Hi John,
On 06/11/2019 23:24, Dey, John F wrote:
Has anyone added ‘sf’ to R with GDAL 3?
I’m doing this; but still get an error about -std=c++11 required. I’ve
also tried using configopts,
('sf', '0.8-0', {
'buildopts': 'CXXFLAGS="$CXXFLAGS -std=c++11"'
}),
That won't work as expected with R CMD INSTALL, you need to use
--configure-args="...", see
https://stackoverflow.com/questions/10921153/c-compilation-flags-from-r .
Try this:
('sf', '0.8-0', {
'installopts': '--configure-args="CXXFLAGS=\\"$CXXFLAGS
-std=c++11\\""',
}),
You need to make sure you're using double quotes so the $CXXFLAGS is
expanded rather than being passed literally, and to install "$CXXFLAGS
-std=c++11" as a whole to CXXFLAGS=
regards,
Kenneth
== 2019-11-06 13:50:59,986 build_log.py:163 ERROR EasyBuild crashed with
an error (at
easybuild/software/EasyBuild/3.9.2/lib/python2.7/site-packages/vsc_base-2.8.4-py2.7.egg/vsc/utils/exceptions.py:124
in __init__): cmd " R CMD INSTALL
/app/easybuild/sources/r/R/extensions/sf_0.8-0.tar.gz
--library=/app/easybuild/software/R/3.6.1-foss-2016b-monocle3/lib/R/library
--no-clean-on-error " exited with exit code 1 and output:
* installing *source* package ‘sf’ ...
** package ‘sf’ successfully unpacked and MD5 sums checked
** using staged installation
configure: CC: gcc
configure: CXX: g++
checking for gdal-config...
/app/easybuild/software/GDAL/3.0.0-foss-2016b-Python-3.7.4/bin/gdal-config
checking gdal-config usability... yes
configure: GDAL: 3.0.0
checking GDAL version >= 2.0.1... 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... /bin/grep
checking for egrep... /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 gdal.h usability... yes
checking gdal.h presence... yes
checking for gdal.h... yes
checking GDAL: linking with --libs only... no
checking GDAL: linking with --libs and --dep-libs... no
In file included from
/app/easybuild/software/GDAL/3.0.0-foss-2016b-Python-3.7.4/include/gdal.h:45:0,
from gdal_test.cpp:1:
/app/easybuild/software/GDAL/3.0.0-foss-2016b-Python-3.7.4/include/cpl_port.h:187:6:
error: #error Must have C++11 or newer.
# error Must have C++11 or newer.
^
https://github.com/easybuilders/easybuild-easyconfigs/blob/develop/easybuild/easyconfigs/r/RQGIS3/RQGIS3-20190903-foss-2019a-R-3.6.0.eb
*John Dey*
*HPC Operations*
SciComp Computing
*O* _206.667.4308_
*M* _360.649.2731_
[email protected] <mailto:[email protected]>
SciComp Office Hours
Wed. 10-noon M4-B102
<http://www.fredhutch.org/>
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*fredhutch.org <http://www.fredhutch.org/>*
