[R-sig-Geo] CRAN releases of sp, rgdal and rgeos

Sun Jun 10 10:45:12 CEST 2018

Thanks for reporting, comments inline below (note that I have no OSX 
access at all):

On Sat, 9 Jun 2018, Thiago V. dos Santos wrote:

> Dear Roger,
> Thank you very much for the excellent work done with those packages.
> Today I update both rgeos and rgdal on my system - macOS 10.13.5 with 
> all dependencies installed via MacPorts. I had updated sp a few days 
> earlier. The dependencies versions on my system are gdal 
> @2.3.0.20180523_0+grib+hdf4+hdf5+jasper+mpich+netcdf and proj @5.1.0_0. 
> Rgeos's update went flawlessly, but I got a few errors while updating 
> rgdal. It still compiled successfully, but I am concerned that some 
> functionality might be compromised due to the errors.
> This is what I got (I have to manually specify the location of proj or 
> rgdal won't find it):> install.packages('rgdal', type = "source", 
> configure.args=c(
> +     '--with-proj-include=/opt/local/lib/proj5/include',
> +     '--with-proj-lib=/opt/local/lib/proj5/lib'))
> Installing package into ‘/Users/thiago/Documents/R-packages’
> (as ‘lib’ is unspecified)
> trying URL 'https://cran.r-project.org/src/contrib/rgdal_1.3-2.tar.gz'
> Content type 'application/x-gzip' length 1667049 bytes (1.6 MB)
> ==================================================
> downloaded 1.6 MB
>
> * installing *source* package ‘rgdal’ ...
> ** package ‘rgdal’ successfully unpacked and MD5 sums checked
> configure: CC: /usr/bin/clang
> configure: CXX: /usr/bin/clang++
> configure: rgdal: 1.3-2
> checking for /usr/bin/svnversion... yes
> 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... no
> checking for suffix of object files... o
> checking whether we are using the GNU C++ compiler... yes
> checking whether /usr/bin/clang++ accepts -g... yes
> checking whether /usr/bin/clang++ supports C++11 features by default... no
> checking whether /usr/bin/clang++ supports C++11 features with -std=gnu++11... yes
> configure: C++11 support available
> checking for gdal-config... /opt/local/bin/gdal-config
> checking gdal-config usability... yes
> configure: GDAL: 2.4.0

All OK up to the GDAL version returned by gdal-config - are you using the 
released GDAL 2.3.0 (probably not) or master?

> checking C++11 support for GDAL >= 2.3.0... yes
> checking GDAL version >= 1.11.4... yes
> checking gdal: linking with --libs only... yes
> checking GDAL: /opt/local/share/gdal/pcs.csv readable... yes
> checking proj_api.h presence and usability... yes
> ./configure: line 3395: test: =: unary operator expected

Will check, that line is:

if test ${PROJ_VERSION} = "" ; then

from configure.ac line 305. Possibly a shell dialect issue.

> checking PROJ version >= 4.8.0... yes
> checking projects.h presence and usability... yes

These relate to configure.ac lines 376-419, and the outcome: epsg found 
and readable is OK - could there be two libproj on your system (maybe for 
different architectures)?

> Undefined symbols for architecture x86_64:
>  "_pj_ctx_fclose", referenced from:
>      _main in proj_conf_test2-06fe7d.o
>  "_pj_get_default_ctx", referenced from:
>      _main in proj_conf_test2-06fe7d.o
>  "_pj_open_lib", referenced from:
>      _main in proj_conf_test2-06fe7d.o
> ld: symbol(s) not found for architecture x86_64
> clang: error: linker command failed with exit code 1 (use -v to see invocation)
> ./configure: line 3511: ./proj_conf_test2: No such file or directory
> checking PROJ.4: epsg found and readable... yes

Same here for next block in configure.ac; conus found and readable.

> Undefined symbols for architecture x86_64:
>  "_pj_ctx_fclose", referenced from:
>      _main in proj_conf_test3-3b7aa2.o
>  "_pj_get_default_ctx", referenced from:
>      _main in proj_conf_test3-3b7aa2.o
>  "_pj_open_lib", referenced from:
>      _main in proj_conf_test3-3b7aa2.o
> ld: symbol(s) not found for architecture x86_64
> clang: error: linker command failed with exit code 1 (use -v to see invocation)
> ./configure: line 3570: ./proj_conf_test3: No such file or directory
> checking PROJ.4: conus found and readable... yes
> configure: Package CPP flags:  -I/opt/local/include -I/opt/local/lib/proj5/include
> configure: Package LIBS:  -L/opt/local/lib -lgdal -L/opt/local/lib/proj5/lib -lproj
> configure: creating ./config.status
> config.status: creating src/Makevars
> ** libs
> clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/local/include -I/opt/local/lib/proj5/include -I"/Users/thiago/Documents/R-packages/sp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c OGR_write.cpp -o OGR_write.o
> clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/local/include -I/opt/local/lib/proj5/include -I"/Users/thiago/Documents/R-packages/sp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c gdal-bindings.cpp -o gdal-bindings.o
> /usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/local/include -I/opt/local/lib/proj5/include -I"/Users/thiago/Documents/R-packages/sp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c init.c -o init.o
> /usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/local/include -I/opt/local/lib/proj5/include -I"/Users/thiago/Documents/R-packages/sp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c inverser.c -o inverser.o
> /usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/local/include -I/opt/local/lib/proj5/include -I"/Users/thiago/Documents/R-packages/sp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c local_stubs.c -o local_stubs.o
> clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/local/include -I/opt/local/lib/proj5/include -I"/Users/thiago/Documents/R-packages/sp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c ogr_geom.cpp -o ogr_geom.o
> /usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/local/include -I/opt/local/lib/proj5/include -I"/Users/thiago/Documents/R-packages/sp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c ogr_polygons.c -o ogr_polygons.o
> clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/local/include -I/opt/local/lib/proj5/include -I"/Users/thiago/Documents/R-packages/sp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c ogr_proj.cpp -o ogr_proj.o
> clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/local/include -I/opt/local/lib/proj5/include -I"/Users/thiago/Documents/R-packages/sp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c ogrdrivers.cpp -o ogrdrivers.o
> clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/local/include -I/opt/local/lib/proj5/include -I"/Users/thiago/Documents/R-packages/sp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c ogrsource.cpp -o ogrsource.o
> clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/local/include -I/opt/local/lib/proj5/include -I"/Users/thiago/Documents/R-packages/sp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c projectit.cpp -o projectit.o
> clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o rgdal.so OGR_write.o gdal-bindings.o init.o inverser.o local_stubs.o ogr_geom.o ogr_polygons.o ogr_proj.o ogrdrivers.o ogrsource.o projectit.o -L/opt/local/lib -lgdal -L/opt/local/lib/proj5/lib -lproj -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
> installing to /Users/thiago/Documents/R-packages/rgdal/libs
> ** R
> ** data
> ** inst
> ** byte-compile and prepare package for lazy loading
> ** help
> *** installing help indices
> ** building package indices
> ** installing vignettes
> ** testing if installed package can be loaded
> * DONE (rgdal)
>
> The downloaded source packages are in
> 
> ‘/private/var/folders/_z/01gg71zs19g816v6m2dddt8w0000gn/T/Rtmp5K6lt8/downloaded_packages’ 
> Is this something that needs to be investigated, or I can just safely 
> ignore those messages?

Please try to run:

tools::testInstalledPackage("rgdal", outDir=tempdir())
list.files(tempdir())
file.show(file.path(tempdir(), "rgdal-Ex.Rout"))

and if the outcomes are as expected, you should be OK, please let us know.

If any OSX users installing from source can contribute, that would be 
useful. It will take a little while before the CRAN OSX binaries catch up 
with new PROJ and GDAL.

Again thanks for reporting!

Roger

> Many thanks, -- Thiago V. dos Santos
> Postdoctoral Research FellowDepartment of Climate and Space Science and EngineeringUniversity of Michigan
>
>    On Friday, June 8, 2018, 2:15:43 PM EDT, Roger Bivand <Roger.Bivand using nhh.no> wrote:
>
> There are new releases of sp, rgdal and rgeos on CRAN. Please install sp
> first, then the other two, which link to the installed sp. They all
> address so-called rchk issues, which have not so far been a problem, but
> might have become more fragile as R's internal memory management is made
> even more efficient. This involves compiled code using memory allocated by
> R to be freed by R's garbage collector, which has to know if an object is
> still being used. Tomas Kalibera, the author of rchk, helped resolve and
> explain the issues encountered - what was good coding practice fifteen
> years ago isn't always still good practice.
>
> In addition, the earliest versions of GDAL and PROJ with which rgdal will
> work have been updated, and set to PROJ 4.8.0 and GDAL 1.11.4. The current
> released versions of PROJ and GDAL are to be prefered, as bugs have been
> fixed and new features and drivers introduced. A check has been put
> in place to trap attempts to install rgdal without a C++11-capable
> compiler when the GDAL version is >=2.3.0 - which requires C++11. rgeos is
> ready for the forthcoming version of GEOS.
>
> The CRAN team has also been very supportive of our efforts to bring
> compiled code in these packages into rchk compliance.
>
> Please get in touch if you see any loose ends in these releases.
>
> Roger
>
>

-- 
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
http://orcid.org/0000-0003-2392-6140
https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en