/usr/lib64/R/library/Rcpp/include' -I'/usr/lib64/R/library/BH/include' -I'/usr/lib64/R/library/RProtoBufLib/include' -I'/usr/lib64/R/library/Rhdf5lib/include' -I'/usr/lib64/R/library/RcppArmadillo/include' -I'/usr/lib64/R/library/RcppParallel/include' -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c boost/libs/filesystem/src/path_traits.cpp -o boost/libs/filesystem/src/path_traits.o g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/usr/lib64/R/library/Rcpp/include' -I'/usr/lib64/R/library/BH/include' -I'/usr/lib64/R/library/RProtoBufLib/include' -I'/usr/lib64/R/library/Rhdf5lib/include' -I'/usr/lib64/R/library/RcppArmadillo/include' -I'/usr/lib64/R/library/RcppParallel/include' -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c boost/libs/filesystem/src/codecvt_error_category.cpp -o boost/libs/filesystem/src/codecvt_error_category.o g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/usr/lib64/R/library/Rcpp/include' -I'/usr/lib64/R/library/BH/include' -I'/usr/lib64/R/library/RProtoBufLib/include' -I'/usr/lib64/R/library/Rhdf5lib/include' -I'/usr/lib64/R/library/RcppArmadillo/include' -I'/usr/lib64/R/library/RcppParallel/include' -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c boost/libs/filesystem/src/utf8_codecvt_facet.cpp -o boost/libs/filesystem/src/utf8_codecvt_facet.o g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/usr/lib64/R/library/Rcpp/include' -I'/usr/lib64/R/library/BH/include' -I'/usr/lib64/R/library/RProtoBufLib/include' -I'/usr/lib64/R/library/Rhdf5lib/include' -I'/usr/lib64/R/library/RcppArmadillo/include' -I'/usr/lib64/R/library/RcppParallel/include' -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c boost/libs/filesystem/src/windows_file_codecvt.cpp -o boost/libs/filesystem/src/windows_file_codecvt.o g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/usr/lib64/R/library/Rcpp/include' -I'/usr/lib64/R/library/BH/include' -I'/usr/lib64/R/library/RProtoBufLib/include' -I'/usr/lib64/R/library/Rhdf5lib/include' -I'/usr/lib64/R/library/RcppArmadillo/include' -I'/usr/lib64/R/library/RcppParallel/include' -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c boost/libs/filesystem/src/exception.cpp -o boost/libs/filesystem/src/exception.o g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/usr/lib64/R/library/Rcpp/include' -I'/usr/lib64/R/library/BH/include' -I'/usr/lib64/R/library/RProtoBufLib/include' -I'/usr/lib64/R/library/Rhdf5lib/include' -I'/usr/lib64/R/library/RcppArmadillo/include' -I'/usr/lib64/R/library/RcppParallel/include' -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c boost/libs/filesystem/src/directory.cpp -o boost/libs/filesystem/src/directory.o g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/usr/lib64/R/library/Rcpp/include' -I'/usr/lib64/R/library/BH/include' -I'/usr/lib64/R/library/RProtoBufLib/include' -I'/usr/lib64/R/library/Rhdf5lib/include' -I'/usr/lib64/R/library/RcppArmadillo/include' -I'/usr/lib64/R/library/RcppParallel/include' -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c boost/libs/filesystem/src/path.cpp -o boost/libs/filesystem/src/path.o g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/usr/lib64/R/library/Rcpp/include' -I'/usr/lib64/R/library/BH/include' -I'/usr/lib64/R/library/RProtoBufLib/include' -I'/usr/lib64/R/library/Rhdf5lib/include' -I'/usr/lib64/R/library/RcppArmadillo/include' -I'/usr/lib64/R/library/RcppParallel/include' -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c boost/libs/filesystem/src/operations.cpp -o boost/libs/filesystem/src/operations.o boost/libs/filesystem/src/operations.cpp: In function ‘boost::filesystem::path boost::filesystem::absolute(const boost::filesystem::path&, const boost::filesystem::path&)’: boost/libs/filesystem/src/operations.cpp:680:6: error: redefinition of ‘boost::filesystem::path boost::filesystem::absolute(const boost::filesystem::path&, const boost::filesystem::path&)’ path absolute(const path& p, const path& base) ^~~~~~~~ In file included from boost/libs/filesystem/src/operations.cpp:71:0: /usr/lib64/R/library/BH/include/boost/filesystem/operations.hpp:258:6: note: ‘boost::filesystem::path boost::filesystem::absolute(const boost::filesystem::path&, const boost::filesystem::path&)’ previously defined here path absolute(const path& p, const path& base=current_path()) {return detail::absolute(p, base);} ^~~~~~~~ boost/libs/filesystem/src/operations.cpp: In function ‘boost::filesystem::path boost::filesystem::detail::canonical(const boost::filesystem::path&, const boost::filesystem::path&, boost::system::error_code*)’: boost/libs/filesystem/src/operations.cpp:747:54: error: call of overloaded ‘absolute(const boost::filesystem::path&, const boost::filesystem::path&)’ is ambiguous path source (p.is_absolute() ? p : absolute(p, base)); ^ In file included from boost/libs/filesystem/src/operations.cpp:71:0: /usr/lib64/R/library/BH/include/boost/filesystem/operations.hpp:96:6: note: candidate: boost::filesystem::path boost::filesystem::detail::absolute(const boost::filesystem::path&, const boost::filesystem::path&, boost::system::error_code*) path absolute(const path& p, const path& base, system::error_code* ec=0); ^~~~~~~~ /usr/lib64/R/library/BH/include/boost/filesystem/operations.hpp:258:6: note: candidate: boost::filesystem::path boost::filesystem::absolute(const boost::filesystem::path&, const boost::filesystem::path&) path absolute(const path& p, const path& base=current_path()) {return detail::absolute(p, base);} ^~~~~~~~ boost/libs/filesystem/src/operations.cpp: In function ‘void boost::filesystem::detail::copy(const boost::filesystem::path&, const boost::filesystem::path&, boost::system::error_code*)’: boost/libs/filesystem/src/operations.cpp:842:41: error: ‘fail_if_exists’ is not a member of ‘boost::filesystem::detail’ detail::copy_file(from, to, detail::fail_if_exists, ec); ^~~~~~~~~~~~~~ boost/libs/filesystem/src/operations.cpp: In function ‘void boost::filesystem::detail::copy_file(const boost::filesystem::path&, const boost::filesystem::path&, boost::filesystem::copy_option, boost::system::error_code*)’: boost/libs/filesystem/src/operations.cpp:867:15: error: ‘fail_if_exists’ was not declared in this scope option == fail_if_exists) ? BOOST_ERRNO : 0, ^ boost/libs/filesystem/src/operations.cpp:232:69: note: in definition of macro ‘BOOST_COPY_FILE’ # define BOOST_COPY_FILE(F,T,FailIfExistsBool)copy_file_api(F, T, FailIfExistsBool) ^~~~~~~~~~~~~~~~ boost/libs/filesystem/src/operations.cpp: In function ‘bool boost::filesystem::detail::create_directories(const boost::filesystem::path&, boost::system::error_code*)’: boost/libs/filesystem/src/operations.cpp:938:32: error: no matching function for call to ‘create_directory(const boost::filesystem::path&, boost::system::error_code*&)’ return create_directory(p, ec); ^ In file included from boost/libs/filesystem/src/operations.cpp:71:0: /usr/lib64/R/library/BH/include/boost/filesystem/operations.hpp:121:6: note: candidate: bool boost::filesystem::detail::create_directory(const boost::filesystem::path&, const boost::filesystem::path*, boost::system::error_code*) bool create_directory(const path& p, const path* existing, system::error_code* ec=0); ^~~~~~~~~~~~~~~~ /usr/lib64/R/library/BH/include/boost/filesystem/operations.hpp:121:6: note: no known conversion for argument 2 from ‘boost::system::error_code*’ to ‘const boost::filesystem::path*’ /usr/lib64/R/library/BH/include/boost/filesystem/operations.hpp:388:6: note: candidate: bool boost::filesystem::create_directory(const boost::filesystem::path&, const boost::filesystem::path&, boost::system::error_code&) bool create_directory(const path& p, const path& existing, system::error_code& ec) BOOST_NOEXCEPT ^~~~~~~~~~~~~~~~ /usr/lib64/R/library/BH/include/boost/filesystem/operations.hpp:388:6: note: candidate expects 3 arguments, 2 provided /usr/lib64/R/library/BH/include/boost/filesystem/operations.hpp:385:6: note: candidate: bool boost::filesystem::create_directory(const boost::filesystem::path&, const boost::filesystem::path&) bool create_directory(const path& p, const path& existing) ^~~~~~~~~~~~~~~~ /usr/lib64/R/library/BH/include/boost/filesystem/operations.hpp:385:6: note: no known conversion for argument 2 from ‘boost::system::error_code*’ to ‘const boost::filesystem::path&’ /usr/lib64/R/library/BH/include/boost/filesystem/operations.hpp:382:6: note: candidate: bool boost::filesystem::create_directory(const boost::filesystem::path&, boost::system::error_code&) bool create_directory(const path& p, system::error_code& ec) BOOST_NOEXCEPT ^~~~~~~~~~~~~~~~ /usr/lib64/R/library/BH/include/boost/filesystem/operations.hpp:382:6: note: no known conversion for argument 2 from ‘boost::system::error_code*’ to ‘boost::system::error_code&’ /usr/lib64/R/library/BH/include/boost/filesystem/operations.hpp:379:6: note: candidate: bool boost::filesystem::create_directory(const boost::filesystem::path&) bool create_directory(const path& p) {return detail::create_directory(p, 0);} ^~~~~~~~~~~~~~~~ /usr/lib64/R/library/BH/include/boost/filesystem/operations.hpp:379:6: note: candidate expects 1 argument, 2 provided boost/libs/filesystem/src/operations.cpp: At global scope: boost/libs/filesystem/src/operations.cpp:381:1: warning: ‘bool boost::filesystem::detail::{anonymous}::copy_file_api(const string&, const string&, bool)’ defined but not used [-Wunused-function] copy_file_api(const std::string& from_p, ^~~~~~~~~~~~~ make: *** [boost/libs/filesystem/src/operations.o] Error 1 ERROR: compilation failed for package ‘cytolib’ * removing ‘/usr/lib64/R/library/cytolib’ Error: Failed to install 'cytolib' from GitHub: (converted from warning) installation of package ‘/tmp/Rtmpzj3ruz/file4948561f90b7/cytolib_2.3.2.tar.gz’ had non-zero exit status

RGLab / cytolib

Installation error in macOS #41