Rashad, apparently, the configuration file it is not sourced in my system. >From a new terminal: alobo@Delia:~$ otbcli bash: otbcli: command not found alobo@Delia:~$ . /home/alobo/OTB-6.6.0-Linux64/otbenv.profile alobo@Delia:~$ otbcli Usage: /home/alobo/OTB-6.6.0-Linux64/bin/otbApplicationLauncherCommandLine module_name [MODULEPATH] [arguments]
otbcli* commands are not recognized until I source otbenv.profile. Same from within R. Agus On Fri, Dec 21, 2018 at 12:13 PM Rashad <[email protected]> wrote: > > > > 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]> 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]> 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. -- -- 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.
