+ case "${usergroup_phase}" in + local run_cmd + run_cmd=run_su + shift + run_su /opt/pkg/bin/bmake stage-install BATCH=1 DEPENDS_TARGET=/nonexistent WRKLOG=/tmp/bulklog/R-FNN-1.1.4.1/work.log + su pbulk -c '"$@"' make /opt/pkg/bin/bmake stage-install BATCH=1 DEPENDS_TARGET=/nonexistent WRKLOG=/tmp/bulklog/R-FNN-1.1.4.1/work.log ===> Installing for R-FNN-1.1.4.1 => Generating pre-install file lists => Creating installation directories * installing *source* package 'FNN' ... file 'src/Makevars' has the wrong MD5 checksum ** using staged installation ** libs using C compiler: 'gcc (GCC) 14.3.0' using C++ compiler: 'g++ (GCC) 14.3.0' g++ -std=gnu++17 -I"/opt/pkg/lib/R/include" -DNDEBUG -Iinclude -DUSING_R -DUSING_RPRINT -I/opt/pkg/include -I/opt/pkg/include/glib-2.0 -I/opt/pkg/include/gio-unix-2.0 -I/opt/pkg/lib/glib-2.0/include -I/usr/include -I/opt/pkg/include/freetype2 -I/opt/pkg/include/harfbuzz -I/opt/pkg/include/ncurses -I/opt/pkg/include/libxml2 -fPIC -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/pkg/include -I/opt/pkg/include/glib-2.0 -I/opt/pkg/include/gio-unix-2.0 -I/opt/pkg/lib/glib-2.0/include -I/usr/include -I/opt/pkg/include/freetype2 -I/opt/pkg/include/harfbuzz -I/opt/pkg/include/ncurses -I/opt/pkg/include/libxml2 -c ANN.cpp -o ANN.o g++ -std=gnu++17 -I"/opt/pkg/lib/R/include" -DNDEBUG -Iinclude -DUSING_R -DUSING_RPRINT -I/opt/pkg/include -I/opt/pkg/include/glib-2.0 -I/opt/pkg/include/gio-unix-2.0 -I/opt/pkg/lib/glib-2.0/include -I/usr/include -I/opt/pkg/include/freetype2 -I/opt/pkg/include/harfbuzz -I/opt/pkg/include/ncurses -I/opt/pkg/include/libxml2 -fPIC -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/pkg/include -I/opt/pkg/include/glib-2.0 -I/opt/pkg/include/gio-unix-2.0 -I/opt/pkg/lib/glib-2.0/include -I/usr/include -I/opt/pkg/include/freetype2 -I/opt/pkg/include/harfbuzz -I/opt/pkg/include/ncurses -I/opt/pkg/include/libxml2 -c KNN_ANN.cpp -o KNN_ANN.o g++ -std=gnu++17 -I"/opt/pkg/lib/R/include" -DNDEBUG -Iinclude -DUSING_R -DUSING_RPRINT -I/opt/pkg/include -I/opt/pkg/include/glib-2.0 -I/opt/pkg/include/gio-unix-2.0 -I/opt/pkg/lib/glib-2.0/include -I/usr/include -I/opt/pkg/include/freetype2 -I/opt/pkg/include/harfbuzz -I/opt/pkg/include/ncurses -I/opt/pkg/include/libxml2 -fPIC -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/pkg/include -I/opt/pkg/include/glib-2.0 -I/opt/pkg/include/gio-unix-2.0 -I/opt/pkg/lib/glib-2.0/include -I/usr/include -I/opt/pkg/include/freetype2 -I/opt/pkg/include/harfbuzz -I/opt/pkg/include/ncurses -I/opt/pkg/include/libxml2 -c KNN_correlation_distance.cpp -o KNN_correlation_distance.o g++ -std=gnu++17 -I"/opt/pkg/lib/R/include" -DNDEBUG -Iinclude -DUSING_R -DUSING_RPRINT -I/opt/pkg/include -I/opt/pkg/include/glib-2.0 -I/opt/pkg/include/gio-unix-2.0 -I/opt/pkg/lib/glib-2.0/include -I/usr/include -I/opt/pkg/include/freetype2 -I/opt/pkg/include/harfbuzz -I/opt/pkg/include/ncurses -I/opt/pkg/include/libxml2 -fPIC -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/pkg/include -I/opt/pkg/include/glib-2.0 -I/opt/pkg/include/gio-unix-2.0 -I/opt/pkg/lib/glib-2.0/include -I/usr/include -I/opt/pkg/include/freetype2 -I/opt/pkg/include/harfbuzz -I/opt/pkg/include/ncurses -I/opt/pkg/include/libxml2 -c KNN_cover_test.cpp -o KNN_cover_test.o g++ -std=gnu++17 -I"/opt/pkg/lib/R/include" -DNDEBUG -Iinclude -DUSING_R -DUSING_RPRINT -I/opt/pkg/include -I/opt/pkg/include/glib-2.0 -I/opt/pkg/include/gio-unix-2.0 -I/opt/pkg/lib/glib-2.0/include -I/usr/include -I/opt/pkg/include/freetype2 -I/opt/pkg/include/harfbuzz -I/opt/pkg/include/ncurses -I/opt/pkg/include/libxml2 -fPIC -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/pkg/include -I/opt/pkg/include/glib-2.0 -I/opt/pkg/include/gio-unix-2.0 -I/opt/pkg/lib/glib-2.0/include -I/usr/include -I/opt/pkg/include/freetype2 -I/opt/pkg/include/harfbuzz -I/opt/pkg/include/ncurses -I/opt/pkg/include/libxml2 -c KNN_cover_tree.cpp -o KNN_cover_tree.o g++ -std=gnu++17 -I"/opt/pkg/lib/R/include" -DNDEBUG -Iinclude -DUSING_R -DUSING_RPRINT -I/opt/pkg/include -I/opt/pkg/include/glib-2.0 -I/opt/pkg/include/gio-unix-2.0 -I/opt/pkg/lib/glib-2.0/include -I/usr/include -I/opt/pkg/include/freetype2 -I/opt/pkg/include/harfbuzz -I/opt/pkg/include/ncurses -I/opt/pkg/include/libxml2 -fPIC -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/pkg/include -I/opt/pkg/include/glib-2.0 -I/opt/pkg/include/gio-unix-2.0 -I/opt/pkg/lib/glib-2.0/include -I/usr/include -I/opt/pkg/include/freetype2 -I/opt/pkg/include/harfbuzz -I/opt/pkg/include/ncurses -I/opt/pkg/include/libxml2 -c KNN_mutual_information.cpp -o KNN_mutual_information.o g++ -std=gnu++17 -I"/opt/pkg/lib/R/include" -DNDEBUG -Iinclude -DUSING_R -DUSING_RPRINT -I/opt/pkg/include -I/opt/pkg/include/glib-2.0 -I/opt/pkg/include/gio-unix-2.0 -I/opt/pkg/lib/glib-2.0/include -I/usr/include -I/opt/pkg/include/freetype2 -I/opt/pkg/include/harfbuzz -I/opt/pkg/include/ncurses -I/opt/pkg/include/libxml2 -fPIC -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/pkg/include -I/opt/pkg/include/glib-2.0 -I/opt/pkg/include/gio-unix-2.0 -I/opt/pkg/lib/glib-2.0/include -I/usr/include -I/opt/pkg/include/freetype2 -I/opt/pkg/include/harfbuzz -I/opt/pkg/include/ncurses -I/opt/pkg/include/libxml2 -c bd_fix_rad_search.cpp -o bd_fix_rad_search.o g++ -std=gnu++17 -I"/opt/pkg/lib/R/include" -DNDEBUG -Iinclude -DUSING_R -DUSING_RPRINT -I/opt/pkg/include -I/opt/pkg/include/glib-2.0 -I/opt/pkg/include/gio-unix-2.0 -I/opt/pkg/lib/glib-2.0/include -I/usr/include -I/opt/pkg/include/freetype2 -I/opt/pkg/include/harfbuzz -I/opt/pkg/include/ncurses -I/opt/pkg/include/libxml2 -fPIC -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/pkg/include -I/opt/pkg/include/glib-2.0 -I/opt/pkg/include/gio-unix-2.0 -I/opt/pkg/lib/glib-2.0/include -I/usr/include -I/opt/pkg/include/freetype2 -I/opt/pkg/include/harfbuzz -I/opt/pkg/include/ncurses -I/opt/pkg/include/libxml2 -c bd_pr_search.cpp -o bd_pr_search.o g++ -std=gnu++17 -I"/opt/pkg/lib/R/include" -DNDEBUG -Iinclude -DUSING_R -DUSING_RPRINT -I/opt/pkg/include -I/opt/pkg/include/glib-2.0 -I/opt/pkg/include/gio-unix-2.0 -I/opt/pkg/lib/glib-2.0/include -I/usr/include -I/opt/pkg/include/freetype2 -I/opt/pkg/include/harfbuzz -I/opt/pkg/include/ncurses -I/opt/pkg/include/libxml2 -fPIC -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/pkg/include -I/opt/pkg/include/glib-2.0 -I/opt/pkg/include/gio-unix-2.0 -I/opt/pkg/lib/glib-2.0/include -I/usr/include -I/opt/pkg/include/freetype2 -I/opt/pkg/include/harfbuzz -I/opt/pkg/include/ncurses -I/opt/pkg/include/libxml2 -c bd_search.cpp -o bd_search.o g++ -std=gnu++17 -I"/opt/pkg/lib/R/include" -DNDEBUG -Iinclude -DUSING_R -DUSING_RPRINT -I/opt/pkg/include -I/opt/pkg/include/glib-2.0 -I/opt/pkg/include/gio-unix-2.0 -I/opt/pkg/lib/glib-2.0/include -I/usr/include -I/opt/pkg/include/freetype2 -I/opt/pkg/include/harfbuzz -I/opt/pkg/include/ncurses -I/opt/pkg/include/libxml2 -fPIC -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/pkg/include -I/opt/pkg/include/glib-2.0 -I/opt/pkg/include/gio-unix-2.0 -I/opt/pkg/lib/glib-2.0/include -I/usr/include -I/opt/pkg/include/freetype2 -I/opt/pkg/include/harfbuzz -I/opt/pkg/include/ncurses -I/opt/pkg/include/libxml2 -c bd_tree.cpp -o bd_tree.o g++ -std=gnu++17 -I"/opt/pkg/lib/R/include" -DNDEBUG -Iinclude -DUSING_R -DUSING_RPRINT -I/opt/pkg/include -I/opt/pkg/include/glib-2.0 -I/opt/pkg/include/gio-unix-2.0 -I/opt/pkg/lib/glib-2.0/include -I/usr/include -I/opt/pkg/include/freetype2 -I/opt/pkg/include/harfbuzz -I/opt/pkg/include/ncurses -I/opt/pkg/include/libxml2 -fPIC -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/pkg/include -I/opt/pkg/include/glib-2.0 -I/opt/pkg/include/gio-unix-2.0 -I/opt/pkg/lib/glib-2.0/include -I/usr/include -I/opt/pkg/include/freetype2 -I/opt/pkg/include/harfbuzz -I/opt/pkg/include/ncurses -I/opt/pkg/include/libxml2 -c brute.cpp -o brute.o gcc -I"/opt/pkg/lib/R/include" -DNDEBUG -Iinclude -DUSING_R -DUSING_RPRINT -I/opt/pkg/include -I/opt/pkg/include/glib-2.0 -I/opt/pkg/include/gio-unix-2.0 -I/opt/pkg/lib/glib-2.0/include -I/usr/include -I/opt/pkg/include/freetype2 -I/opt/pkg/include/harfbuzz -I/opt/pkg/include/ncurses -I/opt/pkg/include/libxml2 -fPIC -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/pkg/include -I/opt/pkg/include/glib-2.0 -I/opt/pkg/include/gio-unix-2.0 -I/opt/pkg/lib/glib-2.0/include -I/usr/include -I/opt/pkg/include/freetype2 -I/opt/pkg/include/harfbuzz -I/opt/pkg/include/ncurses -I/opt/pkg/include/libxml2 -c init_FNN.c -o init_FNN.o g++ -std=gnu++17 -I"/opt/pkg/lib/R/include" -DNDEBUG -Iinclude -DUSING_R -DUSING_RPRINT -I/opt/pkg/include -I/opt/pkg/include/glib-2.0 -I/opt/pkg/include/gio-unix-2.0 -I/opt/pkg/lib/glib-2.0/include -I/usr/include -I/opt/pkg/include/freetype2 -I/opt/pkg/include/harfbuzz -I/opt/pkg/include/ncurses -I/opt/pkg/include/libxml2 -fPIC -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/pkg/include -I/opt/pkg/include/glib-2.0 -I/opt/pkg/include/gio-unix-2.0 -I/opt/pkg/lib/glib-2.0/include -I/usr/include -I/opt/pkg/include/freetype2 -I/opt/pkg/include/harfbuzz -I/opt/pkg/include/ncurses -I/opt/pkg/include/libxml2 -c kd_dump.cpp -o kd_dump.o g++ -std=gnu++17 -I"/opt/pkg/lib/R/include" -DNDEBUG -Iinclude -DUSING_R -DUSING_RPRINT -I/opt/pkg/include -I/opt/pkg/include/glib-2.0 -I/opt/pkg/include/gio-unix-2.0 -I/opt/pkg/lib/glib-2.0/include -I/usr/include -I/opt/pkg/include/freetype2 -I/opt/pkg/include/harfbuzz -I/opt/pkg/include/ncurses -I/opt/pkg/include/libxml2 -fPIC -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/pkg/include -I/opt/pkg/include/glib-2.0 -I/opt/pkg/include/gio-unix-2.0 -I/opt/pkg/lib/glib-2.0/include -I/usr/include -I/opt/pkg/include/freetype2 -I/opt/pkg/include/harfbuzz -I/opt/pkg/include/ncurses -I/opt/pkg/include/libxml2 -c kd_fix_rad_search.cpp -o kd_fix_rad_search.o g++ -std=gnu++17 -I"/opt/pkg/lib/R/include" -DNDEBUG -Iinclude -DUSING_R -DUSING_RPRINT -I/opt/pkg/include -I/opt/pkg/include/glib-2.0 -I/opt/pkg/include/gio-unix-2.0 -I/opt/pkg/lib/glib-2.0/include -I/usr/include -I/opt/pkg/include/freetype2 -I/opt/pkg/include/harfbuzz -I/opt/pkg/include/ncurses -I/opt/pkg/include/libxml2 -fPIC -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/pkg/include -I/opt/pkg/include/glib-2.0 -I/opt/pkg/include/gio-unix-2.0 -I/opt/pkg/lib/glib-2.0/include -I/usr/include -I/opt/pkg/include/freetype2 -I/opt/pkg/include/harfbuzz -I/opt/pkg/include/ncurses -I/opt/pkg/include/libxml2 -c kd_pr_search.cpp -o kd_pr_search.o g++ -std=gnu++17 -I"/opt/pkg/lib/R/include" -DNDEBUG -Iinclude -DUSING_R -DUSING_RPRINT -I/opt/pkg/include -I/opt/pkg/include/glib-2.0 -I/opt/pkg/include/gio-unix-2.0 -I/opt/pkg/lib/glib-2.0/include -I/usr/include -I/opt/pkg/include/freetype2 -I/opt/pkg/include/harfbuzz -I/opt/pkg/include/ncurses -I/opt/pkg/include/libxml2 -fPIC -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/pkg/include -I/opt/pkg/include/glib-2.0 -I/opt/pkg/include/gio-unix-2.0 -I/opt/pkg/lib/glib-2.0/include -I/usr/include -I/opt/pkg/include/freetype2 -I/opt/pkg/include/harfbuzz -I/opt/pkg/include/ncurses -I/opt/pkg/include/libxml2 -c kd_search.cpp -o kd_search.o g++ -std=gnu++17 -I"/opt/pkg/lib/R/include" -DNDEBUG -Iinclude -DUSING_R -DUSING_RPRINT -I/opt/pkg/include -I/opt/pkg/include/glib-2.0 -I/opt/pkg/include/gio-unix-2.0 -I/opt/pkg/lib/glib-2.0/include -I/usr/include -I/opt/pkg/include/freetype2 -I/opt/pkg/include/harfbuzz -I/opt/pkg/include/ncurses -I/opt/pkg/include/libxml2 -fPIC -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/pkg/include -I/opt/pkg/include/glib-2.0 -I/opt/pkg/include/gio-unix-2.0 -I/opt/pkg/lib/glib-2.0/include -I/usr/include -I/opt/pkg/include/freetype2 -I/opt/pkg/include/harfbuzz -I/opt/pkg/include/ncurses -I/opt/pkg/include/libxml2 -c kd_split.cpp -o kd_split.o g++ -std=gnu++17 -I"/opt/pkg/lib/R/include" -DNDEBUG -Iinclude -DUSING_R -DUSING_RPRINT -I/opt/pkg/include -I/opt/pkg/include/glib-2.0 -I/opt/pkg/include/gio-unix-2.0 -I/opt/pkg/lib/glib-2.0/include -I/usr/include -I/opt/pkg/include/freetype2 -I/opt/pkg/include/harfbuzz -I/opt/pkg/include/ncurses -I/opt/pkg/include/libxml2 -fPIC -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/pkg/include -I/opt/pkg/include/glib-2.0 -I/opt/pkg/include/gio-unix-2.0 -I/opt/pkg/lib/glib-2.0/include -I/usr/include -I/opt/pkg/include/freetype2 -I/opt/pkg/include/harfbuzz -I/opt/pkg/include/ncurses -I/opt/pkg/include/libxml2 -c kd_tree.cpp -o kd_tree.o g++ -std=gnu++17 -I"/opt/pkg/lib/R/include" -DNDEBUG -Iinclude -DUSING_R -DUSING_RPRINT -I/opt/pkg/include -I/opt/pkg/include/glib-2.0 -I/opt/pkg/include/gio-unix-2.0 -I/opt/pkg/lib/glib-2.0/include -I/usr/include -I/opt/pkg/include/freetype2 -I/opt/pkg/include/harfbuzz -I/opt/pkg/include/ncurses -I/opt/pkg/include/libxml2 -fPIC -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/pkg/include -I/opt/pkg/include/glib-2.0 -I/opt/pkg/include/gio-unix-2.0 -I/opt/pkg/lib/glib-2.0/include -I/usr/include -I/opt/pkg/include/freetype2 -I/opt/pkg/include/harfbuzz -I/opt/pkg/include/ncurses -I/opt/pkg/include/libxml2 -c kd_util.cpp -o kd_util.o g++ -std=gnu++17 -I"/opt/pkg/lib/R/include" -DNDEBUG -Iinclude -DUSING_R -DUSING_RPRINT -I/opt/pkg/include -I/opt/pkg/include/glib-2.0 -I/opt/pkg/include/gio-unix-2.0 -I/opt/pkg/lib/glib-2.0/include -I/usr/include -I/opt/pkg/include/freetype2 -I/opt/pkg/include/harfbuzz -I/opt/pkg/include/ncurses -I/opt/pkg/include/libxml2 -fPIC -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/pkg/include -I/opt/pkg/include/glib-2.0 -I/opt/pkg/include/gio-unix-2.0 -I/opt/pkg/lib/glib-2.0/include -I/usr/include -I/opt/pkg/include/freetype2 -I/opt/pkg/include/harfbuzz -I/opt/pkg/include/ncurses -I/opt/pkg/include/libxml2 -c label_point.cpp -o label_point.o g++ -std=gnu++17 -I"/opt/pkg/lib/R/include" -DNDEBUG -Iinclude -DUSING_R -DUSING_RPRINT -I/opt/pkg/include -I/opt/pkg/include/glib-2.0 -I/opt/pkg/include/gio-unix-2.0 -I/opt/pkg/lib/glib-2.0/include -I/usr/include -I/opt/pkg/include/freetype2 -I/opt/pkg/include/harfbuzz -I/opt/pkg/include/ncurses -I/opt/pkg/include/libxml2 -fPIC -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/pkg/include -I/opt/pkg/include/glib-2.0 -I/opt/pkg/include/gio-unix-2.0 -I/opt/pkg/lib/glib-2.0/include -I/usr/include -I/opt/pkg/include/freetype2 -I/opt/pkg/include/harfbuzz -I/opt/pkg/include/ncurses -I/opt/pkg/include/libxml2 -c perf.cpp -o perf.o g++ -std=gnu++17 -shared -L/opt/pkg/lib/R/lib -Wl,-R/opt/pkg/lib/R/lib -L/opt/pkg/lib -Wl,-R/opt/pkg/lib -liconv -lintl -pthread -L/usr/lib/amd64 -Wl,-R/usr/lib/amd64 -o FNN.so ANN.o KNN_ANN.o KNN_correlation_distance.o KNN_cover_test.o KNN_cover_tree.o KNN_mutual_information.o bd_fix_rad_search.o bd_pr_search.o bd_search.o bd_tree.o brute.o init_FNN.o kd_dump.o kd_fix_rad_search.o kd_pr_search.o kd_search.o kd_split.o kd_tree.o kd_util.o label_point.o perf.o -L/opt/pkg/lib/R/lib installing to /home/pbulk/build/math/R-FNN/work/.destdir/opt/pkg/lib/R/library/00LOCK-FNN/00new/FNN/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location Error: package or namespace load failed for 'FNN' in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object '/home/pbulk/build/math/R-FNN/work/.destdir/opt/pkg/lib/R/library/00LOCK-FNN/00new/FNN/libs/FNN.so': ld.so.1: R: fatal: libstdc++.so.6: open failed: No such file or directory Error: loading failed Execution halted ERROR: loading failed * removing '/home/pbulk/build/math/R-FNN/work/.destdir/opt/pkg/lib/R/library/FNN' *** Error code 1 Stop. bmake[1]: stopped making "stage-install" in /data/jenkins/workspace/pkgsrc-upstream-trunk/math/R-FNN *** Error code 1 Stop. bmake: stopped making "stage-install" in /data/jenkins/workspace/pkgsrc-upstream-trunk/math/R-FNN