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r-spatial / sf

Simple Features for R
https://r-spatial.github.io/sf/
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Error during "testing" phase on install on Linux: Undefined symbol #2372

Closed stephenashton-dhsc closed 5 months ago

stephenashton-dhsc commented 5 months ago

Describe the bug Apologies if this is something obvious, but I'm getting a failed install of sf due to a missing symbol. Output below:

Installing 1 packages: sf
Installing package into ‘/data/users/hemt/R-library’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/sf_1.0-16.tar.gz'
Content type 'application/x-gzip' length 3493756 bytes (3.3 MB)
==================================================
downloaded 3.3 MB

* installing *source* package ‘sf’ ...
** package ‘sf’ successfully unpacked and MD5 sums checked
** using staged installation
configure: CC: gcc
configure: CXX: g++ -std=gnu++17
checking for gdal-config... /usr/local/packages/gdal/2.4.4/bin/gdal-config
checking gdal-config usability... yes
configure: GDAL: 2.4.4
checking GDAL version >= 2.0.1... yes
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C... yes
checking whether gcc accepts -g... yes
checking for gcc option to enable C11 features... none needed
checking for stdio.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for strings.h... yes
checking for sys/stat.h... yes
checking for sys/types.h... yes
checking for unistd.h... yes
checking for gdal.h... yes
checking GDAL: linking with --libs only... yes
checking GDAL: /usr/local/packages/gdal/2.4.4/share/gdal/pcs.csv readable... yes
checking GDAL: checking whether PROJ is available for linking:... yes
checking GDAL: checking whether PROJ is available for running:... yes
configure: GDAL: 2.4.4
configure: pkg-config proj exists, will use it
checking for proj_api.h... yes
configure: PROJ: 4.9.3
checking for pj_init_plus in -lproj... yes
checking PROJ: epsg found and readable... yes
checking for geos-config... /usr/local/packages/geos/3.11.0/bin/geos-config
checking geos-config usability... yes
configure: GEOS: 3.11.0
checking GEOS version >= 3.4.0... yes
checking for geos_c.h... yes
checking geos: linking with -L/usr/local/packages/geos/3.11.0/lib64 -lgeos_c... yes
configure: Package CPP flags:  -I/usr/local/packages/proj/4.9.3/include   -I/usr/local/packages/gdal/2.4.4/include -I/usr/local/packages/geos/3.11.0/include
configure: Package LIBS: -L/usr/local/packages/proj/4.9.3/lib -lproj     -L/usr/local/packages/gdal/2.4.4/lib -lgdal -L/usr/local/packages/geos/3.11.0/lib64 -lgeos_c
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C++ compiler: ‘g++ (GCC) 13.2.0’
g++ -std=gnu++17 -I"/usr/local/packages/R/4.3.2/lib64/R/include" -DNDEBUG -I/usr/local/packages/proj/4.9.3/include   -I/usr/local/packages/gdal/2.4.4/include -I/usr/local/packages/geos/3.11.0/include -I'/data/users/hemt/R-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/usr/local/packages/R/4.3.2/lib64/R/include" -DNDEBUG -I/usr/local/packages/proj/4.9.3/include   -I/usr/local/packages/gdal/2.4.4/include -I/usr/local/packages/geos/3.11.0/include -I'/data/users/hemt/R-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -c bbox.cpp -o bbox.o
g++ -std=gnu++17 -I"/usr/local/packages/R/4.3.2/lib64/R/include" -DNDEBUG -I/usr/local/packages/proj/4.9.3/include   -I/usr/local/packages/gdal/2.4.4/include -I/usr/local/packages/geos/3.11.0/include -I'/data/users/hemt/R-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -c gdal.cpp -o gdal.o
g++ -std=gnu++17 -I"/usr/local/packages/R/4.3.2/lib64/R/include" -DNDEBUG -I/usr/local/packages/proj/4.9.3/include   -I/usr/local/packages/gdal/2.4.4/include -I/usr/local/packages/geos/3.11.0/include -I'/data/users/hemt/R-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -c gdal_geom.cpp -o gdal_geom.o
g++ -std=gnu++17 -I"/usr/local/packages/R/4.3.2/lib64/R/include" -DNDEBUG -I/usr/local/packages/proj/4.9.3/include   -I/usr/local/packages/gdal/2.4.4/include -I/usr/local/packages/geos/3.11.0/include -I'/data/users/hemt/R-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -c gdal_read.cpp -o gdal_read.o
g++ -std=gnu++17 -I"/usr/local/packages/R/4.3.2/lib64/R/include" -DNDEBUG -I/usr/local/packages/proj/4.9.3/include   -I/usr/local/packages/gdal/2.4.4/include -I/usr/local/packages/geos/3.11.0/include -I'/data/users/hemt/R-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -c gdal_read_stream.cpp -o gdal_read_stream.o
g++ -std=gnu++17 -I"/usr/local/packages/R/4.3.2/lib64/R/include" -DNDEBUG -I/usr/local/packages/proj/4.9.3/include   -I/usr/local/packages/gdal/2.4.4/include -I/usr/local/packages/geos/3.11.0/include -I'/data/users/hemt/R-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -c gdal_utils.cpp -o gdal_utils.o
g++ -std=gnu++17 -I"/usr/local/packages/R/4.3.2/lib64/R/include" -DNDEBUG -I/usr/local/packages/proj/4.9.3/include   -I/usr/local/packages/gdal/2.4.4/include -I/usr/local/packages/geos/3.11.0/include -I'/data/users/hemt/R-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -c gdal_write.cpp -o gdal_write.o
g++ -std=gnu++17 -I"/usr/local/packages/R/4.3.2/lib64/R/include" -DNDEBUG -I/usr/local/packages/proj/4.9.3/include   -I/usr/local/packages/gdal/2.4.4/include -I/usr/local/packages/geos/3.11.0/include -I'/data/users/hemt/R-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -c geos.cpp -o geos.o
g++ -std=gnu++17 -I"/usr/local/packages/R/4.3.2/lib64/R/include" -DNDEBUG -I/usr/local/packages/proj/4.9.3/include   -I/usr/local/packages/gdal/2.4.4/include -I/usr/local/packages/geos/3.11.0/include -I'/data/users/hemt/R-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -c hex.cpp -o hex.o
g++ -std=gnu++17 -I"/usr/local/packages/R/4.3.2/lib64/R/include" -DNDEBUG -I/usr/local/packages/proj/4.9.3/include   -I/usr/local/packages/gdal/2.4.4/include -I/usr/local/packages/geos/3.11.0/include -I'/data/users/hemt/R-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -c mdim.cpp -o mdim.o
g++ -std=gnu++17 -I"/usr/local/packages/R/4.3.2/lib64/R/include" -DNDEBUG -I/usr/local/packages/proj/4.9.3/include   -I/usr/local/packages/gdal/2.4.4/include -I/usr/local/packages/geos/3.11.0/include -I'/data/users/hemt/R-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -c ops.cpp -o ops.o
g++ -std=gnu++17 -I"/usr/local/packages/R/4.3.2/lib64/R/include" -DNDEBUG -I/usr/local/packages/proj/4.9.3/include   -I/usr/local/packages/gdal/2.4.4/include -I/usr/local/packages/geos/3.11.0/include -I'/data/users/hemt/R-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -c polygonize.cpp -o polygonize.o
g++ -std=gnu++17 -I"/usr/local/packages/R/4.3.2/lib64/R/include" -DNDEBUG -I/usr/local/packages/proj/4.9.3/include   -I/usr/local/packages/gdal/2.4.4/include -I/usr/local/packages/geos/3.11.0/include -I'/data/users/hemt/R-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -c proj.cpp -o proj.o
g++ -std=gnu++17 -I"/usr/local/packages/R/4.3.2/lib64/R/include" -DNDEBUG -I/usr/local/packages/proj/4.9.3/include   -I/usr/local/packages/gdal/2.4.4/include -I/usr/local/packages/geos/3.11.0/include -I'/data/users/hemt/R-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -c proj_info.cpp -o proj_info.o
g++ -std=gnu++17 -I"/usr/local/packages/R/4.3.2/lib64/R/include" -DNDEBUG -I/usr/local/packages/proj/4.9.3/include   -I/usr/local/packages/gdal/2.4.4/include -I/usr/local/packages/geos/3.11.0/include -I'/data/users/hemt/R-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -c raster2sf.cpp -o raster2sf.o
g++ -std=gnu++17 -I"/usr/local/packages/R/4.3.2/lib64/R/include" -DNDEBUG -I/usr/local/packages/proj/4.9.3/include   -I/usr/local/packages/gdal/2.4.4/include -I/usr/local/packages/geos/3.11.0/include -I'/data/users/hemt/R-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -c sfc-sfg.cpp -o sfc-sfg.o
g++ -std=gnu++17 -I"/usr/local/packages/R/4.3.2/lib64/R/include" -DNDEBUG -I/usr/local/packages/proj/4.9.3/include   -I/usr/local/packages/gdal/2.4.4/include -I/usr/local/packages/geos/3.11.0/include -I'/data/users/hemt/R-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -c signed_area.cpp -o signed_area.o
g++ -std=gnu++17 -I"/usr/local/packages/R/4.3.2/lib64/R/include" -DNDEBUG -I/usr/local/packages/proj/4.9.3/include   -I/usr/local/packages/gdal/2.4.4/include -I/usr/local/packages/geos/3.11.0/include -I'/data/users/hemt/R-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -c stars.cpp -o stars.o
g++ -std=gnu++17 -I"/usr/local/packages/R/4.3.2/lib64/R/include" -DNDEBUG -I/usr/local/packages/proj/4.9.3/include   -I/usr/local/packages/gdal/2.4.4/include -I/usr/local/packages/geos/3.11.0/include -I'/data/users/hemt/R-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -c wkb.cpp -o wkb.o
g++ -std=gnu++17 -I"/usr/local/packages/R/4.3.2/lib64/R/include" -DNDEBUG -I/usr/local/packages/proj/4.9.3/include   -I/usr/local/packages/gdal/2.4.4/include -I/usr/local/packages/geos/3.11.0/include -I'/data/users/hemt/R-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -c zm_range.cpp -o zm_range.o
g++ -std=gnu++17 -shared -L/usr/local/lib64 -o sf.so RcppExports.o bbox.o gdal.o gdal_geom.o gdal_read.o gdal_read_stream.o gdal_utils.o gdal_write.o geos.o hex.o mdim.o ops.o polygonize.o proj.o proj_info.o raster2sf.o sfc-sfg.o signed_area.o stars.o wkb.o zm_range.o -L/usr/local/packages/proj/4.9.3/lib -lproj -L/usr/local/packages/gdal/2.4.4/lib -lgdal -L/usr/local/packages/geos/3.11.0/lib64 -lgeos_c
installing to /data/users/hemt/R-library/00LOCK-sf/00new/sf/libs
** R
** demo
** inst
** tests
** byte-compile and prepare package for lazy loading
in method for ‘dbWriteTable’ with signature ‘"PostgreSQLConnection","character","sf"’: no definition for class “PostgreSQLConnection”
in method for ‘dbDataType’ with signature ‘"PostgreSQLConnection","sf"’: no definition for class “PostgreSQLConnection”
in method for ‘coerce’ with signature ‘"Spatial","sf"’: no definition for class “Spatial”
in method for ‘coerce’ with signature ‘"Spatial","sfc"’: no definition for class “Spatial”
in method for ‘coerce’ with signature ‘"sf","Spatial"’: no definition for class “Spatial”
in method for ‘coerce’ with signature ‘"sfc","Spatial"’: no definition for class “Spatial”
in method for ‘coerce’ with signature ‘"XY","Spatial"’: no definition for class “Spatial”
in method for ‘coerce’ with signature ‘"crs","CRS"’: no definition for class “CRS”
in method for ‘coerce’ with signature ‘"sgbp","sparseMatrix"’: no definition for class “sparseMatrix”
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for ‘sf’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/data/users/hemt/R-library/00LOCK-sf/00new/sf/libs/sf.so':
  /data/users/hemt/R-library/00LOCK-sf/00new/sf/libs/sf.so: undefined symbol: _Z16CPL_set_data_dirN4Rcpp6VectorILi16ENS_15PreserveStorageEEEb
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/data/users/hemt/R-library/sf’

The downloaded source packages are in
    ‘/tmp/RtmpPSoeGS/downloaded_packages’
``` R version 4.3.2 (2023-10-31) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core) Matrix products: default BLAS: /usr/local/packages/R/4.3.2/lib64/R/lib/libRblas.so LAPACK: /usr/local/packages/R/4.3.2/lib64/R/lib/libRlapack.so; LAPACK version 3.11.0 locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C time zone: Europe/London tzcode source: system (glibc) attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] processx_3.8.2 compiler_4.3.2 R6_2.5.1 cli_3.6.1 [5] pkgcache_2.2.1 tools_4.3.2 pillar_1.9.0 glue_1.7.0 [9] utf8_1.2.4 fansi_1.0.6 vctrs_0.6.5 callr_3.7.3 [13] ps_1.7.5 lifecycle_1.0.4 rlang_1.1.3 pak_0.7.2 [17] pkgdepends_0.7.2 ```
edzer commented 5 months ago

We see that most often on systems that have more than one instance of GDAL, GEOS or PROJ installed; see here.

stephenashton-dhsc commented 5 months ago

Hmmmm. There are multiple versions on the system, but they should be isolated within lmod modules. I’ll check with our tech folks to see if there’s any leakage - thanks 🙂

stephenashton-dhsc commented 5 months ago

I'm not the most familiar with Linux, but here's the portion of the debug return leading up to the error - if you've got any pointers for where to look for duplicate libraries and/or other errors, that'd be great :)

``` 101842: calling init: /usr/local/packages/R/4.3.2/lib64/R/library/grDevices/libs/grDevices.so 101842: 101842: 101842: calling init: /usr/local/packages/R/4.3.2/lib64/R/library/graphics/libs/graphics.so 101842: 101842: find library=libRlapack.so [0]; searching 101842: search path=/usr/local/packages/R/4.3.2/lib64/R/lib:/usr/local/lib64:/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.181-3.b13.el7_5.x86_64/jre/lib/amd64/server:/usr/local/packages/geos/3.11.0/lib64:/usr/local/packages/R/4.3.2/lib64:/usr/local/packages/curl/7.54.1/lib:/usr/local/packages/pcre/8.37/lib:/usr/local/packages/xz/5.2.3/lib:/usr/local/packages/bzip2/1.0.6/lib:/usr/local/packages/zlib/1.2.11/lib:/usr/local/packages/sqlite/3360000/lib:/usr/local/packages/udunits/2.2.28/lib:/usr/local/packages/openmpi/1.6.4/lib:/usr/local/packages/netcdf/4.2.1.1/lib:/usr/local/packages/proj/4.9.3/lib:/usr/local/packages/hdf5/1.8.10/lib:/usr/local/packages/gdal/2.4.4/lib:/usr/local/packages/gcc/13.2.0/lib64:/usr/local/packages/gcc/13.2.0/lib (LD_LIBRARY_PATH) 101842: trying file=/usr/local/packages/R/4.3.2/lib64/R/lib/libRlapack.so 101842: 101842: 101842: calling init: /usr/local/packages/R/4.3.2/lib64/R/lib/libRlapack.so 101842: 101842: 101842: calling init: /usr/local/packages/R/4.3.2/lib64/R/library/stats/libs/stats.so 101842: 101842: 101842: calling init: /usr/local/packages/R/4.3.2/lib64/R/library/tools/libs/tools.so 101842: 101842: 101842: calling init: /data/users/hemt/R-library/Rcpp/libs/Rcpp.so 101842: 101842: 101842: calling init: /data/users/hemt/R-library/proxy/libs/proxy.so 101842: 101842: 101842: calling init: /usr/local/packages/R/4.3.2/lib64/R/library/class/libs/class.so 101842: 101842: 101842: calling init: /data/users/hemt/R-library/e1071/libs/e1071.so 101842: 101842: 101842: calling init: /usr/local/packages/R/4.3.2/lib64/R/library/KernSmooth/libs/KernSmooth.so 101842: 101842: 101842: calling init: /data/users/hemt/R-library/classInt/libs/classInt.so 101842: 101842: 101842: calling init: /usr/local/packages/R/4.3.2/lib64/R/library/grid/libs/grid.so 101842: 101842: 101842: calling init: /usr/local/packages/R/4.3.2/lib64/R/library/magrittr/libs/magrittr.so 101842: 101842: find library=libexpat.so.1 [0]; searching 101842: search path=/usr/local/packages/R/4.3.2/lib64/R/lib:/usr/local/lib64:/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.181-3.b13.el7_5.x86_64/jre/lib/amd64/server:/usr/local/packages/geos/3.11.0/lib64:/usr/local/packages/R/4.3.2/lib64:/usr/local/packages/curl/7.54.1/lib:/usr/local/packages/pcre/8.37/lib:/usr/local/packages/xz/5.2.3/lib:/usr/local/packages/bzip2/1.0.6/lib:/usr/local/packages/zlib/1.2.11/lib:/usr/local/packages/sqlite/3360000/lib:/usr/local/packages/udunits/2.2.28/lib:/usr/local/packages/openmpi/1.6.4/lib:/usr/local/packages/netcdf/4.2.1.1/lib:/usr/local/packages/proj/4.9.3/lib:/usr/local/packages/hdf5/1.8.10/lib:/usr/local/packages/gdal/2.4.4/lib:/usr/local/packages/gcc/13.2.0/lib64:/usr/local/packages/gcc/13.2.0/lib (LD_LIBRARY_PATH) 101842: trying file=/usr/local/packages/R/4.3.2/lib64/R/lib/libexpat.so.1 101842: trying file=/usr/local/lib64/libexpat.so.1 101842: trying file=/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.181-3.b13.el7_5.x86_64/jre/lib/amd64/server/libexpat.so.1 101842: trying file=/usr/local/packages/geos/3.11.0/lib64/libexpat.so.1 101842: trying file=/usr/local/packages/R/4.3.2/lib64/libexpat.so.1 101842: trying file=/usr/local/packages/curl/7.54.1/lib/libexpat.so.1 101842: trying file=/usr/local/packages/pcre/8.37/lib/libexpat.so.1 101842: trying file=/usr/local/packages/xz/5.2.3/lib/libexpat.so.1 101842: trying file=/usr/local/packages/bzip2/1.0.6/lib/libexpat.so.1 101842: trying file=/usr/local/packages/zlib/1.2.11/lib/libexpat.so.1 101842: trying file=/usr/local/packages/sqlite/3360000/lib/libexpat.so.1 101842: trying file=/usr/local/packages/udunits/2.2.28/lib/libexpat.so.1 101842: trying file=/usr/local/packages/openmpi/1.6.4/lib/libexpat.so.1 101842: trying file=/usr/local/packages/netcdf/4.2.1.1/lib/libexpat.so.1 101842: trying file=/usr/local/packages/proj/4.9.3/lib/libexpat.so.1 101842: trying file=/usr/local/packages/hdf5/1.8.10/lib/libexpat.so.1 101842: trying file=/usr/local/packages/gdal/2.4.4/lib/libexpat.so.1 101842: trying file=/usr/local/packages/gcc/13.2.0/lib64/libexpat.so.1 101842: trying file=/usr/local/packages/gcc/13.2.0/lib/libexpat.so.1 101842: search cache=/etc/ld.so.cache 101842: trying file=/lib64/libexpat.so.1 101842: 101842: find library=libudunits2.so.0 [0]; searching 101842: search path=/usr/local/packages/R/4.3.2/lib64/R/lib:/usr/local/lib64:/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.181-3.b13.el7_5.x86_64/jre/lib/amd64/server:/usr/local/packages/geos/3.11.0/lib64:/usr/local/packages/R/4.3.2/lib64:/usr/local/packages/curl/7.54.1/lib:/usr/local/packages/pcre/8.37/lib:/usr/local/packages/xz/5.2.3/lib:/usr/local/packages/bzip2/1.0.6/lib:/usr/local/packages/zlib/1.2.11/lib:/usr/local/packages/sqlite/3360000/lib:/usr/local/packages/udunits/2.2.28/lib:/usr/local/packages/openmpi/1.6.4/lib:/usr/local/packages/netcdf/4.2.1.1/lib:/usr/local/packages/proj/4.9.3/lib:/usr/local/packages/hdf5/1.8.10/lib:/usr/local/packages/gdal/2.4.4/lib:/usr/local/packages/gcc/13.2.0/lib64:/usr/local/packages/gcc/13.2.0/lib (LD_LIBRARY_PATH) 101842: trying file=/usr/local/packages/R/4.3.2/lib64/R/lib/libudunits2.so.0 101842: trying file=/usr/local/lib64/libudunits2.so.0 101842: trying file=/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.181-3.b13.el7_5.x86_64/jre/lib/amd64/server/libudunits2.so.0 101842: trying file=/usr/local/packages/geos/3.11.0/lib64/libudunits2.so.0 101842: trying file=/usr/local/packages/R/4.3.2/lib64/libudunits2.so.0 101842: trying file=/usr/local/packages/curl/7.54.1/lib/libudunits2.so.0 101842: trying file=/usr/local/packages/pcre/8.37/lib/libudunits2.so.0 101842: trying file=/usr/local/packages/xz/5.2.3/lib/libudunits2.so.0 101842: trying file=/usr/local/packages/bzip2/1.0.6/lib/libudunits2.so.0 101842: trying file=/usr/local/packages/zlib/1.2.11/lib/libudunits2.so.0 101842: trying file=/usr/local/packages/sqlite/3360000/lib/libudunits2.so.0 101842: trying file=/usr/local/packages/udunits/2.2.28/lib/libudunits2.so.0 101842: 101842: 101842: calling init: /lib64/libexpat.so.1 101842: 101842: 101842: calling init: /usr/local/packages/udunits/2.2.28/lib/libudunits2.so.0 101842: 101842: 101842: calling init: /data/users/hemt/R-library/units/libs/units.so 101842: 101842: find library=libproj.so.12 [0]; searching 101842: search path=/usr/local/packages/R/4.3.2/lib64/R/lib:/usr/local/lib64:/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.181-3.b13.el7_5.x86_64/jre/lib/amd64/server:/usr/local/packages/geos/3.11.0/lib64:/usr/local/packages/R/4.3.2/lib64:/usr/local/packages/curl/7.54.1/lib:/usr/local/packages/pcre/8.37/lib:/usr/local/packages/xz/5.2.3/lib:/usr/local/packages/bzip2/1.0.6/lib:/usr/local/packages/zlib/1.2.11/lib:/usr/local/packages/sqlite/3360000/lib:/usr/local/packages/udunits/2.2.28/lib:/usr/local/packages/openmpi/1.6.4/lib:/usr/local/packages/netcdf/4.2.1.1/lib:/usr/local/packages/proj/4.9.3/lib:/usr/local/packages/hdf5/1.8.10/lib:/usr/local/packages/gdal/2.4.4/lib:/usr/local/packages/gcc/13.2.0/lib64:/usr/local/packages/gcc/13.2.0/lib (LD_LIBRARY_PATH) 101842: trying file=/usr/local/packages/R/4.3.2/lib64/R/lib/libproj.so.12 101842: trying file=/usr/local/lib64/libproj.so.12 101842: trying file=/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.181-3.b13.el7_5.x86_64/jre/lib/amd64/server/libproj.so.12 101842: trying file=/usr/local/packages/geos/3.11.0/lib64/libproj.so.12 101842: trying file=/usr/local/packages/R/4.3.2/lib64/libproj.so.12 101842: trying file=/usr/local/packages/curl/7.54.1/lib/libproj.so.12 101842: trying file=/usr/local/packages/pcre/8.37/lib/libproj.so.12 101842: trying file=/usr/local/packages/xz/5.2.3/lib/libproj.so.12 101842: trying file=/usr/local/packages/bzip2/1.0.6/lib/libproj.so.12 101842: trying file=/usr/local/packages/zlib/1.2.11/lib/libproj.so.12 101842: trying file=/usr/local/packages/sqlite/3360000/lib/libproj.so.12 101842: trying file=/usr/local/packages/udunits/2.2.28/lib/libproj.so.12 101842: trying file=/usr/local/packages/openmpi/1.6.4/lib/libproj.so.12 101842: trying file=/usr/local/packages/netcdf/4.2.1.1/lib/libproj.so.12 101842: trying file=/usr/local/packages/proj/4.9.3/lib/libproj.so.12 101842: 101842: find library=libgdal.so.20 [0]; searching 101842: search path=/usr/local/packages/R/4.3.2/lib64/R/lib:/usr/local/lib64:/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.181-3.b13.el7_5.x86_64/jre/lib/amd64/server:/usr/local/packages/geos/3.11.0/lib64:/usr/local/packages/R/4.3.2/lib64:/usr/local/packages/curl/7.54.1/lib:/usr/local/packages/pcre/8.37/lib:/usr/local/packages/xz/5.2.3/lib:/usr/local/packages/bzip2/1.0.6/lib:/usr/local/packages/zlib/1.2.11/lib:/usr/local/packages/sqlite/3360000/lib:/usr/local/packages/udunits/2.2.28/lib:/usr/local/packages/openmpi/1.6.4/lib:/usr/local/packages/netcdf/4.2.1.1/lib:/usr/local/packages/proj/4.9.3/lib:/usr/local/packages/hdf5/1.8.10/lib:/usr/local/packages/gdal/2.4.4/lib:/usr/local/packages/gcc/13.2.0/lib64:/usr/local/packages/gcc/13.2.0/lib (LD_LIBRARY_PATH) 101842: trying file=/usr/local/packages/R/4.3.2/lib64/R/lib/libgdal.so.20 101842: trying file=/usr/local/lib64/libgdal.so.20 101842: trying file=/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.181-3.b13.el7_5.x86_64/jre/lib/amd64/server/libgdal.so.20 101842: trying file=/usr/local/packages/geos/3.11.0/lib64/libgdal.so.20 101842: trying file=/usr/local/packages/R/4.3.2/lib64/libgdal.so.20 101842: trying file=/usr/local/packages/curl/7.54.1/lib/libgdal.so.20 101842: trying file=/usr/local/packages/pcre/8.37/lib/libgdal.so.20 101842: trying file=/usr/local/packages/xz/5.2.3/lib/libgdal.so.20 101842: trying file=/usr/local/packages/bzip2/1.0.6/lib/libgdal.so.20 101842: trying file=/usr/local/packages/zlib/1.2.11/lib/libgdal.so.20 101842: trying file=/usr/local/packages/sqlite/3360000/lib/libgdal.so.20 101842: trying file=/usr/local/packages/udunits/2.2.28/lib/libgdal.so.20 101842: trying file=/usr/local/packages/openmpi/1.6.4/lib/libgdal.so.20 101842: trying file=/usr/local/packages/netcdf/4.2.1.1/lib/libgdal.so.20 101842: trying file=/usr/local/packages/proj/4.9.3/lib/libgdal.so.20 101842: trying file=/usr/local/packages/hdf5/1.8.10/lib/libgdal.so.20 101842: trying file=/usr/local/packages/gdal/2.4.4/lib/libgdal.so.20 101842: 101842: find library=libgeos_c.so.1 [0]; searching 101842: search path=/usr/local/packages/R/4.3.2/lib64/R/lib:/usr/local/lib64:/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.181-3.b13.el7_5.x86_64/jre/lib/amd64/server:/usr/local/packages/geos/3.11.0/lib64:/usr/local/packages/R/4.3.2/lib64:/usr/local/packages/curl/7.54.1/lib:/usr/local/packages/pcre/8.37/lib:/usr/local/packages/xz/5.2.3/lib:/usr/local/packages/bzip2/1.0.6/lib:/usr/local/packages/zlib/1.2.11/lib:/usr/local/packages/sqlite/3360000/lib:/usr/local/packages/udunits/2.2.28/lib:/usr/local/packages/openmpi/1.6.4/lib:/usr/local/packages/netcdf/4.2.1.1/lib:/usr/local/packages/proj/4.9.3/lib:/usr/local/packages/hdf5/1.8.10/lib:/usr/local/packages/gdal/2.4.4/lib:/usr/local/packages/gcc/13.2.0/lib64:/usr/local/packages/gcc/13.2.0/lib (LD_LIBRARY_PATH) 101842: trying file=/usr/local/packages/R/4.3.2/lib64/R/lib/libgeos_c.so.1 101842: trying file=/usr/local/lib64/libgeos_c.so.1 101842: trying file=/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.181-3.b13.el7_5.x86_64/jre/lib/amd64/server/libgeos_c.so.1 101842: trying file=/usr/local/packages/geos/3.11.0/lib64/libgeos_c.so.1 101842: 101842: find library=libcrypto.so.10 [0]; searching 101842: search path=/usr/local/packages/gcc/9.4.0/lib/../lib64/tls/x86_64:/usr/local/packages/gcc/9.4.0/lib/../lib64/tls:/usr/local/packages/gcc/9.4.0/lib/../lib64/x86_64:/usr/local/packages/gcc/9.4.0/lib/../lib64 (RPATH from file /usr/local/packages/gdal/2.4.4/lib/libgdal.so.20) 101842: trying file=/usr/local/packages/gcc/9.4.0/lib/../lib64/tls/x86_64/libcrypto.so.10 101842: trying file=/usr/local/packages/gcc/9.4.0/lib/../lib64/tls/libcrypto.so.10 101842: trying file=/usr/local/packages/gcc/9.4.0/lib/../lib64/x86_64/libcrypto.so.10 101842: trying file=/usr/local/packages/gcc/9.4.0/lib/../lib64/libcrypto.so.10 101842: search path=/usr/local/packages/R/4.3.2/lib64/R/lib:/usr/local/lib64:/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.181-3.b13.el7_5.x86_64/jre/lib/amd64/server:/usr/local/packages/geos/3.11.0/lib64:/usr/local/packages/R/4.3.2/lib64:/usr/local/packages/curl/7.54.1/lib:/usr/local/packages/pcre/8.37/lib:/usr/local/packages/xz/5.2.3/lib:/usr/local/packages/bzip2/1.0.6/lib:/usr/local/packages/zlib/1.2.11/lib:/usr/local/packages/sqlite/3360000/lib:/usr/local/packages/udunits/2.2.28/lib:/usr/local/packages/openmpi/1.6.4/lib:/usr/local/packages/netcdf/4.2.1.1/lib:/usr/local/packages/proj/4.9.3/lib:/usr/local/packages/hdf5/1.8.10/lib:/usr/local/packages/gdal/2.4.4/lib:/usr/local/packages/gcc/13.2.0/lib64:/usr/local/packages/gcc/13.2.0/lib (LD_LIBRARY_PATH) 101842: trying file=/usr/local/packages/R/4.3.2/lib64/R/lib/libcrypto.so.10 101842: trying file=/usr/local/lib64/libcrypto.so.10 101842: trying file=/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.181-3.b13.el7_5.x86_64/jre/lib/amd64/server/libcrypto.so.10 101842: trying file=/usr/local/packages/geos/3.11.0/lib64/libcrypto.so.10 101842: trying file=/usr/local/packages/R/4.3.2/lib64/libcrypto.so.10 101842: trying file=/usr/local/packages/curl/7.54.1/lib/libcrypto.so.10 101842: trying file=/usr/local/packages/pcre/8.37/lib/libcrypto.so.10 101842: trying file=/usr/local/packages/xz/5.2.3/lib/libcrypto.so.10 101842: trying file=/usr/local/packages/bzip2/1.0.6/lib/libcrypto.so.10 101842: trying file=/usr/local/packages/zlib/1.2.11/lib/libcrypto.so.10 101842: trying file=/usr/local/packages/sqlite/3360000/lib/libcrypto.so.10 101842: trying file=/usr/local/packages/udunits/2.2.28/lib/libcrypto.so.10 101842: trying file=/usr/local/packages/openmpi/1.6.4/lib/libcrypto.so.10 101842: trying file=/usr/local/packages/netcdf/4.2.1.1/lib/libcrypto.so.10 101842: trying file=/usr/local/packages/proj/4.9.3/lib/libcrypto.so.10 101842: trying file=/usr/local/packages/hdf5/1.8.10/lib/libcrypto.so.10 101842: trying file=/usr/local/packages/gdal/2.4.4/lib/libcrypto.so.10 101842: trying file=/usr/local/packages/gcc/13.2.0/lib64/libcrypto.so.10 101842: trying file=/usr/local/packages/gcc/13.2.0/lib/libcrypto.so.10 101842: search cache=/etc/ld.so.cache 101842: trying file=/lib64/libcrypto.so.10 101842: 101842: find library=libsqlite3.so.0 [0]; searching 101842: search path=/usr/local/packages/gcc/9.4.0/lib/../lib64 (RPATH from file /usr/local/packages/gdal/2.4.4/lib/libgdal.so.20) 101842: trying file=/usr/local/packages/gcc/9.4.0/lib/../lib64/libsqlite3.so.0 101842: search path=/usr/local/packages/R/4.3.2/lib64/R/lib:/usr/local/lib64:/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.181-3.b13.el7_5.x86_64/jre/lib/amd64/server:/usr/local/packages/geos/3.11.0/lib64:/usr/local/packages/R/4.3.2/lib64:/usr/local/packages/curl/7.54.1/lib:/usr/local/packages/pcre/8.37/lib:/usr/local/packages/xz/5.2.3/lib:/usr/local/packages/bzip2/1.0.6/lib:/usr/local/packages/zlib/1.2.11/lib:/usr/local/packages/sqlite/3360000/lib:/usr/local/packages/udunits/2.2.28/lib:/usr/local/packages/openmpi/1.6.4/lib:/usr/local/packages/netcdf/4.2.1.1/lib:/usr/local/packages/proj/4.9.3/lib:/usr/local/packages/hdf5/1.8.10/lib:/usr/local/packages/gdal/2.4.4/lib:/usr/local/packages/gcc/13.2.0/lib64:/usr/local/packages/gcc/13.2.0/lib (LD_LIBRARY_PATH) 101842: trying file=/usr/local/packages/R/4.3.2/lib64/R/lib/libsqlite3.so.0 101842: trying file=/usr/local/lib64/libsqlite3.so.0 101842: trying file=/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.181-3.b13.el7_5.x86_64/jre/lib/amd64/server/libsqlite3.so.0 101842: trying file=/usr/local/packages/geos/3.11.0/lib64/libsqlite3.so.0 101842: trying file=/usr/local/packages/R/4.3.2/lib64/libsqlite3.so.0 101842: trying file=/usr/local/packages/curl/7.54.1/lib/libsqlite3.so.0 101842: trying file=/usr/local/packages/pcre/8.37/lib/libsqlite3.so.0 101842: trying file=/usr/local/packages/xz/5.2.3/lib/libsqlite3.so.0 101842: trying file=/usr/local/packages/bzip2/1.0.6/lib/libsqlite3.so.0 101842: trying file=/usr/local/packages/zlib/1.2.11/lib/libsqlite3.so.0 101842: trying file=/usr/local/packages/sqlite/3360000/lib/libsqlite3.so.0 101842: 101842: find library=libodbc.so.2 [0]; searching 101842: search path=/usr/local/packages/gcc/9.4.0/lib/../lib64 (RPATH from file /usr/local/packages/gdal/2.4.4/lib/libgdal.so.20) 101842: trying file=/usr/local/packages/gcc/9.4.0/lib/../lib64/libodbc.so.2 101842: search path=/usr/local/packages/R/4.3.2/lib64/R/lib:/usr/local/lib64:/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.181-3.b13.el7_5.x86_64/jre/lib/amd64/server:/usr/local/packages/geos/3.11.0/lib64:/usr/local/packages/R/4.3.2/lib64:/usr/local/packages/curl/7.54.1/lib:/usr/local/packages/pcre/8.37/lib:/usr/local/packages/xz/5.2.3/lib:/usr/local/packages/bzip2/1.0.6/lib:/usr/local/packages/zlib/1.2.11/lib:/usr/local/packages/sqlite/3360000/lib:/usr/local/packages/udunits/2.2.28/lib:/usr/local/packages/openmpi/1.6.4/lib:/usr/local/packages/netcdf/4.2.1.1/lib:/usr/local/packages/proj/4.9.3/lib:/usr/local/packages/hdf5/1.8.10/lib:/usr/local/packages/gdal/2.4.4/lib:/usr/local/packages/gcc/13.2.0/lib64:/usr/local/packages/gcc/13.2.0/lib (LD_LIBRARY_PATH) 101842: trying file=/usr/local/packages/R/4.3.2/lib64/R/lib/libodbc.so.2 101842: trying file=/usr/local/lib64/libodbc.so.2 101842: trying file=/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.181-3.b13.el7_5.x86_64/jre/lib/amd64/server/libodbc.so.2 101842: trying file=/usr/local/packages/geos/3.11.0/lib64/libodbc.so.2 101842: trying file=/usr/local/packages/R/4.3.2/lib64/libodbc.so.2 101842: trying file=/usr/local/packages/curl/7.54.1/lib/libodbc.so.2 101842: trying file=/usr/local/packages/pcre/8.37/lib/libodbc.so.2 101842: trying file=/usr/local/packages/xz/5.2.3/lib/libodbc.so.2 101842: trying file=/usr/local/packages/bzip2/1.0.6/lib/libodbc.so.2 101842: trying file=/usr/local/packages/zlib/1.2.11/lib/libodbc.so.2 101842: trying file=/usr/local/packages/sqlite/3360000/lib/libodbc.so.2 101842: trying file=/usr/local/packages/udunits/2.2.28/lib/libodbc.so.2 101842: trying file=/usr/local/packages/openmpi/1.6.4/lib/libodbc.so.2 101842: trying file=/usr/local/packages/netcdf/4.2.1.1/lib/libodbc.so.2 101842: trying file=/usr/local/packages/proj/4.9.3/lib/libodbc.so.2 101842: trying file=/usr/local/packages/hdf5/1.8.10/lib/libodbc.so.2 101842: trying file=/usr/local/packages/gdal/2.4.4/lib/libodbc.so.2 101842: trying file=/usr/local/packages/gcc/13.2.0/lib64/libodbc.so.2 101842: trying file=/usr/local/packages/gcc/13.2.0/lib/libodbc.so.2 101842: search cache=/etc/ld.so.cache 101842: trying file=/lib64/libodbc.so.2 101842: 101842: find library=libodbcinst.so.2 [0]; searching 101842: search path=/usr/local/packages/gcc/9.4.0/lib/../lib64 (RPATH from file /usr/local/packages/gdal/2.4.4/lib/libgdal.so.20) 101842: trying file=/usr/local/packages/gcc/9.4.0/lib/../lib64/libodbcinst.so.2 101842: search path=/usr/local/packages/R/4.3.2/lib64/R/lib:/usr/local/lib64:/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.181-3.b13.el7_5.x86_64/jre/lib/amd64/server:/usr/local/packages/geos/3.11.0/lib64:/usr/local/packages/R/4.3.2/lib64:/usr/local/packages/curl/7.54.1/lib:/usr/local/packages/pcre/8.37/lib:/usr/local/packages/xz/5.2.3/lib:/usr/local/packages/bzip2/1.0.6/lib:/usr/local/packages/zlib/1.2.11/lib:/usr/local/packages/sqlite/3360000/lib:/usr/local/packages/udunits/2.2.28/lib:/usr/local/packages/openmpi/1.6.4/lib:/usr/local/packages/netcdf/4.2.1.1/lib:/usr/local/packages/proj/4.9.3/lib:/usr/local/packages/hdf5/1.8.10/lib:/usr/local/packages/gdal/2.4.4/lib:/usr/local/packages/gcc/13.2.0/lib64:/usr/local/packages/gcc/13.2.0/lib (LD_LIBRARY_PATH) 101842: trying file=/usr/local/packages/R/4.3.2/lib64/R/lib/libodbcinst.so.2 101842: trying file=/usr/local/lib64/libodbcinst.so.2 101842: trying file=/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.181-3.b13.el7_5.x86_64/jre/lib/amd64/server/libodbcinst.so.2 101842: trying file=/usr/local/packages/geos/3.11.0/lib64/libodbcinst.so.2 101842: trying file=/usr/local/packages/R/4.3.2/lib64/libodbcinst.so.2 101842: trying file=/usr/local/packages/curl/7.54.1/lib/libodbcinst.so.2 101842: trying file=/usr/local/packages/pcre/8.37/lib/libodbcinst.so.2 101842: trying file=/usr/local/packages/xz/5.2.3/lib/libodbcinst.so.2 101842: trying file=/usr/local/packages/bzip2/1.0.6/lib/libodbcinst.so.2 101842: trying file=/usr/local/packages/zlib/1.2.11/lib/libodbcinst.so.2 101842: trying file=/usr/local/packages/sqlite/3360000/lib/libodbcinst.so.2 101842: trying file=/usr/local/packages/udunits/2.2.28/lib/libodbcinst.so.2 101842: trying file=/usr/local/packages/openmpi/1.6.4/lib/libodbcinst.so.2 101842: trying file=/usr/local/packages/netcdf/4.2.1.1/lib/libodbcinst.so.2 101842: trying file=/usr/local/packages/proj/4.9.3/lib/libodbcinst.so.2 101842: trying file=/usr/local/packages/hdf5/1.8.10/lib/libodbcinst.so.2 101842: trying file=/usr/local/packages/gdal/2.4.4/lib/libodbcinst.so.2 101842: trying file=/usr/local/packages/gcc/13.2.0/lib64/libodbcinst.so.2 101842: trying file=/usr/local/packages/gcc/13.2.0/lib/libodbcinst.so.2 101842: search cache=/etc/ld.so.cache 101842: trying file=/lib64/libodbcinst.so.2 101842: 101842: find library=libjpeg.so.62 [0]; searching 101842: search path=/usr/local/packages/gcc/9.4.0/lib/../lib64 (RPATH from file /usr/local/packages/gdal/2.4.4/lib/libgdal.so.20) 101842: trying file=/usr/local/packages/gcc/9.4.0/lib/../lib64/libjpeg.so.62 101842: search path=/usr/local/packages/R/4.3.2/lib64/R/lib:/usr/local/lib64:/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.181-3.b13.el7_5.x86_64/jre/lib/amd64/server:/usr/local/packages/geos/3.11.0/lib64:/usr/local/packages/R/4.3.2/lib64:/usr/local/packages/curl/7.54.1/lib:/usr/local/packages/pcre/8.37/lib:/usr/local/packages/xz/5.2.3/lib:/usr/local/packages/bzip2/1.0.6/lib:/usr/local/packages/zlib/1.2.11/lib:/usr/local/packages/sqlite/3360000/lib:/usr/local/packages/udunits/2.2.28/lib:/usr/local/packages/openmpi/1.6.4/lib:/usr/local/packages/netcdf/4.2.1.1/lib:/usr/local/packages/proj/4.9.3/lib:/usr/local/packages/hdf5/1.8.10/lib:/usr/local/packages/gdal/2.4.4/lib:/usr/local/packages/gcc/13.2.0/lib64:/usr/local/packages/gcc/13.2.0/lib (LD_LIBRARY_PATH) 101842: trying file=/usr/local/packages/R/4.3.2/lib64/R/lib/libjpeg.so.62 101842: trying file=/usr/local/lib64/libjpeg.so.62 101842: trying file=/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.181-3.b13.el7_5.x86_64/jre/lib/amd64/server/libjpeg.so.62 101842: trying file=/usr/local/packages/geos/3.11.0/lib64/libjpeg.so.62 101842: trying file=/usr/local/packages/R/4.3.2/lib64/libjpeg.so.62 101842: trying file=/usr/local/packages/curl/7.54.1/lib/libjpeg.so.62 101842: trying file=/usr/local/packages/pcre/8.37/lib/libjpeg.so.62 101842: trying file=/usr/local/packages/xz/5.2.3/lib/libjpeg.so.62 101842: trying file=/usr/local/packages/bzip2/1.0.6/lib/libjpeg.so.62 101842: trying file=/usr/local/packages/zlib/1.2.11/lib/libjpeg.so.62 101842: trying file=/usr/local/packages/sqlite/3360000/lib/libjpeg.so.62 101842: trying file=/usr/local/packages/udunits/2.2.28/lib/libjpeg.so.62 101842: trying file=/usr/local/packages/openmpi/1.6.4/lib/libjpeg.so.62 101842: trying file=/usr/local/packages/netcdf/4.2.1.1/lib/libjpeg.so.62 101842: trying file=/usr/local/packages/proj/4.9.3/lib/libjpeg.so.62 101842: trying file=/usr/local/packages/hdf5/1.8.10/lib/libjpeg.so.62 101842: trying file=/usr/local/packages/gdal/2.4.4/lib/libjpeg.so.62 101842: trying file=/usr/local/packages/gcc/13.2.0/lib64/libjpeg.so.62 101842: trying file=/usr/local/packages/gcc/13.2.0/lib/libjpeg.so.62 101842: search cache=/etc/ld.so.cache 101842: trying file=/lib64/libjpeg.so.62 101842: 101842: find library=libpng15.so.15 [0]; searching 101842: search path=/usr/local/packages/gcc/9.4.0/lib/../lib64 (RPATH from file /usr/local/packages/gdal/2.4.4/lib/libgdal.so.20) 101842: trying file=/usr/local/packages/gcc/9.4.0/lib/../lib64/libpng15.so.15 101842: search path=/usr/local/packages/R/4.3.2/lib64/R/lib:/usr/local/lib64:/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.181-3.b13.el7_5.x86_64/jre/lib/amd64/server:/usr/local/packages/geos/3.11.0/lib64:/usr/local/packages/R/4.3.2/lib64:/usr/local/packages/curl/7.54.1/lib:/usr/local/packages/pcre/8.37/lib:/usr/local/packages/xz/5.2.3/lib:/usr/local/packages/bzip2/1.0.6/lib:/usr/local/packages/zlib/1.2.11/lib:/usr/local/packages/sqlite/3360000/lib:/usr/local/packages/udunits/2.2.28/lib:/usr/local/packages/openmpi/1.6.4/lib:/usr/local/packages/netcdf/4.2.1.1/lib:/usr/local/packages/proj/4.9.3/lib:/usr/local/packages/hdf5/1.8.10/lib:/usr/local/packages/gdal/2.4.4/lib:/usr/local/packages/gcc/13.2.0/lib64:/usr/local/packages/gcc/13.2.0/lib (LD_LIBRARY_PATH) 101842: trying file=/usr/local/packages/R/4.3.2/lib64/R/lib/libpng15.so.15 101842: trying file=/usr/local/lib64/libpng15.so.15 101842: trying file=/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.181-3.b13.el7_5.x86_64/jre/lib/amd64/server/libpng15.so.15 101842: trying file=/usr/local/packages/geos/3.11.0/lib64/libpng15.so.15 101842: trying file=/usr/local/packages/R/4.3.2/lib64/libpng15.so.15 101842: trying file=/usr/local/packages/curl/7.54.1/lib/libpng15.so.15 101842: trying file=/usr/local/packages/pcre/8.37/lib/libpng15.so.15 101842: trying file=/usr/local/packages/xz/5.2.3/lib/libpng15.so.15 101842: trying file=/usr/local/packages/bzip2/1.0.6/lib/libpng15.so.15 101842: trying file=/usr/local/packages/zlib/1.2.11/lib/libpng15.so.15 101842: trying file=/usr/local/packages/sqlite/3360000/lib/libpng15.so.15 101842: trying file=/usr/local/packages/udunits/2.2.28/lib/libpng15.so.15 101842: trying file=/usr/local/packages/openmpi/1.6.4/lib/libpng15.so.15 101842: trying file=/usr/local/packages/netcdf/4.2.1.1/lib/libpng15.so.15 101842: trying file=/usr/local/packages/proj/4.9.3/lib/libpng15.so.15 101842: trying file=/usr/local/packages/hdf5/1.8.10/lib/libpng15.so.15 101842: trying file=/usr/local/packages/gdal/2.4.4/lib/libpng15.so.15 101842: trying file=/usr/local/packages/gcc/13.2.0/lib64/libpng15.so.15 101842: trying file=/usr/local/packages/gcc/13.2.0/lib/libpng15.so.15 101842: search cache=/etc/ld.so.cache 101842: trying file=/lib64/libpng15.so.15 101842: 101842: find library=libpcre.so.1 [0]; searching 101842: search path=/usr/local/packages/gcc/9.4.0/lib/../lib64 (RPATH from file /usr/local/packages/gdal/2.4.4/lib/libgdal.so.20) 101842: trying file=/usr/local/packages/gcc/9.4.0/lib/../lib64/libpcre.so.1 101842: search path=/usr/local/packages/R/4.3.2/lib64/R/lib:/usr/local/lib64:/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.181-3.b13.el7_5.x86_64/jre/lib/amd64/server:/usr/local/packages/geos/3.11.0/lib64:/usr/local/packages/R/4.3.2/lib64:/usr/local/packages/curl/7.54.1/lib:/usr/local/packages/pcre/8.37/lib:/usr/local/packages/xz/5.2.3/lib:/usr/local/packages/bzip2/1.0.6/lib:/usr/local/packages/zlib/1.2.11/lib:/usr/local/packages/sqlite/3360000/lib:/usr/local/packages/udunits/2.2.28/lib:/usr/local/packages/openmpi/1.6.4/lib:/usr/local/packages/netcdf/4.2.1.1/lib:/usr/local/packages/proj/4.9.3/lib:/usr/local/packages/hdf5/1.8.10/lib:/usr/local/packages/gdal/2.4.4/lib:/usr/local/packages/gcc/13.2.0/lib64:/usr/local/packages/gcc/13.2.0/lib (LD_LIBRARY_PATH) 101842: trying file=/usr/local/packages/R/4.3.2/lib64/R/lib/libpcre.so.1 101842: trying file=/usr/local/lib64/libpcre.so.1 101842: trying file=/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.181-3.b13.el7_5.x86_64/jre/lib/amd64/server/libpcre.so.1 101842: trying file=/usr/local/packages/geos/3.11.0/lib64/libpcre.so.1 101842: trying file=/usr/local/packages/R/4.3.2/lib64/libpcre.so.1 101842: trying file=/usr/local/packages/curl/7.54.1/lib/libpcre.so.1 101842: trying file=/usr/local/packages/pcre/8.37/lib/libpcre.so.1 101842: 101842: find library=libxml2.so.2 [0]; searching 101842: search path=/usr/local/packages/gcc/9.4.0/lib/../lib64 (RPATH from file /usr/local/packages/gdal/2.4.4/lib/libgdal.so.20) 101842: trying file=/usr/local/packages/gcc/9.4.0/lib/../lib64/libxml2.so.2 101842: search path=/usr/local/packages/R/4.3.2/lib64/R/lib:/usr/local/lib64:/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.181-3.b13.el7_5.x86_64/jre/lib/amd64/server:/usr/local/packages/geos/3.11.0/lib64:/usr/local/packages/R/4.3.2/lib64:/usr/local/packages/curl/7.54.1/lib:/usr/local/packages/pcre/8.37/lib:/usr/local/packages/xz/5.2.3/lib:/usr/local/packages/bzip2/1.0.6/lib:/usr/local/packages/zlib/1.2.11/lib:/usr/local/packages/sqlite/3360000/lib:/usr/local/packages/udunits/2.2.28/lib:/usr/local/packages/openmpi/1.6.4/lib:/usr/local/packages/netcdf/4.2.1.1/lib:/usr/local/packages/proj/4.9.3/lib:/usr/local/packages/hdf5/1.8.10/lib:/usr/local/packages/gdal/2.4.4/lib:/usr/local/packages/gcc/13.2.0/lib64:/usr/local/packages/gcc/13.2.0/lib (LD_LIBRARY_PATH) 101842: trying file=/usr/local/packages/R/4.3.2/lib64/R/lib/libxml2.so.2 101842: trying file=/usr/local/lib64/libxml2.so.2 101842: trying file=/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.181-3.b13.el7_5.x86_64/jre/lib/amd64/server/libxml2.so.2 101842: trying file=/usr/local/packages/geos/3.11.0/lib64/libxml2.so.2 101842: trying file=/usr/local/packages/R/4.3.2/lib64/libxml2.so.2 101842: trying file=/usr/local/packages/curl/7.54.1/lib/libxml2.so.2 101842: trying file=/usr/local/packages/pcre/8.37/lib/libxml2.so.2 101842: trying file=/usr/local/packages/xz/5.2.3/lib/libxml2.so.2 101842: trying file=/usr/local/packages/bzip2/1.0.6/lib/libxml2.so.2 101842: trying file=/usr/local/packages/zlib/1.2.11/lib/libxml2.so.2 101842: trying file=/usr/local/packages/sqlite/3360000/lib/libxml2.so.2 101842: trying file=/usr/local/packages/udunits/2.2.28/lib/libxml2.so.2 101842: trying file=/usr/local/packages/openmpi/1.6.4/lib/libxml2.so.2 101842: trying file=/usr/local/packages/netcdf/4.2.1.1/lib/libxml2.so.2 101842: trying file=/usr/local/packages/proj/4.9.3/lib/libxml2.so.2 101842: trying file=/usr/local/packages/hdf5/1.8.10/lib/libxml2.so.2 101842: trying file=/usr/local/packages/gdal/2.4.4/lib/libxml2.so.2 101842: trying file=/usr/local/packages/gcc/13.2.0/lib64/libxml2.so.2 101842: trying file=/usr/local/packages/gcc/13.2.0/lib/libxml2.so.2 101842: search cache=/etc/ld.so.cache 101842: trying file=/lib64/libxml2.so.2 101842: 101842: find library=libgeos.so.3.11.0 [0]; searching 101842: search path=/usr/local/packages/R/4.3.2/lib64/R/lib:/usr/local/lib64:/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.181-3.b13.el7_5.x86_64/jre/lib/amd64/server:/usr/local/packages/geos/3.11.0/lib64:/usr/local/packages/R/4.3.2/lib64:/usr/local/packages/curl/7.54.1/lib:/usr/local/packages/pcre/8.37/lib:/usr/local/packages/xz/5.2.3/lib:/usr/local/packages/bzip2/1.0.6/lib:/usr/local/packages/zlib/1.2.11/lib:/usr/local/packages/sqlite/3360000/lib:/usr/local/packages/udunits/2.2.28/lib:/usr/local/packages/openmpi/1.6.4/lib:/usr/local/packages/netcdf/4.2.1.1/lib:/usr/local/packages/proj/4.9.3/lib:/usr/local/packages/hdf5/1.8.10/lib:/usr/local/packages/gdal/2.4.4/lib:/usr/local/packages/gcc/13.2.0/lib64:/usr/local/packages/gcc/13.2.0/lib (LD_LIBRARY_PATH) 101842: trying file=/usr/local/packages/R/4.3.2/lib64/R/lib/libgeos.so.3.11.0 101842: trying file=/usr/local/lib64/libgeos.so.3.11.0 101842: trying file=/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.181-3.b13.el7_5.x86_64/jre/lib/amd64/server/libgeos.so.3.11.0 101842: trying file=/usr/local/packages/geos/3.11.0/lib64/libgeos.so.3.11.0 101842: 101842: find library=libltdl.so.7 [0]; searching 101842: search path=/usr/local/packages/gcc/9.4.0/lib/../lib64 (RPATH from file /usr/local/packages/gdal/2.4.4/lib/libgdal.so.20) 101842: trying file=/usr/local/packages/gcc/9.4.0/lib/../lib64/libltdl.so.7 101842: search path=/usr/local/packages/R/4.3.2/lib64/R/lib:/usr/local/lib64:/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.181-3.b13.el7_5.x86_64/jre/lib/amd64/server:/usr/local/packages/geos/3.11.0/lib64:/usr/local/packages/R/4.3.2/lib64:/usr/local/packages/curl/7.54.1/lib:/usr/local/packages/pcre/8.37/lib:/usr/local/packages/xz/5.2.3/lib:/usr/local/packages/bzip2/1.0.6/lib:/usr/local/packages/zlib/1.2.11/lib:/usr/local/packages/sqlite/3360000/lib:/usr/local/packages/udunits/2.2.28/lib:/usr/local/packages/openmpi/1.6.4/lib:/usr/local/packages/netcdf/4.2.1.1/lib:/usr/local/packages/proj/4.9.3/lib:/usr/local/packages/hdf5/1.8.10/lib:/usr/local/packages/gdal/2.4.4/lib:/usr/local/packages/gcc/13.2.0/lib64:/usr/local/packages/gcc/13.2.0/lib (LD_LIBRARY_PATH) 101842: trying file=/usr/local/packages/R/4.3.2/lib64/R/lib/libltdl.so.7 101842: trying file=/usr/local/lib64/libltdl.so.7 101842: trying file=/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.181-3.b13.el7_5.x86_64/jre/lib/amd64/server/libltdl.so.7 101842: trying file=/usr/local/packages/geos/3.11.0/lib64/libltdl.so.7 101842: trying file=/usr/local/packages/R/4.3.2/lib64/libltdl.so.7 101842: trying file=/usr/local/packages/curl/7.54.1/lib/libltdl.so.7 101842: trying file=/usr/local/packages/pcre/8.37/lib/libltdl.so.7 101842: trying file=/usr/local/packages/xz/5.2.3/lib/libltdl.so.7 101842: trying file=/usr/local/packages/bzip2/1.0.6/lib/libltdl.so.7 101842: trying file=/usr/local/packages/zlib/1.2.11/lib/libltdl.so.7 101842: trying file=/usr/local/packages/sqlite/3360000/lib/libltdl.so.7 101842: trying file=/usr/local/packages/udunits/2.2.28/lib/libltdl.so.7 101842: trying file=/usr/local/packages/openmpi/1.6.4/lib/libltdl.so.7 101842: trying file=/usr/local/packages/netcdf/4.2.1.1/lib/libltdl.so.7 101842: trying file=/usr/local/packages/proj/4.9.3/lib/libltdl.so.7 101842: trying file=/usr/local/packages/hdf5/1.8.10/lib/libltdl.so.7 101842: trying file=/usr/local/packages/gdal/2.4.4/lib/libltdl.so.7 101842: trying file=/usr/local/packages/gcc/13.2.0/lib64/libltdl.so.7 101842: trying file=/usr/local/packages/gcc/13.2.0/lib/libltdl.so.7 101842: search cache=/etc/ld.so.cache 101842: trying file=/lib64/libltdl.so.7 101842: 101842: /data/users/hemt/R-library/00LOCK-sf/00new/sf/libs/sf.so: error: symbol lookup error: undefined symbol: _Z16CPL_set_data_dirN4Rcpp6VectorILi16ENS_15PreserveStorageEEEb (fatal) ```
stephenashton-dhsc commented 5 months ago

Ah - managed to fix it by changing which of the PROJ modules was being loaded via lmod (changed from 4.9.3 to 6.3.2).

senfbrot commented 5 months ago

I'm running into exactly the same issue with version 1.0-16. 1.0-15 works. What have you done to fix it?

library(devtools)
devtools::install_version("sf", version="1.0-16")

...
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for ‘sf’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/home/username/R/x86_64-pc-linux-gnu-library/4.3/00LOCK-sf/00new/sf/libs/sf.so':
  /home/username/R/x86_64-pc-linux-gnu-library/4.3/00LOCK-sf/00new/sf/libs/sf.so: undefined symbol: _Z16CPL_set_data_dirN4Rcpp6VectorILi16ENS_15PreserveStorageEEEb
Error: loading failed
Execution halted
library(devtools)
devtools::install_version("sf", version="1.0-15")

...
** 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 (sf)

geos: 3.9.1 gdal: 2.4.4 proj: 4.9.3

stephenashton-dhsc commented 5 months ago

I've got it working with GEOS 3.11.0, GDAL 2.4.4 and PROJ 6.3.2 (although I'm now running into issues with the interaction between raster and PROJ 6.3.2)

stephenashton-dhsc commented 5 months ago

Although if the error is only appearing in 1.0-16 (but not in 1.0-15), maybe it is an issue with the version?

stephenashton-dhsc commented 5 months ago

Just double checked this myself. For a system with GEOS 3.11.0, GDAL 2.4.4 and PROJ 4.9.3, 1.0-15 works but 1.0-16 does not.

edzer commented 5 months ago

Thanks, this should fix the proj 4.9.3 compile error.

stephenashton-dhsc commented 5 months ago

Fantastic - thanks :)