[R-sig-Geo] problem installing sf

Tue Sep 6 17:06:30 CEST 2022

Dear all,

I'm having problems installing sf on my ubuntu machine (session info
below). Here is the screen output of the installation. I removed the "g++"
output from the log.

The problem might be due to the installation of PROJ 9.0.1 from source. Any
clues on how to remove this?

Best regards,

Thierry

> install.packages("sf")
Installing package into ‘/home/thierry/R/x86_64-pc-linux-gnu-library/4.0’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/sf_1.0-8.tar.gz'
Content type 'application/x-gzip' length 3472914 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... /usr/bin/gdal-config
checking gdal-config usability... yes
configure: GDAL: 3.4.3
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... /bin/grep
checking for egrep... /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: 3.4.3
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... /usr/bin/geos-config
checking geos-config usability... yes
configure: GEOS: 3.10.2
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/lib/x86_64-linux-gnu -lgeos_c... yes
configure: Package CPP flags:  -I/usr/local/include
-I/usr/include/x86_64-linux-gnu -DHAVE_PROJ_H -I/usr/include/gdal
-I/usr/include
configure: Package LIBS: -L/usr/local/lib -lproj   -L/usr/lib -lgdal
-L/usr/lib/x86_64-linux-gnu -lgeos_c
configure: creating ./config.status
config.status: creating src/Makevars
** libs
installing to
/home/thierry/R/x86_64-pc-linux-gnu-library/4.0/00LOCK-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
double free or corruption (out)
Aborted (core dumped)
ERROR: loading failed
* removing ‘/home/thierry/R/x86_64-pc-linux-gnu-library/4.0/sf’

The downloaded source packages are in
‘/tmp/RtmpUVf9he/downloaded_packages’
Warning message:
In install.packages("sf") :
  installation of package ‘sf’ had non-zero exit status

sessioninfo::session_info()
─ Session info
──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.2.1 (2022-06-23)
 os       Ubuntu 20.04.5 LTS
 system   x86_64, linux-gnu
 ui       X11
 language nl_BE:nl
 collate  nl_BE.UTF-8
 ctype    nl_BE.UTF-8
 tz       Europe/Brussels
 date     2022-09-06
 pandoc   2.14.0.3 @ /usr/bin/pandoc

─ Packages
──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
 package     * version date (UTC) lib source
 cli           3.3.0   2022-04-25 [1] CRAN (R 4.2.0)
 fortunes      1.5-4   2016-12-29 [1] CRAN (R 4.2.0)
 sessioninfo   1.2.2   2021-12-06 [1] CRAN (R 4.2.0)

 [1] /home/thierry/R/x86_64-pc-linux-gnu-library/4.0
 [2] /usr/local/lib/R/site-library
 [3] /usr/lib/R/site-library
 [4] /usr/lib/R/library

ir. Thierry Onkelinx
Statisticus / Statistician

Vlaamse Overheid / Government of Flanders
INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE AND
FOREST
Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality Assurance
thierry.onkelinx using inbo.be
Havenlaan 88 bus 73, 1000 Brussel
www.inbo.be

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