Biostrings 2.77.1

- All the functions that went to pwalign in BioC 3.19 and got formally
  deprecated in Biostrings in BioC 3.21 are now defunct.

- After being deprecated in BioC 3.19, XStringPartialMatches objects
  and matchprobes() are now defunct.

- Remove needwunsQS() (was defunct in BioC 3.19).

Author: hpages

DESCRIPTION

@@ -7,7 +7,7 @@ biocViews: SequenceMatching, Alignment, Sequencing, Genetics,
 	DataImport, DataRepresentation, Infrastructure
 URL: https://bioconductor.org/packages/Biostrings
 BugReports: https://github.com/Bioconductor/Biostrings/issues
-Version: 2.77.0
+Version: 2.77.1
 License: Artistic-2.0
 Encoding: UTF-8
 Authors@R: c(
@@ -93,7 +93,6 @@ Collate: utils.R
 	XStringQuality-class.R
 	QualityScaledXStringSet.R
 	pmatchPattern.R
-	needwunsQS.R
 	MultipleAlignment.R
 	matchprobes.R
 	moved_to_pwalign.R

NAMESPACE

@@ -298,7 +298,6 @@ exportMethods(
 ###   XStringQuality-class.R
 ###   QualityScaledXStringSet.R
 ###   pmatchPattern.R
-###   needwunsQS.R
 ###   MultipleAlignment.R
 
 exportClasses(
@@ -341,10 +340,7 @@ export(
     readAAMultipleAlignment,
     consensusViews,
     write.phylip,
-    detail,
-
-    ## Old stuff (Deprecated or Defunct):
-    needwunsQS
+    detail
 )
 
 exportMethods(

R/XStringPartialMatches-class.R

@@ -18,7 +18,7 @@ setClass("XStringPartialMatches",
 setGeneric("subpatterns",
     function(x)
     {
-        .Deprecated()
+        .Defunct()
         standardGeneric("subpatterns")
     }
 )
@@ -33,8 +33,8 @@ setMethod("subpatterns", "XStringPartialMatches", function(x) x@subpatterns)
 setMethod("show", "XStringPartialMatches",
     function(object)
     {
-        msg <- "XStringPartialMatches objects are deprecated"
-        .Deprecated(msg=wmsg(msg))
+        msg <- "XStringPartialMatches objects are defunct"
+        .Defunct(msg=wmsg(msg))
         subject <- subject(object)
         lsub <- length(subject)
         cat("  Views on a ", lsub, "-letter ",
@@ -63,8 +63,8 @@ setMethod("show", "XStringPartialMatches",
 setMethod("[", "XStringPartialMatches",
     function(x, i, j, ..., drop)
     {
-        msg <- "XStringPartialMatches objects are deprecated"
-        .Deprecated(msg=wmsg(msg))
+        msg <- "XStringPartialMatches objects are defunct"
+        .Defunct(msg=wmsg(msg))
         ans <- callNextMethod()
         ans@subpatterns <- ans@subpatterns[i]
         ans

R/matchprobes.R

@@ -1,7 +1,6 @@
 matchprobes <- function(query, records, probepos=FALSE) {
-  msg <- "matchprobes() is deprecated. Please use matchPdict() instead."
-  .Deprecated(msg=msg)
-  .Call2("MP_matchprobes", toupper(query), toupper(records), probepos, PACKAGE="Biostrings")
+  msg <- "matchprobes() is defunct. Please use matchPdict() instead."
+  .Defunct(msg=msg)
 }
 
 longestConsecutive <- function(seq, letter) {

R/moved_to_pwalign.R

@@ -1,26 +1,12 @@
 ### Everything in this file has moved to the pwalign package
 
 
-### TODO: Move this to S4Vectors (or BiocBaseUtils).
-.load_package_gracefully <- function(package, ...)
-{
-    if (!requireNamespace(package, quietly=TRUE))
-        stop("Could not load package ", package, ". Is it installed?\n\n  ",
-             wmsg("Note that ", ..., " requires the ", package, " package. ",
-                  "Please install it with:"),
-             "\n\n    BiocManager::install(\"", package, "\")")
-}
-
 .call_fun_in_pwalign <- function(fun, ...)
 {
-    .load_package_gracefully("pwalign", "starting with BioC 3.19, ",
-                             "calling ", fun, "()")
     msg <- c(fun, "() has moved from Biostrings to the pwalign package, ",
-             "and is formally deprecated in Biostrings >= 2.75.1. ",
-             "Please call pwalign::", fun, "() to get rid of this warning.")
-    .Deprecated(msg=wmsg(msg))
-    FUN <- base::get(fun, envir=asNamespace("pwalign"), inherits=FALSE)
-    do.call(FUN, list(...))
+             "and is formally defunct in Biostrings >= 2.77.1. ",
+             "Please call pwalign::", fun, "() to get rid of this error.")
+    .Defunct(msg=wmsg(msg))
 }
 
 writePairwiseAlignments <-

R/needwunsQS.R

@@ -1,8 +1,11 @@
 \name{matchprobes}
 \alias{matchprobes}
-\title{(Deprecated) A function to match a query sequence to the sequences
+\title{(Defunct) A function to match a query sequence to the sequences
   of a set of probes.}
 \description{
+  WARNING: The \code{matchprobes()} function is defunct in
+  \pkg{Biostrings} >= 2.77.1.
+
   The \code{query} sequence, a character string (probably representing
   a transcript of interest), is scanned for the presence of exact
   matches to the sequences in the character vector \code{records}.

man/matchprobes.Rd

@@ -1110,8 +1110,3 @@ SEXP lcsuffix(
 char compbase(char c);
 SEXP MP_longestConsecutive(SEXP x, SEXP letter);
 
-
-/* matchprobes.c (belonged originally to old matchprobes package) */
-
-SEXP MP_matchprobes(SEXP query, SEXP records, SEXP probepos);
-

man/needwunsQS.Rd

@@ -140,9 +140,6 @@ static const R_CallMethodDef callMethods[] = {
 /* strutils.c (belonged originally to old matchprobes package) */
 	CALLMETHOD_DEF(MP_longestConsecutive, 2),
 
-/* matchprobes.c (belonged originally to old matchprobes package) */
-	CALLMETHOD_DEF(MP_matchprobes, 3),
-
 	{NULL, NULL, 0}
 };