fix problems surfaced by CRAN reviews, push version 2.1-14

.Rbuildignore

@@ -4,3 +4,4 @@
 ^\.gitignore$
 ^\.github$
 ^\.git$
+^CRAN-SUBMISSION$

DESCRIPTION

@@ -1,11 +1,14 @@
 Package: VPdtw
 Type: Package
 Title: Variable Penalty Dynamic Time Warping
-Version: 2.1-13
+Version: 2.1-14
 Date: 2022-07-03
-Author: David Clifford, Glenn Stone
-Maintainer: Ethan Bass <[email protected]>
-Description: Variable Penalty Dynamic Time Warping for aligning GC-MS chromatograms to a master signal and more. With the appropriate penalty this method performs good alignment without altering the shape of peaks in GC-MS data.
-License: GPL-2 | file LICENSE
+Authors@R: c(person("David", "Clifford", , email="[email protected]", role = c("aut")),
+           person("Glenn", "Stone", role = c("aut")),
+           person("Ethan", "Bass", email = "[email protected]", role = c("ctb", "cre"), comment = c(ORCID = "0000-0002-6175-6739"))
+           )
+Description: Variable Penalty Dynamic Time Warping (VPdtw) for aligning chromatographic signals. With an appropriate penalty this method performs good alignment of chromatographic data without deforming the peaks (Clifford, D., Stone, G., Montoliu, I., Rezzi S., Martin F., Guy P., Bruce S., and Kochhar S.(2009) <doi:10.1021/ac802041e>; Clifford, D. and Stone, G. (2012) <doi:10.18637/jss.v047.i08>).
+License: GPL-2
 URL: https://github.com/ethanbass/VPdtw/
 BugReports: https://github.com/ethanbass/VPdtw/issues
+

NEWS.md

@@ -1,3 +1,8 @@
+# VPdtw 2.1-14
+
+* Changed messages so they can be suppressed more easily by the user.
+* Fixed examples and plot.VPdtw function so they no longer change user's par settings.
+
 # VPdtw 2.1-13
 
 * Added a `NEWS.md` file to track changes to the package.

R/VPdtw.R

@@ -1,28 +1,26 @@
-VPdtw <- function(reference,query,penalty=0,maxshift=50,Reference.type=c("random","median","mean","trimmed")) {
+VPdtw <- function(reference, query, penalty=0, maxshift=50,
+                  Reference.type=c("random", "median", "mean", "trimmed")) {
 
   ## We assume Sakoe Chiba DTW to allow for faster computation times
-  if(!is.numeric(maxshift)) {
-    return("Please specify maxshift as an integer value\n")
-  }
+  if(!is.numeric(maxshift))
+    stop("Please specify maxshift as an integer value")
 
   ## Figure out what kind of alignment we are doing -
 
   ## a reference vector to a query vector?
   ## no reference and a matrix of query vectors?
   ## something else = no implementation here
 
-  if(is.null(reference) & !is.matrix(query)) {
-    cat("Please specify a reference when passing a non-matrix query\n")
-    return("Exiting....\n")
-  }
+  if(is.null(reference) & !is.matrix(query))
+    stop("Please specify a reference when passing a non-matrix query")
 
   if(is.null(reference) & is.matrix(query)) {
 
     ## If no reference is specified, we choose one randomly, using
     ## median, mean or trimmed mean of the query matrix depending on
     ## the value of type as specified by the user.
 
-    type <- match.arg(Reference.type,c("random","median","mean","trimmed"))
+    type <- match.arg(Reference.type,c("random", "median", "mean", "trimmed"))
     ss <- sample(1:ncol(query),1)
     reference <- switch(type,
                         random = query[,ss],
@@ -32,12 +30,12 @@ VPdtw <- function(reference,query,penalty=0,maxshift=50,Reference.type=c("random
     reference <- na.omit(reference)
 
     ## if penalty is a number, then this means a constant penalty vector, create that vector
-    if(length(penalty)==1) penalty <- rep(penalty,length(reference))
+    if(length(penalty) ==1 )
+      penalty <- rep(penalty,length(reference))
 
     ## Check penalty vector length
-    if(length(penalty)<length(reference)) {
-      warning("Penalty vector should be at least of length ",length(reference)," but it has length ",length(penalty),"\n")
-      return("Exiting...\n")
+    if(length(penalty) < length(reference)) {
+      stop("Penalty vector should be at least of length ", length(reference)," but it has length ",length(penalty))
     }
 
     ## information used in summary at end - what kind of reference do
@@ -84,7 +82,8 @@ VPdtw <- function(reference,query,penalty=0,maxshift=50,Reference.type=c("random
     information <- paste(information,"Max allowed shift is ",maxshift,".\n",sep="")
     reference <- na.omit(reference)
 
-    if(length(penalty)==1) penalty <- rep(penalty,length(reference))
+    if(length(penalty)==1)
+      penalty <- rep(penalty,length(reference))
 
     result <- DoAlignment(query,reference,penalty,maxshift)
 
@@ -174,10 +173,6 @@ VPdtw <- function(reference,query,penalty=0,maxshift=50,Reference.type=c("random
       output$shift[seq(str,end,by=1),colName] <- result[[ii]][,4]
     }
 
-    ## matplot(output$xVals,output$warpedQuery,type="n",lty=1,col=c(2,3))
-    ## lines(output$xVals,output$reference,lwd=2,col=1)
-    ## matplot(output$xVals,output$warpedQuery,type="l",lty=1,col=c(2,3),add=TRUE)
-
     class(output) <- "VPdtw"
 
     ## Summary Statistics for each query separately
@@ -262,10 +257,6 @@ VPdtw <- function(reference,query,penalty=0,maxshift=50,Reference.type=c("random
       colName <- paste("shift penalty",ii)
       output$shift[seq(str,end,by=1),colName] <- result[[ii]][,4]
     }
-
-    ## matplot(output$xVals,output$warpedQuery,type="n",lty=1,col=c(2,3))
-    ## lines(output$xVals,output$reference,lwd=2,col=1)
-    ## matplot(output$xVals,output$warpedQuery,type="l",lty=1,col=c(2,3),add=TRUE)
     class(output) <- "VPdtw"
 
     ## Summary Statistics for each query separately
@@ -292,9 +283,8 @@ VPdtw <- function(reference,query,penalty=0,maxshift=50,Reference.type=c("random
   }
 
   if(is.matrix(query) & is.matrix(penalty)) {
-    cat("Multiple queries and multiple penalties not yet implemented\n")
-    cat("Please create loops and call VPdtw as required\n")
-    return("Exiting....\n")
+    stop("Multiple queries and multiple penalties not yet implemented.
+         Please create loops and call VPdtw as needed.")
   }
 
   ## finished

R/plot.VPdtw.R

@@ -1,9 +1,12 @@
 
-plot.VPdtw <- function(x,type=c("All","Before","After","Shift"),xlim=NULL,...)
+plot.VPdtw <- function(x, type=c("All", "Before", "After", "Shift"), xlim=NULL,
+                       ...)
   {
     bgcol <- grey(0.9)
     type <- match.arg(type,c("All","Before","After","Shift"))
-
+
+    oldpar <- par(no.readonly = TRUE)
+    on.exit(par(oldpar))
     pp <- switch(type,
                  All=par(mfrow=c(3,1)),
                  Before=par(mfrow=c(1,1)),
@@ -14,7 +17,6 @@ plot.VPdtw <- function(x,type=c("All","Before","After","Shift"),xlim=NULL,...)
       xlim <- c(x$xVals[1],x$xVals[length(x$xVals)])
       ylim <- range(x$query,x$reference,na.rm=TRUE)
     } else {
-
       ind <- 1:length(x$reference)
       ylim <- range(x$reference[which(ind>=xlim[1] & ind <= xlim[2])],na.rm=TRUE)
       ind <- 1:length(x$query)
@@ -28,7 +30,6 @@ plot.VPdtw <- function(x,type=c("All","Before","After","Shift"),xlim=NULL,...)
     }
 
     if(type=="All" | type=="Before") {
-
       if(is.matrix(x$query)) {
         plot(c(1,nrow(x$query)),c(1,ncol(x$query)),type="n",
              xlab="Index",ylab="Sample",
@@ -39,12 +40,10 @@ plot.VPdtw <- function(x,type=c("All","Before","After","Shift"),xlim=NULL,...)
       }
 
       if(is.vector(x$query)) {
-
         plot(xlim,ylim,type="n",xlab="Index",ylab="Intensity",
              main="Query and Reference before Alignment")
         lines(x$xVals,x$reference,lwd=2,col=1)
         lines(x$query,col=2)
-
       }
     }
 
@@ -53,13 +52,15 @@ plot.VPdtw <- function(x,type=c("All","Before","After","Shift"),xlim=NULL,...)
         plot(c(min(x$xVals),max(x$xVals)),c(1,ncol(x$warpedQuery)),type="n",
              xlab="Index",ylab="Sample",
              main="Queries after Alignment")
-        rect(min(x$xVals)-1000,-1000,max(x$xVals)+1000,ncol(x$warpedQuery)+1000,col=bgcol)
+        rect(min(x$xVals)-1000, -1000,
+             max(x$xVals)+1000, ncol(x$warpedQuery)+1000,
+             col=bgcol)
         image(x$xVals,1:ncol(x$warpedQuery),x$warpedQuery,add=TRUE)
         box()
       }
       if(is.vector(x$query) & is.vector(x$penalty)) {
-
-        plot(xlim,ylim,type="n",xlab="Index",ylab="Intensity",main="Query and Reference after Alignment")
+        plot(xlim,ylim,type="n",xlab="Index",ylab="Intensity",
+             main="Query and Reference after Alignment")
         lines(x$xVals,x$reference,lwd=2,col=1)
         lines(x$xVals,x$warpedQuery,col=2)
 
@@ -69,36 +70,33 @@ plot.VPdtw <- function(x,type=c("All","Before","After","Shift"),xlim=NULL,...)
         return("Error, exiting...\n")
       }
       if(is.vector(x$query) & is.matrix(x$penalty)) {
-        ##
         ncols <- ncol(x$warpedQuery)
-        plot(xlim,ylim,type="n",xlab="Index",ylab="Intensity",main="Query and Reference after Alignment")
+        plot(xlim,ylim,type="n",xlab="Index",ylab="Intensity",
+             main="Query and Reference after Alignment")
         lines(x$xVals,x$reference,lwd=2,col=1)
         matplot(x$xVals,x$warpedQuery,type="l",lty=1,add=TRUE,col=2:(ncols+1))
-        legend("topright",legend=c("Reference",paste("penalty  #",1:ncols,sep="")),col=1:(ncols+1),lty=rep(1,ncols+1),lwd=c(2,rep(1,ncols)))
+        legend("topright",legend=c("Reference",paste("penalty  #",1:ncols,sep="")),
+               col=1:(ncols+1),lty=rep(1,ncols+1),lwd=c(2,rep(1,ncols)))
       }
     }
 
-    if(type=="All" | type=="Shift") {
+    if(type == "All" | type == "Shift") {
       if(is.matrix(x$shift)) {
-        ## Image isn't very useful here, matplot is better, though crowded
-        ##image(x$xVals,1:ncol(x$shift),x$shift,xlab="Index",ylab="Sample",main="Shifts after Alignment")
-        ##box()
         ncols <- ncol(x$shift)
-        ##xlim <- range(0,x$shift,na.rm=TRUE)
-
-        matplot(x$xVals,x$shift,type="l",lty=1,xlab="Index",ylab="Shift",main="Shifts required for Alignment",col=2:(ncols+1),xlim=xlim)
-        if(is.matrix(x$penalty)) legend("topleft",legend=paste("penalty  #",1:ncols,sep=""),col=2:(ncols+1),lty=rep(1,ncols))
-        if(is.matrix(x$query)) legend("topleft",legend=paste("query  #",1:ncols,sep=""),col=2:(ncols+1),lty=rep(1,ncols))
+
+        matplot(x$xVals, x$shift, type="l", lty=1, xlab="Index", ylab="Shift",
+                main="Shifts required for Alignment", col=2:(ncols+1), xlim=xlim)
+        if (is.matrix(x$penalty))
+          legend("topleft",legend=paste("penalty  #",1:ncols,sep=""),col=2:(ncols+1),lty=rep(1,ncols))
+        if (is.matrix(x$query))
+          legend("topleft",legend=paste("query  #",1:ncols,sep=""),col=2:(ncols+1),lty=rep(1,ncols))
         abline(h=0,lty=2,col=grey(0.75))
       }
       if(is.vector(x$shift)) {
         plot(x$xVals,x$shift,ylim=range(c(0,x$shift),na.rm=TRUE),xlab="Index",ylab="Shift",main="Shifts required for Alignment",type="n",xlim=xlim)
         abline(h=0,lty=2,col=grey(0.75))
         lines(x$xVals,x$shift)
-
-
       }
     }
-
     par(pp)
   }

R/signalMatchABand.R

@@ -55,7 +55,8 @@ signalMatchABand <- function(reference,query, lambda=rep(0.0,length(reference)),
 
   ## Should we warn when we get close to maxshift?
   shift <- xVals - xIndices
-  if(max(abs(shift),na.rm=TRUE)>(3*maxshift/4)) cat("Warning: Observed shift more than three quarters of maxshift\n")
+  if (max(abs(shift), na.rm=TRUE) > (3*maxshift/4))
+    warning("Observed shift more than three quarters of maxshift")
 
   ## Come up with a nice summary
   output <- matrix(NA,length(xVals),4)
@@ -68,8 +69,6 @@ signalMatchABand <- function(reference,query, lambda=rep(0.0,length(reference)),
   output[,"warped query"] <- query[xIndices]
   output[,"shift"] <- shift
 
-
-  ##cat(range(pp$path - 1:length(pp$path)),"\n")
   zz <- output
   return(invisible(zz))
 }

cran-comments.md

@@ -1,3 +1,16 @@
+## Response to reviews
+
+- Have [the] issues [that caused the original package to be archived] been solved?
+Yes, as far as I know the package was archived because the native routines were not properly registered. This issue has been remedied as of version 2.1-13.
+
+- As requested, the Description was modified to use the Authors@R field and acronyms were removed from the package description. I also added two references to the package description.
+
+- The LICENSE file was removed since it was redundant with the license stated in the package description.
+
+- Functions no longer use the `cat` command to write messages to the console; `message`, `warning` or `stop` (as appropriate) are now used instead.
+
+- Examples were corrected so that they reset the user's par settings after running.
+
 ## R CMD check results
 
 0 errors | 0 warnings | 1 note
@@ -7,5 +20,13 @@
 - While this is marked as a new submission, it was in fact [published on CRAN previously](https://cran.r-project.org/web/packages/VPdtw/index.html).
 VPdtw was removed from CRAN on 2017-03-13 -- apparently, because the
 "native routines" were not properly registered. This issue has been remedied with
-this new version. I  am taking over from David Clifford as maintainer with his 
-permission.
+this new version. I am taking over from David Clifford as maintainer with his 
+permission.
+
+- Found the following (possibly) invalid DOIs:
+  DOI: 10.1021/ac802041e
+    From: DESCRIPTION
+    Status: Service Unavailable
+    Message: 503
+
+^ This is a valid doi.

man/dilation.Rd

@@ -53,10 +53,12 @@ lines(dref,col=2)
 BIN <- (volcano>177)
 dBIN <- t(apply(BIN,1,dilation,span=5))
 dBIN <- apply(dBIN,2,dilation,span=5)
+oldpar <- par(no.readonly = TRUE)
 par(mfrow=c(2,2))
 image(volcano)
 image(BIN)
 image(dBIN)
+par(oldpar)
 }
 
 \keyword{methods}