Bug report #20870

'gdal_fillnodata.bat' is not recognized as an internal or external command

Added by Harm Olthof almost 2 years ago. Updated almost 2 years ago.

Status:Closed
Priority:Normal
Assignee:-
Category:Build/Install
Affected QGIS version:3.4.2 Regression?:No
Operating System:Windows 10 Easy fix?:No
Pull Request or Patch supplied:No Resolution:fixed/implemented
Crashes QGIS or corrupts data:No Copied to github as #:28689

Description

When you run menu item: raster -> Analysis -> Fill no data and use the default settings in the following popup and push run, an error occurs indicating that
gdal_fillnodata.bat is missing from the OSGeo4W setup. Using OSGeo4W setup (advanced), updating GDAL, does not resolve the issue. Nor is gdal_fillnodata.bat visible in the OSGeo4W shell environment.

the complete error log is:

Processing algorithm…
Algorithm 'Fill nodata' starting…
Input parameters:
{ 'BAND' : 1, 'DISTANCE' : 10, 'INPUT' : 'C:/Users/Harm/Downloads/r_02dn1.tif', 'ITERATIONS' : 0, 'MASK_LAYER' : None, 'NO_MASK' : False, 'OUTPUT' : 'C:/Users/Harm/AppData/Local/Temp/processing_5f044c95297b44e69512fd54e6eb7577/7f29e9f1bf05452a9362a0fb74d1666d/OUTPUT.tif' }

GDAL command:
cmd.exe /C gdal_fillnodata.bat -md 10 -b 1 -of GTiff C:/Users/Harm/Downloads/r_02dn1.tif C:/Users/Harm/AppData/Local/Temp/processing_5f044c95297b44e69512fd54e6eb7577/7f29e9f1bf05452a9362a0fb74d1666d/OUTPUT.tif
GDAL command output:
'gdal_fillnodata.bat' is not recognized as an internal or external command,

operable program or batch file.

Schermafdruk 2018-12-31 13.10.20.png - osgeo4w installed GDAL elements (320 KB) Harm Olthof, 2018-12-31 01:10 PM

Associated revisions

Revision b6293f23
Added by Jürgen Fischer almost 2 years ago

osgeo4w: run python scripts with python3 (fixes #20870)

Revision 8b8e6b81
Added by Jürgen Fischer almost 2 years ago

osgeo4w: run python scripts with python3 (fixes #20870)

(cherry picked from commit b6293f23c8c54602f668f980f50d76ef09271e8a)

History

#1 Updated by Alexander Bruy almost 2 years ago

  • Category changed from Rasters to Build/Install

Looks like packaging issue.

#2 Updated by Alexander Bruy almost 2 years ago

  • Status changed from Open to Feedback

Please check if you have GDAL and its python tools and bindings installed.
Can you call any of the GDAL Python tools (like gdal_edit, gdal_fillnodata etc) from the OSGeo shell?

#3 Updated by Harm Olthof almost 2 years ago

According to the OSGeo4W setup GDAL 2.4.0-3 is installed (including Python 3 bindings and Scripts). I can see some commands the OSGeo4W Shell, but not all (esp. not gdal_fillnodata).
Here is a list of commands in the OSGeo4W Shell:
C:\>o-help
={ OSGeo4W Shell Commands }=
cct cs2cs
curl derb
dllupdate fax2ps
fax2tiff gdaladdo
gdalbuildvrt gdaldem
gdalenhance gdalinfo
gdallocationinfo gdalmanage
gdalserver gdalsrsinfo
gdaltindex gdaltransform
gdalwarp gdal_contour
gdal_grid gdal_rasterize
gdal_translate genbrk
genccode gencfu
gencmn gencnval
gendict gennorm2
genrb gensprep
geod gie
gnmanalyse gnmmanage
gpsbabel icuinfo
icupkg makeconv
nad2bin nccopy
ncdump ncgen
ncgen3 nearblack
nircmd nircmdc
ogr2ogr ogrinfo
ogrlineref ogrtindex
osgeo4w-setup-work osgeo4w-setup
pal2rgb pkgdata
ppm2tiff proj
psql python3
pythonw3 qgis-bin
raw2tiff sqlite3
testepsg textreplace
tiff2bw tiff2pdf
tiff2ps tiff2rgba
tiffcmp tiffcp
tiffcrop tiffdither
tiffdump tiffinfo
tiffmedian tiffset
tiffsplit uconv
vcredist_2015_x64 xmlcatalog
xmllint xmlwf
xxmklink o-help
o4w_env py3_env
python-qgis qgis-designer
qgis qt5_env
setup-test setup

GDAL 2.4.0, released 2018/12/14

C:\>

#4 Updated by Giovanni Manghi almost 2 years ago

  • Priority changed from High to Normal
  • Easy fix? changed from Yes to No

Works fine here on a clean install of osgeo4w on Windows 10.

#5 Updated by Harm Olthof almost 2 years ago

I made a clean install also. However I have the same issues as reported before.
What is the supposed path to gdal_fillnodata.bat?
(I do see that the folder C:\OSGeo4W64\bin\gdalplugins is empty)

#6 Updated by Giovanni Manghi almost 2 years ago

Harm Olthof wrote:

I made a clean install also. However I have the same issues as reported before.
What is the supposed path to gdal_fillnodata.bat?
(I do see that the folder C:\OSGeo4W64\bin\gdalplugins is empty)

C:\OSGeo4W64\bin

#7 Updated by Harm Olthof almost 2 years ago

  • Assignee set to Giovanni Manghi

Not in my (clean) install:
C:\OSGeo4W64\bin>dir C:\OSGeo4W64\bin
Volume in drive C is OS
Volume Serial Number is xxx-xxx

Directory of C:\OSGeo4W64\bin

04-01-2019 00:30 <DIR> .
04-01-2019 00:30 <DIR> ..
11-10-2018 16:08 47.616 adrg.dll
29-10-2014 02:36 7.680 boost_atomic-vc110-mt-1_56.dll
29-10-2014 02:36 9.728 boost_atomic-vc110-mt-gd-1_56.dll
29-10-2014 02:36 28.672 boost_chrono-vc110-mt-1_56.dll
29-10-2014 02:36 49.664 boost_chrono-vc110-mt-gd-1_56.dll
29-10-2014 02:36 31.232 boost_container-vc110-mt-1_56.dll
29-10-2014 02:36 108.544 boost_container-vc110-mt-gd-1_56.dll
29-10-2014 02:36 7.168 boost_context-vc110-mt-1_56.dll
29-10-2014 02:36 9.728 boost_context-vc110-mt-gd-1_56.dll
29-10-2014 02:36 57.344 boost_coroutine-vc110-mt-1_56.dll
29-10-2014 02:36 115.712 boost_coroutine-vc110-mt-gd-1_56.dll
29-10-2014 02:36 50.688 boost_date_time-vc110-mt-1_56.dll
29-10-2014 02:36 129.024 boost_date_time-vc110-mt-gd-1_56.dll
29-10-2014 02:36 117.248 boost_filesystem-vc110-mt-1_56.dll
29-10-2014 02:36 218.112 boost_filesystem-vc110-mt-gd-1_56.dll
29-10-2014 02:36 262.144 boost_graph-vc110-mt-1_56.dll
29-10-2014 02:36 740.864 boost_graph-vc110-mt-gd-1_56.dll
29-10-2014 02:36 51.200 boost_iostreams-vc110-mt-1_56.dll
29-10-2014 02:36 83.968 boost_iostreams-vc110-mt-gd-1_56.dll
29-10-2014 02:36 481.280 boost_locale-vc110-mt-1_56.dll
29-10-2014 02:36 1.099.776 boost_locale-vc110-mt-gd-1_56.dll
29-10-2014 02:36 641.024 boost_log-vc110-mt-1_56.dll
29-10-2014 02:36 1.668.096 boost_log-vc110-mt-gd-1_56.dll
29-10-2014 02:36 764.928 boost_log_setup-vc110-mt-1_56.dll
29-10-2014 02:36 2.144.768 boost_log_setup-vc110-mt-gd-1_56.dll
29-10-2014 02:36 34.304 boost_math_c99-vc110-mt-1_56.dll
29-10-2014 02:36 78.336 boost_math_c99-vc110-mt-gd-1_56.dll
29-10-2014 02:36 34.304 boost_math_c99f-vc110-mt-1_56.dll
29-10-2014 02:36 78.848 boost_math_c99f-vc110-mt-gd-1_56.dll
29-10-2014 02:36 32.256 boost_math_c99l-vc110-mt-1_56.dll
29-10-2014 02:36 73.728 boost_math_c99l-vc110-mt-gd-1_56.dll
29-10-2014 02:36 193.024 boost_math_tr1-vc110-mt-1_56.dll
29-10-2014 02:36 453.632 boost_math_tr1-vc110-mt-gd-1_56.dll
29-10-2014 02:36 204.800 boost_math_tr1f-vc110-mt-1_56.dll
29-10-2014 02:36 488.960 boost_math_tr1f-vc110-mt-gd-1_56.dll
29-10-2014 02:36 193.024 boost_math_tr1l-vc110-mt-1_56.dll
29-10-2014 02:36 451.584 boost_math_tr1l-vc110-mt-gd-1_56.dll
29-10-2014 02:36 35.840 boost_prg_exec_monitor-vc110-mt-1_56.dll
29-10-2014 02:36 60.928 boost_prg_exec_monitor-vc110-mt-gd-1_56.dll
29-10-2014 02:36 433.152 boost_program_options-vc110-mt-1_56.dll
29-10-2014 02:36 916.480 boost_program_options-vc110-mt-gd-1_56.dll
29-10-2014 02:36 24.064 boost_random-vc110-mt-1_56.dll
29-10-2014 02:36 39.936 boost_random-vc110-mt-gd-1_56.dll
29-10-2014 02:36 765.440 boost_regex-vc110-mt-1_56.dll
29-10-2014 02:36 2.525.696 boost_regex-vc110-mt-gd-1_56.dll
29-10-2014 02:36 245.760 boost_serialization-vc110-mt-1_56.dll
29-10-2014 02:36 762.368 boost_serialization-vc110-mt-gd-1_56.dll
29-10-2014 02:36 58.880 boost_signals-vc110-mt-1_56.dll
29-10-2014 02:36 165.888 boost_signals-vc110-mt-gd-1_56.dll
29-10-2014 02:36 19.456 boost_system-vc110-mt-1_56.dll
29-10-2014 02:36 32.256 boost_system-vc110-mt-gd-1_56.dll
29-10-2014 02:36 102.912 boost_thread-vc110-mt-1_56.dll
29-10-2014 02:36 220.160 boost_thread-vc110-mt-gd-1_56.dll
29-10-2014 02:36 29.696 boost_timer-vc110-mt-1_56.dll
29-10-2014 02:36 51.712 boost_timer-vc110-mt-gd-1_56.dll
29-10-2014 02:36 535.552 boost_unit_test_framework-vc110-mt-1_56.dll
29-10-2014 02:36 1.444.864 boost_unit_test_framework-vc110-mt-gd-1_56.dll
29-10-2014 02:36 628.736 boost_wave-vc110-mt-1_56.dll
29-10-2014 02:36 1.645.568 boost_wave-vc110-mt-gd-1_56.dll
29-10-2014 02:36 167.936 boost_wserialization-vc110-mt-1_56.dll
29-10-2014 02:36 471.040 boost_wserialization-vc110-mt-gd-1_56.dll
06-08-2013 16:28 408.064 cblas.dll
09-10-2018 22:36 52.736 cct.exe
26-04-2017 15:10 13.824 charset-1.dll
09-10-2018 22:36 48.128 cs2cs.exe
30-06-2018 12:02 352.768 curl.exe
30-06-2018 12:02 888.832 curl.pdb
04-02-2017 20:56 25.600 derb.exe
11-09-2018 12:48 72.192 dllupdate.exe
11-10-2018 16:08 19.968 dtcanada.dll
11-10-2018 16:08 44.032 dted.dll
11-10-2018 16:08 9.216 dtusa.dll
31-07-2013 22:28 136.704 expat.dll
28-05-2017 14:53 20.480 fax2ps.exe
28-05-2017 14:53 18.432 fax2tiff.exe
19-07-2015 14:36 66.560 freexl.dll
20-10-2018 01:15 21.187.072 gdal203.dll
22-12-2018 22:35 21.633.536 gdal204.dll
22-12-2018 22:36 82.944 gdaladdo.exe
22-12-2018 22:36 18.944 gdalbuildvrt.exe
22-12-2018 22:36 78.848 gdaldem.exe
22-12-2018 22:36 101.376 gdalenhance.exe
22-12-2018 22:36 17.408 gdalinfo.exe
22-12-2018 22:36 30.720 gdallocationinfo.exe
22-12-2018 22:36 23.040 gdalmanage.exe
04-01-2019 00:29 <DIR> gdalplugins
22-12-2018 22:36 20.480 gdalserver.exe
22-12-2018 22:36 85.504 gdalsrsinfo.exe
22-12-2018 22:36 32.256 gdaltindex.exe
22-12-2018 22:36 24.064 gdaltransform.exe
22-12-2018 22:36 29.696 gdalwarp.exe
22-12-2018 22:36 29.184 gdal_contour.exe
22-12-2018 22:36 17.408 gdal_grid.exe
22-12-2018 22:36 77.824 gdal_rasterize.exe
22-12-2018 22:36 81.920 gdal_translate.exe
04-02-2017 20:56 21.504 genbrk.exe
04-02-2017 20:56 12.288 genccode.exe
04-02-2017 20:56 17.920 gencfu.exe
04-02-2017 20:56 12.800 gencmn.exe
04-02-2017 20:56 26.624 gencnval.exe
04-02-2017 20:56 28.672 gendict.exe
04-02-2017 20:56 52.736 gennorm2.exe
04-02-2017 20:56 139.264 genrb.exe
04-02-2017 20:56 25.600 gensprep.exe
09-10-2018 22:36 45.568 geod.exe
09-10-2018 22:58 2.023.424 geos.dll
11-10-2018 14:26 482.816 geos_c.dll
09-10-2018 22:36 86.016 gie.exe
22-12-2018 22:36 99.328 gnmanalyse.exe
22-12-2018 22:36 104.960 gnmmanage.exe
23-03-2014 13:08 1.745.920 gpsbabel.exe
06-08-2013 16:30 2.782.720 gsl.dll
14-10-2013 22:48 2.212.864 hdf5.dll
14-10-2013 22:48 99.840 hdf5_hl.dll
26-04-2017 15:10 1.023.488 iconv-2.dll
31-07-2013 22:10 1.332.224 iconv.dll
04-02-2017 20:56 26.277 icu-config
04-02-2017 20:56 25.048.064 icudt56.dll
04-02-2017 20:56 2.713.600 icuin56.dll
04-02-2017 20:56 12.800 icuinfo.exe
04-02-2017 20:56 66.560 icuio56.dll
04-02-2017 20:56 345.088 icule56.dll
04-02-2017 20:56 60.416 iculx56.dll
04-02-2017 20:56 25.600 icupkg.exe
04-02-2017 20:56 73.728 icutest56.dll
04-02-2017 20:56 263.680 icutu56.dll
04-02-2017 20:56 1.818.624 icuuc56.dll
29-08-2016 19:04 146.944 jpeg.dll
29-08-2016 19:04 147.968 jpeg12.dll
30-06-2018 12:02 398.848 libcurl.dll
27-10-2016 23:01 2.265.088 libeay32.dll
28-05-2017 11:01 151.040 liblzma.dll
14-04-2017 17:38 4.107.264 libmysql.dll
23-04-2017 23:11 190.464 libpng16.dll
17-08-2013 18:02 174.080 libpq.dll
28-05-2017 14:53 427.520 libtiff.dll
31-07-2013 20:30 1.392.128 libxml2.dll
11-10-2018 17:40 1.355.776 lwgeom.dll
04-02-2017 20:56 55.296 makeconv.exe
11-10-2018 17:43 9.701.376 mod_spatialite.dll
19-02-2011 21:51 608.080 msvcp100.dll
18-02-2011 23:52 829.264 msvcr100.dll
09-10-2018 22:36 41.472 nad2bin.exe
21-05-2017 20:20 45.568 nccopy.exe
21-05-2017 20:20 73.216 ncdump.exe
21-05-2017 20:21 172.032 ncgen.exe
21-05-2017 20:20 76.800 ncgen3.exe
22-12-2018 22:36 15.872 nearblack.exe
21-05-2017 20:20 1.015.296 netcdf.dll
11-08-2013 14:41 115.712 nircmd.exe
11-08-2013 14:40 113.664 nircmdc.exe
04-11-2018 13:52 852 o-help.bat
27-05-2017 08:53 406 o4w_env.bat
11-10-2018 16:08 158.720 ogdi.dll
22-12-2018 22:36 92.160 ogr2ogr.exe
22-12-2018 22:36 92.672 ogrinfo.exe
22-12-2018 22:36 123.392 ogrlineref.exe
22-12-2018 22:36 90.624 ogrtindex.exe
02-09-2018 18:11 123.392 opencl.dll
08-10-2017 10:25 287.232 openjp2.dll
26-02-2018 20:44 910.304 osgeo4w-setup.exe
28-05-2017 14:53 17.408 pal2rgb.exe
04-02-2017 20:56 41.984 pkgdata.exe
28-05-2017 14:53 17.408 ppm2tiff.exe
04-09-2016 19:51 472.064 proj.dll
09-10-2018 22:36 52.224 proj.exe
09-10-2018 22:36 513.536 proj_5_2.dll
17-08-2013 18:02 379.904 psql.exe
08-10-2018 16:48 141 py3_env.bat
04-01-2019 00:30 481 python-qgis.bat
23-12-2018 07:30 481 python-qgis.bat.tmpl
27-06-2018 04:00 59.032 python3.dll
27-06-2018 04:01 99.992 python3.exe
27-06-2018 04:00 3.844.760 python37.dll
27-06-2018 04:01 98.456 pythonw3.exe
04-01-2019 00:30 852 qgis-bin.env
23-12-2018 05:16 113.152 qgis-bin.exe
22-12-2018 23:26 408 qgis-bin.vars
04-01-2019 00:30 318 qgis-designer.bat
23-12-2018 07:30 318 qgis-designer.bat.tmpl
04-01-2019 00:30 448 qgis.bat
23-12-2018 07:30 448 qgis.bat.tmpl
08-10-2018 01:22 214 qt.conf
08-10-2018 01:22 214 qt5.conf
08-10-2018 01:22 488 qt5_env.bat
28-05-2017 14:53 25.088 raw2tiff.exe
11-10-2018 16:08 40.448 remote.dll
11-10-2018 16:08 68.608 rpf.dll
04-01-2019 00:30 191 setup-test.bat
10-08-2017 08:19 179 setup-test.bat.tmpl
04-01-2019 00:30 178 setup.bat
10-08-2017 08:19 166 setup.bat.tmpl
11-10-2018 16:08 36.352 skeleton.dll
03-11-2014 04:24 538.624 spatialindex-64.dll
03-11-2014 04:24 227.328 spatialindex_c-64.dll
11-10-2018 17:43 9.655.808 spatialite.dll
12-12-2018 15:54 1.412.096 sqlite3.dll
12-12-2018 15:54 170.496 sqlite3.exe
27-10-2016 23:01 383.488 ssleay32.dll
14-10-2013 22:45 45.056 szip.dll
22-12-2018 22:36 67.584 testepsg.exe
11-09-2018 12:48 89.600 textreplace.exe
28-05-2017 14:53 427.520 tiff.dll
28-05-2017 14:53 18.432 tiff2bw.exe
28-05-2017 14:53 75.776 tiff2pdf.exe
28-05-2017 14:53 49.664 tiff2ps.exe
28-05-2017 14:53 18.432 tiff2rgba.exe
28-05-2017 14:53 21.504 tiffcmp.exe
28-05-2017 14:53 35.840 tiffcp.exe
28-05-2017 14:53 108.032 tiffcrop.exe
28-05-2017 14:53 16.384 tiffdither.exe
28-05-2017 14:53 21.504 tiffdump.exe
28-05-2017 14:53 18.944 tiffinfo.exe
28-05-2017 14:53 22.528 tiffmedian.exe
28-05-2017 14:53 14.848 tiffset.exe
28-05-2017 14:53 14.848 tiffsplit.exe
04-02-2017 20:56 55.296 uconv.exe
19-08-2014 10:11 7.188.536 vcredist-2013-x64.exe
21-02-2017 10:15 14.572.000 vcredist_2015_x64.exe
11-10-2018 16:08 194.560 vrf.dll
05-12-2017 20:43 3.095.040 xerces-c_3_2.dll
31-07-2013 20:31 14.336 xmlcatalog.exe
31-07-2013 20:31 50.688 xmllint.exe
31-07-2013 22:28 19.968 xmlwf.exe
01-04-2005 14:01 49.152 xxmklink.exe
04-08-2017 19:41 159.232 zip.dll
31-07-2013 20:27 77.824 zlib1.dll
08-12-2017 21:37 245.760 zstd.dll
227 File(s) 181.771.292 bytes
3 Dir(s) 328.881.299.456 bytes free

#8 Updated by Giovanni Manghi almost 2 years ago

maybe you a particularly aggressive antivirus that do not allow the installer to deploy such .bat files?

#9 Updated by Harm Olthof almost 2 years ago

I just did a "reinstall" and checked gdal-2.4.0-3.tar.bz2 in the download dir.
The files are also missing in the tar. Can you confirm that they are in your version of this tar?
(Just using MS Defender)

#10 Updated by Giovanni Manghi almost 2 years ago

Harm Olthof wrote:

I just did a "reinstall" and checked gdal-2.4.0-3.tar.bz2 in the download dir.
The files are also missing in the tar. Can you confirm that they are in your version of this tar?
(Just using MS Defender)

there you have only the tools that are .exe. Others are python scripts, you have to look into python3-gdal-2.4.0-3.tar.bz2

#11 Updated by Harm Olthof almost 2 years ago

I don't think that is true: in gdal-2.4.0-3.tar.bz2 there are also *.bat files.
In python3-gdal-2.4.0-3.tar.bz2 I also don't find the missing gdal_fillnodata.bat

#12 Updated by Giovanni Manghi almost 2 years ago

Harm Olthof wrote:

I don't think that is true: in gdal-2.4.0-3.tar.bz2 there are also *.bat files.

in this file I see only .exe files, and I have a working copy of qgis/gdal/osgeo4w

In python3-gdal-2.4.0-3.tar.bz2 I also don't find the missing gdal_fillnodata.bat

no, there you have the .py script, the .bat files are generated by the script "make-bat-for-py.bat"

#13 Updated by Giovanni Manghi almost 2 years ago

  • Assignee deleted (Giovanni Manghi)

#14 Updated by Jürgen Fischer almost 2 years ago

Giovanni Manghi wrote:

Harm Olthof wrote:

I don't think that is true: in gdal-2.4.0-3.tar.bz2 there are also *.bat files.

in this file I see only .exe files, and I have a working copy of qgis/gdal/osgeo4w

In python3-gdal-2.4.0-3.tar.bz2 I also don't find the missing gdal_fillnodata.bat

no, there you have the .py script, the .bat files are generated by the script "make-bat-for-py.bat"

The batch files are only generated for py2 (by gdal-python)

#15 Updated by Giovanni Manghi almost 2 years ago

The batch files are only generated for py2 (by gdal-python)

so this may explain: I also did a 2.18 installation, so .bat files are generated. Meanwhile if someone does only a 3.* installation then .bat files are not generated but Processing needs them.

#16 Updated by Harm Olthof almost 2 years ago

I can confirm that I only have QGIS 3.x installed.
So that explains it?

#17 Updated by Giovanni Manghi almost 2 years ago

Harm Olthof wrote:

I can confirm that I only have QGIS 3.x installed.
So that explains it?

try installing also qgis 2.18, then try use the tool in qgis 3.

#18 Updated by Harm Olthof almost 2 years ago

I installed the LTR version (2.18) and I can confirm that raster -> Analysis -> Fill no data now works in QGIS 3.4
So that is a nice workaround until this is fixed in 3.x.

Thanks for the support!
Regards,
Harm

#19 Updated by Jürgen Fischer almost 2 years ago

  • Status changed from Feedback to Closed
  • % Done changed from 0 to 100

#20 Updated by Jürgen Fischer almost 2 years ago

  • Description updated (diff)

#21 Updated by Jürgen Fischer almost 2 years ago

  • Resolution set to fixed/implemented

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