Re: [R-SIG-Mac] Packages with updated spatial libraries.
Dear Roy, thanks for the message. Is it possible that the sf version you
use links to an older version of GDAL/PROJ than the new rgdal does? In
other words: if you update sf from CRAN, does the error persist?
Many regards,
On 6/22/20 9:28 PM, Roy Mendelssohn - NOAA Federal wrote:
> I installed the whole suite available through Prof. Ripley's efforts, and
> finally have gotten time to do extensive testing. I just ran into a problem
> with code that worked previously. It doesn't break all the mapping code,
> only some. The error I get is given below. And yes I realize that this by
> itself it isn't much help. It is a function calling a function in another
> package that causes the problem. I am going to have to get in with the
> debugger and see what is actually being passed, and I will post what is going
> on in more detail when I figure it out. This is more just a heads-up that
> the new versions can indeed break things in existing code. This is what I
> was hoping to find out, because it is going to take some time to pinpoint
> where.
>
> -Roy
>
>> Error in st_crs.character(comment(x)) : invalid crs: GEOGCRS["unknown",
>> DATUM["World Geodetic System 1984",
>> ELLIPSOID["WGS 84",6378137,298.257223563,
>> LENGTHUNIT["metre",1]],
>> ID["EPSG",6326]],
>> PRIMEM["Greenwich",0,
>> ANGLEUNIT["degree",0.0174532925199433],
>> ID["EPSG",8901]],
>> CS[ellipsoidal,2],
>> AXIS["longitude",east,
>> ORDER[1],
>> ANGLEUNIT["degree",0.0174532925199433,
>> ID["EPSG",9122]]],
>> AXIS["latitude",north,
>> ORDER[2],
>> ANGLEUNIT["degree",0.0174532925199433,
>> ID["EPSG",9122
>> In addition: Warning messages:
>> 1: In rgdal::rawTransform(projfrom, projto, nrow(xy), xy[, 1], xy[, :
>> Using PROJ not WKT2 strings
>> 2: In rgdal::rawTransform(projection(obj), crs, nrow(xy), xy[, 1], :
>> Using PROJ not WKT2 strings
>> 3: In rgdal::rawTransform(projto_int, projfrom, nrow(xy), xy[, 1], :
>>
>> Error in st_crs.character(comment(x)) : invalid crs: GEOGCRS["unknown",
>> DATUM["World Geodetic System 1984",
>> ELLIPSOID["WGS 84",6378137,298.257223563,
>> LENGTHUNIT["metre",1]],
>> ID["EPSG",6326]],
>> PRIMEM["Greenwich",0,
>> ANGLEUNIT["degree",0.0174532925199433],
>> ID["EPSG",8901]],
>> CS[ellipsoidal,2],
>> AXIS["longitude",east,
>> ORDER[1],
>> ANGLEUNIT["degree",0.0174532925199433,
>> ID["EPSG",9122]]],
>> AXIS["latitude",north,
>> ORDER[2],
>> ANGLEUNIT["degree",0.0174532925199433,
>> ID["EPSG",9122
>
> -Roy
>
>
>>
>> On Jun 12, 2020, at 7:20 AM, Roy Mendelssohn - NOAA Federal
>> wrote:
>>
>> I will do the install sometime over the weekend, and test what I have
>> (mainly the packages I have that use these). Today is kind of tis up (I
>> mean I can do the install easily enough, just no time to do any testing).
>>
>> Thanks,
>>
>> -Roy
>>
>>
>>> On Jun 12, 2020, at 7:17 AM, Roger Bivand wrote:
>>>
>>> On Fri, 12 Jun 2020, rmendelss gmail wrote:
>>>
Thank you for these efforts. I imagine it will also make it easier to
eventually have these on CRAN.
>>>
>>> Do you have the possibility to try out the affected packages in your
>>> workflows to provide feedback? At the moment, user feedback can help guide
>>> the deployment of CRAN macOS R-spatial binaries.
>>>
>>> Roger
>>>
-Roy
> On Jun 12, 2020, at 7:11 AM, Prof Brian Ripley
> wrote:
>
> I have put binary packages on CRANextras for lwgeom rgdal rgeos sf built
> with GEOS 3.8.1, GDAL 3.1.0, PROJ 6.3.2.
>
> Install with (e.g.)
>
> options(repos="https://www.stats.ox.ac.uk/pub/RWin;)
> install.packages('rgdal', type = 'binary')
>
> (This needed a development version of the rgdal sources.)
>
> This is just to allow early access: it is planned to use these versions
> of the libs on the CRAN builders soon (but they do need package updates,
> e.g. for rgdal and proj4).
>
> These are all using static libraries to make these self-contained.
>
> (In case anyone is wondering why not PROJ 7 -- that would need unreleased
> changes to the PROJ and GDAL sources and changes to many CRAN packages.)
>
> --
> Brian D. Ripley, rip...@stats.ox.ac.uk
> Emeritus Professor of Applied Statistics, University of Oxford
>
> ___
> R-SIG-Mac mailing list
> R-SIG-Mac@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>>
>>> --
>>> Roger Bivand
>>> Department of Economics, Norwegian School of Economics,
>>> Helleveien 30, N-5045 Bergen, Norway.
>>> voice: +47 55 95 93 55; e-mail: roger.biv...@nhh.no
>>>
Re: [R-SIG-Mac] Packages with updated spatial libraries.
I ran package update this morning, so in CRAN terms I should be up to date.
Based on this email:
https://stat.ethz.ch/pipermail/r-sig-mac/2020-June/013599.html
I installed lwgeom rgdal rgeos sf from that repository. These are built with
GEOS 3.8.1, GDAL 3.1.0, PROJ 6.3.2. It installed 'sf' 0.9-4. I assume these
builds are what will eventually make their way onto CRAN, so that is what I
want to test against. It may well be that a CRS is not improperly defined in
the call given the recent changes, That is what I am trying to find out, so I
can have code that will work.
When I can isolate things I will give more information.
-Roy
> On Jun 22, 2020, at 12:34 PM, Edzer Pebesma
> wrote:
>
> Dear Roy, thanks for the message. Is it possible that the sf version you
> use links to an older version of GDAL/PROJ than the new rgdal does? In
> other words: if you update sf from CRAN, does the error persist?
>
> Many regards,
>
> On 6/22/20 9:28 PM, Roy Mendelssohn - NOAA Federal wrote:
>> I installed the whole suite available through Prof. Ripley's efforts, and
>> finally have gotten time to do extensive testing. I just ran into a problem
>> with code that worked previously. It doesn't break all the mapping code,
>> only some. The error I get is given below. And yes I realize that this by
>> itself it isn't much help. It is a function calling a function in another
>> package that causes the problem. I am going to have to get in with the
>> debugger and see what is actually being passed, and I will post what is
>> going on in more detail when I figure it out. This is more just a heads-up
>> that the new versions can indeed break things in existing code. This is
>> what I was hoping to find out, because it is going to take some time to
>> pinpoint where.
>>
>> -Roy
>>
>>> Error in st_crs.character(comment(x)) : invalid crs: GEOGCRS["unknown",
>>>DATUM["World Geodetic System 1984",
>>>ELLIPSOID["WGS 84",6378137,298.257223563,
>>>LENGTHUNIT["metre",1]],
>>>ID["EPSG",6326]],
>>>PRIMEM["Greenwich",0,
>>>ANGLEUNIT["degree",0.0174532925199433],
>>>ID["EPSG",8901]],
>>>CS[ellipsoidal,2],
>>>AXIS["longitude",east,
>>>ORDER[1],
>>>ANGLEUNIT["degree",0.0174532925199433,
>>>ID["EPSG",9122]]],
>>>AXIS["latitude",north,
>>>ORDER[2],
>>>ANGLEUNIT["degree",0.0174532925199433,
>>>ID["EPSG",9122
>>> In addition: Warning messages:
>>> 1: In rgdal::rawTransform(projfrom, projto, nrow(xy), xy[, 1], xy[, :
>>> Using PROJ not WKT2 strings
>>> 2: In rgdal::rawTransform(projection(obj), crs, nrow(xy), xy[, 1], :
>>> Using PROJ not WKT2 strings
>>> 3: In rgdal::rawTransform(projto_int, projfrom, nrow(xy), xy[, 1], :
>>>
>>> Error in st_crs.character(comment(x)) : invalid crs: GEOGCRS["unknown",
>>>DATUM["World Geodetic System 1984",
>>>ELLIPSOID["WGS 84",6378137,298.257223563,
>>>LENGTHUNIT["metre",1]],
>>>ID["EPSG",6326]],
>>>PRIMEM["Greenwich",0,
>>>ANGLEUNIT["degree",0.0174532925199433],
>>>ID["EPSG",8901]],
>>>CS[ellipsoidal,2],
>>>AXIS["longitude",east,
>>>ORDER[1],
>>>ANGLEUNIT["degree",0.0174532925199433,
>>>ID["EPSG",9122]]],
>>>AXIS["latitude",north,
>>>ORDER[2],
>>>ANGLEUNIT["degree",0.0174532925199433,
>>>ID["EPSG",9122
>>
>> -Roy
>>
>>
>>>
>>> On Jun 12, 2020, at 7:20 AM, Roy Mendelssohn - NOAA Federal
>>> wrote:
>>>
>>> I will do the install sometime over the weekend, and test what I have
>>> (mainly the packages I have that use these). Today is kind of tis up (I
>>> mean I can do the install easily enough, just no time to do any testing).
>>>
>>> Thanks,
>>>
>>> -Roy
>>>
>>>
On Jun 12, 2020, at 7:17 AM, Roger Bivand wrote:
On Fri, 12 Jun 2020, rmendelss gmail wrote:
> Thank you for these efforts. I imagine it will also make it easier to
> eventually have these on CRAN.
>
Do you have the possibility to try out the affected packages in your
workflows to provide feedback? At the moment, user feedback can help guide
the deployment of CRAN macOS R-spatial binaries.
Roger
> -Roy
>
>
>> On Jun 12, 2020, at 7:11 AM, Prof Brian Ripley
>> wrote:
>>
>> I have put binary packages on CRANextras for lwgeom rgdal rgeos sf built
>> with GEOS 3.8.1, GDAL 3.1.0, PROJ 6.3.2.
>>
>> Install with (e.g.)
>>
>> options(repos="https://www.stats.ox.ac.uk/pub/RWin;)
>> install.packages('rgdal', type = 'binary')
>>
>> (This needed a development version of the rgdal sources.)
>>
>> This is just to allow early access: it is planned to use these versions
>> of the libs on the CRAN builders soon (but they do need package
Re: [R-SIG-Mac] Packages with updated spatial libraries.
I installed the whole suite available through Prof. Ripley's efforts, and
finally have gotten time to do extensive testing. I just ran into a problem
with code that worked previously. It doesn't break all the mapping code, only
some. The error I get is given below. And yes I realize that this by itself it
isn't much help. It is a function calling a function in another package that
causes the problem. I am going to have to get in with the debugger and see
what is actually being passed, and I will post what is going on in more detail
when I figure it out. This is more just a heads-up that the new versions can
indeed break things in existing code. This is what I was hoping to find out,
because it is going to take some time to pinpoint where.
-Roy
> Error in st_crs.character(comment(x)) : invalid crs: GEOGCRS["unknown",
> DATUM["World Geodetic System 1984",
> ELLIPSOID["WGS 84",6378137,298.257223563,
> LENGTHUNIT["metre",1]],
> ID["EPSG",6326]],
> PRIMEM["Greenwich",0,
> ANGLEUNIT["degree",0.0174532925199433],
> ID["EPSG",8901]],
> CS[ellipsoidal,2],
> AXIS["longitude",east,
> ORDER[1],
> ANGLEUNIT["degree",0.0174532925199433,
> ID["EPSG",9122]]],
> AXIS["latitude",north,
> ORDER[2],
> ANGLEUNIT["degree",0.0174532925199433,
> ID["EPSG",9122
> In addition: Warning messages:
> 1: In rgdal::rawTransform(projfrom, projto, nrow(xy), xy[, 1], xy[, :
> Using PROJ not WKT2 strings
> 2: In rgdal::rawTransform(projection(obj), crs, nrow(xy), xy[, 1], :
> Using PROJ not WKT2 strings
> 3: In rgdal::rawTransform(projto_int, projfrom, nrow(xy), xy[, 1], :
>
> Error in st_crs.character(comment(x)) : invalid crs: GEOGCRS["unknown",
> DATUM["World Geodetic System 1984",
> ELLIPSOID["WGS 84",6378137,298.257223563,
> LENGTHUNIT["metre",1]],
> ID["EPSG",6326]],
> PRIMEM["Greenwich",0,
> ANGLEUNIT["degree",0.0174532925199433],
> ID["EPSG",8901]],
> CS[ellipsoidal,2],
> AXIS["longitude",east,
> ORDER[1],
> ANGLEUNIT["degree",0.0174532925199433,
> ID["EPSG",9122]]],
> AXIS["latitude",north,
> ORDER[2],
> ANGLEUNIT["degree",0.0174532925199433,
> ID["EPSG",9122
-Roy
>
> On Jun 12, 2020, at 7:20 AM, Roy Mendelssohn - NOAA Federal
> wrote:
>
> I will do the install sometime over the weekend, and test what I have
> (mainly the packages I have that use these). Today is kind of tis up (I
> mean I can do the install easily enough, just no time to do any testing).
>
> Thanks,
>
> -Roy
>
>
>> On Jun 12, 2020, at 7:17 AM, Roger Bivand wrote:
>>
>> On Fri, 12 Jun 2020, rmendelss gmail wrote:
>>
>>> Thank you for these efforts. I imagine it will also make it easier to
>>> eventually have these on CRAN.
>>>
>>
>> Do you have the possibility to try out the affected packages in your
>> workflows to provide feedback? At the moment, user feedback can help guide
>> the deployment of CRAN macOS R-spatial binaries.
>>
>> Roger
>>
>>> -Roy
>>>
>>>
On Jun 12, 2020, at 7:11 AM, Prof Brian Ripley
wrote:
I have put binary packages on CRANextras for lwgeom rgdal rgeos sf built
with GEOS 3.8.1, GDAL 3.1.0, PROJ 6.3.2.
Install with (e.g.)
options(repos="https://www.stats.ox.ac.uk/pub/RWin;)
install.packages('rgdal', type = 'binary')
(This needed a development version of the rgdal sources.)
This is just to allow early access: it is planned to use these versions of
the libs on the CRAN builders soon (but they do need package updates, e.g.
for rgdal and proj4).
These are all using static libraries to make these self-contained.
(In case anyone is wondering why not PROJ 7 -- that would need unreleased
changes to the PROJ and GDAL sources and changes to many CRAN packages.)
--
Brian D. Ripley, rip...@stats.ox.ac.uk
Emeritus Professor of Applied Statistics, University of Oxford
___
R-SIG-Mac mailing list
R-SIG-Mac@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>>
>>>
>>
>> --
>> Roger Bivand
>> Department of Economics, Norwegian School of Economics,
>> Helleveien 30, N-5045 Bergen, Norway.
>> voice: +47 55 95 93 55; e-mail: roger.biv...@nhh.no
>> https://orcid.org/-0003-2392-6140
>> https://scholar.google.no/citations?user=AWeghB0J=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
Re: [R-SIG-Mac] Packages with updated spatial libraries.
On Fri, 12 Jun 2020, rmendelss gmail wrote:
Thank you for these efforts. I imagine it will also make it easier to
eventually have these on CRAN.
Do you have the possibility to try out the affected packages in your
workflows to provide feedback? At the moment, user feedback can help guide
the deployment of CRAN macOS R-spatial binaries.
Roger
-Roy
On Jun 12, 2020, at 7:11 AM, Prof Brian Ripley wrote:
I have put binary packages on CRANextras for lwgeom rgdal rgeos sf built with
GEOS 3.8.1, GDAL 3.1.0, PROJ 6.3.2.
Install with (e.g.)
options(repos="https://www.stats.ox.ac.uk/pub/RWin;)
install.packages('rgdal', type = 'binary')
(This needed a development version of the rgdal sources.)
This is just to allow early access: it is planned to use these versions of the
libs on the CRAN builders soon (but they do need package updates, e.g. for
rgdal and proj4).
These are all using static libraries to make these self-contained.
(In case anyone is wondering why not PROJ 7 -- that would need unreleased
changes to the PROJ and GDAL sources and changes to many CRAN packages.)
--
Brian D. Ripley, rip...@stats.ox.ac.uk
Emeritus Professor of Applied Statistics, University of Oxford
___
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--
Roger Bivand
Department of Economics, Norwegian School of Economics,
Helleveien 30, N-5045 Bergen, Norway.
voice: +47 55 95 93 55; e-mail: roger.biv...@nhh.no
https://orcid.org/-0003-2392-6140
https://scholar.google.no/citations?user=AWeghB0J=en
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Re: [R-SIG-Mac] Packages with updated spatial libraries.
I will do the install sometime over the weekend, and test what I have (mainly
the packages I have that use these). Today is kind of tis up (I mean I can do
the install easily enough, just no time to do any testing).
Thanks,
-Roy
> On Jun 12, 2020, at 7:17 AM, Roger Bivand wrote:
>
> On Fri, 12 Jun 2020, rmendelss gmail wrote:
>
>> Thank you for these efforts. I imagine it will also make it easier to
>> eventually have these on CRAN.
>>
>
> Do you have the possibility to try out the affected packages in your
> workflows to provide feedback? At the moment, user feedback can help guide
> the deployment of CRAN macOS R-spatial binaries.
>
> Roger
>
>> -Roy
>>
>>
>>> On Jun 12, 2020, at 7:11 AM, Prof Brian Ripley
>>> wrote:
>>>
>>> I have put binary packages on CRANextras for lwgeom rgdal rgeos sf built
>>> with GEOS 3.8.1, GDAL 3.1.0, PROJ 6.3.2.
>>>
>>> Install with (e.g.)
>>>
>>> options(repos="https://www.stats.ox.ac.uk/pub/RWin;)
>>> install.packages('rgdal', type = 'binary')
>>>
>>> (This needed a development version of the rgdal sources.)
>>>
>>> This is just to allow early access: it is planned to use these versions of
>>> the libs on the CRAN builders soon (but they do need package updates, e.g.
>>> for rgdal and proj4).
>>>
>>> These are all using static libraries to make these self-contained.
>>>
>>> (In case anyone is wondering why not PROJ 7 -- that would need unreleased
>>> changes to the PROJ and GDAL sources and changes to many CRAN packages.)
>>>
>>> --
>>> Brian D. Ripley, rip...@stats.ox.ac.uk
>>> Emeritus Professor of Applied Statistics, University of Oxford
>>>
>>> ___
>>> R-SIG-Mac mailing list
>>> R-SIG-Mac@r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>
>>
>
> --
> Roger Bivand
> Department of Economics, Norwegian School of Economics,
> Helleveien 30, N-5045 Bergen, Norway.
> voice: +47 55 95 93 55; e-mail: roger.biv...@nhh.no
> https://orcid.org/-0003-2392-6140
> https://scholar.google.no/citations?user=AWeghB0J=en
**
"The contents of this message do not reflect any position of the U.S.
Government or NOAA."
**
Roy Mendelssohn
Supervisory Operations Research Analyst
NOAA/NMFS
Environmental Research Division
Southwest Fisheries Science Center
***Note new street address***
110 McAllister Way
Santa Cruz, CA 95060
Phone: (831)-420-3666
Fax: (831) 420-3980
e-mail: roy.mendelss...@noaa.gov www: https://www.pfeg.noaa.gov/
"Old age and treachery will overcome youth and skill."
"From those who have been given much, much will be expected"
"the arc of the moral universe is long, but it bends toward justice" -MLK Jr.
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Re: [R-SIG-Mac] Packages with updated spatial libraries.
Thank you for these efforts. I imagine it will also make it easier to
eventually have these on CRAN.
-Roy
> On Jun 12, 2020, at 7:11 AM, Prof Brian Ripley wrote:
>
> I have put binary packages on CRANextras for lwgeom rgdal rgeos sf built with
> GEOS 3.8.1, GDAL 3.1.0, PROJ 6.3.2.
>
> Install with (e.g.)
>
> options(repos="https://www.stats.ox.ac.uk/pub/RWin;)
> install.packages('rgdal', type = 'binary')
>
> (This needed a development version of the rgdal sources.)
>
> This is just to allow early access: it is planned to use these versions of
> the libs on the CRAN builders soon (but they do need package updates, e.g.
> for rgdal and proj4).
>
> These are all using static libraries to make these self-contained.
>
> (In case anyone is wondering why not PROJ 7 -- that would need unreleased
> changes to the PROJ and GDAL sources and changes to many CRAN packages.)
>
> --
> Brian D. Ripley, rip...@stats.ox.ac.uk
> Emeritus Professor of Applied Statistics, University of Oxford
>
> ___
> R-SIG-Mac mailing list
> R-SIG-Mac@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
___
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[R-SIG-Mac] Packages with updated spatial libraries.
I have put binary packages on CRANextras for lwgeom rgdal rgeos sf built
with GEOS 3.8.1, GDAL 3.1.0, PROJ 6.3.2.
Install with (e.g.)
options(repos="https://www.stats.ox.ac.uk/pub/RWin;)
install.packages('rgdal', type = 'binary')
(This needed a development version of the rgdal sources.)
This is just to allow early access: it is planned to use these versions
of the libs on the CRAN builders soon (but they do need package updates,
e.g. for rgdal and proj4).
These are all using static libraries to make these self-contained.
(In case anyone is wondering why not PROJ 7 -- that would need
unreleased changes to the PROJ and GDAL sources and changes to many CRAN
packages.)
--
Brian D. Ripley, rip...@stats.ox.ac.uk
Emeritus Professor of Applied Statistics, University of Oxford
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