CRAN releases of sp, rgdal and rgeos
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 at 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 at 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 at nhh.no http://orcid.org/0000-0003-2392-6140 https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en [[alternative HTML version deleted]]