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 >> > >> > You received this message because you are subscribed to the Google >> > Groups "otb-users" group. >> > To post to this group, send email to [email protected] >> > To unsubscribe from this group, send email to >> > [email protected] >> > For more options, visit this group at >> > http://groups.google.com/group/otb-users?hl=en >> > --- >> > You received this message because you are subscribed to the Google >> > Groups "otb-users" group. >> > To unsubscribe from this group and stop receiving emails from it, >> > send an email to [email protected]. >> > For more options, visit https://groups.google.com/d/optout. >> >> >> -- >> -- >> 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. >> To post to this group, send email to [email protected] >> To unsubscribe from this group, send email to >> [email protected] >> For more options, visit this group at >> http://groups.google.com/group/otb-users?hl=en >> --- >> You received this message because you are subscribed to the Google Groups >> "otb-users" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to [email protected]. >> For more options, visit https://groups.google.com/d/optout. > > -- -- -- 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. To post to this group, send email to [email protected] To unsubscribe from this group, send email to [email protected] For more options, visit this group at http://groups.google.com/group/otb-users?hl=en --- You received this message because you are subscribed to the Google Groups "otb-users" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. For more options, visit https://groups.google.com/d/optout.
