[R-sig-Geo] MODIS package's runGdal() returns error: dataFormat='GTiff', format not supported
chris english
englishchristophera at gmail.com
Thu May 19 06:10:54 CEST 2016
Logging out (Log out?!?, do people still do that?), which is mentioned in
the manual, though actually means more than closing and opening a new
terminal, actually restarting the kernel, results in system update where
after MRT is recognized but still, in my case, drivers are not:
>library(MODIS)
> MODISoptions()
All suggested packages are installed
Detecting available write drivers!
Found: 64 candidate drivers, detecting file extensions...
ERROR 1: --format option given with format 'VRT-raster-', but that format
not
recognised. Use the --formats option to get a list of available formats,
and use the short code (ie. GTiff or HFA) as the format identifier.
ERROR 1: --format option given with format 'GTiff-raster-', but that format
not
recognised. Use the --formats option to get a list of available formats,
and use the short code (ie. GTiff or HFA) as the format identifier.
0 usable drivers detected!
STORAGE:
_______________
localArcPath : /home/chris/MODIS_ARC
outDirPath : /home/chris/MODIS_ARC/PROCESSED
DOWNLOAD:
_______________
MODISserverOrder : LPDAAC, LAADS
dlmethod : auto
stubbornness : high
PROCESSING:
_______________
GDAL : GDAL 2.1.0dev, released 2015/99/99
MRT : Version 4.1 (March 2011)
pixelSize : asIn
outProj : asIn
resamplingType : NN
dataFormat : GTiff
DEPENDENCIES:
_______________
>
So, a little more digging.
Chris
On Wed, May 18, 2016 at 2:13 PM, chris english <
englishchristophera at gmail.com> wrote:
> 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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