Hi Agus,
On Thu 20-Dec-2018 at 11:08:52 +01, Agustin Lobo <[email protected]> wrote:
> Thanks Guillaume. I think I have "environment problems"!!
>
Some will say this is fake news.
I would suggest removing any OTB install at the system level using the
packages for your distribution. Using the binaries that you have in your
$HOME should not be a problem in this case. With the self extracting
binary, you have a configuration file which sets the right paths for
you.
I would also suggest avoid sourcing this configuration file in your
.bashrc, because it can generate issues with your gdal version for
instance when using QGis. I would just source it when needed : in a
terminal for the command line or from the script that you call from R
with the "system" function.
Good luck.
Jordi
> 1. Outside R
> Whenever I start a shell (Xfce Terminal) I get
> bash: LD_LIBRARY_PATH: command not found
> (do not know why and do not know if it matters)
>
> Then I do
> alobo@Delia:~$ echo $OTB_APPLICATION_PATH
>
> alobo@Delia:~$ echo $LD_LIBRARY_PATH
> :/usr/local/lib/otb
>
> All otbcli work:
> alobo@Delia:~$ otbcli
> Usage: /usr/bin/otbApplicationLauncherCommandLine module_name
> [MODULEPATH] [arguments]
>
> But
> alobo@Delia:~$ which otbcli
> /usr/bin/otbcli
>
> And BandMathX does not work:
> alobo@Delia:~$ BandMathX
> bash: BandMathX: command not found
>
> BandMathX works if I use the path:
> alobo@Delia:~$ /home/alobo/OTB-6.6.0-Linux64/bin/otbcli_BandMathX
> ERROR: Waiting for at least one parameter.
> etc
>
> Then I do
> alobo@Delia:~$ source /home/alobo/OTB-6.6.0-Linux64/otbenv.profile
> alobo@Delia:~$ echo $OTB_APPLICATION_PATH
> /home/alobo/OTB-6.6.0-Linux64/lib/otb/applications
> alobo@Delia:~$ echo $LD_LIBRARY_PATH
> :/usr/local/lib/otb
>
> Which sets the path for the new version
> alobo@Delia:~$ which otbcli
> /home/alobo/OTB-6.6.0-Linux64/bin/otbcli
> alobo@Delia:~$ which otbcli_BandMathX
> /home/alobo/OTB-6.6.0-Linux64/bin/otbcli_BandMathX
>
> 2. Given test.scr
> source /home/alobo/OTB-6.6.0-Linux64/otbenv.profile
> echo $OTB_APPLICATION_PATH
> echo $LD_LIBRARY_PATH
> otbcli
> /home/alobo/OTB-6.6.0-Linux64/bin/otbcli_BandMathX
>
> Running from within R with system("sh /home/alobo/test.scr") I get:
>
> /home/alobo/test.scr: 1: /home/alobo/test.scr: source: not found
> Usage: /usr/bin/otbApplicationLauncherCommandLine module_name
> [MODULEPATH] [arguments]
> /home/alobo/OTB-6.6.0-Linux64/bin/otbApplicationLauncherCommandLine:
> symbol lookup error: /usr/lib/x86_64-linux-gnu/libOTBCommon-6.6.so.1:
> undefined symbol:
> _ZN3itk10LoggerBase5WriteENS0_17PriorityLevelTypeERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE
> Error in system("sh /home/alobo/test.scr", intern = TRUE) :
> error in running command
>
> So, from within R, otbcli commands work,
> /home/alobo/OTB-6.6.0-Linux64/bin/otbcli_BandMathX does not work
> source is unknown (!!!??)
>
> I think I have found a clue, because
> /home/alobo/OTB-6.6.0-Linux64/bin/otbcli
> does not work either from within R (same error as otbcli_BandMathX)
> so the otbcli that is run from within R is a different one.
>
> Running an script with
> echo $OTB_APPLICATION_PATH
> echo $LD_LIBRARY_PATH
> which otbcli
>
> from within R results in:
> [1] ""
> [2]
> "/usr/lib/R/lib::/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/default-java/lib/server"
> [3] "/usr/bin/otbcli"
>
> Which means I have an older otbcli that is the one actually working
> from within R (but otbcli_BandMatX did not exist yet),
> and I have a problem for running the new version OTB-6.6.0-Linux64
> from within R because I cannot source otbenv.profile
> from within R, but why???
>
> Any help appreciated...
> Agus
>
> On Wed, Dec 19, 2018 at 6:00 PM PASERO Guillaume
> <[email protected]> wrote:
>>
>> Hi,
>>
>> I would say it is a conflict between your standalone package
>> '/home/alobo/OTB-6.6.0-Linux64' and your system OTB libs
>> '/usr/lib/x86_64-linux-gnu/libOTBCommon-6.6.so.1'.
>>
>> Maybe add some prints in the ./tmp/test.scr script to check the
>> content of variables like OTB_APPLICATION_PATH, LD_LIBRARY_PATH, just
>> before calling otbcli_BandMathX
>>
>> Regards,
>> Guillaume
>>
>> Quoting Agustin Lobo <[email protected]>:
>>
>> > In order to run otbcli* commands from within R, I normally use the R
>> > system() command that let run any system command as if it were on the
>> > terminal.
>> >
>> > For otbcli_BandMathX I have a problem. I write from within R a simple
>> > text file with the following script (as ./tmp/test.scr)
>> >
>> > source /home/alobo/OTB-6.6.0-Linux64/otbenv.profile
>> > /home/alobo/OTB-6.6.0-Linux64/bin/otbcli_BandMathX -il ima1.tif
>> > ima2.tif -out result.tif -exp 'im1 div im2'
>> >
>> > and then try to execute with
>> > system("sh ./tmp/test.scr")
>> >
>> > But surprisingly I get a weird error:
>> >
>> > /home/alobo/OTB-6.6.0-Linux64/bin/otbApplicationLauncherCommandLine:
>> > symbol lookup error: /usr/lib/x86_64-linux-gnu/libOTBCommon-6.6.so.1:
>> > undefined symbol:
>> > _ZN3itk10LoggerBase5WriteENS0_17PriorityLevelTypeERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE
>> >
>> > I can run
>> > sh ./tmp/test.scr
>> > on the terminal with no problems.
>> >
>> > Does this error mean anything to you?
>> > I'm not trying that you solve an R problem, but I guess this is rather
>> > a problem with otbcli_BandMathX, because the same approach works for
>> > the rest of otbcli* commands.
>> >
>> > Agus
>> >
>> > --
>> > --
>> > Check the OTB FAQ at
>> > http://www.orfeo-toolbox.org/FAQ.html
>> >
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>>
>> --
>> --
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>> http://www.orfeo-toolbox.org/FAQ.html
>>
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>
> --
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