[R-sig-Geo] MODIS package's runGdal() returns error: dataFormat='GTiff', format not supported
chris english
englishchristophera at gmail.com
Wed May 18 13:13:00 CEST 2016
Hakim,
Your installation and mine share the same defect:
> MODIS:::checkGdalDriver()
[1] TRUE
> MODIS:::checkGdalDriver(GTiff)
Error in correctPath(path) : object 'GTiff' not found
> MODIS:::checkGdalDriver
function (path = NULL)
{
inW <- getOption("warn")
on.exit(options(warn = inW))
options(warn = -1)
path <- correctPath(path)
cmd <- paste0(path, "gdalinfo --formats")
if (.Platform$OS == "windows") {
driver <- try(shell(cmd, intern = TRUE), silent = TRUE)
}
else {
driver <- try(system(cmd, intern = TRUE), silent = TRUE)
}
if (class(driver) == "try-error") {
options(warn = inW)
warning("No gdal installation found please install 'gdal' on your
system first!")
return(FALSE)
}
if (length(grep(driver, pattern = "HDF4")) == 0) {
return(FALSE)
}
else {
return(TRUE)
}
}
<bytecode: 0x7ddc970>
<environment: namespace:MODIS>
>
If we hard code:
> cmd <- "/usr/local/bin/gdalinfo --formats"
> driver <- try(system(cmd, intern = TRUE), silent = TRUE)
> driver
[1] "Supported Formats:"
[2] " VRT -raster- (rw+v): Virtual Raster"
[3] " GTiff -raster- (rw+vs): GeoTIFF"
[4] " NITF -raster- (rw+vs): National Imagery Transmission Format"
[5] " RPFTOC -raster- (rovs): Raster Product Format TOC format"
[6] " ECRGTOC -raster- (rovs): ECRG TOC format"
[7] " HFA -raster- (rw+v): Erdas Imagine Images (.img)"
[8] " SAR_CEOS -raster- (rov): CEOS SAR Image"
[9] " CEOS -raster- (rov): CEOS Image"
[10] " JAXAPALSAR -raster- (rov): JAXA PALSAR Product Reader (Level
1.1/1.5)"
I am still looking for where correctPath() comes from as well as trying to
get my MRT recognized, but slowly slowly.
Seems we're looking at environment variables (MRT, and likely gdal_config)
and some other special sause that we've overlooked in installation of MODIS.
Chris
On Wed, May 18, 2016 at 8:53 AM, chris english <
englishchristophera at gmail.com> wrote:
> > ?MODISoptions
> > MODIS:::checkTools("GDAL")
> Checking availabillity of GDAL:
> OK, GDAL 2.1.0dev, released 2015/99/99 found!
> > getOption("MODIS_gdalOutDriver")
> [1] name description extension
> <0 rows> (or 0-length row.names)
> >
> Interestingly not finding even GTiff default. Well, more digging, but
> these outputs explain runGdal error output.
>
> On Tue, May 17, 2016 at 10:07 AM, Hakim Abdi <hakim.abdi at nateko.lu.se>
> wrote:
>
>> Same here. Loading rgdal didn't make a difference.
>>
>> On Tue, May 17, 2016 at 9:05 AM, chris english <
>> englishchristophera at gmail.com> wrote:
>>
>>> I suspect it is an incomplete Modis build even though library(Modis)
>>> loads without complaint, but will have to check into this later. I recall
>>> not seeing MRT complete...which I think is inscribing a folder though is
>>> probably much more.
>>> Having rgdal loaded as against your sessionInfo() didn't make a
>>> difference.
>>> Chris
>>>
>>> On Tue, May 17, 2016 at 9:52 AM, chris english <
>>> englishchristophera at gmail.com> wrote:
>>>
>>>> Hi Hakim,
>>>>
>>>> Interesting and unexpected as I am on a linux box but I have the same
>>>> problem, or I can reproduce your's:
>>>> > sessionInfo()
>>>> R version 3.2.2 (2015-08-14)
>>>> Platform: x86_64-pc-linux-gnu (64-bit)
>>>> Running under: Ubuntu 14.04.4 LTS
>>>>
>>>> locale:
>>>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
>>>> LC_TIME=en_US.UTF-8
>>>> [4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8
>>>> LC_MESSAGES=en_US.UTF-8
>>>> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C
>>>>
>>>> [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8
>>>> LC_IDENTIFICATION=C
>>>>
>>>> attached base packages:
>>>> [1] stats graphics grDevices utils datasets methods base
>>>>
>>>>
>>>> other attached packages:
>>>> [1] rgdal_1.1-3 MODIS_0.10-34 raster_2.5-2 sp_1.2-1
>>>>
>>>> loaded via a namespace (and not attached):
>>>> [1] rsconnect_0.4.1.11 tools_3.2.2 Rcpp_0.12.4 grid_3.2.2
>>>> lattice_0.20-33
>>>> > dates <- as.POSIXct( as.Date(c("01/01/2010","01/05/2016"),format
>>>> ="%d/%m/%Y") )
>>>> > dates <- transDate(dates[1],dates[2])
>>>> > product <- "MOD13Q1"
>>>> > bands <- "010"
>>>> > h = c("21","22")
>>>> > v = c("07","08")
>>>> > runGdal(product=product,begin=dates$beginDOY,end = dates$endDOY,tileH
>>>> =
>>>> + h,tileV = v, SDSstring = bands, outProj="4326")
>>>> Error in runGdal(product = product, begin = dates$beginDOY, end =
>>>> dates$endDOY, :
>>>> in argument dataFormat='GTiff', format not supported by GDAL type:
>>>> 'gdalWriteDriver()' (column 'name') to list available inputs
>>>>
>>>> debugonce(runGdal)
>>>> #output
>>>> Browse[2]> n
>>>> debug: stop("in argument dataFormat='", opts$dataFormat, "', format not
>>>> supported by GDAL type: 'gdalWriteDriver()' (column 'name') to list
>>>> available inputs")
>>>> Browse[2]> n
>>>> Error in runGdal(product = product, begin = dates$beginDOY, end =
>>>> dates$endDOY, :
>>>> in argument dataFormat='GTiff', format not supported by GDAL type:
>>>> 'gdalWriteDriver()' (column 'name') to list available inputs
>>>> >
>>>> Hmmmm. More digging. Sorry to not be helpful to this point.
>>>> Chris
>>>>
>>>> On Mon, May 16, 2016 at 11:47 AM, Hakim Abdi <hakim.abdi at nateko.lu.se>
>>>> wrote:
>>>>
>>>>> Hi Alex,
>>>>>
>>>>> The OS is a 64 bit Windows 7 as specified in the sessionInfo() output
>>>>> I posted. When I upgraded QGIS, I did so by uninstalling the previous one
>>>>> and reinstalling the new version. I'm not quite sure what it means to
>>>>> upgrade GDAL since I installed it fresh with OSGeo4W. In R, I reinstall all
>>>>> the packages I need fresh off the repository using the install.views
>>>>> command.
>>>>>
>>>>> gdalDrivers() produces the output that's attached.
>>>>>
>>>>> Cheers,
>>>>>
>>>>> Hakim
>>>>>
>>>>>
>>>>> On Wed, May 11, 2016 at 5:09 PM, Alex Mandel <
>>>>> tech_dev at wildintellect.com> wrote:
>>>>>
>>>>>> What operating system?
>>>>>> When you upgraded QGIS did you also upgrade GDAL?
>>>>>> When you upgraded R, did you update your packages (or rebuild any
>>>>>> packages)?
>>>>>>
>>>>>> What do you get from the following command?
>>>>>> gdalDrivers()
>>>>>>
>>>>>> Thanks,
>>>>>> Alex
>>>>>>
>>>>>> On 05/02/2016 02:11 PM, Hakim Abdi wrote:
>>>>>> > Hello everyone,
>>>>>> >
>>>>>> > I'm having problems with the MODIS package, specifically, the
>>>>>> runGdal()
>>>>>> > command after the recent update to R 3.2.5. The error I get is this:
>>>>>> >
>>>>>> > Error in runGdal(product = product, begin = dates$beginDOY, end =
>>>>>> > dates$endDOY, : in argument dataFormat='GTiff', format not
>>>>>> supported by
>>>>>> > GDAL type: 'gdalWriteDriver()' (column 'name') to list available
>>>>>> inputs
>>>>>> >
>>>>>> > I'm not quite sure why this is happening, and I haven't found a
>>>>>> solution
>>>>>> > online. Does anyone have an idea? The package was working fine
>>>>>> before I
>>>>>> > upgraded R from 3.1.1. to 3.2.5, QGIS from 2.12.3 to 2.14.1 and
>>>>>> RStudio to
>>>>>> > version 0.99.467.
>>>>>> >
>>>>>> > My details are below, thanks for the assistance:
>>>>>> >
>>>>>> > R version 3.2.5 (2016-04-14) -- "Very, Very Secure Dishes"
>>>>>> > Copyright (C) 2016 The R Foundation for Statistical Computing
>>>>>> > Platform: x86_64-w64-mingw32/x64 (64-bit)
>>>>>> >
>>>>>> > R is free software and comes with ABSOLUTELY NO WARRANTY.
>>>>>> > You are welcome to redistribute it under certain conditions.
>>>>>> > Type 'license()' or 'licence()' for distribution details.
>>>>>> >
>>>>>> > R is a collaborative project with many contributors.
>>>>>> > Type 'contributors()' for more information and
>>>>>> > 'citation()' on how to cite R or R packages in publications.
>>>>>> >
>>>>>> > Type 'demo()' for some demos, 'help()' for on-line help, or
>>>>>> > 'help.start()' for an HTML browser interface to help.
>>>>>> > Type 'q()' to quit R.
>>>>>> >
>>>>>> >> require(MODIS)
>>>>>> > Loading required package: MODIS
>>>>>> > Loading required package: raster
>>>>>> > Loading required package: sp
>>>>>> > MODIS_manual:
>>>>>> >
>>>>>> https://ivfl-rio.boku.ac.at/owncloud/public.php?service=files&t=660dc830afb091237cc40b3dea2fdf6b
>>>>>> >
>>>>>> > Attaching package: ‘MODIS’
>>>>>> >
>>>>>> > The following object is masked from ‘package:base’:
>>>>>> >
>>>>>> > file.size
>>>>>> >
>>>>>> >> MODISoptions()
>>>>>> > All suggested packages are installed
>>>>>> > Detecting available write drivers!
>>>>>> > Found: 64 candidate drivers, detecting file extensions...
>>>>>> > 0 usable drivers detected!
>>>>>> >
>>>>>> > STORAGE:
>>>>>> > _______________
>>>>>> > localArcPath : C:/Users/Hakim/Documents/MODIS_ARC/
>>>>>> > outDirPath : C:/Users/Hakim/Documents/MODIS_ARC/PROCESSED/
>>>>>> >
>>>>>> >
>>>>>> > DOWNLOAD:
>>>>>> > _______________
>>>>>> > MODISserverOrder : LPDAAC, LAADS
>>>>>> > dlmethod : auto
>>>>>> > stubbornness : 5
>>>>>> >
>>>>>> >
>>>>>> > PROCESSING:
>>>>>> > _______________
>>>>>> > GDAL : GDAL 2.0.2, released 2016/01/26
>>>>>> > MRT : Version 4.1 (March 2011)
>>>>>> > pixelSize : asIn
>>>>>> > outProj : GEOGRAPHIC
>>>>>> > resamplingType : NN
>>>>>> > dataFormat : GTiff
>>>>>> >
>>>>>> >
>>>>>> > DEPENDENCIES:
>>>>>> > _______________
>>>>>> >
>>>>>> >> dates <- as.POSIXct( as.Date(c("01/01/2010","01/05/2016"),format =
>>>>>> > "%d/%m/%Y") )
>>>>>> >> dates <- transDate(dates[1],dates[2])
>>>>>> >> product <- "MOD13Q1"
>>>>>> >> bands <- "010"
>>>>>> >> h = c("21","22")
>>>>>> >> v = c("07","08")
>>>>>> > *> runGdal(product=product,begin=dates$beginDOY,end =
>>>>>> dates$endDOY,tileH =
>>>>>> > h,tileV = v, SDSstring = bands, outProj="4326")*
>>>>>> > *Error in runGdal(product = product, begin = dates$beginDOY, end =
>>>>>> > dates$endDOY, : **in argument dataFormat='GTiff', format not
>>>>>> supported by
>>>>>> > GDAL type: 'gdalWriteDriver()' (column 'name') to list available
>>>>>> inputs*
>>>>>> >> sessionInfo()
>>>>>> > R version 3.2.5 (2016-04-14)
>>>>>> > Platform: x86_64-w64-mingw32/x64 (64-bit)
>>>>>> > Running under: Windows 7 x64 (build 7601) Service Pack 1
>>>>>> >
>>>>>> > locale:
>>>>>> > [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United
>>>>>> > States.1252
>>>>>> > [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
>>>>>> >
>>>>>> > [5] LC_TIME=English_United States.1252
>>>>>> >
>>>>>> > attached base packages:
>>>>>> > [1] stats graphics grDevices utils datasets methods base
>>>>>> >
>>>>>> > other attached packages:
>>>>>> > [1] MODIS_0.10-34 raster_2.5-2 sp_1.2-3
>>>>>> >
>>>>>> > loaded via a namespace (and not attached):
>>>>>> > [1] tools_3.2.5 Rcpp_0.12.4 grid_3.2.5 lattice_0.20-33
>>>>>> >
>>>>>> >
>>>>>> >
>>>>>> > __________________________________________________
>>>>>> >
>>>>>> > Hakim Abdi | PhD Candidate
>>>>>> > Center for Geobiosphere Science
>>>>>> >
>>>>>> > Department of Physical Geography and Ecosystem Science
>>>>>> > Lund University, Sölvegatan 12, SE-223 62 Lund, Sweden
>>>>>> >
>>>>>> > [[alternative HTML version deleted]]
>>>>>> >
>>>>>> > _______________________________________________
>>>>>> > R-sig-Geo mailing list
>>>>>> > R-sig-Geo at r-project.org
>>>>>> > https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>>>>> >
>>>>>>
>>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> R-sig-Geo mailing list
>>>>> R-sig-Geo at r-project.org
>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>>>>
>>>>
>>>>
>>>
>>
>
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