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

Robin Lovelace rob00x @end|ng |rom gm@||@com
Sat May 30 21:40:53 CEST 2020 

Hi all,

For what it's worth I'm having the same issue and am getting this message:

inverser.c:5:10: fatal error: projects.h: No such file or directory
 #include <projects.h>
          ^~~~~~~~~~~~
compilation terminated.
/usr/lib/R/etc/Makeconf:168: recipe for target 'inverser.o' failed
make: *** [inverser.o] Error 1
ERROR: compilation failed for package ‘rgdal’
* removing ‘/home/robin/R/x86_64-pc-linux-gnu-library/3.6/rgdal’
* restoring previous ‘/home/robin/R/x86_64-pc-linux-gnu-library/3.6/rgdal’

The development version of sf installs OK. I'm on Ubuntu with the following
versions:

sf::sf_extSoftVersion()
          GEOS           GDAL         proj.4 GDAL_with_GEOS     USE_PROJ_H
       "3.8.0"        "3.0.4"        "7.0.0"         "true"         "true"

I think I need to set the proj path. My projinfo binary is at

which projinfo
# /usr/bin/projinfo

From the thread I guess I should add the argument ,
 configure.args=c("--with-proj-include=...") but so far my attempts have
been in vain.

As a test I tried installing older versions with the following results:

remotes::install_version(package = "rgdal", version = "1.4-8") # works
remotes::install_version(package = "rgdal", version = "1.4-7") # works
remotes::install_version(package = "rgdal", version = "1.5-8") # fails

Any pointers for installation on my set-up appreciated.

I should say huge thanks to Roger and other developers in the community for
amazing work keeping track of rapidly changing upstream dependencies. It's
a small miracle that R can be used as a powerful geographic data processing
tool, with a vast array of statistical functionality a few keystrokes away.
Hope sharing my experience is useful.




On Sat, May 30, 2020 at 7:47 PM chris english <englishchristophera using gmail.com>
wrote:

> Roy,
>
> I'm not OSX but generally I see them as conceptually similar and where I
> have stumbled (at what appears to be 'this stage') is in permissions so I
> would check the 'geneaology' of permissions and your ownership there upon
> the entire path of permissions that allows dynlib to execute
> comprehensively. And as you pass the rgdal hurdle so the same for gdal,
> geos. As applies to OSX, this may appear as voodoo, but if there is a sudo
> analog in OSX, try it. My voodoo (that is possibly disconcerting to those
> who view computers as logical systems. I would have advocated base 3 were I
> there at the beginning...)
>
> Chris
>
> On Sat, May 30, 2020 at 2:12 PM Roy Mendelssohn - NOAA Federal via
> R-sig-Geo <r-sig-geo using r-project.org> wrote:
>
> > Hi All:
> >
> > Okay after some fiddling I was able to get it to sort of successfully
> > compile,  where I am having problems is in finding the dynamic libraries,
> > such as I get this error:
> >
> > > dyld: Library not loaded: @rpath/libproj.19.dylib
> >
> > and
> >
> > > Error: package or namespace load failed for ‘rgdal’ in dyn.load(file,
> > DLLpath = DLLpath, ...):
> > >  unable to load shared object
> >
> '/Users/rmendels/Library/R/4.0/library/00LOCK-rgdal/00new/rgdal/libs/rgdal.so':
> > >
> >
> dlopen(/Users/rmendels/Library/R/4.0/library/00LOCK-rgdal/00new/rgdal/libs/rgdal.so,
> > 6): Library not loaded: @rpath/libgdal.26.dylib
> > >   Referenced from:
> >
> /Users/rmendels/Library/R/4.0/library/00LOCK-rgdal/00new/rgdal/libs/rgdal.so
> > >   Reason: image not found
> > > Error: loading failed
> >
> > It has to do with these are defined in terms of @rpath.  I thought
> > defining this in $LD_LIBRARY_PATH would do it,  but I have:
> >
> > > echo $LD_LIBRARY_PATH
> > > /Users/rmendels/Library/R/4.0/library:/Users/rmendels/anaconda3/lib
> >
> > I also tried setting    $DYLD_LIBRARY_PATH same problem.  If someone can
> > tell me how to set it so @rpath finds the dynamic libraries I might be
> able
> > to get this to work.
> >
> > Thanks,
> >
> > -Roy
> >
> >
> >
> > > On May 30, 2020, at 8:04 AM, chris english <
> > englishchristophera using gmail.com> wrote:
> > >
> > > my setup - albeit on 20.04 as reported by sf
> > >
> > > > library(sf)
> > > Linking to GEOS 3.9.0dev, GDAL 3.1.0, PROJ 7.0.1
> > >
> > > Note I'm using release gdal, that I none the less built from source as
> I
> > had to enable Mr. Sid for some particular
> > >  data. Couldn't get GDAL 3.2.*dev working but still toying around with
> > it. Roger's discussion of the history of all
> > > of this on r-spatial and the path forward is very much worth the read
> as
> > and relates to his following message here.
> > >
> > >
> > >
> > > On Sat, May 30, 2020 at 10:33 AM Roy Mendelssohn - NOAA Federal <
> > roy.mendelssohn using noaa.gov> wrote:
> > > Yes thanks.  As I said in reply to Roger I am far from an expert in
> > these things,  but if I can get it to build,  then I will try to post
> > somewhere for others to use.
> > >
> > > -Roy
> > >
> > > > On May 30, 2020, at 7:03 AM, chris english <
> > englishchristophera using gmail.com> wrote:
> > > >
> > > > Roy,
> > > > From a related prior post Roger shared this link to rgdal-1.5-9,
> > http://spatial.nhh.no/R/rgdal/ . I followed discussions
> > > > from the 'sf' github readme and purged all prior proj/geos/gdal
> > iterations that have lingered around over the past five
> > > > years and built them from source on ubuntu 20.04. This upgrade to
> > 20.04 was perhaps my first mistake in a month
> > > > long effort to bring back my full spatial capabilities as it doesn't
> > become the official LTS until sometime mid this month.
> > > > I don't know how Anaconda packages and may require sym links or
> > copying files from down in the depths to visible,
> > > > but it worked before and can be made to work again.
> > > > HTH-
> > > > Chris
> > > >
> > > > On Sat, May 30, 2020 at 8:08 AM Roger Bivand <Roger.Bivand using nhh.no>
> > wrote:
> > > > 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 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_______________________________________________
> > > > R-sig-Geo mailing list
> > > > R-sig-Geo using r-project.org
> > > > https://stat.ethz.ch/mailman/listinfo/r-sig-geo
> > >
> > > **********************
> > > "The contents of this message do not reflect any position of the U.S.
> > Government or NOAA."
> > > **********************
> > > Roy Mendelssohn
> > > Supervisory Operations Research Analyst
> > > NOAA/NMFS
> > > Environmental Research Division
> > > Southwest Fisheries Science Center
> > > ***Note new street address***
> > > 110 McAllister Way
> > > Santa Cruz, CA 95060
> > > Phone: (831)-420-3666
> > > Fax: (831) 420-3980
> > > e-mail: Roy.Mendelssohn using noaa.gov www: https://www.pfeg.noaa.gov/
> > >
> > > "Old age and treachery will overcome youth and skill."
> > > "From those who have been given much, much will be expected"
> > > "the arc of the moral universe is long, but it bends toward justice"
> > -MLK Jr.
> > >
> >
> > **********************
> > "The contents of this message do not reflect any position of the U.S.
> > Government or NOAA."
> > **********************
> > Roy Mendelssohn
> > Supervisory Operations Research Analyst
> > NOAA/NMFS
> > Environmental Research Division
> > Southwest Fisheries Science Center
> > ***Note new street address***
> > 110 McAllister Way
> > Santa Cruz, CA 95060
> > Phone: (831)-420-3666
> > Fax: (831) 420-3980
> > e-mail: Roy.Mendelssohn using noaa.gov www: https://www.pfeg.noaa.gov/
> >
> > "Old age and treachery will overcome youth and skill."
> > "From those who have been given much, much will be expected"
> > "the arc of the moral universe is long, but it bends toward justice" -MLK
> > Jr.
> >
> > _______________________________________________
> > R-sig-Geo mailing list
> > R-sig-Geo using r-project.org
> > https://stat.ethz.ch/mailman/listinfo/r-sig-geo
> >
>
>         [[alternative HTML version deleted]]
>
> _______________________________________________
> R-sig-Geo mailing list
> R-sig-Geo using r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>

	[[alternative HTML version deleted]]

More information about the R-sig-Geo mailing list