[R-sig-Geo] rgdal error in pj_transform: failed to load datum shift file

Fri Jan 27 10:32:06 CET 2017

You didn't say that you were using OSX, and probably originally the CRAN 
OSX rgdal binary. If that is the case, 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")

The problem you most likely found was that the person building CRAN rgdal 
OSX binaries forgot to set configure arguments to package these two 
folders. You also probably ignored a startup warning.

For rgdal queries, always state verbatim the output of sessionInfo() and 
the output of the startup messages shown when rgdal is loaded and 
attached.

Roger

On Fri, 27 Jan 2017, Olivia Burge wrote:

> Dear all,
>
> Fixed eventually after using a number of different install options, of
> which only this one worked:
>
> 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',
> '--with-data-copy=yes',
> '--with-proj-data=/Library/Frameworks/PROJ.framework/unix/share/proj'))
>
> The latter two made the difference.
>
> Note in my .bash_profile I also added the gdal path:
> export PATH=/Library/Frameworks/GDAL.framework/Programs:$PATH
>
> Regards,
>
> Olivia
>
> On Fri, Jan 27, 2017 at 3:02 PM Olivia Burge <olivia.burge at gmail.com> wrote:
>
>> Dear list,
>>
>> I am having some trouble transforming data (ie reprojecting) after
>> installing rgdal, etc on a new mac.
>>
>> The error message is:
>>> wgs84 <- CRS("+proj=longlat +datum=WGS84 +no_defs ")
>>> df <- spTransform(locs_sp, CRS = wgs84)
>> Error in spTransform(xSP, CRSobj, ...) :
>>   error in pj_transform: failed to load datum shift file.
>>
>> locs_sp dput output:
>>
>> new("SpatialPointsDataFrame"
>>     , data = structure(list(Plot = c(1L, 2L, 3L, 4L, 5L, 6L, 1L, 1L, 4L,
>> 9L,
>> 19L, 20L), Wetland = structure(c(2L, 2L, 2L, 2L, 2L, 2L, 3L,
>> 4L, 4L, 4L, 4L, 4L), .Label = c("", "Awarua", "Bayswater", "Dunearn"
>> ), class = "factor")), .Names = c("Plot", "Wetland"), row.names = c(NA,
>> 12L), class = "data.frame")
>>     , coords.nrs = numeric(0)
>>     , coords = structure(c(2159130, 2159243, 2159242, 2159240, 2159504,
>> 2157624,
>> 2126982, 2138135, 2138087, 2137919, 2137472, 2137450, 5397279,
>> 5397304, 5397304, 5392166, 5397215, 5395541, 5439946, 5456416,
>> 5456657, 5456657, 5456659, 5456662), .Dim = c(12L, 2L), .Dimnames = list(
>>     c("1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11",
>>     "12"), c("NZMGE", "NZMGN")))
>>     , bbox = structure(c(2126982, 5392166, 2159504, 5456662), .Dim = c(2L,
>> 2L), .Dimnames = list(c("NZMGE", "NZMGN"), c("min", "max")))
>>     , proj4string = new("CRS"
>>     , projargs = "+proj=nzmg +lat_0=-41 +lon_0=173 +x_0=2510000
>> +y_0=6023150 +ellps=intl +units=m +nadgrids=nzgd2kgrid0005.gsb"
>> )
>> )
>>
>> I have a windows computer with rgdal & R on and it works fine on there.
>>
>> When I load rgdal, I get:
>>> require(rgdal)
>> Loading required package: rgdal
>> Loading required package: sp
>> rgdal: version: 1.2-5, (SVN revision 648)
>>  Geospatial Data Abstraction Library extensions to R successfully loaded
>>  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, [PJ_VERSION: 491]
>>  Path to PROJ.4 shared files: (autodetected)
>>  Linking to sp version: 1.2-3
>>
>> I have seen reference to the output of this:
>>> system.file("proj", package= "rgdal")
>> elsewhere. The output is simply ""
>>
>> SessionInfo:
>> R version 3.3.2 (2016-10-31)
>> Platform: x86_64-apple-darwin13.4.0 (64-bit)
>> Running under: macOS Sierra 10.12.1
>>
>> locale:
>> [1] en_NZ.UTF-8/en_NZ.UTF-8/en_NZ.UTF-8/C/en_NZ.UTF-8/en_NZ.UTF-8
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>> other attached packages:
>> [1] ggmap_2.7          ggplot2_2.2.1.9000 rgdal_1.2-5        sp_1.2-4
>>
>>
>> loaded via a namespace (and not attached):
>>  [1] Rcpp_0.12.9       magrittr_1.5      maps_3.1.1        munsell_0.4.3
>>   colorspace_1.3-2  geosphere_1.5-5
>>  [7] lattice_0.20-34   R6_2.2.0          rjson_0.2.15      jpeg_0.1-8
>>    dplyr_0.5.0       stringr_1.1.0
>> [13] plyr_1.8.4        tools_3.3.2       grid_3.3.2        gtable_0.2.0
>>    png_0.1-7         DBI_0.5-1
>> [19] lazyeval_0.2.0    assertthat_0.1    tibble_1.2        mapproj_1.2-4
>>   reshape2_1.4.2    bitops_1.0-6
>> [25] stringi_1.1.2     RgoogleMaps_1.4.1 scales_0.4.1      proto_1.0.0
>>
>> Any help would be greatly appreciated. I will be out the office for a week
>> on fieldwork in a couple of hours, after which I won't be able to test
>> anything until I return.
>>
>> Kind regards,
>>
>> Olivia
>>
>>
>>
>>
>
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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.Bivand at nhh.no
http://orcid.org/0000-0003-2392-6140
https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en
http://depsy.org/person/434412