1

I am attempting to install leaflet in R version 4.0.5 on RHEL 8 via a Putty shell. In R I am using

install.packages("leaflet", repos="cloud.r-project.org")

The installation fails with

Error in parse(outFile) :
  /tmp/RtmpWWabtG/R.INSTALL13f2149d5f91/terra/R/zonal.R:72:42: unexpected input
71:                         r <- !relate(x, z, "disjoint")
72:                         i <- apply(r, 1, \
                                             ^
ERROR: unable to collate and parse R files for package ‘terra’
* removing ‘/opt/R/4.0.5/lib/R/library/terra’
ERROR: dependency ‘terra’ is not available for package ‘raster’
* removing ‘/opt/R/4.0.5/lib/R/library/raster’
ERROR: dependency ‘raster’ is not available for package ‘leaflet’
* removing ‘/opt/R/4.0.5/lib/R/library/leaflet’

The downloaded source packages are in
        ‘/tmp/RtmpwfKfHa/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning messages:
1: In install.packages("leaflet", repos = "https://cloud.r-project.org") :
  installation of package ‘terra’ had non-zero exit status
2: In install.packages("leaflet", repos = "https://cloud.r-project.org") :
  installation of package ‘raster’ had non-zero exit status
3: In install.packages("leaflet", repos = "https://cloud.r-project.org") :
  installation of package ‘leaflet’ had non-zero exit status

I've also tried using repos = https://cran.us.r-project.org with the same result.

I have installed gdal 3.0.4 proj 6.3.2 and geos 3.7.2. I originally installed the latest version of R and then noticed that leaflet wasn't available for that version so installed 4.0.5 based on How to update to specific R version on Linux (Red Hat/CentOS), keeping the previous version? R --version now shows 4.0.5 when logged in as myself or as sudo.

The full installation reply is below. I thought perhaps that installation of the second version of R was the problem so tested an install of the stringr package - this was successful (I can see stringr in my local library now).

I notice that the library section below now uses quotes around the include path (i.e. -I"/opt/R/4.0.5/lib/R/include") while the other -I sections do not.

Thanks in advance.

* installing *source* package ‘terra’ ...
** package ‘terra’ successfully unpacked and MD5 sums checked
** using staged installation
configure: CC: gcc
configure: CXX: g++ -std=gnu++11
checking for gdal-config... /usr/bin/gdal-configchecking 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 we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking gdal.h usability... yes
checking gdal.h presence... yes
checking for gdal.h... yes
checking GDAL: linking with --libs only... yes
checking GDAL: /usr/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: 6.3.2
checking PROJ: checking whether PROJ and sqlite3 are available for linking:... yes
checking for geos-config... /usr/bin/geos-config
checking geos-config usability... yes
configure: GEOS: 3.7.2
checking GEOS version >= 3.4.0... yes
checking geos_c.h usability... yes
checking geos_c.h presence... yes
checking for geos_c.h... yes
checking geos: linking with -L/usr/lib64 -lgeos_c... yes
configure: Package CPP flags:   -DHAVE_PROJ_H -I/usr/include/gdal -I/usr/include
configure: Package LIBS: -lproj    -L/usr/lib64 -lgdal -L/usr/lib64 -lgeos_c
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++ -std=gnu++11 -I"/opt/R/4.0.5/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/include/gdal -I/usr/include -I'/opt/R/4.0.5/lib/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/opt/R/4.0.5/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/include/gdal -I/usr/include -I'/opt/R/4.0.5/lib/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c RcppFunctions.cpp -o RcppFunctions.o
g++ -std=gnu++11 -I"/opt/R/4.0.5/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/include/gdal -I/usr/include -I'/opt/R/4.0.5/lib/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c RcppModule.cpp -o RcppModule.o
g++ -std=gnu++11 -I"/opt/R/4.0.5/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/include/gdal -I/usr/include -I'/opt/R/4.0.5/lib/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c arith.cpp -o arith.o
g++ -std=gnu++11 -I"/opt/R/4.0.5/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/include/gdal -I/usr/include -I'/opt/R/4.0.5/lib/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c crs.cpp -o crs.o
g++ -std=gnu++11 -I"/opt/R/4.0.5/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/include/gdal -I/usr/include -I'/opt/R/4.0.5/lib/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c distRaster.cpp -o distRaster.o
g++ -std=gnu++11 -I"/opt/R/4.0.5/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/include/gdal -I/usr/include -I'/opt/R/4.0.5/lib/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c distance.cpp -o distance.o
g++ -std=gnu++11 -I"/opt/R/4.0.5/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/include/gdal -I/usr/include -I'/opt/R/4.0.5/lib/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c extract.cpp -o extract.o
g++ -std=gnu++11 -I"/opt/R/4.0.5/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/include/gdal -I/usr/include -I'/opt/R/4.0.5/lib/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c file_utils.cpp -o file_utils.o
g++ -std=gnu++11 -I"/opt/R/4.0.5/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/include/gdal -I/usr/include -I'/opt/R/4.0.5/lib/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c focal.cpp -o focal.o
g++ -std=gnu++11 -I"/opt/R/4.0.5/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/include/gdal -I/usr/include -I'/opt/R/4.0.5/lib/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c gcp.cpp -o gcp.o
g++ -std=gnu++11 -I"/opt/R/4.0.5/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/include/gdal -I/usr/include -I'/opt/R/4.0.5/lib/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c gdal_algs.cpp -o gdal_algs.o
g++ -std=gnu++11 -I"/opt/R/4.0.5/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/include/gdal -I/usr/include -I'/opt/R/4.0.5/lib/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c gdal_multidimensional.cpp -o gdal_multidimensional.o
g++ -std=gnu++11 -I"/opt/R/4.0.5/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/include/gdal -I/usr/include -I'/opt/R/4.0.5/lib/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c gdalio.cpp -o gdalio.o
gcc -I"/opt/R/4.0.5/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/include/gdal -I/usr/include -I'/opt/R/4.0.5/lib/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c geodesic.c -o geodesic.o
g++ -std=gnu++11 -I"/opt/R/4.0.5/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/include/gdal -I/usr/include -I'/opt/R/4.0.5/lib/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c geos_methods.cpp -o geos_methods.o
g++ -std=gnu++11 -I"/opt/R/4.0.5/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/include/gdal -I/usr/include -I'/opt/R/4.0.5/lib/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c geosphere.cpp -o geosphere.o
g++ -std=gnu++11 -I"/opt/R/4.0.5/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/include/gdal -I/usr/include -I'/opt/R/4.0.5/lib/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c graticule.cpp -o graticule.o
g++ -std=gnu++11 -I"/opt/R/4.0.5/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/include/gdal -I/usr/include -I'/opt/R/4.0.5/lib/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c math_utils.cpp -o math_utils.o
g++ -std=gnu++11 -I"/opt/R/4.0.5/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/include/gdal -I/usr/include -I'/opt/R/4.0.5/lib/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c mediancut.cpp -o mediancut.o
g++ -std=gnu++11 -I"/opt/R/4.0.5/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/include/gdal -I/usr/include -I'/opt/R/4.0.5/lib/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c memory.cpp -o memory.o
g++ -std=gnu++11 -I"/opt/R/4.0.5/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/include/gdal -I/usr/include -I'/opt/R/4.0.5/lib/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c ncdf.cpp -o ncdf.o
g++ -std=gnu++11 -I"/opt/R/4.0.5/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/include/gdal -I/usr/include -I'/opt/R/4.0.5/lib/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c ram.cpp -o ram.o
g++ -std=gnu++11 -I"/opt/R/4.0.5/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/include/gdal -I/usr/include -I'/opt/R/4.0.5/lib/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c raster_methods.cpp -o raster_methods.o
g++ -std=gnu++11 -I"/opt/R/4.0.5/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/include/gdal -I/usr/include -I'/opt/R/4.0.5/lib/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c raster_stats.cpp -o raster_stats.o
g++ -std=gnu++11 -I"/opt/R/4.0.5/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/include/gdal -I/usr/include -I'/opt/R/4.0.5/lib/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c rasterize.cpp -o rasterize.o
g++ -std=gnu++11 -I"/opt/R/4.0.5/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/include/gdal -I/usr/include -I'/opt/R/4.0.5/lib/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c read.cpp -o read.o
g++ -std=gnu++11 -I"/opt/R/4.0.5/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/include/gdal -I/usr/include -I'/opt/R/4.0.5/lib/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c read_gdal.cpp -o read_gdal.o
g++ -std=gnu++11 -I"/opt/R/4.0.5/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/include/gdal -I/usr/include -I'/opt/R/4.0.5/lib/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c read_ogr.cpp -o read_ogr.o
g++ -std=gnu++11 -I"/opt/R/4.0.5/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/include/gdal -I/usr/include -I'/opt/R/4.0.5/lib/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c sample.cpp -o sample.o
g++ -std=gnu++11 -I"/opt/R/4.0.5/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/include/gdal -I/usr/include -I'/opt/R/4.0.5/lib/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c spatBase.cpp -o spatBase.o
g++ -std=gnu++11 -I"/opt/R/4.0.5/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/include/gdal -I/usr/include -I'/opt/R/4.0.5/lib/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c spatDataframe.cpp -o spatDataframe.o
g++ -std=gnu++11 -I"/opt/R/4.0.5/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/include/gdal -I/usr/include -I'/opt/R/4.0.5/lib/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c spatFactor.cpp -o spatFactor.o
g++ -std=gnu++11 -I"/opt/R/4.0.5/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/include/gdal -I/usr/include -I'/opt/R/4.0.5/lib/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c spatRaster.cpp -o spatRaster.o
g++ -std=gnu++11 -I"/opt/R/4.0.5/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/include/gdal -I/usr/include -I'/opt/R/4.0.5/lib/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c spatSources.cpp -o spatSources.o
g++ -std=gnu++11 -I"/opt/R/4.0.5/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/include/gdal -I/usr/include -I'/opt/R/4.0.5/lib/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c spatTime.cpp -o spatTime.o
g++ -std=gnu++11 -I"/opt/R/4.0.5/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/include/gdal -I/usr/include -I'/opt/R/4.0.5/lib/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c spatVector.cpp -o spatVector.o
g++ -std=gnu++11 -I"/opt/R/4.0.5/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/include/gdal -I/usr/include -I'/opt/R/4.0.5/lib/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c string_utils.cpp -o string_utils.o
g++ -std=gnu++11 -I"/opt/R/4.0.5/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/include/gdal -I/usr/include -I'/opt/R/4.0.5/lib/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c vecmath.cpp -o vecmath.o
g++ -std=gnu++11 -I"/opt/R/4.0.5/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/include/gdal -I/usr/include -I'/opt/R/4.0.5/lib/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c vector_methods.cpp -o vector_methods.o
g++ -std=gnu++11 -I"/opt/R/4.0.5/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/include/gdal -I/usr/include -I'/opt/R/4.0.5/lib/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c write.cpp -o write.o
g++ -std=gnu++11 -I"/opt/R/4.0.5/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/include/gdal -I/usr/include -I'/opt/R/4.0.5/lib/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c write_gdal.cpp -o write_gdal.o
g++ -std=gnu++11 -I"/opt/R/4.0.5/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/include/gdal -I/usr/include -I'/opt/R/4.0.5/lib/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c write_ogr.cpp -o write_ogr.o
g++ -std=gnu++11 -shared -L/opt/R/4.0.5/lib/R/lib -L/usr/local/lib -o terra.so RcppExports.o RcppFunctions.o RcppModule.o arith.o crs.o distRaster.o distance.o extract.o file_utils.o focal.o gcp.o gdal_algs.o gdal_multidimensional.o gdalio.o geodesic.o geos_methods.o geosphere.o graticule.o math_utils.o mediancut.o memory.o ncdf.o ram.o raster_methods.o raster_stats.o rasterize.o read.o read_gdal.o read_ogr.o sample.o spatBase.o spatDataframe.o spatFactor.o spatRaster.o spatSources.o spatTime.o spatVector.o string_utils.o vecmath.o vector_methods.o write.o write_gdal.o write_ogr.o -lproj -L/usr/lib64 -lgdal -L/usr/lib64 -lgeos_c -L/opt/R/4.0.5/lib/R/lib -lR
installing to /home/iparfitt/R/x86_64-pc-linux-gnu-library/4.0/00LOCK-terra/00new/terra/libs
** R
Error in parse(outFile) :
  /tmp/RtmpmT4nui/R.INSTALL28bf58555f8f/terra/R/zonal.R:72:42: unexpected input
71:                         r <- !relate(x, z, "disjoint")
72:                         i <- apply(r, 1, \
                                             ^
ERROR: unable to collate and parse R files for package ‘terra’
* removing ‘/home/iparfitt/R/x86_64-pc-linux-gnu-library/4.0/terra’

The downloaded source packages are in
        ‘/tmp/RtmprSVhnM/downloaded_packages’
Warning message:
In install.packages("terra", repos = "cloud.r-project.org") :
  installation of package ‘terra’ had non-zero exit status
Ian Parfitt
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1 Answers1

0

This happens because the current released version of terra is dependent on R >= 4.1; that was not intended and will be fixed in the next release (early August). For now, you can either update your R version, or install the development version of "terra". On windows you can do that with install.packages('terra', repos='https://rspatial.r-universe.dev'). For other platforms see https://github.com/rspatial/terra

Robert Hijmans
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