[R-sig-Geo] MODIS package's runGdal() returns error: dataFormat='GTiff', format not supported
chris english
englishchristophera at gmail.com
Thu May 19 12:31:00 CEST 2016
Playing with MODISoptions.R lines 155-162:
> gdalPath = '/usr/local/bin' # take out correctPath as can't find where
defined at present ln 157
> if(length(grep(dir(gdalPath),pattern="gdalinfo"))==0)
+ {
+ stop(paste0("The 'gdalPath' you have provided
'",normalizePath(gdalPath,"/",FALSE) ,
+ "' does not contain any gdal utilities, make sure to address the
+ folder with GDAL executables (ie: gdalinfo)!"))
+ }
>
The preceding executes without complaint or stop as gdalinfo was found in
/usr/local/bin to have length >0.
>gdalDrivers()
47 GTiff GeoTIFF TRUE TRUE FALSE
51 HDF4Image HDF4 Dataset TRUE FALSE FALSE
We have the necessary drivers. Hard coding MODIS_Opts.R gdalPath doesn't
work. Ah well.
On Thu, May 19, 2016 at 7:10 AM, chris english <
englishchristophera at gmail.com> wrote:
> 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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