private void reindexPackage(RPackage rPackage, RPackage indexPackage) { // replace package RHelperUtil.LOG.info("detecting methods in " + rPackage.getName()); String allFunsConcat = RHelperUtil.runCommand("cat(getNamespaceExports('" + rPackage.getName() + "'))").trim(); List<String> allFuns = Splitter.on(" ").trimResults().splitToList(allFunsConcat); List<Function> functions = Lists.transform( allFuns, new com.google.common.base.Function<String, Function>() { @Override public Function apply(String s) { return new Function(s, "NA"); } }); rPackage.setFunctions(functions); if (indexPackage != null) { allPackages.remove(indexPackage); } allPackages.add(rPackage); }