+ case "${usergroup_phase}" in
+ local run_cmd
+ run_cmd=run_su
+ shift
+ run_su /opt/pkg/bin/bmake stage-install BATCH=1 DEPENDS_TARGET=/nonexistent WRKLOG=/tmp/bulklog/R-ncdf4-1.23nb6/work.log
+ su pbulk -c '"$@"' make /opt/pkg/bin/bmake stage-install BATCH=1 DEPENDS_TARGET=/nonexistent WRKLOG=/tmp/bulklog/R-ncdf4-1.23nb6/work.log
===> Installing for R-ncdf4-1.23nb6
=> Generating pre-install file lists
=> Creating installation directories
* installing *source* package 'ncdf4' ...
file 'configure' has the wrong MD5 checksum
** using staged installation
configure.ac: starting
checking for nc-config... yes
Using nc-config: nc-config
Output of nc-config --all:

This netCDF 4.9.2 has been built with the following features: 

  --cc            -> gcc
  --cflags        -> -I/opt/pkg/include -I/usr/include -I/opt/pkg/include -I/opt/pkg/include/libxml2
  --libs          -> -L/opt/pkg/lib  -lnetcdf
  --static        -> -lhdf5_hl -lhdf5 -lm -lz -lsz -lbz2 -lxml2 -lcurl 
  --has-dap          -> yes
  --has-dap2         -> yes
  --has-dap4         -> yes
  --has-nc2          -> yes
  --has-nc4          -> yes
  --has-hdf5         -> yes
  --has-hdf4         -> no
  --has-logging      -> no
  --has-pnetcdf      -> no
  --has-szlib        -> yes
  --has-cdf5         -> yes
  --has-parallel4    -> no
  --has-parallel     -> no
  --has-nczarr       -> yes
  --has-zstd         -> no
  --has-benchmarks   -> no
  --has-multifilters -> yes
  --has-stdfilters   -> deflate bz2
  --has-quantize     -> yes

  --prefix           -> /opt/pkg
  --includedir       -> /opt/pkg/include
  --libdir           -> /opt/pkg/lib
  --plugindir        -> 
  --version          -> netCDF 4.9.2

---
netcdf.m4: about to set rpath, here is source string: >-L/opt/pkg/lib -lnetcdf<
netcdf.m4: final rpath:   -Wl,-rpath,/opt/pkg/lib
Netcdf library version: netCDF 4.9.2
Netcdf library has version 4 interface present: yes
Netcdf library was compiled with C compiler: gcc
configure: creating ./config.status
config.status: creating src/Makevars
 
**********************  Results of ncdf4 package configure *******************
 
netCDF v4 CPP flags      = -I/opt/pkg/include -I/usr/include -I/opt/pkg/include -I/opt/pkg/include/libxml2
netCDF v4 LD flags       =   -Wl,-rpath,/opt/pkg/lib -L/opt/pkg/lib -lnetcdf -L/opt/pkg/lib -Wl,-R/opt/pkg/lib -lintl -liconv -L/usr/lib/amd64 -Wl,-R/usr/lib/amd64
netCDF v4 runtime path   =   -Wl,-rpath,/opt/pkg/lib
 
netCDF C compiler used   = gcc
R      C compiler used   = gcc -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
 
******************************************************************************
 
** 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 -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 ncdf4.so ncdf.o -Wl,-rpath,/opt/pkg/lib -L/opt/pkg/lib -lnetcdf -L/opt/pkg/lib -Wl,-R/opt/pkg/lib -lintl -liconv -L/usr/lib/amd64 -Wl,-R/usr/lib/amd64 -Wl,-R/opt/pkg/lib/R/lib -L/opt/pkg/lib/R/lib -lR
installing to /home/pbulk/build/math/R-ncdf4/work/.destdir/opt/pkg/lib/R/library/00LOCK-ncdf4/00new/ncdf4/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 'ncdf4' in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/home/pbulk/build/math/R-ncdf4/work/.destdir/opt/pkg/lib/R/library/00LOCK-ncdf4/00new/ncdf4/libs/ncdf4.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-ncdf4/work/.destdir/opt/pkg/lib/R/library/ncdf4'
*** Error code 1

Stop.
bmake[1]: stopped making "stage-install" in /data/jenkins/workspace/pkgsrc-upstream-trunk/math/R-ncdf4
*** Error code 1

Stop.
bmake: stopped making "stage-install" in /data/jenkins/workspace/pkgsrc-upstream-trunk/math/R-ncdf4