[R-sig-Geo] rgdal installation on Fedora 28

[Thiago V. dos Santos]

The following lines in your config.log:

/usr/bin/ld: /tmp/cc9pfZ1b.o: relocation R_X86_64_32 against .rodata' can not be used when making a shared object; recompile with -fPIC

make me wonder: maybe there is a -fPIC compilation flag lacking for you platform in the makefile?

Greetings, -- Thiago V. dos Santos
Postdoctoral Research FellowDepartment of Climate and Space Science and EngineeringUniversity of Michigan 

    On Friday, June 15, 2018, 3:27:44 PM EDT, Sarah Goslee <sarah.goslee using gmail.com> wrote:  
 
 Hi folks,

I updated all of my linux computers to Fedora 28, and now can’t install rgdal.

I can install sf with no problems, so it doesn't appear to be an issue
with GDAL or with proj.

I checked with Roger Bivand, the package maintainer, who asked me to
confirm whether I could install sf, to make sure it wasn’t a
dependency issue, and to post the logs online, then ask on the
R-sig-geo mailing list. I’m putting the full problem here, and the
abbreviated version on the mailing list.

I’d appreciate any thoughts: I rely very heavily on the incredibly
useful rgdal package.

> sessionInfo()
R version 3.5.0 (2018-04-23)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: Fedora 28 (Workstation Edition)

Matrix products: default
BLAS/LAPACK: /usr/lib64/R/lib/libRblas.so

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_3.5.0 tools_3.5.0</code>


The install message is:

installing *source* package ‘rgdal’ ...
** package ‘rgdal’ successfully unpacked and MD5 sums checked
configure: CC: gcc -m64
configure: CXX: g++ -m64
configure: rgdal: 1.3-2
checking for /usr/bin/svnversion... no
configure: svn revision: 755
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
`/tmp/RtmpfMGBY5/R.INSTALL66c3b8deddb/rgdal':
configure: error: cannot run C++ compiled programs.
If you meant to cross compile, use `--host'.
See `config.log' for more details
ERROR: configuration failed for package ‘rgdal’
* removing ‘/usr/lib64/R/library/rgdal’
* restoring previous ‘/usr/lib64/R/library/rgdal’


The complete information and config.log are posted online at:

http://numberwright.com/2018/06/stuck-on-rgdal/


Any ideas? Or any other information that would be useful?

Thanks!
Sarah

-- 
Sarah Goslee
http://www.functionaldiversity.org

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