+ case "${usergroup_phase}" in
+ local run_cmd
+ run_cmd=run_su
+ shift
+ run_su /opt/pkg/bin/bmake stage-install BATCH=1 DEPENDS_TARGET=/nonexistent WRKLOG=/tmp/bulklog/R-ncdf-1.6.6nb31/work.log
+ su pbulk -c '"$@"' make /opt/pkg/bin/bmake stage-install BATCH=1 DEPENDS_TARGET=/nonexistent WRKLOG=/tmp/bulklog/R-ncdf-1.6.6nb31/work.log
===> Installing for R-ncdf-1.6.6nb31
=> Generating pre-install file lists
=> Creating installation directories
* installing *source* package 'ncdf' ...
** package 'ncdf' successfully unpacked and MD5 sums checked
** using staged installation
configure: WARNING: unrecognized options: --with-netcdf_incdir, --with-netcdf_libdir
checking for nc-config... /opt/pkg/bin/nc-config
configure: creating ./config.status
config.status: creating src/Makevars
configure: WARNING: unrecognized options: --with-netcdf_incdir, --with-netcdf_libdir
** libs
using C compiler: 'gcc (GCC) 13.3.0'
gcc -I"/opt/pkg/lib/R/include" -DNDEBUG -I/opt/pkg/include -I/usr/include -I/opt/pkg/include -I/opt/pkg/include/libxml2  -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 ncdf.c -o ncdf.o
gcc -I"/opt/pkg/lib/R/include" -DNDEBUG -I/opt/pkg/include -I/usr/include -I/opt/pkg/include -I/opt/pkg/include/libxml2  -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 ncdf2.c -o ncdf2.o
gcc -I"/opt/pkg/lib/R/include" -DNDEBUG -I/opt/pkg/include -I/usr/include -I/opt/pkg/include -I/opt/pkg/include/libxml2  -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 ncdf3.c -o ncdf3.o
gcc -shared -Wl,-R/opt/pkg/lib/R/lib -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 ncdf.so ncdf.o ncdf2.o ncdf3.o -L/opt/pkg/lib -lnetcdf -Wl,-R/opt/pkg/lib/R/lib -L/opt/pkg/lib/R/lib -lR
installing to /home/pbulk/build/math/R-ncdf/work/.destdir/opt/pkg/lib/R/library/00LOCK-ncdf/00new/ncdf/libs
** R
** 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 'ncdf' in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/home/pbulk/build/math/R-ncdf/work/.destdir/opt/pkg/lib/R/library/00LOCK-ncdf/00new/ncdf/libs/ncdf.so':
  ld.so.1: R: fatal: relocation error: file /opt/pkg/lib/libhdf5.so.310: symbol __truncsfhf2: referenced symbol not found
Error: loading failed
Execution halted
ERROR: loading failed
* removing '/home/pbulk/build/math/R-ncdf/work/.destdir/opt/pkg/lib/R/library/ncdf'
*** Error code 1

Stop.
bmake[1]: stopped making "stage-install" in /data/jenkins/workspace/pkgsrc-upstream-trunk/math/R-ncdf
*** Error code 1

Stop.
bmake: stopped making "stage-install" in /data/jenkins/workspace/pkgsrc-upstream-trunk/math/R-ncdf