fix broken tests

- struct::struct_class now correctly checks for bibtex format of citations
- fixed incorrect use of testthat::expect_output when testing ontology classes

Author: grlloyd

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: struct
 Type: Package
 Title: Statistics in R Using Class-based Templates
-Version: 1.20.0
+Version: 1.20.1
 Authors@R: c(
     person(
         c("Gavin","Rhys"),

NEWS

@@ -1,3 +1,6 @@
+Changes 1.20.1
++ fix broken tests
+
 Changes 1.15.5
 + update automated documentation generation
 

R/struct_class.R

@@ -77,12 +77,12 @@ struct_class = function(
     }
 
     # check all citations are Bibtex
-    if (length(citations>0)) {
-        ok=unlist(lapply(citations,is,class='bibentry'))
-        if (!(all(ok))){
-            stop('all citations must be in "bibentry" format')
-        }
-    }
+    #if (length(citations>0)) {
+    #    ok=unlist(lapply(citations,is,class='bibentry'))
+    #    if (!(all(ok))){
+    #        stop('all citations must be in "bibentry" format')
+    #    }
+    #}
 
     # new object
     out = .struct_class(
@@ -123,7 +123,7 @@ setValidity('struct_class', method = function(object) {
 
     citations=object$citations
     # check all citations are Bibtex
-    if (length(citations>0)) {
+    if (length(citations)>0) {
         ok=unlist(lapply(citations,is,class='bibentry'))
         if (!(all(ok))){
             str=c(str,('All citations must be in "bibentry" format'))

tests/testthat/test-ontology.R

@@ -47,7 +47,7 @@ test_that('ontology works as expected',{
 
     expect_error(O$cake)
 
-    expect_output(show(O[1]),"STATO:0000555",regexp = 'STATO:0000555')
+    expect_output(show(O[1]),regexp = 'STATO:0000555')
 
     O=ontology_list()
     expect_equal(length(O),0)