Solved by following your advice!
After uninstalling all otb* items with synaptic, just starting the script with
. /home/alobo/OTB-6.6.0-Linux64/otbenv.profile
let otbcli* and otbcli_BandMathX work fine from within R
Thanks!
Agus
On Thu, Dec 20, 2018 at 1:42 PM Jordi Inglada <jordi.ingl...@cesbio.eu> wrote:
>
>
> I think that the remaining problem comes from the fact that you have OTB
> libraries in /usr/lib/x86_64-linux-gnu/. This is why I suggest avoiding
> packages from the distribution.
>
> Your LD_LIBRARY_PATH contains /usr/lib/x86_64-linux-gnu/ and does not contain
> /home/alobo/OTB-6.6.0-Linux64/lib where the good library is located.
>
> The fact that the correct otbcli_* is found is misleading, because the
> command line applications are just wrappers for shared libs.
>
> On Thu 20-Dec-2018 at 13:02:13 +01, Agustin Lobo <alobolis...@gmail.com>
> wrote:
> > Thanks.
> > ok, I can solve the source problem, but not the main problem. If my
> > script is just
> > . /home/alobo/OTB-6.6.0-Linux64/otbenv.profile
> > echo $OTB_APPLICATION_PATH
> > echo $LD_LIBRARY_PATH
> > which otbcli
> > which otbcli_BandMathX
> >
> > I run from within R with system() and get:
> >> system("sh /home/alobo/test.scr", intern=TRUE)
> > [1] "/home/alobo/OTB-6.6.0-Linux64/lib/otb/applications"
> > [2]
> > "/usr/lib/R/lib::/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/default-java/lib/server"
> > [3] "/home/alobo/OTB-6.6.0-Linux64/bin/otbcli"
> > [4] "/home/alobo/OTB-6.6.0-Linux64/bin/otbcli_BandMathX"
> >
> > which is correct.
> >
> > But the poblem with otbcli_BandMathX remains. As soon as I add
> > otbcli_BandMathX
> > . /home/alobo/OTB-6.6.0-Linux64/otbenv.profile
> > echo $OTB_APPLICATION_PATH
> > echo $LD_LIBRARY_PATH
> > which otbcli
> > which otbcli_BandMathX
> > otbcli_BandMathX
> >
> > I get:
> >
> >> system("sh /home/alobo/test.scr", intern=TRUE)
> > /home/alobo/OTB-6.6.0-Linux64/bin/otbApplicationLauncherCommandLine:
> > symbol lookup error: /usr/lib/x86_64-linux-gnu/libOTBCommon-6.6.so.1:
> > undefined symbol:
> > _ZN3itk10LoggerBase5WriteENS0_17PriorityLevelTypeERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE
> > Error in system("sh /home/alobo/test.scr", intern = TRUE) :
> > error in running command
> >
> > Same problem for otbcli commands (which are now
> > /home/alobo/OTB-6.6.0-Linux64/bin/otbcli)
> >
> > So, something else has to be set for these commands to work from
> > within R, both otbcli and otbcli_BandMathX run ok from the terminal.
> > What could be different between this version and the older one that
> > actually works from within R?
> >
> > Agus
> >
> > On Thu, Dec 20, 2018 at 11:37 AM Jordi Inglada <jordi.ingl...@cesbio.eu>
> > wrote:
> >>
> >>
> >> The problem you have when sourcing from R is that "source" is not a
> >> command, but a built-in bash function which may not be available.
> >>
> >> Try with '.' instead of source, or include the contents of the config
> >> script in your scr file.
> >>
> >> On Thu 20-Dec-2018 at 11:08:52 +01, Agustin Lobo <alobolis...@gmail.com>
> >> wrote:
> >> > Thanks Guillaume. I think I have "environment problems"!!
> >> >
> >> > 1. Outside R
> >> > Whenever I start a shell (Xfce Terminal) I get
> >> > bash: LD_LIBRARY_PATH: command not found
> >> > (do not know why and do not know if it matters)
> >> >
> >> > Then I do
> >> > alobo@Delia:~$ 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
> >> > <guillaume.pas...@c-s.fr> 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 <alobolis...@gmail.com>:
> >> >>
> >> >> > 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
> >> >> >
> >> >> > You received this message because you are subscribed to the Google
> >> >> > Groups "otb-users" group.
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> >> >> > To unsubscribe from this group, send email to
> >> >> > otb-users+unsubscr...@googlegroups.com
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> >> >> > http://groups.google.com/group/otb-users?hl=en
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> >> >>
> >> >>
> >> >> --
> >> >> --
> >> >> 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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>
> --
> --
> Check the OTB FAQ at
> http://www.orfeo-toolbox.org/FAQ.html
>
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