CRAN releases of sp, rgdal and rgeos

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 at 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 at 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 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.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 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]]

--
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