version 1.6.4

ChangeLog

@@ -1,3 +1,11 @@
+05-31-2016: 1.6.4
+	* changed description language as per CRAN rules. 
+05-25-2016: 1.6.3
+	* added pow_bounded function in misc.h
+	* replaced pow function with pow_bounded in maf.c and sufficient_stats.c
+	  to handle overflow
+	* added seed for phyloP testing
+
 8-14-2013: 1.5
         * fixed bug and added examples to translate.msa; also changed default
 	  frame to 1

DESCRIPTION

@@ -1,27 +1,29 @@
-Copyright: All code is Copyright (c) 2002-2015 University of
-        California, Cornell University.
+Copyright: All code is Copyright (c) 2002-2016 University of
+        California, Cornell University, Cold Spring Harbor Laboratory.
 Package: rphast
 Maintainer: Melissa Hubisz <mjhubisz@cornell.edu>
 License: BSD_3_clause + file LICENSE
 Title: Interface to PHAST Software for Comparative Genomics
 Author: Melissa Hubisz, Katherine Pollard, and Adam Siepel
-Description: RPHAST is an R interface to the PHAST software 
+Description: Provides an R interface to the PHAST software
     (Phylogenetic Analysis with Space/Time Models).  It can be used for
     many types of analysis in comparative and evolutionary genomics,
     such as estimating models of evolution from sequence data, scoring
     alignments for conservation or acceleration, and predicting
     elements based on conservation or custom phylogenetic hidden Markov
     models.  It can also perform many basic operations on multiple
     sequence alignments and phylogenetic trees.
-Version: 1.6
+Version: 1.6.4
 URL: http://compgen.cshl.edu/rphast
-Date: 2015-01-13
+Date: 2016-05-25
+Imports: methods
 Depends: stats
 Suggests: ape, seqLogo
 Collate: 'bgc.R' 'checkArgs.R' 'feat.R' 'hmm.R' 'listOfLists.R' 'msa.R'
         'optim.R' 'phastCons.R' 'phyloFit.R' 'phyloP.R' 'plot.R'
         'rphast.R' 'treeModel.R' 'trees.R' 'zzz.R'
-Packaged: 2015-01-14 04:15:59 UTC; mhubisz
+RoxygenNote: 5.0.1
+Packaged: 2016-06-01 18:50:26 UTC; rramani
 NeedsCompilation: yes
 Repository: CRAN
-Date/Publication: 2015-01-14 06:03:53
+Date/Publication: 2016-06-02 05:58:21

LICENSE

@@ -1,3 +1,3 @@
-YEAR: 2002-2015
+YEAR: 2002-2016
 COPYRIGHT HOLDER: University of California, Cornell University 
 ORGANIZATION: University of California, Cornell University

NAMESPACE

@@ -1,4 +1,4 @@
-# Generated by roxygen2 (4.1.0): do not edit by hand
+# Generated by roxygen2: do not edit by hand
 
 S3method("[",msa)
 S3method(as.data.frame,feat)
@@ -181,3 +181,7 @@ export(write.wig.feat)
 importFrom(stats,density)
 importFrom(stats,simulate)
 useDynLib(rphast)
+importFrom(graphics, abline, axis, hist, lines, mtext,
+           par, plot, points, rect, segments, text)
+importFrom(methods, as, is)
+importFrom(utils, URLencode, packageDescription, read.csv)

R/feat.R

@@ -1180,17 +1180,29 @@ tagval <- function(x, tag) {
 
 ##' Combine adjacent features with the same "feature" field
 ##' @param x An object of type feat
+##' @param weightedAverageScore If TRUE, scores of merged features
+##' are given by the average of those features, weighted by their
+##' original lengths. Otherwise, scores of merged features are
+##' simply summed.
+##' @param minScore If TRUE, scores of merged features are given
+##' by the minimum score of the combined features.
 ##' @return A features object in which adjacent features are
 ##' combined into one longer feature.
 ##' @note If x is stored as a pointer to a C structure, then
 ##' x will be modified to the return value.
 ##' @author Melissa J. Hubisz and Adam Siepel
 ##' @export
-flatten.feat <- function(x) {
+flatten.feat <- function(x, weightedAverageScore=FALSE, minScore=FALSE) {
+  if (minScore && weightedAverageScore) {
+    stop("flatten.feat: only one of minScore, weightedAverageScore can be TRUE")
+  }
   isPointer <- !is.null(x$externalPtr)
   if (!isPointer) x <- as.pointer.feat(x)
+  if (!is.logical(weightedAverageScore))
+      stop("Expected weightedAverageScore to be a logical")
   sort.feat(x)
-  .Call.rphast("rph_gff_flatten", x$externalPtr)
+  .Call.rphast("rph_gff_flatten", x$externalPtr, weightedAverageScore,
+               minScore)
   if (!isPointer) return(from.pointer.feat(x))
   x
 }

configure

@@ -2137,7 +2137,7 @@ CC=`"${R_HOME}/bin/R" CMD config CC`
 #RCFLAGS=`"${R_HOME}/bin/R" CMD config CFLAGS`
 RCFLAGS="-g"
 #CFLAGS="${RCFLAGS} ${CFLAGS}"
-CFLAGS=" -g"
+CFLAGS="${CFLAGS} -g"
 { $as_echo "$as_me:${as_lineno-$LINENO}: result: ${CFLAGS}" >&5
 $as_echo "${CFLAGS}" >&6; }
 ac_ext=c

configure.ac

@@ -13,7 +13,7 @@ CC=`"${R_HOME}/bin/R" CMD config CC`
 #RCFLAGS=`"${R_HOME}/bin/R" CMD config CFLAGS`
 RCFLAGS="-g"
 #CFLAGS="${RCFLAGS} ${CFLAGS}"
-CFLAGS=" -g"
+CFLAGS="${CFLAGS} -g"
 AC_MSG_RESULT(${CFLAGS})
 AC_PROG_CC
 AC_MSG_RESULT(${CFLAGS})