[R-sig-Geo] problem installing sf

Edzer Pebesma edzer@pebe@m@ @end|ng |rom un|-muen@ter@de
Tue Sep 6 17:53:55 CEST 2022 

Remove any other installations of PROJ from your machine, and recompile 
anything that linked to it to the new PROJ install.

On 06/09/2022 17:06, Thierry Onkelinx via R-sig-Geo wrote:
> 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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-- 
Edzer Pebesma
Institute for Geoinformatics
Heisenbergstrasse 2, 48151 Muenster, Germany
Phone: +49 251 8333081

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