[R] rgdal functions: spTransform and CRS not working

[Ossenbruggen, Paul]

The following are examples from the rgdal library help file.

Neither functions operate properly.

Help is appreciated.
Paul

Example 1
> EPSG <- make_EPSG()
Error in make_EPSG() : Error opening epsg file
> EPSG[grep("Oslo", EPSG$note), 1:2]
Error: object 'EPSG' not found
> EPSG[1925:1927, 3]
Error: object 'EPSG' not found


Example 2
> data(meuse)
> coordinates(meuse) <- c("x", "y")
> proj4string(meuse) <- CRS(paste("+init=epsg:28992",
+ "+towgs84=565.237,50.0087,465.658,-0.406857,0.350733,-1.87035,4.0812"))
NOTE: rgdal::checkCRSArgs: no proj_defs.dat in PROJ.4 shared files
Error in CRS(paste("+init=epsg:28992", "+towgs84=565.237,50.0087,465.658,-0.406857,0.350733,-1.87035,4.0812")) :
no system list, errno: 2
> # see http://trac.osgeo.org/gdal/ticket/1987
> summary(meuse)
Object of class SpatialPointsDataFrame
Coordinates:
min max
x 178605 181390
y 329714 333611
Is projected: NA
proj4string : [NA]
Number of points: 155
Data attributes:
cadmium copper lead zinc
Min. : 0.200 Min. : 14.00 Min. : 37.0 Min. : 113.0
1st Qu.: 0.800 1st Qu.: 23.00 1st Qu.: 72.5 1st Qu.: 198.0
Median : 2.100 Median : 31.00 Median :123.0 Median : 326.0
Mean : 3.246 Mean : 40.32 Mean :153.4 Mean : 469.7
3rd Qu.: 3.850 3rd Qu.: 49.50 3rd Qu.:207.0 3rd Qu.: 674.5
Max. :18.100 Max. :128.00 Max. :654.0 Max. :1839.0

elev dist om ffreq soil lime
Min. : 5.180 Min. :0.00000 Min. : 1.000 1:84 1:97 0:111
1st Qu.: 7.546 1st Qu.:0.07569 1st Qu.: 5.300 2:48 2:46 1: 44
Median : 8.180 Median :0.21184 Median : 6.900 3:23 3:12
Mean : 8.165 Mean :0.24002 Mean : 7.478
3rd Qu.: 8.955 3rd Qu.:0.36407 3rd Qu.: 9.000
Max. :10.520 Max. :0.88039 Max. :17.000
NA's :2
landuse dist.m
W :50 Min. : 10.0
Ah :39 1st Qu.: 80.0
Am :22 Median : 270.0
Fw :10 Mean : 290.3
Ab : 8 3rd Qu.: 450.0
(Other):25 Max. :1000.0
NA's : 1
> meuse.utm <- spTransform(meuse, CRS("+proj=utm +zone=32 +datum=WGS84"))
NOTE: rgdal::checkCRSArgs: no proj_defs.dat in PROJ.4 shared files
Error in spTransform(xSP, CRSobj, ...) :
No transformation possible from NA reference system
> summary(meuse.utm)
Error in summary(meuse.utm) : object 'meuse.utm' not found
>
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[David Winsemius]

> On Jan 13, 2017, at 1:21 PM, Ossenbruggen, Paul <Paul.Oss...@unh.edu> wrote:
>
> The following are examples from the rgdal library help file.
>
> Neither functions operate properly.
>
> Help is appreciated.
> Paul
>
> Example 1
>> EPSG <- make_EPSG()
> Error in make_EPSG() : Error opening epsg file

I get the same error. Using OSX:

Built: R 3.3.2; x86_64-apple-darwin13.4.0; 2016-12-17 14:34:29 UTC; unix

.... with recently updated rgdal but did not update either GDAL or PROJ4

Loaded GDAL runtime: GDAL 2.1.2, released 2016/10/24
Path to GDAL shared files:
Loaded PROJ.4 runtime: Rel. 4.9.1, 04 March 2015,

which I am seeing some documented problems with

... when I search on the warning message:

WARNING: no proj_defs.dat in PROJ.4 shared files

... I got when loading rgdal:

https://github.com/OSGeo/proj.4/issues/351

So I'm wondering what OS you have and what version of GDAL and PROJ4 you are using. I'm quitting my session so I can update my system structure. I've had success in hte past with the KingChaos disk images:

GDAL 2.1 Complete
http://www.kyngchaos.com/files/software/frameworks/GDAL_Complete-2.1.dmg

Used the disk image from Finder.app

That failed to resolve the warning or the error from rgdal::make_EPSG. Tried (re-)installing rgdal from current source tar.gz file using install.packages. Got an error relating to missing gdal-config

So based on a stackOverflow solution from Fran Villamil: http://stackoverflow.com/questions/34333624/trouble-installing-rgdal/37829420#37829420, I tried (from the R console):

install.packages('rgdal', type = "source", configure.args=c(
'--with-gdal-config=/Library/Frameworks/GDAL.framework/Programs/gdal-config',
'--with-proj-include=/Library/Frameworks/PROJ.framework/Headers',
'--with-proj-lib=/Library/Frameworks/PROJ.framework/unix/lib'))


reloaded R and ... no warnings or errors

I'm a somewhat clueless, albeit noisy user of R. I don't really have the development skills to figure out how to construct the code to tie together all these compiled bits, but I do find that searching is often sufficient to solve problems. If this is not an exact match to your situation, then you should first read the posting guide and include sufficient information about _your_ OS, your system tools, and versions of external-to-R packages to support a more focussed discussion.

Best;
David.

David Winsemius
Alameda, CA, USA

[Roger Bivand]

I apologise for not following up in-thread, as I used to use Gmane to
reply to postings read digested before its (hopefully temporary) demise.

The problem is that the CRAN OSX binaries for rgdal are shipping without
two key folders, proj/ and gdal/. Until we get it fixed, please see if you
can download the equivalent Windows binary package:

https://cran.r-project.org/bin/windows/contrib/3.3/rgdal_1.2-5.zip

unzip it (do not install it), and copy the proj/ and gdal/ folders with
their contents to the folder shown (in R) by:

system.file("", package="rgdal")

For OSX-specific questions like this, you could try R-sig-mac, for spatial
data R-sig-geo. Always show the output of sessionInfo() when reporting
issues.

--
Roger Bivand
Department of Economics, Norwegian School of Economics,
Helleveien 30, N-5045 Bergen, Norway.
voice: +47 55 95 93 55; e-mail: Roger....@nhh.no
http://orcid.org/0000-0003-2392-6140
https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en
http://depsy.org/person/434412

[Ossenbruggen, Paul]

Thank you for your assistance.

David Winsemius gave me a work around solution that addresses the issue.

I thank both of you.

Paul

Sent from my iPad

> On Jan 16, 2017, at 5:02 AM, Roger Bivand <Roger....@nhh.no> wrote:
>
> I apologise for not following up in-thread, as I used to use Gmane to reply to postings read digested before its (hopefully temporary) demise.
>
> The problem is that the CRAN OSX binaries for rgdal are shipping without two key folders, proj/ and gdal/. Until we get it fixed, please see if you can download the equivalent Windows binary package:
>

> https://urldefense.proofpoint.com/v2/url?u=https-3A__cran.r-2Dproject.org_bin_windows_contrib_3.3_rgdal-5F1.2-2D5.zip&d=DwIBAg&c=c6MrceVCY5m5A_KAUkrdoA&r=WDD4_Yg52kDcV1-aTnZGuPa5XvnE9sRyJLzwnTtaEa4&m=dgU0yI25qorGYcBVyZbsn1WJw773Uh-jx0lQHACi8t0&s=wnPJ31FbUqePLKa2rQgFFPi0-GvGKY8XFGUZQHoEmGY&e=

> unzip it (do not install it), and copy the proj/ and gdal/ folders with
> their contents to the folder shown (in R) by:
>
> system.file("", package="rgdal")
>
> For OSX-specific questions like this, you could try R-sig-mac, for spatial data R-sig-geo. Always show the output of sessionInfo() when reporting issues.
>
> --
> Roger Bivand
> Department of Economics, Norwegian School of Economics,
> Helleveien 30, N-5045 Bergen, Norway.
> voice: +47 55 95 93 55; e-mail: Roger....@nhh.no

> https://urldefense.proofpoint.com/v2/url?u=http-3A__orcid.org_0000-2D0003-2D2392-2D6140&d=DwIBAg&c=c6MrceVCY5m5A_KAUkrdoA&r=WDD4_Yg52kDcV1-aTnZGuPa5XvnE9sRyJLzwnTtaEa4&m=dgU0yI25qorGYcBVyZbsn1WJw773Uh-jx0lQHACi8t0&s=vkKFU5pFCkqarbvnL7h3LHTf2FOeqRHz5kXzN-LepwE&e= https://urldefense.proofpoint.com/v2/url?u=https-3A__scholar.google.no_citations-3Fuser-3DAWeghB0AAAAJ-26hl-3Den&d=DwIBAg&c=c6MrceVCY5m5A_KAUkrdoA&r=WDD4_Yg52kDcV1-aTnZGuPa5XvnE9sRyJLzwnTtaEa4&m=dgU0yI25qorGYcBVyZbsn1WJw773Uh-jx0lQHACi8t0&s=BzwpcCxeGE8YMisKdas7VFF6YDAXFoMyLygD2PI5XGU&e= https://urldefense.proofpoint.com/v2/url?u=http-3A__depsy.org_person_434412&d=DwIBAg&c=c6MrceVCY5m5A_KAUkrdoA&r=WDD4_Yg52kDcV1-aTnZGuPa5XvnE9sRyJLzwnTtaEa4&m=dgU0yI25qorGYcBVyZbsn1WJw773Uh-jx0lQHACi8t0&s=vDry50VlCgUoz7ZoJu5j2rg-DBKK2fPQ9jjWxOLNoIc&e=