[R-sig-Geo] cannot install rgdal after updating to fedora32

[Roger Bivand]

Vero,

On Sat, 27 Jun 2020, Veronica Andreo wrote:

> See the attached config.log file
>

How did you install R itself? If an rpm, then

https://github.com/r-spatial/sf/issues/1369

may be relevant, also if you see errors installing sf. You would need to 
unset LDFLAGS before installing:

https://github.com/r-spatial/sf/issues/1369#issuecomment-614096865

Please report back on this.

Roger

> El sáb., 27 jun. 2020 a las 21:29, Veronica Andreo (<veroandreo using gmail.com>)
> escribió:
>
>> Hello everyone
>>
>> I have just updated my system to fedora 32 (which fetched GDAL 3 and PROJ
>> 6) and when updating my R packages, I get the following error for rgdal.
>> Can someone help me out here? What does it mean that it cannot run C++
>> compiled programs?  And do I want to crosscompile?
>>
>> Thanks much in advance
>>
>> Vero
>>
>> ---
>>
>> install.packages("rgdal")
>> Installing package into
>> ‘/home/veroandreo/R/x86_64-redhat-linux-gnu-library/3.6’
>> (as ‘lib’ is unspecified)
>> trying URL 'http://cran.rstudio.com/src/contrib/rgdal_1.5-12.tar.gz'
>> Content type 'application/x-gzip' length 2302403 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: /usr/lib64/R
>> configure: CC: gcc -m64
>> configure: CXX: g++ -m64 -std=gnu++11
>> configure: CXX11 is: g++ -m64, CXX11STD is: -std=gnu++11
>> configure: CXX is: g++ -m64 -std=gnu++11
>> configure: C++11 support available
>> configure: rgdal: 1.5-12
>> checking for /usr/bin/svnversion... yes
>> configure: svn revision: 1018
>> checking for gdal-config... /usr/bin/gdal-config
>> checking gdal-config usability... yes
>> configure: GDAL: 3.0.4
>> 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/stateplane.csv readable... yes
>> configure: pkg-config proj exists, will use it
>> configure: PROJ version: 6.3.2
>> configure: PROJ CPP flags: -DPROJ_H_API
>> configure: PROJ LIBS: -lproj
>> checking PROJ header API:... yes
>> 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... configure: error: in
>> `/home/veroandreo/tmp/Rtmpo7AtPr/R.INSTALL12cc66f8f895/rgdal':
>> configure: error: cannot run C++ compiled programs. <<<<--- here
>> If you meant to cross compile, use `--host'.
>> See `config.log' for more details
>> ERROR: configuration failed for package ‘rgdal’
>> * removing ‘/home/veroandreo/R/x86_64-redhat-linux-gnu-library/3.6/rgdal’
>> * restoring previous
>> ‘/home/veroandreo/R/x86_64-redhat-linux-gnu-library/3.6/rgdal’
>> Warning in install.packages :
>>   installation of package ‘rgdal’ had non-zero exit status
>>
>> ---
>>
>> sessionInfo()
>> R version 3.6.3 (2020-02-29)
>> Platform: x86_64-redhat-linux-gnu (64-bit)
>> Running under: Fedora 32 (Thirty Two)
>>
>> Matrix products: default
>> BLAS/LAPACK: /usr/lib64/libopenblas-r0.3.9.so
>>
>> Random number generation:
>>  RNG:     Mersenne-Twister
>>  Normal:  Inversion
>>  Sample:  Rounding
>>
>> locale:
>>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>>  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>> loaded via a namespace (and not attached):
>> [1] compiler_3.6.3 tools_3.6.3
>>
>

-- 
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