Fix syntax of error parameter of tryCatch.

nsoranzo · Oct 15, 2015 · 73ca4c7 · 73ca4c7
1 parent 296dab0
commit 73ca4c7
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py b/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
@@ -1372,7 +1372,7 @@ def execute_step( self, tool_dependency, package_name, actions, action_dict, fil
                     # Use raw strings so that python won't automatically unescape the quotes before passing the command
                     # to subprocess.Popen.
                     cmd = r'''PATH=$PATH:$R_HOME/bin; export PATH; R_LIBS=$INSTALL_DIR:$R_LIBS; export R_LIBS;
-                        Rscript -e "tryCatch( install.packages(c('%s'),lib='$INSTALL_DIR', repos=NULL, dependencies=FALSE), error = quit(status = 1))"''' % \
+                        Rscript -e "tryCatch( { install.packages(c('%s'), lib = '$INSTALL_DIR', repos = NULL, dependencies = FALSE) }, error = function(e) { print(e); quit(status = 1) } )"''' % \
                         ( str( tarball_name ) )
                     cmd = install_environment.build_command( basic_util.evaluate_template( cmd, install_environment ) )
                     return_code = install_environment.handle_command( tool_dependency=tool_dependency,