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

Sat May 30 17:04:10 CEST 2020

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.
>
>

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