[R-sig-Geo] rgdal configure errors for proj test

Sun Jun 14 21:25:01 CEST 2020

Thanks, I've only checked your patch locally. Please try rev. 1010 when/if 
it completes building on R-Forge. I'd be grateful if others can also check 
the current rgdal status, as quite a number of changes have entered 
configure.ac since 1.5-8, and only some are in 1.5-10.

Roger

On Sun, 14 Jun 2020, Bennet Fauber wrote:

> Summary
>
> I was getting errors from the configure script that it could not find
> the proj library file when it is installed outside of /usr/local.  A
> one line change to configure.ac and rerunning autoreconf solves the
> problem.  This problem exists both in the tar ball supplied by CRAN
> mirrors and in the version provided by
>
> $ svn checkout svn://scm.r-forge.r-project.org/svnroot/rgdal/
> . . . .
> Checked out revision 1009.
>
> I hope that sufficient detail is provided in what follows to understand
> the environment, the error, and why the proposed fix works.  There is
> almost certainly a better way to resolve the issue, but the proposed one
> does work.  I hope it will isolate the problem sufficiently that a more
> correct fix can be created.
>
>
> Environment description
>
> #------------------------------------------------------------------------
> CentOS Linux release 7.7.1908 (Core)
> 3.10.0-1062.9.1.el7.x86_64
>
> GCC 8.2.0  Compiled from source
> R version 3.6.3 (2020-02-29)  Compiled from source with gcc/8.2.0
>
> #------------------------------------------------------------------------
> 06-11-2020 09:22 $ wget http://download.osgeo.org/geos/geos-3.8.1.tar.bz2
>
> ./configure --prefix=/sw/arcts/centos7/gcc_8_2_0/geos/3.8.1
>
> #------------------------------------------------------------------------
> 06-11-2020 09:26 $ wget http://download.osgeo.org/gdal/CURRENT/gdal-3.1.0.tar.gz
>
> ./configure --prefix=/sw/arcts/centos7/gcc_8_2_0/gdal/3.1.0 \
>    --with-libtiff=$IMG_LIBS_HOME \
>    --with-libjpeg=$IMG_LIBS_HOME --with-gif=$IMG_LIBS_HOME \
>    --with-hdf4=$HDF4_ROOT --with-hdf5=$HDF5_ROOT \
>    --with-geos=$GEOS_HOME --with-proj=$PROJ_HOME
>
> #------------------------------------------------------------------------
> 06-11-2020 19:44 $ wget https://download.osgeo.org/proj/proj-6.2.1.tar.gz
>
> ./configure --prefix=/sw/arcts/centos7/gcc_8_2_0/proj/6.2.1
>
> # Into the build directory, and before running make ; make install, we
>
> unzip -o /sw/src/arcts/proj/proj-datumgrid-1.8.zip -d data
>
> #------------------------------------------------------------------------
>
> All of the base libraries pass tests and are known to work properly.
>
>
>
> All R libraries obtained from a mirror of CRAN.
>
> The prerequisite libraries for rgdal were install with these commands
> and were successful.
>
> install.packages('tidyverse', "/sw/arcts/centos7/Rgeospatial/062020")
> install.packages('sf', "/sw/arcts/centos7/Rgeospatial/062020")
> install.packages('rgeos', "/sw/arcts/centos7/Rgeospatial/062020")
>
>
> Rgdal installation
>
> # First attempted this install.packages(rgdal) command, which has worked
> # in past years with slightly different versions
> # (comand line broken for legibility)
>
> install.packages('rgdal',
>    configure.args=c("--with-proj-include=${PROJ_INCLUDE}",
>                     "--with-proj-lib=${PROJ_LIB}",
>                     "--with-proj-share=${PROJ_SHARE}")
>                    )
>
> That failed on the configure test of `proj_create_context` because it is
> unable to find the library with this message from `configure`.  See note
> at the end of this message for the complete transcript of the first attempt
> at installation.
>
>>> /usr/bin/ld: cannot find -lproj
>
> The rgdal installation reports that it can find proj, and it is usable.  The
> following excerpt from the transcript shows configure properly finding
> the proj libraries from pkg-config, and that it knows the proper PROJ_LIBS.
>
> configure: pkg-config proj exists, will use it
> configure: PROJ version: 6.2.1
> configure: proj CPP flags: -DPROJ_H_API
> -I/sw/arcts/centos7/gcc_8_2_0/proj/6.2.1/include
> configure: PROJ LIBS: -L/sw/arcts/centos7/gcc_8_2_0/proj/6.2.1/lib -lproj
> checking PROJ header API:... yes
>
> Somewhere between that test and compilation of the test code for
> proj_context_create shown above, it clearly loses the needed
> '-L/sw/arcts/centos7/gcc_8_2_0/proj/6.2.1/lib' portion of PROJ LIBS.
>
>
> Debugging information
>
> To debug this, I unpacked the .tar.gz of the R package and ran `configure`
> by hand.  I obtained the same result.
>
> Looking in the config.log generated by `configure`, I find that the compile
> command used was.  This confirms that the library location if reported
> finding is not being used on the compile command for this test.
>
>    configure:3894: gcc -o conftest -O3 -mtune=native -I/usr/local/include
>    -DPROJ_H_API -I/sw/arcts/centos7/gcc_8_2_0/proj/6.2.1/include
>    -L/usr/local/lib64 conftest.c -lproj
>    -L/sw/arcts/centos7/gcc_8_2_0/gdal/3.1.0/lib -lgdal >&5
>
>
> Nonetheless, I confirmed that by extracting the test code and compiling it
> by hand with the correct library flag provided, it compiles.  I modified
> the `configure` script to include the missing library specification, and
> `configure` also then runs to completion.  That confirms that the problem
> really is the missing '-L/sw/arcts/centos7/gcc_8_2_0/proj/6.2.1/lib' portion
> of PROJ LIBS.
>
> I then tried to locate where in the configure.ac file the library was
> being lost or not set for the test, but I was only able to determine that
> by adding $PKG_LIBS to LIBS manually after the block where the proj-libs
> are determined, configure would now run to completion; it did.
>
> I then applied the patch and recreated the installation tar ball to be used
> with install.packages().
>
> The procedure for doing that is to unpack rgdal_1.5-10.tar.gz as distributed
> by CRAN mirrors, change to the rgdal directory, apply this patch,
>
>
> *** configure.ac.original    2020-06-14 10:44:31.999142923 -0400
> --- configure.ac    2020-06-14 10:47:59.830661680 -0400
> ***************
> *** 397,402 ****
> --- 397,403 ----
>    fi # proj_config_ok
>  fi # proj_lib_path
>
> + LIBS="${PKG_LIBS} ${LIBS}"
>  AC_MSG_NOTICE([PROJ LIBS: ${PKG_LIBS}])
>
>
> run autoreconf to regenerate the configure script, obtain new md5sums for
> configure and configure.ac, patch the MD5 file, change to the directory
> above, tar the rgdal directory that contains the patched files, and use
> that to install rgdal with install.packages().
>
>
> After installation of the patched version, I get this upon loading the rgdal
> library.
>
>> library(rgdal)
> Loading required package: sp
> rgdal: version: 1.5-10, (SVN revision 1006)
> Geospatial Data Abstraction Library extensions to R successfully loaded
> Loaded GDAL runtime: GDAL 3.1.0, released 2020/05/03
> Path to GDAL shared files: /sw/arcts/centos7/gcc_8_2_0/gdal/3.1.0/share/gdal
> GDAL binary built with GEOS: FALSE
> Loaded PROJ runtime: Rel. 6.2.1, November 1st, 2019, [PJ_VERSION: 621]
> Path to PROJ shared files: /sw/arcts/centos7/gcc_8_2_0/proj/6.2.1/share/proj
> Linking to sp version:1.4-2
> To mute warnings of possible GDAL/OSR exportToProj4() degradation,
> use options("rgdal_show_exportToProj4_warnings"="none") before loading rgdal.
>
>
>
>
> #============================================================================
> #
> # Transcript of the first, failed installation attempt
> #
> #============================================================================
>
>> install.packages('rgdal', "/sw/arcts/centos7/Rgeospatial/062020", repos="https://repo.miserver.it.umich.edu/cran/")
> trying URL 'https://repo.miserver.it.umich.edu/cran/src/contrib/rgdal_1.5-10.tar.gz'
> Content type 'application/octet-stream' length 2300923 bytes (2.2 MB)
> ==================================================
> downloaded 2.2 MB
>
> * installing *source* package ‘rgdal’ ...
> ** package ‘rgdal’ successfully unpacked and MD5 sums checked
> ** using staged installation
> configure: R_HOME: /sw/arcts/centos7/R/3.6.3/lib64/R
> configure: CC: gcc
> configure: CXX: g++ -std=gnu++11
> configure: CXX11 is: g++, CXX11STD is: -std=gnu++11
> configure: CXX is: g++ -std=gnu++11
> configure: C++11 support available
> configure: rgdal: 1.5-10
> checking for /usr/bin/svnversion... yes
> configure: svn revision: 1006
> checking for gdal-config...
> /sw/arcts/centos7/gcc_8_2_0/gdal/3.1.0/bin/gdal-config
> checking gdal-config usability... yes
> configure: GDAL: 3.1.0
> 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: /sw/arcts/centos7/gcc_8_2_0/gdal/3.1.0/share/gdal/stateplane.csv
> readable... yes
> configure: pkg-config proj exists, will use it
> configure: PROJ version: 6.2.1
> configure: proj CPP flags: -DPROJ_H_API
> -I/sw/arcts/centos7/gcc_8_2_0/proj/6.2.1/include
> configure: PROJ LIBS: -L/sw/arcts/centos7/gcc_8_2_0/proj/6.2.1/lib -lproj
> checking PROJ header API:... 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 proj.h usability... yes
> checking proj.h presence... yes
> checking for proj.h... yes
> checking for proj_context_create in -lproj... no
> configure: error: proj_context_create not found in libproj.
> ERROR: configuration failed for package ‘rgdal’
>
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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 using nhh.no
https://orcid.org/0000-0003-2392-6140
https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en