rgdal 1.5-8 released on CRAN

classic Classic list List threaded Threaded
24 messages Options
12
Reply | Threaded
Open this post in threaded view
|

rgdal 1.5-8 released on CRAN

Roger Bivand
Administrator
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: [hidden email]
https://orcid.org/0000-0003-2392-6140
https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en

_______________________________________________
R-sig-Geo mailing list
[hidden email]
https://stat.ethz.ch/mailman/listinfo/r-sig-geo
Roger Bivand
Department of Economics
Norwegian School of Economics
Helleveien 30
N-5045 Bergen, Norway
Reply | Threaded
Open this post in threaded view
|

Re: rgdal 1.5-8 released on CRAN

R-sig-geo mailing list
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 <[hidden email]> 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: [hidden email]
https://orcid.org/0000-0003-2392-6140
https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en

_______________________________________________
R-sig-Geo mailing list
[hidden email]
https://stat.ethz.ch/mailman/listinfo/r-sig-geo

_______________________________________________
R-sig-Geo mailing list
[hidden email]
https://stat.ethz.ch/mailman/listinfo/r-sig-geo
Reply | Threaded
Open this post in threaded view
|

Re: rgdal 1.5-8 released on CRAN

R-sig-geo mailing list
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>
>          ^~~~~~~~~~~~


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 <[hidden email]> 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 <[hidden email]> 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: [hidden email]
> https://orcid.org/0000-0003-2392-6140
> https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en
>
> _______________________________________________
> R-sig-Geo mailing list
> [hidden email]
> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>
> _______________________________________________
> R-sig-Geo mailing list
> [hidden email]
> https://stat.ethz.ch/mailman/listinfo/r-sig-geo


        [[alternative HTML version deleted]]

_______________________________________________
R-sig-Geo mailing list
[hidden email]
https://stat.ethz.ch/mailman/listinfo/r-sig-geo
Reply | Threaded
Open this post in threaded view
|

Re: rgdal 1.5-8 released on CRAN

chris english-2
And not desiring to muddy Thiago's clear waters, but when is Proj7*
transition expected?

Chris

On Fri, May 29, 2020 at 5:46 PM Roy Mendelssohn - NOAA Federal via
R-sig-Geo <[hidden email]> 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>
> >          ^~~~~~~~~~~~
>
>
> 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 <
> [hidden email]> 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 <
> [hidden email]> 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: [hidden email]
> > https://orcid.org/0000-0003-2392-6140
> > https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en
> >
> > _______________________________________________
> > R-sig-Geo mailing list
> > [hidden email]
> > https://stat.ethz.ch/mailman/listinfo/r-sig-geo
> >
> > _______________________________________________
> > R-sig-Geo mailing list
> > [hidden email]
> > https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>
>
>         [[alternative HTML version deleted]]
>
> _______________________________________________
> R-sig-Geo mailing list
> [hidden email]
> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>

        [[alternative HTML version deleted]]

_______________________________________________
R-sig-Geo mailing list
[hidden email]
https://stat.ethz.ch/mailman/listinfo/r-sig-geo
Reply | Threaded
Open this post in threaded view
|

Re: rgdal 1.5-8 released on CRAN

chris english-2
My problems of install of sf and dependencies were fixed by rgdal-1.5-9 and
additionally
upgrading lwgeom and all other dependencies. Thank you all for your efforts
and I am
in ubuntu 20.04.

On Fri, May 29, 2020 at 5:57 PM chris english <[hidden email]>
wrote:

> And not desiring to muddy Thiago's clear waters, but when is Proj7*
> transition expected?
>
> Chris
>
> On Fri, May 29, 2020 at 5:46 PM Roy Mendelssohn - NOAA Federal via
> R-sig-Geo <[hidden email]> 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>
>> >          ^~~~~~~~~~~~
>>
>>
>> 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 <
>> [hidden email]> 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 <
>> [hidden email]> 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: [hidden email]
>> > https://orcid.org/0000-0003-2392-6140
>> > https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en
>> >
>> > _______________________________________________
>> > R-sig-Geo mailing list
>> > [hidden email]
>> > https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>> >
>> > _______________________________________________
>> > R-sig-Geo mailing list
>> > [hidden email]
>> > https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>
>>
>>         [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> R-sig-Geo mailing list
>> [hidden email]
>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>
>

        [[alternative HTML version deleted]]

_______________________________________________
R-sig-Geo mailing list
[hidden email]
https://stat.ethz.ch/mailman/listinfo/r-sig-geo
Reply | Threaded
Open this post in threaded view
|

Re: rgdal 1.5-8 released on CRAN

R-sig-geo mailing list

Where did you get  rgdal-1.5-9?  On CRAN I see  rgdal-1.5-8 and that is what I was trying.

Thanks,

-Roy

> On May 29, 2020, at 5:27 PM, chris english <[hidden email]> wrote:
>
> My problems of install of sf and dependencies were fixed by rgdal-1.5-9 and additionally
> upgrading lwgeom and all other dependencies. Thank you all for your efforts and I am
> in ubuntu 20.04.
>
> On Fri, May 29, 2020 at 5:57 PM chris english <[hidden email]> wrote:
> And not desiring to muddy Thiago's clear waters, but when is Proj7* transition expected?
>
> Chris
>
> On Fri, May 29, 2020 at 5:46 PM Roy Mendelssohn - NOAA Federal via R-sig-Geo <[hidden email]> 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>
> >          ^~~~~~~~~~~~
>
>
> 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 <[hidden email]> 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 <[hidden email]> 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: [hidden email]
> > https://orcid.org/0000-0003-2392-6140
> > https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en
> >
> > _______________________________________________
> > R-sig-Geo mailing list
> > [hidden email]
> > https://stat.ethz.ch/mailman/listinfo/r-sig-geo
> >
> > _______________________________________________
> > R-sig-Geo mailing list
> > [hidden email]
> > https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>
>
>         [[alternative HTML version deleted]]
>
> _______________________________________________
> R-sig-Geo mailing list
> [hidden email]
> 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: [hidden email] 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
[hidden email]
https://stat.ethz.ch/mailman/listinfo/r-sig-geo
Reply | Threaded
Open this post in threaded view
|

Re: rgdal 1.5-8 released on CRAN

Roger Bivand
Administrator
On Sat, 30 May 2020, Roy Mendelssohn - NOAA Federal via R-sig-Geo wrote:

>
> Where did you get rgdal-1.5-9?  On CRAN I see rgdal-1.5-8 and that is
> what I was trying.

See earlier posts on this list May 29.

Roger

>
> Thanks,
>
> -Roy
>
>> On May 29, 2020, at 5:27 PM, chris english <[hidden email]> wrote:
>>
>> My problems of install of sf and dependencies were fixed by rgdal-1.5-9 and additionally
>> upgrading lwgeom and all other dependencies. Thank you all for your efforts and I am
>> in ubuntu 20.04.
>>
>> On Fri, May 29, 2020 at 5:57 PM chris english <[hidden email]> wrote:
>> And not desiring to muddy Thiago's clear waters, but when is Proj7* transition expected?
>>
>> Chris
>>
>> On Fri, May 29, 2020 at 5:46 PM Roy Mendelssohn - NOAA Federal via R-sig-Geo <[hidden email]> 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>
>>>          ^~~~~~~~~~~~
>>
>>
>> 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 <[hidden email]> 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 <[hidden email]> 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: [hidden email]
>>> https://orcid.org/0000-0003-2392-6140
>>> https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en
>>>
>>> _______________________________________________
>>> R-sig-Geo mailing list
>>> [hidden email]
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>>
>>> _______________________________________________
>>> R-sig-Geo mailing list
>>> [hidden email]
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>
>>
>>         [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> R-sig-Geo mailing list
>> [hidden email]
>> 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: [hidden email] 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
> [hidden email]
> 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: [hidden email]
https://orcid.org/0000-0003-2392-6140
https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en
_______________________________________________
R-sig-Geo mailing list
[hidden email]
https://stat.ethz.ch/mailman/listinfo/r-sig-geo
Roger Bivand
Department of Economics
Norwegian School of Economics
Helleveien 30
N-5045 Bergen, Norway
Reply | Threaded
Open this post in threaded view
|

Re: rgdal 1.5-8 released on CRAN

Roger Bivand
Administrator
In reply to this post by R-sig-geo mailing list
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 <[hidden email]> 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 <[hidden email]> 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: [hidden email]
>> https://orcid.org/0000-0003-2392-6140
>> https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en
>>
>> _______________________________________________
>> R-sig-Geo mailing list
>> [hidden email]
>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>
>> _______________________________________________
>> R-sig-Geo mailing list
>> [hidden email]
>> 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: [hidden email]
https://orcid.org/0000-0003-2392-6140
https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en
_______________________________________________
R-sig-Geo mailing list
[hidden email]
https://stat.ethz.ch/mailman/listinfo/r-sig-geo
Roger Bivand
Department of Economics
Norwegian School of Economics
Helleveien 30
N-5045 Bergen, Norway
Reply | Threaded
Open this post in threaded view
|

Re: rgdal 1.5-8 released on CRAN

Roger Bivand
Administrator
In reply to this post by R-sig-geo mailing list
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 <[hidden email]> 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: [hidden email]
https://orcid.org/0000-0003-2392-6140
https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en
_______________________________________________
R-sig-Geo mailing list
[hidden email]
https://stat.ethz.ch/mailman/listinfo/r-sig-geo
Roger Bivand
Department of Economics
Norwegian School of Economics
Helleveien 30
N-5045 Bergen, Norway
Reply | Threaded
Open this post in threaded view
|

Re: rgdal 1.5-8 released on CRAN

chris english-2
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 <[hidden email]> 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 <
> [hidden email]> 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: [hidden email]
> https://orcid.org/0000-0003-2392-6140
> https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en
> _______________________________________________
> R-sig-Geo mailing list
> [hidden email]
> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>

        [[alternative HTML version deleted]]

_______________________________________________
R-sig-Geo mailing list
[hidden email]
https://stat.ethz.ch/mailman/listinfo/r-sig-geo
Reply | Threaded
Open this post in threaded view
|

Re: rgdal 1.5-8 released on CRAN

R-sig-geo mailing list
In reply to this post by Roger Bivand
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.

-Roy


> On May 30, 2020, at 4:56 AM, Roger Bivand <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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: [hidden email]
>>> https://orcid.org/0000-0003-2392-6140
>>> https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en
>>>
>>> _______________________________________________
>>> R-sig-Geo mailing list
>>> [hidden email]
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>>
>>> _______________________________________________
>>> R-sig-Geo mailing list
>>> [hidden email]
>>> 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: [hidden email]
> 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: [hidden email] 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
[hidden email]
https://stat.ethz.ch/mailman/listinfo/r-sig-geo
Reply | Threaded
Open this post in threaded view
|

Re: rgdal 1.5-8 released on CRAN

R-sig-geo mailing list
In reply to this post by chris english-2
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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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: [hidden email]
> https://orcid.org/0000-0003-2392-6140
> https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en_______________________________________________
> R-sig-Geo mailing list
> [hidden email]
> 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: [hidden email] 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
[hidden email]
https://stat.ethz.ch/mailman/listinfo/r-sig-geo
Reply | Threaded
Open this post in threaded view
|

Re: rgdal 1.5-8 released on CRAN

Roger Bivand
Administrator
In reply to this post by R-sig-geo mailing list
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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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: [hidden email]
>>>> https://orcid.org/0000-0003-2392-6140
>>>> https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en
>>>>
>>>> _______________________________________________
>>>> R-sig-Geo mailing list
>>>> [hidden email]
>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>>>
>>>> _______________________________________________
>>>> R-sig-Geo mailing list
>>>> [hidden email]
>>>> 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: [hidden email]
>> 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: [hidden email] 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: [hidden email]
https://orcid.org/0000-0003-2392-6140
https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en
_______________________________________________
R-sig-Geo mailing list
[hidden email]
https://stat.ethz.ch/mailman/listinfo/r-sig-geo
Roger Bivand
Department of Economics
Norwegian School of Economics
Helleveien 30
N-5045 Bergen, Norway
Reply | Threaded
Open this post in threaded view
|

Re: rgdal 1.5-8 released on CRAN

R-sig-geo mailing list
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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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: [hidden email]
>>>>> https://orcid.org/0000-0003-2392-6140
>>>>> https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en
>>>>>
>>>>> _______________________________________________
>>>>> R-sig-Geo mailing list
>>>>> [hidden email]
>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>>>>
>>>>> _______________________________________________
>>>>> R-sig-Geo mailing list
>>>>> [hidden email]
>>>>> 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: [hidden email]
>>> 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: [hidden email] 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: [hidden email]
> 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: [hidden email] 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
[hidden email]
https://stat.ethz.ch/mailman/listinfo/r-sig-geo
Reply | Threaded
Open this post in threaded view
|

Re: rgdal 1.5-8 released on CRAN

chris english-2
In reply to this post by R-sig-geo mailing list
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 <
[hidden email]> 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 <
> [hidden email]> 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 <[hidden email]>
> 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 <
> [hidden email]> 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: [hidden email]
> > https://orcid.org/0000-0003-2392-6140
> >
> https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en_______________________________________________
> > R-sig-Geo mailing list
> > [hidden email]
> > 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: [hidden email] 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.
>
>

        [[alternative HTML version deleted]]

_______________________________________________
R-sig-Geo mailing list
[hidden email]
https://stat.ethz.ch/mailman/listinfo/r-sig-geo
Reply | Threaded
Open this post in threaded view
|

Re: rgdal 1.5-8 released on CRAN

R-sig-geo mailing list
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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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: [hidden email]
> > https://orcid.org/0000-0003-2392-6140
> > https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en_______________________________________________
> > R-sig-Geo mailing list
> > [hidden email]
> > 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: [hidden email] 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: [hidden email] 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
[hidden email]
https://stat.ethz.ch/mailman/listinfo/r-sig-geo
Reply | Threaded
Open this post in threaded view
|

Re: rgdal 1.5-8 released on CRAN

chris english-2
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 <[hidden email]> 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 <
> [hidden email]> 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 <
> [hidden email]> 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 <
> [hidden email]> 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 <[hidden email]>
> 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 <
> [hidden email]> 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: [hidden email]
> > > https://orcid.org/0000-0003-2392-6140
> > >
> https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en_______________________________________________
> > > R-sig-Geo mailing list
> > > [hidden email]
> > > 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: [hidden email] 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: [hidden email] 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
> [hidden email]
> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>

        [[alternative HTML version deleted]]

_______________________________________________
R-sig-Geo mailing list
[hidden email]
https://stat.ethz.ch/mailman/listinfo/r-sig-geo
Reply | Threaded
Open this post in threaded view
|

Re: rgdal 1.5-8 released on CRAN

robinlovelace
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 <[hidden email]>
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 <[hidden email]> 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 <
> > [hidden email]> 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 <
> > [hidden email]> 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 <
> > [hidden email]> 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 <[hidden email]>
> > 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 <
> > [hidden email]> 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: [hidden email]
> > > > https://orcid.org/0000-0003-2392-6140
> > > >
> >
> https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en_______________________________________________
> > > > R-sig-Geo mailing list
> > > > [hidden email]
> > > > 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: [hidden email] 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: [hidden email] 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
> > [hidden email]
> > https://stat.ethz.ch/mailman/listinfo/r-sig-geo
> >
>
>         [[alternative HTML version deleted]]
>
> _______________________________________________
> R-sig-Geo mailing list
> [hidden email]
> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>

        [[alternative HTML version deleted]]

_______________________________________________
R-sig-Geo mailing list
[hidden email]
https://stat.ethz.ch/mailman/listinfo/r-sig-geo
Reply | Threaded
Open this post in threaded view
|

Re: rgdal 1.5-8 released on CRAN

R-sig-geo mailing list


> On May 30, 2020, at 12:40 PM, Robin Lovelace <[hidden email]> wrote:
>
> 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.

-Ditto.  I am just interested in seeing if I can get it to work.  It is not always possible for developers to have every OS right at hand to develop and test on. It helped in my case to get version 1.59,  and I since things were in non-standard places I had to set those.

-Roy


**********************
"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: [hidden email] 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
[hidden email]
https://stat.ethz.ch/mailman/listinfo/r-sig-geo
Reply | Threaded
Open this post in threaded view
|

Re: rgdal 1.5-8 released on CRAN

chris english-2
And I'm very grateful for Robin's
https://bookdown.org/robinlovelace/geocompr/intro.html, because at this
point my lazy days
of rstudio are broken and his book provides a very helpful and informative
re-introduction to accomplishing what I need from
the command line. Roy, did permissions figure in your difficulties or was
that an ubuntu based herring whose checking bore no
fruit?
Chris

On Sat, May 30, 2020 at 4:02 PM Roy Mendelssohn - NOAA Federal via
R-sig-Geo <[hidden email]> wrote:

>
>
> > On May 30, 2020, at 12:40 PM, Robin Lovelace <[hidden email]> wrote:
> >
> > 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.
>
> -Ditto.  I am just interested in seeing if I can get it to work.  It is
> not always possible for developers to have every OS right at hand to
> develop and test on. It helped in my case to get version 1.59,  and I since
> things were in non-standard places I had to set those.
>
> -Roy
>
>
> **********************
> "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: [hidden email] 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
> [hidden email]
> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>

        [[alternative HTML version deleted]]

_______________________________________________
R-sig-Geo mailing list
[hidden email]
https://stat.ethz.ch/mailman/listinfo/r-sig-geo
12