On Thursday, December 20, 2018 at 11:34:37 AM UTC+1, jordi.inglada wrote:
>
> Hi Agus,
>
> On Thu 20-Dec-2018 at 11:08:52 +01, Agustin Lobo <[email protected]
> <javascript:>> 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
> $HOME should not be a problem in this case. With the self extracting
> binary, you have a configuration file which sets the right paths for
> you.
>
> I would also suggest avoid sourcing this configuration file in your
> .bashrc, because it can generate issues with your gdal version for
> instance when using QGis. I would just source it when needed : in a
> terminal for the command line or from the script that you call from R
> with the "system" function.
>
configuration file is sourced by otbcli.sh in of package. so simply otbcli_
is expected to work without additional export.
@alobo
> /home/alobo/test.scr: 1: /home/alobo/test.scr: source: not found
seems like you weren't using bash or your default /bin/sh is not bash
>
> Good luck.
>
> Jordi
>
>
> > 1. Outside R
> > Whenever I start a shell (Xfce Terminal) I get
> > bash: LD_LIBRARY_PATH: command not found
> > (do not know why and do not know if it matters)
> >
> > Then I do
> > alobo@Delia:~$ 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] <javascript:>> 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] <javascript:>>:
> >>
> >> > 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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> <javascript:>
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> >>
> >> --
> >> --
> >> Check the OTB FAQ at
> >> http://www.orfeo-toolbox.org/FAQ.html
> >>
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