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 $LD_LIBRARY_PATH
which otbcli
which otbcli_BandMathX
otbcli_BandMathX
I get:
> system("sh /home/alobo/test.scr", intern=TRUE)
/home/alobo/OTB-6.6.0-Linux64/bin/otbApplicationLauncherCommandLine:
symbol lookup error: /usr/lib/x86_64-linux-gnu/libOTBCommon-6.6.so.1:
undefined symbol:
_ZN3itk10LoggerBase5WriteENS0_17PriorityLevelTypeERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE
Error in system("sh /home/alobo/test.scr", intern = TRUE) :
error in running command
Same problem for otbcli commands (which are now
/home/alobo/OTB-6.6.0-Linux64/bin/otbcli)
So, something else has to be set for these commands to work from
within R, both otbcli and otbcli_BandMathX run ok from the terminal.
What could be different between this version and the older one that
actually works from within R?
Agus
On Thu, Dec 20, 2018 at 11:37 AM Jordi Inglada <[email protected]> wrote:
>
>
> The problem you have when sourcing from R is that "source" is not a command,
> but a built-in bash function which may not be available.
>
> Try with '.' instead of source, or include the contents of the config script
> in your scr file.
>
> On Thu 20-Dec-2018 at 11:08:52 +01, Agustin Lobo <[email protected]>
> wrote:
> > Thanks Guillaume. I think I have "environment problems"!!
> >
> > 1. Outside R
> > Whenever I start a shell (Xfce Terminal) I get
> > bash: LD_LIBRARY_PATH: command not found
> > (do not know why and do not know if it matters)
> >
> > Then I do
> > alobo@Delia:~$ 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
> > <[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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> >> http://www.orfeo-toolbox.org/FAQ.html
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