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

[Roger Bivand]

On Sun, 28 Jun 2020, Roger Bivand wrote:

> 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.

LDFLAGS needs unsetting. Revision 1020 on R-Forge

https://r-forge.r-project.org/R/?group_id=884

includes a new configure argument --disable-loadflags to assist in 
unsetting the very specific R rpm LDFLAGS. Please report if this fixes the 
problem.

Roger


>
> 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