[R-sig-Geo] rgdal 1.5-8 released on CRAN

Fri May 29 23:25:37 CEST 2020

Dear Roger,

Many thanks for the effort keeping rgdal up-to-date with proj6.

I'd like to report that I am unable to install rgdal 1.5.8 on my macOS system. I am reporting this error here on the list because I thought it would be the best channel in terms of reaching future users experiencing the same error. Please apologize if my rationale is not right, and ignore this message.

GDAL was installed via MacPorts and is at its latest version, 3.1.0 (at the time of this writing). Proj6 has also been installed via Macports.

This is how I am trying to install it:

export PKG_CONFIG_PATH=/opt/local/lib/proj6/lib/pkgconfig
R
install.packages('rgdal', type="source", configure.args=c(
     '--with-proj-include=/opt/local/lib/proj6/include',
     '--with-proj-lib=/opt/local/lib/proj6/lib'))

and this is the output I get:

R version 4.0.0 (2020-04-24) -- "Arbor Day"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> install.packages('rgdal', type="source", configure.args=c(
+      '--with-proj-include=/opt/local/lib/proj6/include',
+      '--with-proj-lib=/opt/local/lib/proj6/lib'))
Installing package into ‘/Users/thiago/Documents/R-packages’
(as ‘lib’ is unspecified)

    trying URL 'https://cran.r-project.org/src/contrib/rgdal_1.5-8.tar.gz'
Content type 'application/x-gzip' length 2299235 bytes (2.2 MB)
==================================================
downloaded 2.2 MB

* installing *source* package ‘rgdal’ ...
** package ‘rgdal’ successfully unpacked and MD5 sums checked
** using staged installation
configure: R_HOME: /Library/Frameworks/R.framework/Resources
configure: CC: /opt/local/bin/gcc
configure: CXX: /opt/local/bin/g++
configure: C++11 support available
configure: rgdal: 1.5-8
checking for /usr/bin/svnversion... yes
configure: svn revision: 990
checking for gdal-config... /opt/local/bin/gdal-config
checking gdal-config usability... yes
configure: GDAL: 3.1.0
checking GDAL version >= 1.11.4... yes
checking GDAL version <= 2.5 or >= 3.0... yes
checking gdal: linking with --libs only... yes
checking GDAL: gdal-config data directory readable... yes
checking GDAL: /opt/local/share/gdal/stateplane.csv readable... yes
configure: pkg-config proj exists, will use it
configure: PROJ version: 6.3.2
configure: proj CPP flags: -DPROJ_H_API -I/opt/local/lib/proj6/include
configure: PROJ LIBS: -L/opt/local/lib/proj6/lib
checking PROJ header API:... proj.h
checking for gcc... /opt/local/bin/gcc
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 /opt/local/bin/gcc accepts -g... yes
checking for /opt/local/bin/gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... /opt/local/bin/gcc -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... rm: conftest.dSYM: is a directory
rm: conftest.dSYM: is a directory
yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking proj.h usability... yes
checking proj.h presence... yes
checking for proj.h... yes
checking for proj_context_create in -lproj... no
configure: error: proj_context_create not found in libproj.
ERROR: configuration failed for package ‘rgdal’
* removing ‘/Users/thiago/Documents/R-packages/rgdal’
* restoring previous ‘/Users/thiago/Documents/R-packages/rgdal’

The downloaded source packages are in
    ‘/private/var/folders/_z/01gg71zs19g816v6m2dddt8w0000gn/T/RtmpvZAChj/downloaded_packages’
Warning message:
In install.packages("rgdal", type = "source", configure.args = c("--with-proj-include=/opt/local/lib/proj6/include",  :
  installation of package ‘rgdal’ had non-zero exit status

I found this error to be quite mysterious, and could not find any previous discussion about it.

Are you familiar with it? Is there any other argument that I can pass to install.packages to solve it?

Greetings,
 -- Thiago V. dos Santos

ThiagoDosSantos.com
MudancasClimaticasBrasil.com

On Thursday, May 28, 2020, 08:53:50 AM GMT-3, Roger Bivand <roger.bivand using nhh.no> wrote: 

With sp 1.4-2 and rgdal 1.5-8, those using GDAL 3 and PROJ 6 (including 
users of the CRAN Windows binary when it comes) will be part of the big 
migration to WKT2 from Proj4 strings for CRS representation. See

https://cran.r-project.org/web/packages/rgdal/vignettes/CRS_projections_transformations.html

or for a better rendering of "\phi" and bib-handling:

https://rgdal.r-forge.r-project.org/articles/CRS_projections_transformations.html

for background and https://www.r-spatial.org/r/2020/03/17/wkt.html for the 
full sf and sp story.

You will see lots of warnings, they should grab your attention, that is 
what they are for. We need your attention to be as sure as we can be that 
your results - if affected by the transition - have been checked by you.

I plan to flip the warnings to default off from rgdal 1.6-*, and sp 1.5-*. 
In some weeks but before flipping the defaults, I'll follow up showing 
ways of muting them, but we really need to be confident that this 
necessary and future-proofing change isn't silently destroying your work 
first. So please don't treat the many warnings as just pesky and nagging - 
they are priming your immune system to check for unwanted consequences of 
your legacy CRS representation choices.

I'd also like to thank the maintainers of packages importing 
from/depending on sp/rgdal for largely positive responses to issues raised 
and emails sent, often less polite than they might have been, but grabbing 
attention was more important. From over 70 broken reverse dependency 
packages we are now well under 20, and I've contacted all of those, with 
only a couple not responding. Edzer has seen similar responsiveness for 
the parallel migration of sf.

Enjoy!

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
https://orcid.org/0000-0003-2392-6140
https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en

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