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

[Barry Rowlingson]

Just a quick note to point out that you can test installations on systems
without having to install such a system by using Docker. Fedora 28 images
are available on Docker Hub.

You have to figure out how to install the toolchain and other components
for building R etc but that helps make a reproducible installation
procedure.

Is everyone doing this already?

Barry


On Sun, Jun 17, 2018 at 2:50 PM, Sarah Goslee <sarah.goslee using gmail.com>
wrote:

> I can confirm that the patched R-Forge version of rgdal installs
> correctly on my systems with no other change.
>
> Thank you to Roger and Colin, and everyone else who took a look. The R
> community is the BEST.
>
> Sarah
>
> On Sat, Jun 16, 2018 at 5:55 PM, Roger Bivand <Roger.Bivand using nhh.no> wrote:
> > On Sat, 16 Jun 2018, Colin Rundel wrote:
> >
> >> As I mentioned in the tweet, I was able to fix this on both a Fedora 23
> >> and
> >> Fedora 27 machine by making the following change to configure.ac:
> >>
> >> diff --git a/configure.ac b/configure.ac
> >> index 8ff72be..ab4c772 100644
> >> --- a/configure.ac
> >> +++ b/configure.ac
> >> @@ -3,6 +3,8 @@ define([pkgversion], esyscmd([sh -c "grep Version:
> >> DESCRIPTION | cut -d' ' -f2 |
> >> AC_INIT(rgdal, [pkgversion], Roger.Bivand using nhh.no)
> >> AC_CONFIG_SRCDIR(src/gdal-bindings.cpp)
> >>
> >> +AC_PROG_CXX()
> >> +
> >> # find R home and set correct compiler + flags
> >> : ${R_HOME=`R RHOME`}
> >> if test -z "${R_HOME}"; then
> >>
> >> rerunning autoconf (also assuming m4/ax_cxx_compile_stdcxx.m4 is added)
> >> results in ./configure working for me. I don't have a deep enough
> >> understanding of the vagaries of autoconf to know why exactly this is
> >> necessary on redhat systems and why this fixes it but at least
> everything
> >> seems to work.
> >
> >
> > Thanks very much, committed to R-forge as revision 758.
> >
> > Roger
> >
> >
> >>
> >> -Colin
> >>
> >> On Fri, Jun 15, 2018 at 7:29 PM Thiago V. dos Santos via R-sig-Geo <
> >> r-sig-geo using r-project.org> wrote:
> >>
> >>> 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
> >>>
>
> _______________________________________________
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>

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