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

Tue Jun 12 19:49:51 CEST 2018

What is the setup that CRAN uses?  Where can I find this information?

I install most of the R packages on my mac from source and I will be happy
to help (mostly with answering questions and sharing my notes about how I
get packages to compile).

On Tue, Jun 12, 2018 at 12:00 PM, Edzer Pebesma <
edzer.pebesma using uni-muenster.de> wrote:

> proj.5 contains new features, but none of these are, or will in the near
> future be available to R users. All our (= Roger + me) efforts so far
> have been to get software (rgdal, sf) running with proj.5, not to expose
> any of its new features.
> See also https://github.com/r-spatial/sf/issues/545
>
> Also: if anyone insists on installing rgdal or sf from source on a Mac
> but doesn't use the setup CRAN uses for building binaries, neither Roger
> nor I can assist in case of problems beyond wildly guessing. Of course,
> any help from anyone else on these kind of issues is highly appreciated.
>
> On 06/12/2018 04:41 PM, Vijay Lulla wrote:
> > Thank you for the explanation of difference between proj.h and proj_api.h
> > and the recommendation of setting environment variable for pkg-config.  I
> > had tried using pkg-config by setting env variables but haven't had much
> > luck getting it to work.
> > Cordially,
> > Vijay.
> >
> > On Tue, Jun 12, 2018 at 3:11 AM, Roger Bivand <Roger.Bivand using nhh.no>
> wrote:
> >
> >> On Tue, 12 Jun 2018, Vijay Lulla wrote:
> >>
> >> 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.
> >>>
> >>>
> >> Neither sp/rgdal nor sf plan to accomodate the proj.h interface until
> the
> >> GDAL barn-raising project is completed. Even then, most software using
> proj
> >> will have to support the proj_api.h and the proj.h APIs because many
> >> platforms are bound to move at the speed of the slowest package using
> proj.
> >> The proj_api.h API does use the new mechanisms internally, but it isn't
> >> obvious how or whether proj.h pipelines should be exposed (GRASS has a
> >> prototype implementation).
> >>
> >> If you work in geodetics and need sub-cm precision, this may matter; in
> >> which case please follow the GDAL barn-raising project and provide use
> >> cases where the proj.h API is required. The main difference is that the
> >> proj_api.h API always transforms to the WGS84 datum first then
> transforms
> >> to the target datum (many to one then one to many). When this was chosen
> >> 1984 was not so long ago; the new proj.h API suggests transforming
> along a
> >> pipeline from source to target datum without going through WGS84 (many
> to
> >> many).
> >>
> >> If your question is about how to install rgdal from source on OSX, you
> may
> >> need to ensure that you only have one version of proj installed, or use
> >> configure arguments and load path modifications on your own
> responsibility.
> >>
> >> From rgdal 1.3-1, the pkg-config mechanism is used if the path to
> proj.pc
> >> is set correctly (environment variable), but will fall back on standard
> >> locations if pkg-config proj fails.
> >>
> >> Roger
> >>
> >>
> >>
> >>> 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.frame
> >>>>> work/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.frame
> >>>>> work/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.frame
> >>>>> work/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.frame
> >>>>> work/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.frame
> >>>>> work/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.frame
> >>>>> work/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.frame
> >>>>> work/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
> >>>>         [[alternative HTML version deleted]]
> >>>>
> >>>> _______________________________________________
> >>>> R-sig-Geo mailing list
> >>>> R-sig-Geo using r-project.org
> >>>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
> >>>>
> >>>>
> >>>
> >>>
> >>>
> >>>
> >> --
> >> 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
> >>
> >
> >
> >
>
> --
> Edzer Pebesma
> Institute for Geoinformatics
> Heisenbergstrasse 2, 48151 Muenster, Germany
> Phone: +49 251 8333081
>
> _______________________________________________
> R-sig-Geo mailing list
> R-sig-Geo using r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>

-- 
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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