Installation error

[zhengchencai]

Hello,

I was trying to install sf on a Linux cluster. I did module load proj, geos, udunits and gdal, and their versions are quite new. The installation failed at the very end while testing if installed package can be loaded from temporary location. Could you please help to fix this issue? Thank you very much.

** testing if installed package can be loaded from temporary location
sh: line 1: 536421 Aborted                 (core dumped) R_TESTS= '/cvmfs/[soft.computecanada.ca/easybuild/software/2020/avx2/Core/r/4.1.2/lib64/R/bin/R](http://soft.computecanada.ca/easybuild/software/2020/avx2/Core/r/4.1.2/lib64/R/bin/R)' --no-save --no-restore --no-echo 2>&1 < '/tmp/RtmpR4z5mU/file7c6032dc3fd74'
free(): invalid pointer
ERROR: loading failed
* removing ‘/home/djangoc/R/x86_64-pc-linux-gnu-library/4.1/sf’
Warning message:
In i.p(...) :
  installation of package ‘/tmp/Rtmpcu0hYr/file790786b68c1e5/sf_1.0-10.tar.gz’ had non-zero exit status

[zhengchencai]

Sorry I just noticed you may want the whole installation message

Selection: 1
trying URL 'https://cloud.r-project.org/src/contrib/sf_1.0-9.tar.gz'
Content type 'application/x-gzip' length 3480774 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++11
checking for gdal-config... /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Compiler/intel2020/gdal/3.0.4/bin/gdal-config
checking gdal-config usability... yes
configure: GDAL: 3.0.4
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: /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Compiler/intel2020/gdal/3.0.4/share/gdal/pcs.csv readable... no
checking GDAL: checking whether PROJ is available for linking:... yes
checking GDAL: checking whether PROJ is available fur running:... yes
configure: GDAL: 3.0.4
configure: pkg-config proj exists, will use it
configure: using proj.h.
configure: PROJ: 9.0.1
checking PROJ: checking whether PROJ and sqlite3 are available for linking:... yes
checking for geos-config... /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/geos/3.10.2/bin/geos-config
checking geos-config usability... yes
configure: GEOS: 3.10.2
checking GEOS version >= 3.4.0... yes
checking for geos_c.h... yes
checking geos: linking with -L/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/geos/3.10.2/lib64 -lgeos_c... yes
configure: Package CPP flags:   -DHAVE_PROJ_H -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Compiler/intel2020/gdal/3.0.4/include -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/geos/3.10.2/include
configure: Package LIBS: -L/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/proj/9.0.1/lib64 -lproj   -L/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Compiler/intel2020/gdal/3.0.4/lib -lgdal -L/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/geos/3.10.2/lib64 -lgeos_c
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++ -std=gnu++11 -I"/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/r/4.1.2/lib64/R/include" -DNDEBUG -DHAVE_PROJ_H -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Compiler/intel2020/gdal/3.0.4/include -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/geos/3.10.2/include -I'/home/djangoc/R/x86_64-pc-linux-gnu-library/4.1/Rcpp/include' -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/java/13.0.2/include -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/flexiblas/3.0.4/include -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/flexiblas/3.0.4/include/flexiblas   -fpic  -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/r/4.1.2/lib64/R/include" -DNDEBUG -DHAVE_PROJ_H -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Compiler/intel2020/gdal/3.0.4/include -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/geos/3.10.2/include -I'/home/djangoc/R/x86_64-pc-linux-gnu-library/4.1/Rcpp/include' -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/java/13.0.2/include -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/flexiblas/3.0.4/include -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/flexiblas/3.0.4/include/flexiblas   -fpic  -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno  -c bbox.cpp -o bbox.o
g++ -std=gnu++11 -I"/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/r/4.1.2/lib64/R/include" -DNDEBUG -DHAVE_PROJ_H -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Compiler/intel2020/gdal/3.0.4/include -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/geos/3.10.2/include -I'/home/djangoc/R/x86_64-pc-linux-gnu-library/4.1/Rcpp/include' -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/java/13.0.2/include -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/flexiblas/3.0.4/include -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/flexiblas/3.0.4/include/flexiblas   -fpic  -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno  -c gdal.cpp -o gdal.o
g++ -std=gnu++11 -I"/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/r/4.1.2/lib64/R/include" -DNDEBUG -DHAVE_PROJ_H -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Compiler/intel2020/gdal/3.0.4/include -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/geos/3.10.2/include -I'/home/djangoc/R/x86_64-pc-linux-gnu-library/4.1/Rcpp/include' -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/java/13.0.2/include -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/flexiblas/3.0.4/include -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/flexiblas/3.0.4/include/flexiblas   -fpic  -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno  -c gdal_geom.cpp -o gdal_geom.o
g++ -std=gnu++11 -I"/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/r/4.1.2/lib64/R/include" -DNDEBUG -DHAVE_PROJ_H -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Compiler/intel2020/gdal/3.0.4/include -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/geos/3.10.2/include -I'/home/djangoc/R/x86_64-pc-linux-gnu-library/4.1/Rcpp/include' -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/java/13.0.2/include -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/flexiblas/3.0.4/include -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/flexiblas/3.0.4/include/flexiblas   -fpic  -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno  -c gdal_read.cpp -o gdal_read.o
g++ -std=gnu++11 -I"/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/r/4.1.2/lib64/R/include" -DNDEBUG -DHAVE_PROJ_H -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Compiler/intel2020/gdal/3.0.4/include -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/geos/3.10.2/include -I'/home/djangoc/R/x86_64-pc-linux-gnu-library/4.1/Rcpp/include' -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/java/13.0.2/include -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/flexiblas/3.0.4/include -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/flexiblas/3.0.4/include/flexiblas   -fpic  -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno  -c gdal_utils.cpp -o gdal_utils.o
g++ -std=gnu++11 -I"/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/r/4.1.2/lib64/R/include" -DNDEBUG -DHAVE_PROJ_H -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Compiler/intel2020/gdal/3.0.4/include -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/geos/3.10.2/include -I'/home/djangoc/R/x86_64-pc-linux-gnu-library/4.1/Rcpp/include' -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/java/13.0.2/include -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/flexiblas/3.0.4/include -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/flexiblas/3.0.4/include/flexiblas   -fpic  -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno  -c gdal_write.cpp -o gdal_write.o
g++ -std=gnu++11 -I"/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/r/4.1.2/lib64/R/include" -DNDEBUG -DHAVE_PROJ_H -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Compiler/intel2020/gdal/3.0.4/include -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/geos/3.10.2/include -I'/home/djangoc/R/x86_64-pc-linux-gnu-library/4.1/Rcpp/include' -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/java/13.0.2/include -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/flexiblas/3.0.4/include -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/flexiblas/3.0.4/include/flexiblas   -fpic  -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno  -c geos.cpp -o geos.o
g++ -std=gnu++11 -I"/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/r/4.1.2/lib64/R/include" -DNDEBUG -DHAVE_PROJ_H -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Compiler/intel2020/gdal/3.0.4/include -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/geos/3.10.2/include -I'/home/djangoc/R/x86_64-pc-linux-gnu-library/4.1/Rcpp/include' -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/java/13.0.2/include -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/flexiblas/3.0.4/include -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/flexiblas/3.0.4/include/flexiblas   -fpic  -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno  -c hex.cpp -o hex.o
g++ -std=gnu++11 -I"/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/r/4.1.2/lib64/R/include" -DNDEBUG -DHAVE_PROJ_H -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Compiler/intel2020/gdal/3.0.4/include -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/geos/3.10.2/include -I'/home/djangoc/R/x86_64-pc-linux-gnu-library/4.1/Rcpp/include' -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/java/13.0.2/include -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/flexiblas/3.0.4/include -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/flexiblas/3.0.4/include/flexiblas   -fpic  -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno  -c mdim.cpp -o mdim.o
g++ -std=gnu++11 -I"/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/r/4.1.2/lib64/R/include" -DNDEBUG -DHAVE_PROJ_H -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Compiler/intel2020/gdal/3.0.4/include -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/geos/3.10.2/include -I'/home/djangoc/R/x86_64-pc-linux-gnu-library/4.1/Rcpp/include' -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/java/13.0.2/include -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/flexiblas/3.0.4/include -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/flexiblas/3.0.4/include/flexiblas   -fpic  -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno  -c ops.cpp -o ops.o
g++ -std=gnu++11 -I"/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/r/4.1.2/lib64/R/include" -DNDEBUG -DHAVE_PROJ_H -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Compiler/intel2020/gdal/3.0.4/include -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/geos/3.10.2/include -I'/home/djangoc/R/x86_64-pc-linux-gnu-library/4.1/Rcpp/include' -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/java/13.0.2/include -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/flexiblas/3.0.4/include -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/flexiblas/3.0.4/include/flexiblas   -fpic  -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno  -c polygonize.cpp -o polygonize.o
g++ -std=gnu++11 -I"/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/r/4.1.2/lib64/R/include" -DNDEBUG -DHAVE_PROJ_H -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Compiler/intel2020/gdal/3.0.4/include -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/geos/3.10.2/include -I'/home/djangoc/R/x86_64-pc-linux-gnu-library/4.1/Rcpp/include' -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/java/13.0.2/include -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/flexiblas/3.0.4/include -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/flexiblas/3.0.4/include/flexiblas   -fpic  -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno  -c proj.cpp -o proj.o
g++ -std=gnu++11 -I"/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/r/4.1.2/lib64/R/include" -DNDEBUG -DHAVE_PROJ_H -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Compiler/intel2020/gdal/3.0.4/include -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/geos/3.10.2/include -I'/home/djangoc/R/x86_64-pc-linux-gnu-library/4.1/Rcpp/include' -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/java/13.0.2/include -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/flexiblas/3.0.4/include -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/flexiblas/3.0.4/include/flexiblas   -fpic  -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno  -c proj_info.cpp -o proj_info.o
g++ -std=gnu++11 -I"/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/r/4.1.2/lib64/R/include" -DNDEBUG -DHAVE_PROJ_H -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Compiler/intel2020/gdal/3.0.4/include -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/geos/3.10.2/include -I'/home/djangoc/R/x86_64-pc-linux-gnu-library/4.1/Rcpp/include' -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/java/13.0.2/include -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/flexiblas/3.0.4/include -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/flexiblas/3.0.4/include/flexiblas   -fpic  -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno  -c raster2sf.cpp -o raster2sf.o
g++ -std=gnu++11 -I"/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/r/4.1.2/lib64/R/include" -DNDEBUG -DHAVE_PROJ_H -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Compiler/intel2020/gdal/3.0.4/include -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/geos/3.10.2/include -I'/home/djangoc/R/x86_64-pc-linux-gnu-library/4.1/Rcpp/include' -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/java/13.0.2/include -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/flexiblas/3.0.4/include -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/flexiblas/3.0.4/include/flexiblas   -fpic  -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno  -c sfc-sfg.cpp -o sfc-sfg.o
g++ -std=gnu++11 -I"/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/r/4.1.2/lib64/R/include" -DNDEBUG -DHAVE_PROJ_H -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Compiler/intel2020/gdal/3.0.4/include -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/geos/3.10.2/include -I'/home/djangoc/R/x86_64-pc-linux-gnu-library/4.1/Rcpp/include' -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/java/13.0.2/include -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/flexiblas/3.0.4/include -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/flexiblas/3.0.4/include/flexiblas   -fpic  -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno  -c signed_area.cpp -o signed_area.o
g++ -std=gnu++11 -I"/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/r/4.1.2/lib64/R/include" -DNDEBUG -DHAVE_PROJ_H -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Compiler/intel2020/gdal/3.0.4/include -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/geos/3.10.2/include -I'/home/djangoc/R/x86_64-pc-linux-gnu-library/4.1/Rcpp/include' -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/java/13.0.2/include -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/flexiblas/3.0.4/include -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/flexiblas/3.0.4/include/flexiblas   -fpic  -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno  -c stars.cpp -o stars.o
g++ -std=gnu++11 -I"/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/r/4.1.2/lib64/R/include" -DNDEBUG -DHAVE_PROJ_H -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Compiler/intel2020/gdal/3.0.4/include -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/geos/3.10.2/include -I'/home/djangoc/R/x86_64-pc-linux-gnu-library/4.1/Rcpp/include' -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/java/13.0.2/include -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/flexiblas/3.0.4/include -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/flexiblas/3.0.4/include/flexiblas   -fpic  -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno  -c wkb.cpp -o wkb.o
g++ -std=gnu++11 -I"/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/r/4.1.2/lib64/R/include" -DNDEBUG -DHAVE_PROJ_H -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Compiler/intel2020/gdal/3.0.4/include -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/geos/3.10.2/include -I'/home/djangoc/R/x86_64-pc-linux-gnu-library/4.1/Rcpp/include' -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/java/13.0.2/include -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/flexiblas/3.0.4/include -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/flexiblas/3.0.4/include/flexiblas   -fpic  -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno  -c zm_range.cpp -o zm_range.o
g++ -std=gnu++11 -shared -L/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/r/4.1.2/lib64/R/lib -L/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/java/13.0.2/lib -L/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/flexiblas/3.0.4/lib64 -L/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/flexiblas/3.0.4/lib -L/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/gcccore/9.3.0/lib64 -L/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/gcccore/9.3.0/lib -o sf.so RcppExports.o bbox.o gdal.o gdal_geom.o gdal_read.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/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/proj/9.0.1/lib64 -lproj -L/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Compiler/intel2020/gdal/3.0.4/lib -lgdal -L/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/geos/3.10.2/lib64 -lgeos_c -L/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/r/4.1.2/lib64/R/lib -lR
installing to /home/djangoc/R/x86_64-pc-linux-gnu-library/4.1/00LOCK-sf/00new/sf/libs
** R
** demo
** inst
** 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
sh: line 1: 688419 Aborted                 (core dumped) R_TESTS= '/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/r/4.1.2/lib64/R/bin/R' --no-save --no-restore --no-echo 2>&1 < '/tmp/RtmpejJQXV/filea189d4c42a564'
free(): invalid pointer
ERROR: loading failed
* removing ‘/home/djangoc/R/x86_64-pc-linux-gnu-library/4.1/sf’

The downloaded source packages are in
        ‘/tmp/Rtmpcu0hYr/downloaded_packages’
Warning message:
In install.packages("sf") :
  installation of package ‘sf’ had non-zero exit status

[rsbivand]

Almost certainly https://r-spatial.github.io/sf/#multiple-gdal-geos-andor-proj-versions-on-your-system.

[zhengchencai]

Thanks a lot. After reading it through I still don't know how to solve it. It seems #844 (comment) is a solution but I don't know the path of libgeos_c.so on the cluster I use. Could you please explain a bit more?

[rsbivand]

You do not need to know. Ask the cluster admin to detect multiple installs of GEOS, PROJ or GDAL, and eliminate all but the most recent. Better, remove all installs completely (of everything installed when they were installed), then install GDAL, which hopefully will install PROJ and GEOS as it needs them.

[zhengchencai]

Thank you very much. Will do it and let you know.

[zhengchencai]

Hi @rsbivand, our tech support suggested to module load gcc and it worked. Thank you very much.