From 6113663f91e18a2c4e2189fb008a1e1478684cf9 Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Mon, 12 Oct 2015 13:44:07 +0200 Subject: [PATCH] replace exit() with quit(), this is more portable --- .../galaxy_install/tool_dependencies/recipe/step_handler.py | 2 +- 1 file changed, 1 insertion(+), 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 index 6935f42d1d6..dbcc1e3f3ec 100755 --- 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 @@ class SetupREnvironment( Download, RecipeStep ): # 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='$INSTALL_DIR', repos=NULL, dependencies=FALSE), error = exit(1))"''' % \ + Rscript -e "tryCatch( install.packages(c('%s'),lib='$INSTALL_DIR', repos=NULL, dependencies=FALSE), error = 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,