Fixed warning on BBS

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: Structstrings
 Title: Implementation of the dot bracket annotations with Biostrings
-Version: 1.19.0
-Date: 2020-12-13
+Version: 1.19.1
+Date: 2024-03-19
 Authors@R: person("Felix G.M.","Ernst",
                   email = "felix.gm.ernst@outlook.com",
                   role = c("aut", "cre"),
@@ -43,7 +43,7 @@ Suggests:
     tRNAscanImport,
     BiocStyle
 VignetteBuilder: knitr
-RoxygenNote: 7.1.1
+RoxygenNote: 7.3.1
 Collate: 
     'Structstrings.R'
     'AllGenerics.R'

NAMESPACE

@@ -1,5 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method(add_colors,DotBracket)
 export("dotbracket<-")
 export(DB)
 export(DBDF)

R/Structstrings-DotBracketString.R

@@ -208,7 +208,7 @@ make_DOTBRACKET_COLORED_LETTERS <- function()
 }
 
 add_colors <- function(x) UseMethod("add_colors")
-add_colors.default <- identity
+#' @export
 add_colors.DotBracket <- .add_DotBracket_colors
 
 setMethod("show", "DotBracketString",

R/Structstrings.R

@@ -47,10 +47,12 @@
 #' tRNA Genes." Nucleic Acids Research 37 (suppl_1): D159–D162.
 #' \href{https://doi.org/10.1093/nar/gkn772}{doi:10.1093/nar/gkn772}.
 #' 
-#' @docType package
 #' @name Structstrings
 NULL
 
+#' @keywords internal
+"_PACKAGE"
+
 #' @useDynLib Structstrings
 #' @import methods
 #' @import S4Vectors

README.md

@@ -1,7 +1,7 @@
 # Structstrings: implementation of the dot bracket annotations with Biostrings <img src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/Structstrings/Structstrings.png" height="300" align="right">
 
 <!-- badges: start -->
-[![R-CMD-check](https://github.com/FelixErnst/Structstrings/workflows/R-CMD-check-bioc/badge.svg)](https://github.com/FelixErnst/Structstrings/actions?query=workflow:R-CMD-check-bioc)
+[![R-CMD-check](https://github.com/FelixErnst/Structstrings/workflows/R-CMD-check-bioc-devel/badge.svg)](https://github.com/FelixErnst/EpiTxDb/actions/)
 [![BioC Build](https://bioconductor.org/shields/build/devel/bioc/Structstrings.svg)](http://bioconductor.org/checkResults/devel/bioc-LATEST/Structstrings/)
 [![codecov](https://codecov.io/gh/FelixErnst/Structstrings/branch/master/graph/badge.svg)](https://codecov.io/gh/FelixErnst/Structstrings)
 [![BioC Years](https://bioconductor.org/shields/years-in-bioc/Structstrings.svg)](https://doi.org/doi:10.18129/B9.bioc.Structstrings)

src/DotBracketDataFrame_class.c

@@ -23,10 +23,7 @@ SEXP new_DotBracketDFrameList(SEXP unlistData, SEXP partitioning)
   return ans;
 }
 
-long *get_base_pairing_per_char_pair(R_xlen_t length, 
-                                     const char *str,
-                                     char bracket_open,
-                                     char bracket_close)
+long *get_base_pairing_per_char_pair(R_xlen_t length, const char *str, char bracket_open, char bracket_close)
 {
   long *table, *stack, i,j,hx;
 
@@ -40,9 +37,7 @@ long *get_base_pairing_per_char_pair(R_xlen_t length,
     } else if(str[i-1] == bracket_close){
       j = stack[--hx];
       if (hx<0) {
-        error("unbalanced '%s%s' brackets in dot bracket structure",
-              bracket_open,
-              bracket_close);
+        error("unbalanced '%s%s' brackets in dot bracket structure", bracket_open, bracket_close);
         free(stack);
         return NULL;
       }
@@ -54,9 +49,7 @@ long *get_base_pairing_per_char_pair(R_xlen_t length,
   }
   free(stack);
   if (hx != 0) {
-    error("unbalanced '%s%s' brackets in dot bracket structure",
-          bracket_open,
-          bracket_close);
+    error("unbalanced '%s%s' brackets in dot bracket structure", bracket_open,  bracket_close);
     return NULL;
   }
   return(table);