############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL cytolib ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’ * 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=2.6.2 configure: creating ./config.status config.status: creating inst/include/cytolib/cytolibConfig.h config.status: creating src/Makevars ** libs g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DBOOST_FILESYSTEM_NO_CXX20_ATOMIC_REF -DBOOST_FILESYSTEM_SINGLE_THREADED -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c dummy.cpp -o dummy.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DBOOST_FILESYSTEM_NO_CXX20_ATOMIC_REF -DBOOST_FILESYSTEM_SINGLE_THREADED -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c boost/libs/system/src/error_code.cpp -o boost/libs/system/src/error_code.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DBOOST_FILESYSTEM_NO_CXX20_ATOMIC_REF -DBOOST_FILESYSTEM_SINGLE_THREADED -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c boost/libs/filesystem/src/path_traits.cpp -o boost/libs/filesystem/src/path_traits.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DBOOST_FILESYSTEM_NO_CXX20_ATOMIC_REF -DBOOST_FILESYSTEM_SINGLE_THREADED -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c boost/libs/filesystem/src/codecvt_error_category.cpp -o boost/libs/filesystem/src/codecvt_error_category.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DBOOST_FILESYSTEM_NO_CXX20_ATOMIC_REF -DBOOST_FILESYSTEM_SINGLE_THREADED -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c boost/libs/filesystem/src/utf8_codecvt_facet.cpp -o boost/libs/filesystem/src/utf8_codecvt_facet.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DBOOST_FILESYSTEM_NO_CXX20_ATOMIC_REF -DBOOST_FILESYSTEM_SINGLE_THREADED -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c boost/libs/filesystem/src/windows_file_codecvt.cpp -o boost/libs/filesystem/src/windows_file_codecvt.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DBOOST_FILESYSTEM_NO_CXX20_ATOMIC_REF -DBOOST_FILESYSTEM_SINGLE_THREADED -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c boost/libs/filesystem/src/exception.cpp -o boost/libs/filesystem/src/exception.o In file included from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/arg.hpp:25, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/filesystem/path.hpp:22, from boost/libs/filesystem/src/exception.cpp:17: /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses] 194 | failed ************ (Pred::************ | ^ /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses] 199 | failed ************ (boost::mpl::not_::************ | ^ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DBOOST_FILESYSTEM_NO_CXX20_ATOMIC_REF -DBOOST_FILESYSTEM_SINGLE_THREADED -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c boost/libs/filesystem/src/directory.cpp -o boost/libs/filesystem/src/directory.o In file included from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/arg.hpp:25, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/filesystem/path.hpp:22, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/filesystem/directory.hpp:20, from boost/libs/filesystem/src/directory.cpp:17: /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses] 194 | failed ************ (Pred::************ | ^ /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses] 199 | failed ************ (boost::mpl::not_::************ | ^ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DBOOST_FILESYSTEM_NO_CXX20_ATOMIC_REF -DBOOST_FILESYSTEM_SINGLE_THREADED -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c boost/libs/filesystem/src/path.cpp -o boost/libs/filesystem/src/path.o In file included from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/arg.hpp:25, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/filesystem/path.hpp:22, from boost/libs/filesystem/src/path.cpp:14: /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses] 194 | failed ************ (Pred::************ | ^ /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses] 199 | failed ************ (boost::mpl::not_::************ | ^ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DBOOST_FILESYSTEM_NO_CXX20_ATOMIC_REF -DBOOST_FILESYSTEM_SINGLE_THREADED -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c boost/libs/filesystem/src/operations.cpp -o boost/libs/filesystem/src/operations.o In file included from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/arg.hpp:25, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/filesystem/path.hpp:22, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/filesystem/operations.hpp:20, from boost/libs/filesystem/src/operations.cpp:18: /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses] 194 | failed ************ (Pred::************ | ^ /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses] 199 | failed ************ (boost::mpl::not_::************ | ^ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DBOOST_FILESYSTEM_NO_CXX20_ATOMIC_REF -DBOOST_FILESYSTEM_SINGLE_THREADED -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c boost/libs/filesystem/src/unique_path.cpp -o boost/libs/filesystem/src/unique_path.o In file included from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/arg.hpp:25, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/filesystem/path.hpp:22, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/filesystem/operations.hpp:20, from boost/libs/filesystem/src/unique_path.cpp:93: /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses] 194 | failed ************ (Pred::************ | ^ /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses] 199 | failed ************ (boost::mpl::not_::************ | ^ boost/libs/filesystem/src/unique_path.cpp:173:5: warning: ‘int boost::filesystem::detail::{anonymous}::fill_random_getrandom(void*, std::size_t)’ defined but not used [-Wunused-function] 173 | int fill_random_getrandom(void* buf, std::size_t len) | ^~~~~~~~~~~~~~~~~~~~~ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DBOOST_FILESYSTEM_NO_CXX20_ATOMIC_REF -DBOOST_FILESYSTEM_SINGLE_THREADED -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c boost/libs/filesystem/src/portability.cpp -o boost/libs/filesystem/src/portability.o In file included from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/arg.hpp:25, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/filesystem/path.hpp:22, from boost/libs/filesystem/src/portability.cpp:15: /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses] 194 | failed ************ (Pred::************ | ^ /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses] 199 | failed ************ (boost::mpl::not_::************ | ^ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DBOOST_FILESYSTEM_NO_CXX20_ATOMIC_REF -DBOOST_FILESYSTEM_SINGLE_THREADED -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c CytoFrameView.cpp -o CytoFrameView.o In file included from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/arg.hpp:25, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/as_literal.hpp:18, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19, from /home/biocbuild/bbs-3.14-bioc/R/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: /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses] 194 | failed ************ (Pred::************ | ^ /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses] 199 | failed ************ (boost::mpl::not_::************ | ^ 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:58:20: warning: comparison of integer expressions of different signedness: ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 58 | if(valVec.size() != 1+n+n*n){ | ~~~~~~~~~~~~~~^~~~~~~~~~ ../inst/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 62 | if(valVec.size() == 1+n+2*n*n){ | ~~~~~~~~~~~~~~^~~~~~~~~~~~ ../inst/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 68 | for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2) | ~~^~~~~~~~~~~~~~~~~~~~~ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DBOOST_FILESYSTEM_NO_CXX20_ATOMIC_REF -DBOOST_FILESYSTEM_SINGLE_THREADED -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c GatingHierarchy.cpp -o GatingHierarchy.o In file included from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/arg.hpp:25, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/as_literal.hpp:18, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19, from /home/biocbuild/bbs-3.14-bioc/R/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: /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses] 194 | failed ************ (Pred::************ | ^ /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses] 199 | failed ************ (boost::mpl::not_::************ | ^ 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:58:20: warning: comparison of integer expressions of different signedness: ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 58 | if(valVec.size() != 1+n+n*n){ | ~~~~~~~~~~~~~~^~~~~~~~~~ ../inst/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 62 | if(valVec.size() == 1+n+2*n*n){ | ~~~~~~~~~~~~~~^~~~~~~~~~~~ ../inst/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 68 | for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2) | ~~^~~~~~~~~~~~~~~~~~~~~ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DBOOST_FILESYSTEM_NO_CXX20_ATOMIC_REF -DBOOST_FILESYSTEM_SINGLE_THREADED -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5CytoFrame.cpp -o H5CytoFrame.o In file included from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/arg.hpp:25, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/as_literal.hpp:18, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19, from /home/biocbuild/bbs-3.14-bioc/R/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: /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses] 194 | failed ************ (Pred::************ | ^ /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses] 199 | failed ************ (boost::mpl::not_::************ | ^ 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:58:20: warning: comparison of integer expressions of different signedness: ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 58 | if(valVec.size() != 1+n+n*n){ | ~~~~~~~~~~~~~~^~~~~~~~~~ ../inst/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 62 | if(valVec.size() == 1+n+2*n*n){ | ~~~~~~~~~~~~~~^~~~~~~~~~~~ ../inst/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 68 | for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2) | ~~^~~~~~~~~~~~~~~~~~~~~ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DBOOST_FILESYSTEM_NO_CXX20_ATOMIC_REF -DBOOST_FILESYSTEM_SINGLE_THREADED -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c spline.cpp -o spline.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DBOOST_FILESYSTEM_NO_CXX20_ATOMIC_REF -DBOOST_FILESYSTEM_SINGLE_THREADED -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c trans_group.cpp -o trans_group.o In file included from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/arg.hpp:25, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/as_literal.hpp:18, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19, from /home/biocbuild/bbs-3.14-bioc/R/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: /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses] 194 | failed ************ (Pred::************ | ^ /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses] 199 | failed ************ (boost::mpl::not_::************ | ^ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DBOOST_FILESYSTEM_NO_CXX20_ATOMIC_REF -DBOOST_FILESYSTEM_SINGLE_THREADED -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c ellipse2points.cpp -o ellipse2points.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DBOOST_FILESYSTEM_NO_CXX20_ATOMIC_REF -DBOOST_FILESYSTEM_SINGLE_THREADED -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c transformation.cpp -o transformation.o In file included from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/arg.hpp:25, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/as_literal.hpp:18, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string.hpp:19, from ../inst/include/cytolib/transformation.hpp:18, from transformation.cpp:3: /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses] 194 | failed ************ (Pred::************ | ^ /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses] 199 | failed ************ (boost::mpl::not_::************ | ^ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DBOOST_FILESYSTEM_NO_CXX20_ATOMIC_REF -DBOOST_FILESYSTEM_SINGLE_THREADED -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c GatingSet.cpp -o GatingSet.o In file included from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/arg.hpp:25, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/as_literal.hpp:18, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19, from /home/biocbuild/bbs-3.14-bioc/R/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: /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses] 194 | failed ************ (Pred::************ | ^ /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses] 199 | failed ************ (boost::mpl::not_::************ | ^ 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:58:20: warning: comparison of integer expressions of different signedness: ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 58 | if(valVec.size() != 1+n+n*n){ | ~~~~~~~~~~~~~~^~~~~~~~~~ ../inst/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 62 | if(valVec.size() == 1+n+2*n*n){ | ~~~~~~~~~~~~~~^~~~~~~~~~~~ ../inst/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 68 | 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::string, bool, bool, std::vector, std::allocator > >, bool, cytolib::CytoCtx)’: ../inst/include/cytolib/global.hpp:29:3: warning: ‘fmt’ may be used uninitialized in this function [-Wmaybe-uninitialized] 29 | switch(fmt) | ^~~~~~ GatingSet.cpp:30:14: note: ‘fmt’ was declared here 30 | FileFormat fmt; | ^~~ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DBOOST_FILESYSTEM_NO_CXX20_ATOMIC_REF -DBOOST_FILESYSTEM_SINGLE_THREADED -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c CytoVFS.cpp -o CytoVFS.o In file included from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/arg.hpp:25, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/filesystem/path.hpp:22, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/filesystem.hpp:16, from ../inst/include/cytolib/CytoVFS.hpp:17, from CytoVFS.cpp:8: /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses] 194 | failed ************ (Pred::************ | ^ /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses] 199 | failed ************ (boost::mpl::not_::************ | ^ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DBOOST_FILESYSTEM_NO_CXX20_ATOMIC_REF -DBOOST_FILESYSTEM_SINGLE_THREADED -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c POPINDICES.cpp -o POPINDICES.o In file included from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/arg.hpp:25, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/as_literal.hpp:18, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19, from /home/biocbuild/bbs-3.14-bioc/R/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: /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses] 194 | failed ************ (Pred::************ | ^ /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses] 199 | failed ************ (boost::mpl::not_::************ | ^ 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:58:20: warning: comparison of integer expressions of different signedness: ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 58 | if(valVec.size() != 1+n+n*n){ | ~~~~~~~~~~~~~~^~~~~~~~~~ ../inst/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 62 | if(valVec.size() == 1+n+2*n*n){ | ~~~~~~~~~~~~~~^~~~~~~~~~~~ ../inst/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 68 | for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2) | ~~^~~~~~~~~~~~~~~~~~~~~ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DBOOST_FILESYSTEM_NO_CXX20_ATOMIC_REF -DBOOST_FILESYSTEM_SINGLE_THREADED -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c MemCytoFrame.cpp -o MemCytoFrame.o MemCytoFrame.cpp:538: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] 538 | #pragma omp parallel for | In file included from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/arg.hpp:25, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/as_literal.hpp:18, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19, from /home/biocbuild/bbs-3.14-bioc/R/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: /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses] 194 | failed ************ (Pred::************ | ^ /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses] 199 | failed ************ (boost::mpl::not_::************ | ^ 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:58:20: warning: comparison of integer expressions of different signedness: ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 58 | if(valVec.size() != 1+n+n*n){ | ~~~~~~~~~~~~~~^~~~~~~~~~ ../inst/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 62 | if(valVec.size() == 1+n+2*n*n){ | ~~~~~~~~~~~~~~^~~~~~~~~~~~ ../inst/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 68 | for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2) | ~~^~~~~~~~~~~~~~~~~~~~~ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DBOOST_FILESYSTEM_NO_CXX20_ATOMIC_REF -DBOOST_FILESYSTEM_SINGLE_THREADED -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c calibrationTable.cpp -o calibrationTable.o In file included from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/foreach.hpp:76, from calibrationTable.cpp:5: /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses] 194 | failed ************ (Pred::************ | ^ /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses] 199 | failed ************ (boost::mpl::not_::************ | ^ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DBOOST_FILESYSTEM_NO_CXX20_ATOMIC_REF -DBOOST_FILESYSTEM_SINGLE_THREADED -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c CytoFrame.cpp -o CytoFrame.o In file included from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/arg.hpp:25, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/as_literal.hpp:18, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19, from /home/biocbuild/bbs-3.14-bioc/R/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: /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses] 194 | failed ************ (Pred::************ | ^ /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses] 199 | failed ************ (boost::mpl::not_::************ | ^ 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:58:20: warning: comparison of integer expressions of different signedness: ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 58 | if(valVec.size() != 1+n+n*n){ | ~~~~~~~~~~~~~~^~~~~~~~~~ ../inst/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 62 | if(valVec.size() == 1+n+2*n*n){ | ~~~~~~~~~~~~~~^~~~~~~~~~~~ ../inst/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 68 | for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2) | ~~^~~~~~~~~~~~~~~~~~~~~ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DBOOST_FILESYSTEM_NO_CXX20_ATOMIC_REF -DBOOST_FILESYSTEM_SINGLE_THREADED -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c global.cpp -o global.o In file included from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/arg.hpp:25, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/filesystem/path.hpp:22, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/filesystem.hpp:16, from ../inst/include/cytolib/CytoVFS.hpp:17, from ../inst/include/cytolib/global.hpp:21, from global.cpp:3: /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses] 194 | failed ************ (Pred::************ | ^ /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses] 199 | failed ************ (boost::mpl::not_::************ | ^ global.cpp: In function ‘std::string cytolib::s3_to_http(std::string)’: global.cpp:46:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 46 | for(int i = 1; i < tokens.size(); i++) | ~~^~~~~~~~~~~~~~~ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DBOOST_FILESYSTEM_NO_CXX20_ATOMIC_REF -DBOOST_FILESYSTEM_SINGLE_THREADED -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c in_polygon.cpp -o in_polygon.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DBOOST_FILESYSTEM_NO_CXX20_ATOMIC_REF -DBOOST_FILESYSTEM_SINGLE_THREADED -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c gate.cpp -o gate.o In file included from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/arg.hpp:25, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/as_literal.hpp:18, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19, from /home/biocbuild/bbs-3.14-bioc/R/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: /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses] 194 | failed ************ (Pred::************ | ^ /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses] 199 | failed ************ (boost::mpl::not_::************ | ^ 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:58:20: warning: comparison of integer expressions of different signedness: ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 58 | if(valVec.size() != 1+n+n*n){ | ~~~~~~~~~~~~~~^~~~~~~~~~ ../inst/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 62 | if(valVec.size() == 1+n+2*n*n){ | ~~~~~~~~~~~~~~^~~~~~~~~~~~ ../inst/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 68 | for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2) | ~~^~~~~~~~~~~~~~~~~~~~~ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DBOOST_FILESYSTEM_NO_CXX20_ATOMIC_REF -DBOOST_FILESYSTEM_SINGLE_THREADED -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c nodeProperties.cpp -o nodeProperties.o In file included from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/arg.hpp:25, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/as_literal.hpp:18, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19, from /home/biocbuild/bbs-3.14-bioc/R/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: /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses] 194 | failed ************ (Pred::************ | ^ /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses] 199 | failed ************ (boost::mpl::not_::************ | ^ 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:58:20: warning: comparison of integer expressions of different signedness: ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 58 | if(valVec.size() != 1+n+n*n){ | ~~~~~~~~~~~~~~^~~~~~~~~~ ../inst/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 62 | if(valVec.size() == 1+n+2*n*n){ | ~~~~~~~~~~~~~~^~~~~~~~~~~~ ../inst/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 68 | for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2) | ~~^~~~~~~~~~~~~~~~~~~~~ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DBOOST_FILESYSTEM_NO_CXX20_ATOMIC_REF -DBOOST_FILESYSTEM_SINGLE_THREADED -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c compensation.cpp -o compensation.o In file included from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/arg.hpp:25, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/as_literal.hpp:18, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19, from /home/biocbuild/bbs-3.14-bioc/R/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: /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses] 194 | failed ************ (Pred::************ | ^ /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses] 199 | failed ************ (boost::mpl::not_::************ | ^ In file included from compensation.cpp:3: ../inst/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’: ../inst/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 58 | if(valVec.size() != 1+n+n*n){ | ~~~~~~~~~~~~~~^~~~~~~~~~ ../inst/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 62 | if(valVec.size() == 1+n+2*n*n){ | ~~~~~~~~~~~~~~^~~~~~~~~~~~ ../inst/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 68 | for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2) | ~~^~~~~~~~~~~~~~~~~~~~~ mkdir -p "/home/biocbuild/bbs-3.14-bioc/R/library/00LOCK-cytolib/00new/cytolib/lib" ar rs "/home/biocbuild/bbs-3.14-bioc/R/library/00LOCK-cytolib/00new/cytolib/lib/libcytolib.a" CytoFrameView.o GatingHierarchy.o H5CytoFrame.o spline.o trans_group.o ellipse2points.o dummy.o transformation.o GatingSet.o CytoVFS.o POPINDICES.o MemCytoFrame.o calibrationTable.o CytoFrame.o global.o in_polygon.o gate.o nodeProperties.o compensation.o boost/libs/filesystem/src/path_traits.o boost/libs/filesystem/src/codecvt_error_category.o boost/libs/filesystem/src/utf8_codecvt_facet.o boost/libs/filesystem/src/windows_file_codecvt.o boost/libs/filesystem/src/exception.o boost/libs/filesystem/src/directory.o boost/libs/filesystem/src/path.o boost/libs/filesystem/src/operations.o boost/libs/filesystem/src/unique_path.o boost/libs/filesystem/src/portability.o boost/libs/system/src/error_code.o ar: creating /home/biocbuild/bbs-3.14-bioc/R/library/00LOCK-cytolib/00new/cytolib/lib/libcytolib.a g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.14-bioc/R/lib -L/usr/local/lib -o cytolib.so dummy.o -L/home/biocbuild/bbs-3.14-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.14-bioc/R/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 ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (cytolib)