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

[Roger Bivand]

On Sat, 30 May 2020, Roy Mendelssohn - NOAA Federal wrote:

> Thanks. I used "R CMD" and I did state where most things were found, the 
> compilation wasn't unhappy about that. It was unhappy about the header 
> file that didn't exist in my installation.  When I get a chance I will 
> find the other tarball and see if i can it compiled.  I would just like 
> to get Mac version of rgdal, sp and sf using the latest libraries, and 
> post them somewhere for others to use.  Alas, I am not an expert in 
> parts of this, just know that Anaconda looks like it did install the 
> needed files, so it is a start.

Looking for an internal file last used almost ten years ago only suggests 
that your system has defeated the over-complicated logic of ./configure. 
Access to is not needed unless PROJ is < 4.9.3.

Roger

>
> -Roy
>
>
>> On May 30, 2020, at 4:56 AM, Roger Bivand <Roger.Bivand using nhh.no> wrote:
>>
>> On Fri, 29 May 2020, Roy Mendelssohn - NOAA Federal wrote:
>>
>>> I just tried using the Anaconda setup Mine dies on not being able to find “projects.h”.
>>>
>>>> inverser.c:5:10: fatal error: 'projects.h' file not found
>>>> #include <projects.h>
>>>>         ^~~~~~~~~~~~
>>
>> This might happen for particular mixes of versions of PROJ and GDAL, and depending on whether pkg-config proj --exists or not. Try draft 1.5-9 as mentioned in other threads. You need to state PROJ and GDAL versions and how they are detected.
>>
>> Roger
>>
>>>
>>>
>>> Doing internet searches,  for PROJ6 and beyond,  this was made private,  and is not suppose to be for public linking, see:
>>>
>>> https://github.com/OSGeo/PROJ/issues/835 <https://github.com/OSGeo/PROJ/issues/835>
>>> https://code.mpimet.mpg.de/boards/1/topics/1184 <https://code.mpimet.mpg.de/boards/1/topics/1184>
>>>
>>> The discussion in the second one suggests that it should be linking to the public header proj_api.h rather than the private header projects.h.  proj_api.h does exist in the installation I have.  Unless there is an easy fix I can do,  more than I want to mess with.
>>>
>>> -Roy
>>>
>>>
>>>
>>>> On May 29, 2020, at 2:25 PM, Thiago V. dos Santos via R-sig-Geo <r-sig-geo using r-project.org> 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
>>>> 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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>>>>
>>>> _______________________________________________
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>>>
>>>
>>
>> --
>> 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
>
> **********************
> "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***
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>
> "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.
>
>

-- 
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