Problems installing rgdal on ubuntu 18.04 from ubuntu-unstable GDAL: 3.0.2 / PROJ version: 6.2.1

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
Look at about line 41 (search for PJ_VERSION) in all the files found by:

locate proj_api.h

The one pointed to by pkg-config --cflags proj is the one stating 621, but 
there must be another earlier in the includes search path.

Happy hunting!

Roger

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 at r-project.org> p? vegne av Tomislav
 Hengl <tom.hengl at gmail.com>
 *Sendt:* mandag 9. mars 2020, 15.23
 *Til:* r-sig-geo at 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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Roger Bivand
Department of Economics, Norwegian School of Economics,
Helleveien 30, N-5045 Bergen, Norway.
voice: +47 55 95 93 55; e-mail: Roger.Bivand at nhh.no
https://orcid.org/0000-0003-2392-6140
https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en

Problems installing rgdal on ubuntu 18.04 from ubuntu-unstable GDAL: 3.0.2 / PROJ version: 6.2.1

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