############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL flowCore ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’ * installing *source* package ‘flowCore’ ... ** using staged installation ** libs using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’ using C++17 /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -DBOOST_NO_AUTO_PTR -w -Wfatal-errors -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/cpp11/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/cytolib/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RProtoBufLib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c FastLogicle.cpp -o FastLogicle.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -DBOOST_NO_AUTO_PTR -w -Wfatal-errors -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/cpp11/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/cytolib/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RProtoBufLib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c Hyperlog.cpp -o Hyperlog.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -DBOOST_NO_AUTO_PTR -w -Wfatal-errors -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/cpp11/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/cytolib/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RProtoBufLib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c Logicle.cpp -o Logicle.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -DBOOST_NO_AUTO_PTR -w -Wfatal-errors -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/cpp11/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/cytolib/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RProtoBufLib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c biexponential.cpp -o biexponential.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -DBOOST_NO_AUTO_PTR -w -Wfatal-errors -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/cpp11/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/cytolib/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RProtoBufLib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c convertRawBytes.cpp -o convertRawBytes.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -DBOOST_NO_AUTO_PTR -w -Wfatal-errors -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/cpp11/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/cytolib/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RProtoBufLib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c cpp11.cpp -o cpp11.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -DBOOST_NO_AUTO_PTR -w -Wfatal-errors -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/cpp11/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/cytolib/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RProtoBufLib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c fcsTextParse.cpp -o fcsTextParse.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -DBOOST_NO_AUTO_PTR -w -Wfatal-errors -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/cpp11/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/cytolib/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RProtoBufLib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c hyperlogTransform.cpp -o hyperlogTransform.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -DBOOST_NO_AUTO_PTR -w -Wfatal-errors -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/cpp11/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/cytolib/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RProtoBufLib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c inPolygon.cpp -o inPolygon.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -DBOOST_NO_AUTO_PTR -w -Wfatal-errors -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/cpp11/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/cytolib/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RProtoBufLib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c inPolytope.cpp -o inPolytope.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -DBOOST_NO_AUTO_PTR -w -Wfatal-errors -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/cpp11/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/cytolib/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RProtoBufLib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c logicleTransform.cpp -o logicleTransform.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -DBOOST_NO_AUTO_PTR -w -Wfatal-errors -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/cpp11/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/cytolib/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RProtoBufLib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c poly_centroid.cpp -o poly_centroid.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -DBOOST_NO_AUTO_PTR -w -Wfatal-errors -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/cpp11/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/cytolib/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RProtoBufLib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c sortBytes.cpp -o sortBytes.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -DBOOST_NO_AUTO_PTR -w -Wfatal-errors -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/cpp11/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/cytolib/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RProtoBufLib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c uint2double.cpp -o uint2double.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -DBOOST_NO_AUTO_PTR -w -Wfatal-errors -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/cpp11/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/cytolib/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RProtoBufLib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c zeroin.cpp -o zeroin.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -shared -L/home/biocbuild/R/R/lib -L/usr/local/lib -o flowCore.so FastLogicle.o Hyperlog.o Logicle.o biexponential.o convertRawBytes.o cpp11.o fcsTextParse.o hyperlogTransform.o inPolygon.o inPolytope.o logicleTransform.o poly_centroid.o sortBytes.o uint2double.o zeroin.o /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/cytolib/lib/libcytolib.a -L/home/biocbuild/R/R/lib -lR if [ `uname -s` = 'Darwin' ]; then install_name_tool -change /usr/local/clang4/lib/libc++.1.dylib /usr/lib/libc++.1.dylib flowCore.so; fi installing to /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/00LOCK-flowCore/00new/flowCore/libs ** R ** data ** 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 (flowCore)