[R-sig-Geo] Reporting an issue with rgdal in macOS BigSur

[Roger Bivand]

Dear Gilberto,

On Thu, 26 Nov 2020, GilbertoCamara wrote:

> Dear R-SIG-GEO and Roger
>
> I am developing an R package (https://github.com/e-sensing/sits 
> <https://github.com/e-sensing/sits>) to analyse satellite image time 
> series (SITS) which is heavily dependent on “rgdal”.
>
> I would like to report an issue with rgdal in the new macOS BigSur. 
> While I agree with Roger that it is not wise to install a new OS until 
> it is stable, I hope the information below will be useful.
>
> For starters, let me praise Roger, Edzer and all those involved in 
> “rgdal”. I did some debugging on the source code and was humbled by the 
> effort involved in making the code an operational software many of us 
> rely on. Chapeau bas!
>
> That said, please allow me to report on three issues:
>
> 1. Installation
>
> I have installed GDAL-3.2.0 using Homebrew on BigSur; it works fine. 
> When installing the binary version of rgdal-1.5-18 (SVN revision 1082) 
> from CRAN, recently released by Simon Urbanek, “rgdal" reports that is 
> is using GDAL-3.1.1, which is not installed. The actual message is: 
> "Loaded GDAL runtime: GDAL 3.1.1, released 2020/06/22”.
>
> When installing from source, rgdal recognises GDAL-3.2.0, if the 
> Homebrew libraries are on the path. The message changes to: "Loaded GDAL 
> runtime: GDAL 3.2.0, released 2020/10/26."
>
> It is odd that the binary version would report using a runtime that is 
> not there.

On MacOS and Windows, CRAN binary packages are built using static linking, 
for a number of reasons.  One is to limit installation difficulties, 
another to make support easier, as all users of a updated package/R 
version will be using the same set of external software components (of 
course, locales will vary, but most variables are fixed).

>
> 2. Errors in /vsis3 file access
>
> In earlier versions of macOS, rgdal had no problems with accessing files 
> in AWS with commands such as:
>
>> s3_file <- "/vsis3/sentinel-s2-l2a/tiles/20/L/KP/2018/8/17/0/R20m/B02.jp2”
>> rgdal::GDALinfo(s3_file)
>
> In BigSur, it produces an error. Debugging the rgdal code, I found the 
> error to arise from line 723 of the “gdal-bindings.cpp” file. This is 
> one of the places where rgdal calls the GDAL function “GDALOpenEx”, as 
> follows:

Please first check on running systems with pre-Big Sur and Big Sur that 
the returned lists of drivers match. Crucially, jp2 (Jpeg 2000) needs GDAL 
built against openjpeg. If one of the systems has GDAL built with the 
driver, and the other without, this outcome would be expected. I suspect 
that the Big Sur GDAL (or the CRAN MacOS rgdal binary) has 
missing/defective drivers.

For my Fedora 33 system with GDAL installed from source, I have:

drvs <- rgdal::gdalDrivers()$name; drvs[grep("JP2", drvs)]
## [1] "JP2OpenJPEG"

There are other JP2* drivers, but they need closed source libraries when 
GDAL itself is built, and cannot be redistributed from CRAN.

>
>  GDALDataset *pDataset = (GDALDataset *) GDALOpenEx(fn, RWFlag,
>    papszAllowedDrivers, papszOpenOptions, NULL);
>
> The function call returns a NULL pointer. Since calling gdalinfo 
> externally or using gdalUtils::gdalinfo works, it seems there is a 
> problem with the return parameters which are provided to rgdal by GDAL.
>
> To reproduce the issue, one needs AWS credentials. If Roger and/or Edzer 
> wish to have a go at this issue, I can provide a temporary credential 
> for doing so.

First, we need to be sure that the driver is present, then present and 
working.

>
> 3. Errors in TIFF Decoding
>
> Running devtools::check() produces a strange error on TIFF decoding on a 
> very small file. The error is odd:
>
> "TIFFReadDirectory: Warning, Unknown field with tag 42112 (0xa480) encountered."
>
> The call stack is as follows:
>
>   1: .Call("RGDAL_OpenDataset", .normalize_if_path(filename, mustWork = NA),     TRUE, silent, allowedDrivers, options, PACKAGE = "rgdal")
>   2: .local(.Object, ...)
>   3: initialize(value, ...)
>   4: initialize(value, ...)
>   5: new("GDALReadOnlyDataset", filename, silent = silent, allowedDrivers = allowedDrivers,     options = options)
>   6: GDAL.open(fname, silent = silent, allowedDrivers = allowedDrivers,     options = options)
>   7: rgdal::GDALinfo(file, silent = FALSE)
>
> The error appears to be in the same place as the one reported above. 
> However, it is hard to reproduce, because when running on the console, 
> rgdal works.

This feels again like a driver mismatch. Please try with the CRAN MacOS 
binary package, for which 
https://cran.r-project.org/web/checks/check_results_rgdal.html looks 
clean. The examples for rgdal::readGDAL() include reading TIFF files, so 
are run in CRAN daily checks.

I have no access to any MacOS platform, so cannot do more than arm's 
length debug. My clear suspicion is that the GDAL you are using has 
drivers missing/defective. A small JP2 raster could be added to the 
examples to trap driver malfunction.

Best wishes,

Roger

>
>> ndvi_file <- c(system.file("extdata/raster/mod13q1/sinop-ndvi-2014.tif", package = "sits”))
>> rgdal::GDALinfo(ndvi_file, silent = FALSE)
>
> However, given that the place on the “rgdal” code where the error occurs 
> is the same, it might be worthwhile to look into the RGDAL-GDAL 
> interface in more detail.
>
> I know it’s my responsibility to have moved to macOS BigSur too soon. 
> Thus, I do not expect that you address the issue. That said, any help 
> would be much appreciated.
>
> Best regards
> Gilberto
> ===========================
> Prof Dr Gilberto Camara
> Secretariat Director
> GEO - Group on Earth Observations
> 7 bis, Avenue de La Paix
> CH-1211 Geneva - Switzerland
> Tel: +41227308480
> Web: www.earthobservations.org <http://www.earthobservations.org/>
>
>
>
>

-- 
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