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@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.biv...@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.biv...@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.biv...@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@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 vlu...@iupui.edu ORCID: https://orcid.org/0000-0002-0823-2522 Webpage: http://vijaylulla.com [[alternative HTML version deleted]] _______________________________________________ R-sig-Geo mailing list R-sig-Geo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-geo