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

[Vijay Lulla]

I too use R on a mac but I cannot get rgdal to use proj5 (port info proj).
rgdal still uses proj4 even when there is a newer version of proj already
on my computer.  Neither of these proj packages (proj4 or proj) use
pkg-config mechanism even though there are proj.pc files in both versions
of the package.  Maybe using the pkg-config mechanism to detect version of
packages during source installation might help?  I don't know whether this
is a "proj" or a "macports" issue though.


On Mon, Jun 11, 2018 at 7:54 PM, Thiago V. dos Santos via R-sig-Geo <
r-sig-geo using r-project.org> wrote:

> Hi Roger, thanks for the follow up. Answering to your comments:
>
> a) I am using Macports's gdal version 2.3.0.20180523. I am pretty sure
> that its source code (i.e. the one that is compiled on my machine) is
> downloaded from OSGEO (at least according to https://github.com/
> macports/macports-ports/blob/master/gis/gdal/Portfile);
>
> b) I do have more than one libproj installed on my system (as QGIS for
> macOS requires its own gdal and proj stuff), but only the Macports one is
> on my path;
>
>
> c) I tried running:
> tools::testInstalledPackage("rgdal", outDir=tempdir())list.files(
> tempdir())file.show(file.path(tempdir(), "rgdal-Ex.Rout"))
>
> but it unexpectedly returned "Error in library("rgdal") : there is no
> package called ‘rgdal’. Execution halted".
>
> It looks weird but so far I am able to normally load and use at least a
> couple of rgdal's functions.
>
> I will keep monitoring it though, and report any other issue.
>
> Cheers,
>  -- Thiago V. dos Santos
> Postdoctoral Research FellowDepartment of Climate and Space Science and
> EngineeringUniversity of Michigan
>
>     On Sunday, June 10, 2018, 4:46:04 AM EDT, Roger Bivand <
> Roger.Bivand using nhh.no> wrote:
>
>  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
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>
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-- 
Vijay Lulla

Assistant Professor,
Dept. of Geography, IUPUI
425 University Blvd, CA-207C.
Indianapolis, IN-46202
vlulla using iupui.edu
ORCID: https://orcid.org/0000-0002-0823-2522
Webpage: http://vijaylulla.com

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