[R-sig-Geo] Problems installing rgdal on ubuntu 18.04 from ubuntu-unstable GDAL: 3.0.2 / PROJ version: 6.2.1

[Tomislav Hengl]

The example below is with the rgdal from R-Forge:

R CMD INSTALL rgdal_1.4-8.tar.gz
* installing to library ‘/home/tomislav/R/x86_64-pc-linux-gnu-library/3.5’
* installing *source* package ‘rgdal’ ...
** package ‘rgdal’ successfully unpacked and MD5 sums checked
configure: R_HOME: /opt/microsoft/ropen/3.5.1/lib64/R
configure: CC: gcc -std=gnu99
configure: CXX: g++
configure: C++11 support available
configure: rgdal: 1.4-7
checking for /usr/bin/svnversion... yes
configure: svn revision: 845
checking for gdal-config... /usr/bin/gdal-config
checking gdal-config usability... yes
configure: GDAL: 3.0.2
checking GDAL version >= 1.11.4... yes
checking GDAL version <= 2.5 or >= 3.0... yes
checking gdal: linking with --libs only... yes
checking GDAL: gdal-config data directory readable... yes
checking GDAL: /usr/share/gdal/pcs.csv readable... yes
configure: pkg-config proj exists, will use it
configure: PROJ version: 6.2.1
configure: Support for PROJ >= 6.0.0 not yet available, deprecated API 
defined
configure: proj CPP flags: -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H
configure: PROJ LIBS: -lproj
checking PROJ header API:... proj_api.h
checking proj_api.h presence and usability... yes
checking PROJ version agreement... no
configure: error: proj_api.h and pkg-config give different versions
ERROR: configuration failed for package ‘rgdal’
* removing ‘/home/tomislav/R/x86_64-pc-linux-gnu-library/3.5/rgdal’


The error message suggests that I might have 2 versions of proj, but 
when I check pkg-config it all looks fine:

which proj
/usr/local/bin/proj

pkg-config --modversion proj
6.2.1


On 3/9/20 3:28 PM, Roger Bivand wrote:
> Sorry, no idea, only ever install PROJ and GDAL from source. Multiple 
> PROJ installs? Does rgdal install from R-Forge?
> 
> 
> Roger Bivand
> Norwegian School of Economics
> Bergen, Norway
> 
> ------------------------------------------------------------------------
> *Fra:* R-sig-Geo <r-sig-geo-bounces using r-project.org> på vegne av Tomislav 
> Hengl <tom.hengl using gmail.com>
> *Sendt:* mandag 9. mars 2020, 15.23
> *Til:* r-sig-geo using r-project.org
> *Emne:* [R-sig-Geo] Problems installing rgdal on ubuntu 18.04 from 
> ubuntu-unstable GDAL: 3.0.2 / PROJ version: 6.2.1
> 
> I'm trying to install rgdal using ubuntu-unstable. First I do: sudo 
> apt-get install libproj-dev libgdal-dev Then I get 2 different messages 
> depending on the rgdal version: R CMD INSTALL rgdal_1.4-8.tar.gz * 
> installing to library ‘/home/tomislav/R/x86_64-pc-linux-gnu-library/3.5’ 
> * installing *source* package ‘rgdal’ ... ** package ‘rgdal’ 
> successfully unpacked and MD5 sums checked configure: R_HOME: 
> /opt/microsoft/ropen/3.5.1/lib64/R configure: CC: gcc -std=gnu99 
> configure: CXX: g++ configure: C++11 support available configure: rgdal: 
> 1.4-7 checking for /usr/bin/svnversion... yes configure: svn revision: 
> 845 checking for gdal-config... /usr/bin/gdal-config checking 
> gdal-config usability... yes configure: GDAL: 3.0.2 checking GDAL 
> version >= 1.11.4... yes checking GDAL version <= 2.5 or >= 3.0... yes 
> checking gdal: linking with --libs only... yes checking GDAL: 
> gdal-config data directory readable... yes checking GDAL: 
> /usr/share/gdal/pcs.csv readable... yes configure: pkg-config proj 
> exists, will use it configure: PROJ version: 6.2.1 configure: Support 
> for PROJ >= 6.0.0 not yet available, deprecated API defined configure: 
> proj CPP flags: -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H configure: PROJ 
> LIBS: -lproj checking PROJ header API:... proj_api.h checking proj_api.h 
> presence and usability... yes checking PROJ version agreement... no 
> configure: error: proj_api.h and pkg-config give different versions 
> ERROR: configuration failed for package ‘rgdal’ * removing 
> ‘/home/tomislav/R/x86_64-pc-linux-gnu-library/3.5/rgdal’ > 
> install.packages("rgdal") Installing package into 
> ‘/home/tomislav/R/x86_64-pc-linux-gnu-library/3.5’ (as ‘lib’ is 
> unspecified) % Total % Received % Xferd Average Speed Time Time Time 
> Current Dload Upload Total Spent Left Speed 100 1631k 100 1631k 0 0 722k 
> 0 0:00:02 0:00:02 --:--:-- 722k * installing *source* package ‘rgdal’ 
> ... ** package ‘rgdal’ successfully unpacked and MD5 sums checked 
> checking for g++... g++ 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 g++ accepts -g... yes 
> configure: CC: gcc -std=gnu99 configure: CXX: g++ configure: rgdal: 
> 1.3-3 checking for /usr/bin/svnversion... yes configure: svn revision: 
> 759 checking whether g++ supports C++11 features by default... yes 
> configure: C++11 support available checking for gdal-config... 
> /usr/bin/gdal-config checking gdal-config usability... yes configure: 
> GDAL: 3.0.2 checking GDAL version >= 1.11.4... yes checking gdal: 
> linking with --libs only... yes checking GDAL: /usr/share/gdal/pcs.csv 
> readable... yes configure: pkg-config proj exists, will use it 
> configure: PROJ version: 6.2.1 checking proj_api.h presence and 
> usability... no configure: error: proj_api.h not found in standard or 
> given locations. ERROR: configuration failed for package ‘rgdal’ * 
> removing ‘/home/tomislav/R/x86_64-pc-linux-gnu-library/3.5/rgdal’ 
> Warning in install.packages : installation of package ‘rgdal’ had 
> non-zero exit status The downloaded source packages are in 
> ‘/data/RTMP/RtmpZtTz9T/downloaded_packages’ pkg-config proj --libs 
> -lproj > devtools::session_info() Session info 
> --------------------------------------------------------------------------------------------------- 
> setting value version R version 3.5.1 (2018-07-02) system x86_64, 
> linux-gnu ui RStudio (1.2.1335) language en_US collate en_US.UTF-8 tz 
> Europe/Amsterdam date 2020-03-09 Packages 
> ------------------------------------------------------------------------------------------------------- 
> package * version date source base * 3.5.1 2018-08-05 local compiler 
> 3.5.1 2018-08-05 local datasets * 3.5.1 2018-08-05 local devtools 1.13.6 
> 2018-06-27 CRAN (R 3.5.1) digest 0.6.18 2018-10-10 CRAN (R 3.5.1) 
> graphics * 3.5.1 2018-08-05 local grDevices * 3.5.1 2018-08-05 local 
> grid 3.5.1 2018-08-05 local lattice 0.20-35 2017-03-25 CRAN (R 3.5.1) 
> memoise 1.1.0 2017-04-21 CRAN (R 3.5.1) methods * 3.5.1 2018-08-05 local 
> RevoUtils * 11.0.1 2018-08-01 local RevoUtilsMath * 11.0.0 2018-08-01 
> local sp * 1.3-1 2018-06-05 CRAN (R 3.5.1) stats * 3.5.1 2018-08-05 
> local tools 3.5.1 2018-08-05 local utils * 3.5.1 2018-08-05 local withr 
> 2.1.2 2018-03-15 CRAN (R 3.5.1) I have tried removing all installations 
> of GDAL, proj and QGIS 2x but no luck - always the same problem with 
> "proj_api.h". What are my best options? thank you! 
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