rgdal 1.5-8 released on CRAN
On Fri, 29 May 2020, Thiago V. dos Santos wrote:
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
So far so good, but you chose to override pkg-config proj by passing configure arguments. You should let pkg-config proj provide those values.
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
Also OK.
checking for proj_context_create in -lproj... no configure: error: proj_context_create not found in libproj.
The directory where libproj should be does not contain it - whether you got it wrong, pkg-config got it wrong, or for some other reason, the library was not found.
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.
Try to avoid googling, it is usually misleading. Running ./configure in the untarred source package directory, and running ./configure --help to show the arguments to configure can be much more helpful. Crucially, they are up to date, while most search hits are old, and they are ordered by hit counts, which is certainly no guarantee of precision.
Are you familiar with it? Is there any other argument that I can pass to install.packages to solve it?
Try not setting configure arguments and let pkg-config proj do the work if you feel you can trust it. If, however, you have multiple installs of GDAL and/or PROJ, the proj.pc file may point to a deleted install. Download and untar the source package, and run just ./configure with its argumments, or setting PKG_CONFIG_PATH= until you find a recipe that works that far. Roger
Greetings, ?-- Thiago V. dos Santos ThiagoDosSantos.com MudancasClimaticasBrasil.com On Thursday, May 28, 2020, 08:53:50 AM GMT-3, Roger Bivand <roger.bivand at 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 at nhh.no https://orcid.org/0000-0003-2392-6140 https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en