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

Thiago V. dos Santos thi_velo@o @ending from y@hoo@com@br
Sat Jun 9 21:46:15 CEST 2018 

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