[R-SIG-Mac] Mac-only problem using readOGR() to read a shapefile from a directory on a USB pen drive

D G. Rossiter d.g.rossiter at cornell.edu
Mon Mar 6 20:48:03 CET 2017 

Good idea. From the shell, ogrInfo correctly reads the shapefile:

$ ogrInfo /Volumes/DRENTHE/ds/NEweather/ gdd50_7100j | more
INFO: Open of `/Volumes/DRENTHE/ds/NEweather/'
      using driver `ESRI Shapefile' successful.

Layer name: gdd50_7100j
Geometry: Point
Feature Count: 5556
Extent: (-177.350000, -14.330000) - (174.100000, 71.280000)
Layer SRS WKT:
GEOGCS["GCS_North_American_1927",
    DATUM["North_American_Datum_1927",
        SPHEROID["Clarke_1866",6378206.4,294.9786982]],
    PRIMEM["Greenwich",0.0],
    UNIT["Degree",0.0174532925199433]]
STATION_ID: Integer (6.0)
STATE: String (2.0)
STATION_NA: String (24.0)

etc.

This is indeed an MS-DOS USB device (which came from a meeting at the Drenthe (NL) provincial enviromental bureau, hence the volume name):

$ mount | grep DRENTHE
/dev/disk3s1 on /Volumes/DRENTHE (msdos, local, nodev, nosuid, noowners)

From R comes the failure with readOGR:

> usa <- readOGR(dsn="/Volumes/DRENTHE/ds/NEweather/", layer=“gdd50_7100”)
Error in ogrInfo(dsn = dsn, layer = layer, encoding = encoding, use_iconv = use_iconv,  : 
  Cannot open data source

D G (David) Rossiter
Section of Soil & Crop Sciences
Cornell University
http://www.css.cornell.edu/faculty/dgr2/

> On 06 Mar 2017, at 12:56, MacQueen, Don <macqueen1 at llnl.gov> wrote:
> 
> It would be informative to try ogrInfo from the shell prompt (i.e., outside of R) to find out if this is an R problem or an ogrInfo problem.
> 
> -Don
> 
> -- 
> Don MacQueen
> 
> Lawrence Livermore National Laboratory
> 7000 East Ave., L-627
> Livermore, CA 94550
> 925-423-1062
> 
> 
> On 3/4/17, 3:40 AM, "R-SIG-Mac on behalf of D G. Rossiter" <r-sig-mac-bounces at r-project.org on behalf of d.g.rossiter at cornell.edu> wrote:
> 
>    Thanks to Ken Beath, this indeed was the problem. I tested by formatting a USB drive to Mac format with Disk Info, copying the shapefiles onto it, and then reading with readOGR().
> 
>    Problem solved, although the Mac-formatted USB drive could not be used to transfer files to and from Windows machines.
> 
>    D G (David) Rossiter
>    Section of Soil & Crop Sciences
>    Cornell University
>    http://www.css.cornell.edu/faculty/dgr2/
> 
> 
>      1. Re:  Mac-only problem using readOGR(), which uses ogrInfo(),
>         to read a shapefile from a directory on a USB pen drive (Ken Beath)
> 
>    From: Ken Beath <ken at kjbeath.com.au<mailto:ken at kjbeath.com.au>>
>    Subject: Re: [R-SIG-Mac] Mac-only problem using readOGR(), which uses ogrInfo(), to read a shapefile from a directory on a USB pen drive
>    Date: 3 March 2017 at 20:28:33 GMT-5
>    To: "D G. Rossiter" <d.g.rossiter at cornell.edu<mailto:d.g.rossiter at cornell.edu>>
>    Cc: "r-sig-mac at r-project.org<mailto:r-sig-mac at r-project.org>" <r-sig-mac at r-project.org<mailto:r-sig-mac at r-project.org>>
> 
> 
>    My thought is that it might be that USB drives are usually MSDOS formatted. Usually not a problem but rgdal works with directories. Formatting  in a Mac with Disk Utility might be a work-around, with the limitation that the USB will only work in Macs.
> 
>    I would also try verbose=TRUE which may give more information.
> 
>    In the absence of other ideas contacting the package author can help.
> 
>    Ken
> 
>    On 4 Mar 2017, at 3:32 am, D G. Rossiter <d.g.rossiter at cornell.edu<mailto:d.g.rossiter at cornell.edu>> wrote:
> 
>    I ran across a Mac-only problem using readOGR(), which uses ogrInfo(), to read a shapefile from a directory on a USB pen drive. I tested the behaviour on a Windows 10 machine and did not get the problem.
> 
>    Trying to read from the USB drive, with relative and full paths:
> 
>    setwd("/Volumes/ISPRS/“) # this is my connected USB drive
>    list.files()
>    [1] "map7100.dbf"                      "map7100.prj"
>    [3] "map7100.sbn"                      "map7100.sbx"
>    [5] "map7100.shp"                      "map7100.shp.xml"
>    [7] "map7100.shx"
>    file.exists("map7100.shp")
>    [1] TRUE
>    usa <- readOGR(dsn=".", layer="map7100")
>    Error in ogrInfo(dsn = dsn, layer = layer, encoding = encoding, use_iconv = use_iconv,  :
>    Cannot open data source
>    usa <- readOGR(dsn="/Volumes/ISPRS", layer="map7100")
>    Error in ogrInfo(dsn = dsn, layer = layer, encoding = encoding, use_iconv = use_iconv,  :
>    Cannot open data source
> 
>    But, readOGR reads the shapefile correctly if it’s located on the Mac’s internal drive:
> 
>    setwd("/Users/rossiter/data/edu/dgeostats/ex")
>    file.exists("./ds/NEweather/map7100.shp")
>    [1] TRUE
>    usa <- readOGR(dsn="./ds/NEweather", layer="map7100")
>    OGR data source with driver: ESRI Shapefile
>    Source: "./ds/NEweather", layer: "map7100"
>    with 7926 features
>    It has 19 fields
> 
>    All packages are up to date. Here is the sessionInfo():
> 
>    R version 3.3.2 (2016-10-31)
>    Platform: x86_64-apple-darwin13.4.0 (64-bit)
>    Running under: OS X El Capitan 10.11.6
> 
>    locale:
>    [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
> 
>    attached base packages:
>    [1] stats     graphics  grDevices utils     datasets  methods   base
> 
>    other attached packages:
>    [1] ggplot2_2.2.1  sf_0.3-4       maptools_0.9-1 rgdal_1.2-5
>    [5] sp_1.2-4       gstat_1.1-4
> 
>    loaded via a namespace (and not attached):
>    [1] Rcpp_0.12.9      plyr_1.8.4       xts_0.9-7        tools_3.3.2
>    [5] digest_0.6.12    evaluate_0.10    tibble_1.2       gtable_0.2.0
>    [9] lattice_0.20-34  DBI_0.5-1        yaml_2.1.14      stringr_1.2.0
>    [13] knitr_1.15.1     rprojroot_1.2    grid_3.3.2       spacetime_1.2-0
>    [17] foreign_0.8-67   rmarkdown_1.3    udunits2_0.13    magrittr_1.5
>    [21] backports_1.0.5  scales_0.4.1     intervals_0.15.1 htmltools_0.3.5
>    [25] units_0.4-2      rsconnect_0.7    assertthat_0.1   colorspace_1.3-2
>    [29] labeling_0.3     stringi_1.1.2    lazyeval_0.2.0   munsell_0.4.3
>    [33] FNN_1.1          zoo_1.7-14
> 
>    This is a problem because several of my students have OS/X machines and like to work from USB-connected external drives.
> 
>    D G (David) Rossiter
>    Section of Soil & Crop Sciences
>    Cornell University
>    http://www.css.cornell.edu/faculty/dgr2/
> 
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