On Thu 20-Dec-2018 at 14:57:38 +01, Agustin Lobo <alobolis...@gmail.com> wrote:
> 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
>
I think you should ask for official R bindings for OTB. I will ask for Julia
and Haskell ;)
> 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
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>> >> >> > For more options, visit this group at
>> >> >> > 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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>> >> >> Groups "otb-users" group.
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>> >> >
>> >> > --
>> >>
>> >> --
>> >> --
>> >> Check the OTB FAQ at
>> >> 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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>
> --
--
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