Merge pull request #33 from Chris1221/devel

Bug checks and fixes

R/RcppExports.R

@@ -1,4 +1,4 @@
-# This file was generated by Rcpp::compileAttributes
+# Generated by using Rcpp::compileAttributes() -> do not edit by hand
 # Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
 
 #' @title Match terms

R/goldi.R

@@ -5,7 +5,7 @@
 #'
 #' @keywords Text Mining, Gene Ontology, Databases
 #'
-#' @author Christopher B. Cole <[email protected]>
+#' @author Christopher B. Cole <chris.c.1221@@gmail.com>
 #'
 #' @references See ArXiv prepubliation.
 #'
@@ -151,7 +151,7 @@ Note that any interactively created lists may be saved and inputed.
 
 		lims <- as.list(lims)
 
-		flog.warn("Trying to coerce limits to list format.")
+		flog.debug("Trying to coerce limits to list format.")
 		flog.info("Printing your lims to log file. You can use this to recreate your list later:")
 
 		flog.info("%s", capture.output(dput(lims)))
@@ -460,12 +460,12 @@ Note that any interactively created lists may be saved and inputed.
 
   # Clean this up after, it's really messy right now
 
-  out %>% as.data.frame %>% data.matrix -> input_pdf_tdm
+  suppressWarnings( out %>% as.data.frame %>% data.matrix ) -> input_pdf_tdm
   colnames(input_pdf_tdm) <- NULL
   row.names(input_pdf_tdm) <- NULL
 
   input_term_tdm <- as.matrix(TDM.go.df)
-  input_term_tdm %<>% as.data.frame %>% data.matrix
+  input_term_tdm %<>% as.data.frame %>% data.matrix %>% suppressWarnings()
   colnames(input_term_tdm) <- NULL
   row.names(input_term_tdm) <- NULL
 
@@ -511,6 +511,8 @@ Note that any interactively created lists may be saved and inputed.
 
 	flog.info("Everything was successful. Ending logging now. Have a nice day.")
 
+	colnames(terms) <- c("Identified Terms", "Context")
+
 	if(!object){
 
 		flog.info("Returning as List, either for internal use or for testing.")

cran-comments.md

@@ -1,7 +1,7 @@
 ## Test environments
-* Local OS X Install, R 3.3.1
-* Linux Ubuntu 12.04 LTS Server Edition 64 bit (through Travis-CI), R 3.3.1
-* Windows through Appveyor, R R.3.3.1
+* Local OS X Install, R 3.3.1 + R Devel 
+* Linux Ubuntu 12.04 LTS Server Edition 64 bit (through Travis-CI), R 3.3.1 + R Devel
+* Windows through Appveyor, R 3.3.1 + R Devel
 
 ## R CMD check results
 There were no ERRORs or WARNINGs.

src/RcppExports.cpp

@@ -1,4 +1,4 @@
-// This file was generated by Rcpp::compileAttributes
+// Generated by using Rcpp::compileAttributes() -> do not edit by hand
 // Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
 
 #include <RcppArmadillo.h>
@@ -10,16 +10,16 @@ using namespace Rcpp;
 Rcpp::CharacterMatrix match(arma::uvec term_vector, arma::mat pdf_tdm, arma::mat term_tdm, arma::vec thresholds, arma::uvec pdf_index, std::vector<std::string> terms, std::vector<std::string> sentences);
 RcppExport SEXP goldi_match(SEXP term_vectorSEXP, SEXP pdf_tdmSEXP, SEXP term_tdmSEXP, SEXP thresholdsSEXP, SEXP pdf_indexSEXP, SEXP termsSEXP, SEXP sentencesSEXP) {
 BEGIN_RCPP
-    Rcpp::RObject __result;
-    Rcpp::RNGScope __rngScope;
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
     Rcpp::traits::input_parameter< arma::uvec >::type term_vector(term_vectorSEXP);
     Rcpp::traits::input_parameter< arma::mat >::type pdf_tdm(pdf_tdmSEXP);
     Rcpp::traits::input_parameter< arma::mat >::type term_tdm(term_tdmSEXP);
     Rcpp::traits::input_parameter< arma::vec >::type thresholds(thresholdsSEXP);
     Rcpp::traits::input_parameter< arma::uvec >::type pdf_index(pdf_indexSEXP);
     Rcpp::traits::input_parameter< std::vector<std::string> >::type terms(termsSEXP);
     Rcpp::traits::input_parameter< std::vector<std::string> >::type sentences(sentencesSEXP);
-    __result = Rcpp::wrap(match(term_vector, pdf_tdm, term_tdm, thresholds, pdf_index, terms, sentences));
-    return __result;
+    rcpp_result_gen = Rcpp::wrap(match(term_vector, pdf_tdm, term_tdm, thresholds, pdf_index, terms, sentences));
+    return rcpp_result_gen;
 END_RCPP
 }

tests/testthat/test-goldi.R

@@ -12,9 +12,11 @@ log = "/dev/null"
 ouput = "/dev/null"
 
 os <- .Platform$OS.type
-out <- structure(c("ribosomal_chaperone_activity", "Ribosomal chaperone activity"), .Dim = 1:2)
-
+#out <- structure(c("ribosomal_chaperone_activity", "Ribosomal chaperone activity"), .Dim = 1:2)
 
+out <- structure(c("ribosomal_chaperone_activity", "Ribosomal chaperone activity"
+		  ), .Dim = 1:2, .Dimnames = list(NULL, c("Identified Terms", "Context"
+							 ))) 
 test_that("testing main function", {
   if(os != "unix") skip("Tests are not currently performed on windows.")