[R-sig-Geo] rgdal 1.5-8 released on CRAN
Roy Mendelssohn - NOAA Federal
roy@mende|@@ohn @end|ng |rom no@@@gov
Sat May 30 16:56:30 CEST 2020
Thanks. I will make certain that all paths to everything (gdal, proj and geos if needed are fully specified in the command). As I said, gdal-conf and geos-conf are there, as well as the include files for gdal, geos and proj, and they are definitely the more recent versions.
-Roy
> On May 30, 2020, at 7:46 AM, Roger Bivand <Roger.Bivand using nhh.no> wrote:
>
> 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
>>>>>
>>>>> _______________________________________________
>>>>> R-sig-Geo mailing list
>>>>> R-sig-Geo using r-project.org
>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>>>>
>>>>> _______________________________________________
>>>>> R-sig-Geo mailing list
>>>>> R-sig-Geo using r-project.org
>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>>>
>>>>
>>>
>>> --
>>> 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***
>> 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.
>>
>>
>
> --
> 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***
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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