[R-sig-Geo] Unable to perform intersection operations with vectors

[Roger Bivand]

On Wed, 15 Jul 2020, Coyo Tepe wrote:

> Dear Doctor Roger Bivand,
>
> First I have to say thank you for your quick response and secondly I
> am sorry for the confusion. I did not mean you to think I don´t trust
> your comments. Not at all, you are the reference in this matter..

OK, not a problem.

>
>
> I first sent an incomplete message and when I realized it I sent the
> complete one,  that´s why the message was sent twice and I did not
> read your reply before sending this second message.
>

I mis-understood this - you might have added a comment at the head of your 
post. Had I looked at 
https://stat.ethz.ch/pipermail/r-sig-geo/2020-July/thread.html, I would 
have seen that you were replying to yourself, not to my reply.

>
> Regarding your message, you are right, this is a warning, not an error
> and I agree with you that is much better to have warnings that
> problems at the end of the process and not knowing what could be
> wrong.
>
>
> I was not aware thae using the Proj4 strings should not be relied on
> and of course you are right about the comment with shapefile() call,
> this should not be part of the REPEX. Thanks also for the
> recommendation regarding the downgrading or R packages. I have read
> the links you shared regarding the GDAL and PROJ development and is
> more clear to me now.
>

Excellent! Now you and others following the thread have been alerted. What 
we do not know is which workflows will be affected - if we did, we could 
check and only warn those affected. So awareness of changes in 
sp::CRS/raster::crs/sf::st_crs will be needed to let users check whether 
their current workflows (written before the changes) are affected.

Roger

>
> Thank you!!  and again  I am really sorry for the misunderstanding,
>
> El mar., 14 jul. 2020 a las 6:36, Roger Bivand (<Roger.Bivand using nhh.no>) escribió:
>>
>> On Mon, 13 Jul 2020, Coyo Tepe wrote:
>>
>>> Platform and versions
>>> Windows 64 bit
>>> R version 4.0.2 (2020-06-22) -- "Taking Off Again"
>>> Rstudio Version 1.3.959
>>> rgdal: 1.5-12 / gdal: 3.0.4
>>> rgeos version: 0.5-3, (SVN revision 634)
>>> GEOS runtime version: 3.8.0-CAPI-1.13.1
>>> Linking to sp version: 1.4-2
>>> Polygon checking: TRUE
>>>
>>> Problem
>>> We are trying to perform an intersection operation between two vector
>>> layers in shapefile format and we get an error:
>>>
>>> Warning message:
>>> In proj4string(x) : CRS object has comment, which is lost in output
>>
>> As I replied before (and I know with complete certainty, because I wrote
>> and maintain the code), this is a warning, not an error. You (no
>> affiliation, I have no idea what work/research you are doing) and
>> everybody else using R spatial software needs to be aware that Proj4
>> strings (the ones starting with "+proj=") are almost defunct and should
>> not be relied on. Hence the warning. If your workflow is affected by
>> degradation as described in
>> https://www.r-spatial.org/r/2020/03/17/wkt.html and
>> https://rgdal.r-forge.r-project.org/articles/CRS_projections_transformations.html,
>> you will suffer increased imprecision by about 150m.
>>
>> You should in principle trust information from package authors and
>> maintainers much more than random google search hits. I do not contribute
>> to stackoverflow, and while the answer you refer to does concern this
>> issue, it is basically wrong in saying that regular users do not need to
>> pay attention. I have noted why in that thread. Downgrading R/packages
>> makes absolutely no sense, and you should only consider installing old
>> versions of R and packages to reproduce old results.
>>
>> Again, you  are not seeing any errors in your example, only two warnings
>> in the released version of raster, which are (wrongly) suppressed in the
>> development version.
>>
>> Please demonstrate that anything here is an error, and show the output of
>> traceback in your case, which the reprex obviously does not capture. Your
>> reprex also contains totally irrelevant calls to raster::shapefile(),
>> which just writes the polygons to disk but are otherwise without effect.
>>
>> Roger
>>
>>>
>>> Below you can have a REPEX:
>>> ´´
>>> library(rgdal)
>>> library(raster)
>>> library(rgeos)
>>>
>>> #layer a
>>> bbox_a<-c(497555,500000,137000,138000)
>>> extent_a<-extent(bbox_a)
>>> extent_a
>>> capa_a<-as(extent_a,'SpatialPolygons') #creamos un objeto tipo SpatialPolygons
>>> crs(capa_a)<- "+proj=utm +zone=16 +datum=WGS84 +units=m +no_defs"
>>> crs(capa_a)
>>> shapefile(capa_a,paste("capa_a_re",sep="/"),overwrite=TRUE)
>>> plot(capa_a,col="green") #plot(capa_a,col="green")
>>>
>>> #layer b
>>> bbox_b<-c(497995,500050,137100,138100)
>>> extent_b<-extent(bbox_b)
>>> extent_b
>>> capa_b<-as(extent_b,'SpatialPolygons') #creamos un objeto tipo SpatialPolygons
>>> crs(capa_b)<- "+proj=utm +zone=16 +datum=WGS84 +units=m +no_defs"
>>> crs(capa_b)
>>> shapefile(capa_b,paste("capa_b_re",sep="/"),overwrite=TRUE)
>>> plot(capa_b,add=T)
>>>
>>> #buffer
>>> b_buf<-buffer(capa_b,width=50)
>>> plot(b_buf,add=T) #plot(b_buf,add=T,col="blue")
>>>
>>> #intersect
>>> b_intersect<-intersect(capa_a,b_buf)
>>>
>>> #Warning messages:
>>> # 1: In proj4string(x) : CRS object has comment, which is lost in output
>>> # 2: In proj4string(y) : CRS object has comment, which is lost in output
>>>
>>> ´´´
>>>
>>> We have found in the following link:
>>>
>>> https://gis.stackexchange.com/questions/364667/r-4-0-1-not-sure-i-understand-this-message-warning-message-in-proj4stringx
>>>
>>> some comment about this problem: “This is not related to R 4.0.1 but
>>> to rgdal 1.5-8 and the migration to gdal 3 and proj 6. This is a very
>>> long and complex process that impact hundreds maybe thouthands of
>>> packages. All the packages are not yet up-to-date with what is coming.
>>> As a regular user you do not need to pay too much attention on these
>>> warnings but should be aware of what is coming in the geospatial
>>> world.
>>>
>>> You can have a look to ?rgdal::set_thin_PROJ6_warnings() to eliminate
>>> those warnings.”
>>>
>>> However, this warning for us is a problem since it does not allow us
>>> to perform the intersection operation between the 2 layers.
>>>
>>> What we have tried is to pass our R and rgdal to a previous version
>>> (Version rgdal 1.4-8) and R version 3.6.1 (2019-07-05) - "Action of
>>> the Toes" but we would like to know if this is the way to go or there
>>> other options.
>>>
>>> Currently we have managed to get the 3.6.1 R version and but we have
>>> trouble passing to the Rgdal version 1.4-8, hoping that this version
>>> does not have these problems with the warning that we can not perform
>>> the operation of intersection.
>>>
>>> Regarding how to install an older rgdal version we found an interesting link
>>>
>>> (https://stackoverflow.com/questions/51749860/installing-rgdal-backdate-rgdal-version-versus-update-gdal-version-and-how)
>>> that explains how to do it with the following commands:
>>>
>>> require(devtools)
>>> install_version("rgdal", version="1.4-8")
>>> But we get the following error:
>>> ERROR: lazy loading failed for package 'rgdal'
>>> * removing 'C:/Users/pepe/Documents/R/win-library/3.6/rgdal'
>>> * restoring previous 'C:/Users/pepe/Documents/R/win-library/3.6/rgdal'
>>> Error: Failed to install 'unknown package' from URL:
>>>  (converted from warning) installation of
>>> package ‘C:/Users/pepe /AppData/Local/Temp/RtmpqCxtfw/remotes26c7f616614/rgdal’
>>> had non-zero exit status
>>>
>>> Thank you for your help,
>>>
>>> _______________________________________________
>>> R-sig-Geo mailing list
>>> R-sig-Geo using r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>>
>>
>> --
>> Roger Bivand
>> Department of Economics, Norwegian School of Economics,
>> Helleveien 30, N-5045 Bergen, Norway.
>> voice: +47 55 95 93 55; e-mail: Roger.Bivand using nhh.no
>> https://orcid.org/0000-0003-2392-6140
>> https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en
>

-- 
Roger Bivand
Department of Economics, Norwegian School of Economics,
Helleveien 30, N-5045 Bergen, Norway.
voice: +47 55 95 93 55; e-mail: Roger.Bivand using nhh.no
https://orcid.org/0000-0003-2392-6140
https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en