* installing *source* package ‘alcyon’ ... ** package ‘alcyon’ successfully unpacked and MD5 sums checked ** using staged installation R_HOME set at: /data/gannet/ripley/R/R-devel configure: creating ./config.status config.status: creating src/Makevars R has been built with OpenMP support, enabling -- The C compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/local/bin/gcc-14 - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/local/bin/g++-14 - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Configuring done (8.0s) -- 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/data/gannet/ripley/R/packages/tests-devel/alcyon/src/libs/salalib/salaprogram.cpp [ 55%] Building CXX object salalib/CMakeFiles/salalib.dir/shapemap.cpp.o cd /data/gannet/ripley/R/packages/tests-devel/alcyon/src/build-Release/salalib && /usr/local/bin/g++-14 -std=gnu++17 -DSALALIB_LIBRARY -D_DEPTHMAP -D_USE_MATH_DEFINES -I/data/gannet/ripley/R/packages/tests-devel/alcyon/src/libs/. -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -O3 -DNDEBUG -std=gnu++17 -fPIC -Wall -Wextra -fopenmp -MD -MT salalib/CMakeFiles/salalib.dir/shapemap.cpp.o -MF CMakeFiles/salalib.dir/shapemap.cpp.o.d -o CMakeFiles/salalib.dir/shapemap.cpp.o -c /data/gannet/ripley/R/packages/tests-devel/alcyon/src/libs/salalib/shapemap.cpp [ 55%] Building CXX object salalib/CMakeFiles/salalib.dir/spacepix.cpp.o cd /data/gannet/ripley/R/packages/tests-devel/alcyon/src/build-Release/salalib && 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salalib/CMakeFiles/salalib.dir/gridproperties.cpp.o cd /data/gannet/ripley/R/packages/tests-devel/alcyon/src/build-Release/salalib && /usr/local/bin/g++-14 -std=gnu++17 -DSALALIB_LIBRARY -D_DEPTHMAP -D_USE_MATH_DEFINES -I/data/gannet/ripley/R/packages/tests-devel/alcyon/src/libs/. -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -O3 -DNDEBUG -std=gnu++17 -fPIC -Wall -Wextra -fopenmp -MD -MT salalib/CMakeFiles/salalib.dir/gridproperties.cpp.o -MF CMakeFiles/salalib.dir/gridproperties.cpp.o.d -o CMakeFiles/salalib.dir/gridproperties.cpp.o -c /data/gannet/ripley/R/packages/tests-devel/alcyon/src/libs/salalib/gridproperties.cpp [ 58%] Building CXX object salalib/CMakeFiles/salalib.dir/attributetable.cpp.o cd /data/gannet/ripley/R/packages/tests-devel/alcyon/src/build-Release/salalib && /usr/local/bin/g++-14 -std=gnu++17 -DSALALIB_LIBRARY -D_DEPTHMAP 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CMakeFiles/salalib.dir/attributetableview.cpp.o.d -o CMakeFiles/salalib.dir/attributetableview.cpp.o -c /data/gannet/ripley/R/packages/tests-devel/alcyon/src/libs/salalib/attributetableview.cpp [ 60%] Building CXX object salalib/CMakeFiles/salalib.dir/geometrygenerators.cpp.o cd /data/gannet/ripley/R/packages/tests-devel/alcyon/src/build-Release/salalib && /usr/local/bin/g++-14 -std=gnu++17 -DSALALIB_LIBRARY -D_DEPTHMAP -D_USE_MATH_DEFINES -I/data/gannet/ripley/R/packages/tests-devel/alcyon/src/libs/. -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -O3 -DNDEBUG -std=gnu++17 -fPIC -Wall -Wextra -fopenmp -MD -MT salalib/CMakeFiles/salalib.dir/geometrygenerators.cpp.o -MF CMakeFiles/salalib.dir/geometrygenerators.cpp.o.d -o CMakeFiles/salalib.dir/geometrygenerators.cpp.o -c 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-Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -O3 -DNDEBUG -std=gnu++17 -fPIC -Wall -Wextra -fopenmp -MD -MT salalib/CMakeFiles/salalib.dir/alllinemap.cpp.o -MF CMakeFiles/salalib.dir/alllinemap.cpp.o.d -o CMakeFiles/salalib.dir/alllinemap.cpp.o -c /data/gannet/ripley/R/packages/tests-devel/alcyon/src/libs/salalib/alllinemap.cpp [ 63%] Building CXX object salalib/CMakeFiles/salalib.dir/axialminimiser.cpp.o cd /data/gannet/ripley/R/packages/tests-devel/alcyon/src/build-Release/salalib && /usr/local/bin/g++-14 -std=gnu++17 -DSALALIB_LIBRARY -D_DEPTHMAP -D_USE_MATH_DEFINES -I/data/gannet/ripley/R/packages/tests-devel/alcyon/src/libs/. -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -O3 -DNDEBUG -std=gnu++17 -fPIC -Wall -Wextra -fopenmp -MD -MT salalib/CMakeFiles/salalib.dir/axialminimiser.cpp.o -MF CMakeFiles/salalib.dir/axialminimiser.cpp.o.d -o CMakeFiles/salalib.dir/axialminimiser.cpp.o -c /data/gannet/ripley/R/packages/tests-devel/alcyon/src/libs/salalib/axialminimiser.cpp [ 64%] Building CXX object salalib/CMakeFiles/salalib.dir/axialpolygons.cpp.o cd /data/gannet/ripley/R/packages/tests-devel/alcyon/src/build-Release/salalib && /usr/local/bin/g++-14 -std=gnu++17 -DSALALIB_LIBRARY -D_DEPTHMAP -D_USE_MATH_DEFINES -I/data/gannet/ripley/R/packages/tests-devel/alcyon/src/libs/. -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -O3 -DNDEBUG -std=gnu++17 -fPIC -Wall -Wextra -fopenmp -MD -MT salalib/CMakeFiles/salalib.dir/axialpolygons.cpp.o -MF CMakeFiles/salalib.dir/axialpolygons.cpp.o.d -o CMakeFiles/salalib.dir/axialpolygons.cpp.o -c /data/gannet/ripley/R/packages/tests-devel/alcyon/src/libs/salalib/axialpolygons.cpp [ 64%] Building CXX object salalib/CMakeFiles/salalib.dir/tidylines.cpp.o cd /data/gannet/ripley/R/packages/tests-devel/alcyon/src/build-Release/salalib && /usr/local/bin/g++-14 -std=gnu++17 -DSALALIB_LIBRARY -D_DEPTHMAP -D_USE_MATH_DEFINES -I/data/gannet/ripley/R/packages/tests-devel/alcyon/src/libs/. -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -O3 -DNDEBUG -std=gnu++17 -fPIC -Wall -Wextra -fopenmp -MD -MT salalib/CMakeFiles/salalib.dir/tidylines.cpp.o -MF CMakeFiles/salalib.dir/tidylines.cpp.o.d -o CMakeFiles/salalib.dir/tidylines.cpp.o -c /data/gannet/ripley/R/packages/tests-devel/alcyon/src/libs/salalib/tidylines.cpp [ 65%] Building CXX object salalib/CMakeFiles/salalib.dir/mapconverter.cpp.o cd /data/gannet/ripley/R/packages/tests-devel/alcyon/src/build-Release/salalib && /usr/local/bin/g++-14 -std=gnu++17 -DSALALIB_LIBRARY -D_DEPTHMAP -D_USE_MATH_DEFINES 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-I/data/gannet/ripley/R/packages/tests-devel/alcyon/src/libs/. -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -O3 -DNDEBUG -std=gnu++17 -fPIC -Wall -Wextra -fopenmp -MD -MT salalib/CMakeFiles/salalib.dir/parsers/tigerp.cpp.o -MF CMakeFiles/salalib.dir/parsers/tigerp.cpp.o.d -o CMakeFiles/salalib.dir/parsers/tigerp.cpp.o -c /data/gannet/ripley/R/packages/tests-devel/alcyon/src/libs/salalib/parsers/tigerp.cpp [ 97%] Building CXX object salalib/CMakeFiles/salalib.dir/agents/agent.cpp.o cd /data/gannet/ripley/R/packages/tests-devel/alcyon/src/build-Release/salalib && /usr/local/bin/g++-14 -std=gnu++17 -DSALALIB_LIBRARY -D_DEPTHMAP -D_USE_MATH_DEFINES -I/data/gannet/ripley/R/packages/tests-devel/alcyon/src/libs/. -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong 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CMakeFiles/salalib.dir/agents/agentprogram.cpp.o CMakeFiles/salalib.dir/agents/agentga.cpp.o CMakeFiles/salalib.dir/agents/agentanalysis.cpp.o /usr/bin/ranlib libsalalib.a make[3]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/alcyon/src/build-Release' [100%] Built target salalib make[2]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/alcyon/src/build-Release' /usr/bin/cmake -E cmake_progress_start /data/gannet/ripley/R/packages/tests-devel/alcyon/src/build-Release/CMakeFiles 0 make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/alcyon/src/build-Release' ** libs using C compiler: ‘gcc-14 (GCC) 14.2.0’ using C++ compiler: ‘g++-14 (GCC) 14.2.0’ using C++17 make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/alcyon/src' g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../src/libs -I../../inst/include/ -I.. -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/cli/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c main.cpp -o build-Release/main.o g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../src/libs -I../../inst/include/ -I.. -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/cli/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c communicator.cpp -o build-Release/communicator.o g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../src/libs -I../../inst/include/ -I.. -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/cli/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c rcpp_ShapeMap.cpp -o build-Release/rcpp_ShapeMap.o rcpp_ShapeMap.cpp: In function 'std::vector<std::__cxx11::basic_string<char> > getShapeMapAttributeNames(ShapeMap*)': rcpp_ShapeMap.cpp:28:23: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 28 | for (int i = 0; i < attributes.getNumColumns(); ++i) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ rcpp_ShapeMap.cpp: In function 'Rcpp::GenericVector getShapesAsPolylineCoords(Rcpp::XPtr<ShapeMap>)': rcpp_ShapeMap.cpp:122:21: warning: unused variable 'firstPoint' [-Wunused-variable] 122 | const auto &firstPoint = *shape.second.points.begin(); | ^~~~~~~~~~ rcpp_ShapeMap.cpp:123:21: warning: unused variable 'lastPoint' [-Wunused-variable] 123 | const auto &lastPoint = *shape.second.points.rbegin(); | ^~~~~~~~~ rcpp_ShapeMap.cpp:114:11: warning: unused variable 'TOLERANCE' [-Wunused-variable] 114 | float TOLERANCE = 0.0001; | ^~~~~~~~~ rcpp_ShapeMap.cpp: In function 'Rcpp::List getShapeAttributes(Rcpp::XPtr<ShapeMap>, int)': rcpp_ShapeMap.cpp:184:31: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 184 | for (int col = 0; col < attributes.getNumColumns(); ++col) { | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ rcpp_ShapeMap.cpp:179:11: warning: unused variable 'TOLERANCE' [-Wunused-variable] 179 | float TOLERANCE = 0.0001; | ^~~~~~~~~ g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../src/libs -I../../inst/include/ -I.. -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/cli/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c rcpp_ShapeGraph.cpp -o build-Release/rcpp_ShapeGraph.o g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../src/libs -I../../inst/include/ -I.. -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/cli/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c rcpp_AllLineMap.cpp -o build-Release/rcpp_AllLineMap.o rcpp_ShapeGraph.cpp: In function 'std::map<std::__cxx11::basic_string<char>, std::vector<int> > getAxialConnections(Rcpp::XPtr<ShapeMap>)': rcpp_ShapeGraph.cpp:17:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<Connector>::size_type' {aka 'long unsigned int'} [-Wsign-compare] 17 | for (int i = 0; i < connectors.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../src/libs -I../../inst/include/ -I.. -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/cli/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c rcpp_PointMap.cpp -o build-Release/rcpp_PointMap.o g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../src/libs -I../../inst/include/ -I.. -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/cli/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c rcpp_metagraphdata.cpp -o build-Release/rcpp_metagraphdata.o rcpp_PointMap.cpp: In function 'Rcpp::NumericMatrix getGridCoordinates(Rcpp::XPtr<PointMap>)': rcpp_PointMap.cpp:219:23: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 219 | for (int i = 0; i < pointMapPtr->getRows(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~ rcpp_PointMap.cpp:220:27: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 220 | for (int j = 0; j < pointMapPtr->getCols(); j++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~ rcpp_PointMap.cpp: In function 'std::vector<std::__cxx11::basic_string<char> > getPointMapAttributeNames(PointMap*)': rcpp_PointMap.cpp:240:23: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 240 | for (int i = 0; i < attributes.getNumColumns(); ++i) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ rcpp_PointMap.cpp: In function 'std::map<std::__cxx11::basic_string<char>, std::vector<double> > getPointMapAttributeData(Rcpp::XPtr<PointMap>, std::vector<std::__cxx11::basic_string<char> >)': rcpp_PointMap.cpp:260:31: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 260 | for (int i = 0; i < pointMap->getRows(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~~ rcpp_PointMap.cpp:261:35: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 261 | for (int j = 0; j < pointMap->getCols(); j++) { | ~~^~~~~~~~~~~~~~~~~~~~~ rcpp_PointMap.cpp:274:31: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 274 | for (int i = 0; i < pointMap->getRows(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~~ rcpp_PointMap.cpp:275:35: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 275 | for (int j = 0; j < pointMap->getCols(); j++) { | ~~^~~~~~~~~~~~~~~~~~~~~ rcpp_PointMap.cpp: In function 'std::map<std::__cxx11::basic_string<char>, std::vector<double> > getPointMapPropertyData(Rcpp::XPtr<PointMap>, std::vector<std::__cxx11::basic_string<char> >)': rcpp_PointMap.cpp:307:27: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 307 | for (int i = 0; i < pointMap->getRows(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~~ rcpp_PointMap.cpp:308:31: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 308 | for (int j = 0; j < pointMap->getCols(); j++) { | ~~^~~~~~~~~~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../src/libs -I../../inst/include/ -I.. -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/cli/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c process_convertInternal.cpp -o build-Release/process_convertInternal.o process_convertInternal.cpp: In function 'Rcpp::List shapeMapToSegment(Rcpp::XPtr<ShapeMap>, Rcpp::Nullable<std::__cxx11::basic_string<char> >, Rcpp::Nullable<bool>, Rcpp::Nullable<bool>, Rcpp::Nullable<bool>)': process_convertInternal.cpp:78:10: warning: unused variable 'keeporiginal' [-Wunused-variable] 78 | auto keeporiginal = NullableValue::get(keeporiginalNV, true); | ^~~~~~~~~~~~ process_convertInternal.cpp:82:10: warning: unused variable 'converted' [-Wunused-variable] 82 | bool converted = true; | ^~~~~~~~~ g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../src/libs -I../../inst/include/ -I.. -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/cli/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c process_convertExternal.cpp -o build-Release/process_convertExternal.o g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../src/libs -I../../inst/include/ -I.. -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/cli/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c process_link.cpp -o build-Release/process_link.o g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../src/libs -I../../inst/include/ -I.. -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/cli/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c process_isovist.cpp -o build-Release/process_isovist.o g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../src/libs -I../../inst/include/ -I.. -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/cli/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c analysis_axial.cpp -o build-Release/analysis_axial.o g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../src/libs -I../../inst/include/ -I.. -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/cli/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c analysis_segment.cpp -o build-Release/analysis_segment.o g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../src/libs -I../../inst/include/ -I.. -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/cli/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c analysis_segmentDepth.cpp -o build-Release/analysis_segmentDepth.o analysis_axial.cpp: In lambda function: analysis_axial.cpp:55:35: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 55 | for (int i = 0; i < table.getNumColumns(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~ analysis_axial.cpp: In lambda function: analysis_axial.cpp:121:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long unsigned int'} [-Wsign-compare] 121 | for (int i = 0; i < stepDepthPointsX.size(); ++i) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~ analysis_segment.cpp: In lambda function: analysis_segment.cpp:64:35: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 64 | for (int i = 0; i < table.getNumColumns(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~ analysis_segment.cpp: In function 'Rcpp::List runSegmentAnalysis(Rcpp::XPtr<ShapeGraph>, Rcpp::NumericVector, int, int, Rcpp::Nullable<std::__cxx11::basic_string<char> >, Rcpp::Nullable<bool>, Rcpp::Nullable<int>, Rcpp::Nullable<bool>, Rcpp::Nullable<bool>, Rcpp::Nullable<bool>, Rcpp::Nullable<bool>)': analysis_segment.cpp:38:10: warning: unused variable 'selOnly' [-Wunused-variable] 38 | auto selOnly = NullableValue::get(selOnlyNV, false); | ^~~~~~~ analysis_segmentDepth.cpp: In lambda function: analysis_segmentDepth.cpp:46:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long unsigned int'} [-Wsign-compare] 46 | for (int i = 0; i < stepDepthPointsX.size(); ++i) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../src/libs -I../../inst/include/ -I.. -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/cli/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c analysis_segmentShortestPath.cpp -o build-Release/analysis_segmentShortestPath.o g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../src/libs -I../../inst/include/ -I.. -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/cli/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c analysis_allFewest.cpp -o build-Release/analysis_allFewest.o g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../src/libs -I../../inst/include/ -I.. -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/cli/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c analysis_vgaGlobal.cpp -o build-Release/analysis_vgaGlobal.o g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../src/libs -I../../inst/include/ -I.. -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/cli/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c analysis_vgaLocal.cpp -o build-Release/analysis_vgaLocal.o g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../src/libs -I../../inst/include/ -I.. -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/cli/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c analysis_vgaIsovist.cpp -o build-Release/analysis_vgaIsovist.o g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../src/libs -I../../inst/include/ -I.. -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/cli/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c analysis_vgaDepth.cpp -o build-Release/analysis_vgaDepth.o g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../src/libs -I../../inst/include/ -I.. -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/cli/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c analysis_vgaShortestPath.cpp -o build-Release/analysis_vgaShortestPath.o g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../src/libs -I../../inst/include/ -I.. -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/cli/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c analysis_agent.cpp -o build-Release/analysis_agent.o g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../src/libs -I../../inst/include/ -I.. -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/cli/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c RcppExports.cpp -o build-Release/RcppExports.o analysis_vgaShortestPath.cpp: In function 'Rcpp::List vgaVisualShortestPath(Rcpp::XPtr<PointMap>, Rcpp::NumericMatrix, Rcpp::NumericMatrix, Rcpp::Nullable<bool>, Rcpp::Nullable<bool>, Rcpp::Nullable<bool>)': analysis_vgaShortestPath.cpp:25:10: warning: unused variable 'verbose' [-Wunused-variable] 25 | auto verbose = NullableValue::get(verboseNV, false); | ^~~~~~~ analysis_vgaShortestPath.cpp: In function 'Rcpp::List vgaMetricShortestPath(Rcpp::XPtr<PointMap>, Rcpp::NumericMatrix, Rcpp::NumericMatrix, Rcpp::Nullable<bool>, Rcpp::Nullable<bool>, Rcpp::Nullable<bool>)': analysis_vgaShortestPath.cpp:89:10: warning: unused variable 'verbose' [-Wunused-variable] 89 | auto verbose = NullableValue::get(verboseNV, false); | ^~~~~~~ analysis_vgaShortestPath.cpp: In function 'Rcpp::List vgaAngularShortestPath(Rcpp::XPtr<PointMap>, Rcpp::NumericMatrix, Rcpp::NumericMatrix, Rcpp::Nullable<bool>, Rcpp::Nullable<bool>, Rcpp::Nullable<bool>)': analysis_vgaShortestPath.cpp:153:10: warning: unused variable 'verbose' [-Wunused-variable] 153 | auto verbose = NullableValue::get(verboseNV, false); | ^~~~~~~ g++-14 -std=gnu++17 -shared -L/usr/local/gcc14/lib64 -L/usr/local/lib64 -o alcyon.so build-Release/main.o build-Release/communicator.o build-Release/rcpp_ShapeMap.o build-Release/rcpp_ShapeGraph.o build-Release/rcpp_AllLineMap.o build-Release/rcpp_PointMap.o build-Release/rcpp_metagraphdata.o build-Release/process_convertInternal.o build-Release/process_convertExternal.o build-Release/process_link.o build-Release/process_isovist.o build-Release/analysis_axial.o build-Release/analysis_segment.o build-Release/analysis_segmentDepth.o build-Release/analysis_segmentShortestPath.o build-Release/analysis_allFewest.o build-Release/analysis_vgaGlobal.o build-Release/analysis_vgaLocal.o build-Release/analysis_vgaIsovist.o build-Release/analysis_vgaDepth.o build-Release/analysis_vgaShortestPath.o build-Release/analysis_agent.o build-Release/RcppExports.o -fopenmp build-Release/libalcyon_gensala.a make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/alcyon/src' make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/alcyon/src' make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/alcyon/src' installing to /data/gannet/ripley/R/packages/tests-devel/alcyon.Rcheck/00LOCK-alcyon/00new/alcyon/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 (alcyon)