Merge branch 'master' into devel

* master: (24 commits) temporarily disable updateObject test - see issue #166 torture test script Fix class version problem for Spectrum1 and Spectrum2 new lines cleanup set version in initialise for Spectum only Use getClassVersion function to get class versions. Add class version to C-constructors set Spectrum class in initialize revert to previous NAnnotatedDataFrame fix new error quantifying msnexp with empty phenodata set class version in NAnnotatedDataFrame initialize fix iPQF unit test to take into account new class versions fix MSnProcess and MIAPE initialize to set class version earlier set class version in MIAPE initialize new rcpp attribs class version helper functions MSnProcess has class set in initialize and validity checks for version Initiating removal or new() class version construction inside prototype. Tix removeReporters,OnDiskMSnExp Reverting to old initialize,Spectrum (see issue #163) ... From: Laurent <lg390@cam.ac.uk> git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MSnbase@122190 bc3139a8-67e5-0310-9ffc-ced21a209358
lgatto · Oct 11, 2016 · a1cb083 · a1cb083
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: MSnbase
 Title: Base Functions and Classes for MS-based Proteomics
-Version: 1.99.5
+Version: 1.99.6
 Description: Basic plotting, data manipulation and processing
  of MS-based Proteomics data.
 Authors@R: c(person(given = "Laurent", family = "Gatto",

diff --git a/NEWS b/NEWS
@@ -1,3 +1,11 @@
+CHANGES IN VERSION 1.99.6
+-------------------------
+ o Reverting to old initialize,Spectrum (see issue #163)
+ <2016-10-07 Fri>
+ o Setting Spectrum class versions outside of prototype (see issue
+ #163). For this, there is now a vector of class version in
+ .MSnbaseEnv <2016-10-10 Mon>
+
 CHANGES IN VERSION 1.99.5
 -------------------------
  o Add removeReporters,OnDiskMSnExp (see issue #161 for details)

diff --git a/R/DataClasses.R b/R/DataClasses.R
@@ -1,26 +1,44 @@
+## Returns of class version as documented in .MSnBaseEnd$ClassVersions
+## as and instance of class Versions.
+getClassVersion <- function(x) {
+ if (!is.character(x))
+ x <- class(x)[1]
+ ## This get class versions from parent classes (if any)
+ ver <- classVersion(x)
+ ## Adds (or overwrites) x's class version to the list of class
+ ## versions
+ ver[x] <- getClassVersionString(x)
+ ver
+}
+## Utility to just extract the version string from the environment.
+getClassVersionString <- function(x) {
+ if (!is.character(x))
+ x <- class(x)[1]
+ return(.MSnbaseEnv$ClassVersions[x])
+}
+
 ######################################################################
 ## MSnProcess: Container for MSnExp and MSnSet processing information
 ## See online documentation for more information.
 setClass("MSnProcess",
  representation = representation(
- files="character",
- processing="character",
- merged="logical",
- cleaned="logical",
- removedPeaks="character",
- smoothed="logical",
- trimmed="numeric",
- normalised="logical",
- MSnbaseVersion="character"),
- contains=c("Versioned"),
- prototype = prototype(
- new("Versioned", versions=c(MSnProcess="0.1.3")),
- processing=character(),
- files=character(),
- trimmed=numeric(),
- removedPeaks=character(),
- MSnbaseVersion=character()) ## set in initialize()
- )
+ files = "character",
+ processing = "character",
+ merged = "logical",
+ cleaned = "logical",
+ removedPeaks = "character",
+ smoothed = "logical",
+ trimmed = "numeric",
+ normalised = "logical",
+ MSnbaseVersion = "character"),
+ contains = c("Versioned"),
+ prototype = prototype(
+ new("Versioned", versions = c(MSnProcess = "0.1.3")),
+ processing = character(),
+ files = character(),
+ trimmed = numeric(),
+ removedPeaks = character(),
+ MSnbaseVersion = character())) ## set in initialize()
 
 #################################################################
 ## The 'Minimum Information About a Proteomics Experiment' Class
@@ -36,7 +54,7 @@ setClass("MIAPE",
  samples = "list",
  preprocessing = "list",
  other = "list",
-##########################
+ ## ########################
  ## Based on MIAPE-MS 2.24
  ## will be updated with MIAPE-MSI and MIAPE-Quant
  ## 1. General features - (a) Global descriptors
@@ -79,7 +97,8 @@ setClass("MIAPE",
  ),
  contains = c("MIAxE"),
  prototype = prototype(
- new("Versioned", versions=c(classVersion("MIAxE"), MIAPE="0.2.2")),
+ new("Versioned",
+ versions = c(classVersion("MIAxE"), MIAPE = "0.2.2")),
  name = "",
  lab = "",
  contact = "",
@@ -90,8 +109,7 @@ setClass("MIAPE",
  email = "",
  samples = list(),
  preprocessing = list(),
- other = list())
- )
+ other = list()))
 
 ############################################################################
 ## NAnnotatedDataFrame: As Biobase's AnnotatedDataFrame, it is composed of
@@ -105,7 +123,7 @@ setClass("NAnnotatedDataFrame",
  multiLabels = "character"),
  contains = c("AnnotatedDataFrame"),
  prototype = prototype(
- new("Versioned", versions=list(NAnnotatedDataFrame="0.0.3")),
+  new("Versioned", versions = list(NAnnotatedDataFrame="0.0.3")),
  multiplex = 1,
  multiLabels = "Single run"),
  validity = function(object) {
@@ -149,7 +167,7 @@ setClass("pSet",
  "VIRTUAL"),
  contains = "Versioned",
  prototype = prototype(
- new("Versioned", versions=c(pSet="0.1.1")),
+ new("Versioned", versions = c(pSet = "0.1.1")),
  assayData = new.env(parent=emptyenv()),
  experimentData = new("MIAPE"),
  phenoData = new("NAnnotatedDataFrame",
@@ -193,7 +211,6 @@ setClass("Spectrum",
  "VIRTUAL"),
  contains=c("Versioned"),
  prototype = prototype(
- new("Versioned", versions=c(Spectrum="0.4.0")),
  rt = numeric(),
  polarity = NA_integer_,
  acquisitionNum = NA_integer_,
@@ -235,8 +252,6 @@ setClass("Spectrum2",
  collisionEnergy = "numeric"),
  contains=c("Spectrum"),
  prototype = prototype(
- new("Versioned",
- versions=c(classVersion("Spectrum"), Spectrum2="0.2.0")),
  merged = 1,
  acquisitionNum = integer(),
  precScanNum = integer(),
@@ -262,7 +277,6 @@ setClass("Spectrum2",
 setClass("Spectrum1",
  contains=c("Spectrum"),
  prototype = prototype(
- new("Versioned", versions=c(classVersion("Spectrum"), Spectrum1="0.2.0")),
  polarity=integer(),
  msLevel = as.integer(1)),
  validity = function(object) {
@@ -280,27 +294,27 @@ setClass("Spectrum1",
 ## See online documentation for more information.
 setClass("ReporterIons",
  representation = representation(
- name="character",
- reporterNames="character",
- description="character",
- mz="numeric",
- col="character",
- width="numeric"),
- contains=c("Versioned"),
- prototype = prototype(
- new("Versioned", versions=c(ReporterIons="0.1.0")),
- name=character(),
- reporterNames=character(),
- description=character(),
- mz=numeric(),
- col=character(),
- width=numeric()),
+ name = "character",
+ reporterNames = "character",
+ description = "character",
+ mz = "numeric",
+ col = "character",
+ width = "numeric"),
+ contains = c("Versioned"),
+ prototype  =  prototype(
+ new("Versioned", versions = c(ReporterIons = "0.1.0")),
+ name = character(),
+ reporterNames = character(),
+ description = character(),
+ mz = numeric(),
+ col = character(),
+ width = numeric()),
  validity = function(object) {
  msg <- validMsg(NULL, NULL)
- if (length(object@mz)==0) {
- msg <- validMsg(msg,"No reporter ions defined.")
+ if (length(object@mz) == 0) {
+ msg <- validMsg(msg, "No reporter ions defined.")
  } else {
- if (length(object@col)!=length(object@mz))
+ if (length(object@col) != length(object@mz))
  warning("Missing color(s) for the reporter ions.")
  }
  if (is.null(msg)) TRUE

diff --git a/R/RcppExports.R b/R/RcppExports.R
@@ -1,4 +1,4 @@
-# This file was generated by Rcpp::compileAttributes
+# Generated by using Rcpp::compileAttributes() -> do not edit by hand
 # Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
 
 imp_neighbour_avg <- function(x, k) {

diff --git a/R/environment.R b/R/environment.R
@@ -1,4 +1,18 @@
-.MSnbaseEnv <- new.env(parent=emptyenv(), hash=TRUE)
+.MSnbaseEnv <- new.env(parent = emptyenv(), hash = TRUE)
+
+## As discussed in issue #163 for details, the random errors we see
+## (see issue #138) seem to come (partially at least) from using new
+## in the prototype. As a result, these will be setn (and tested in
+## validity methods) outside of the prototype. The vector below stores
+## the respective class versions. When a class doesn't have one, the
+## version should be defined as NA_character_.
+
+ClassVersions <- c(
+ Spectrum = "0.4.0",
+ Spectrum1 = "0.2.0",
+ Spectrum2 = "0.2.0")
+
+assign("ClassVersions", ClassVersions, envir = .MSnbaseEnv)
 
 assign("amino.acids",
  data.frame(AA = c("peg","A","R","N","D","C","E",

diff --git a/R/functions-Spectrum1.R b/R/functions-Spectrum1.R
@@ -8,7 +8,9 @@ show_Spectrum1 <- function(spectrum) {
 
 ############################################################
 ## Constructor function for Spectrum1 objects. This one uses C-code and
-## is faster than a call to "new"
+## is faster than a call to "new".
+## It calls the "versioned" constructor in C that adds also the class version(s)
+## (see issue #163).
 Spectrum1 <- function(peaksCount = length(mz), rt = numeric(),
  acquisitionNum = NA_integer_, scanIndex = integer(),
  tic = 0, mz = numeric(), intensity = numeric(),
@@ -28,16 +30,29 @@ Spectrum1 <- function(peaksCount = length(mz), rt = numeric(),
  if (!is.logical(centroided)) centroided <- as.logical(centroided)
  if (!is.logical(smoothed)) smoothed <- as.logical(smoothed)
  if (!is.integer(polarity)) polarity <- as.integer(polarity)
+ ## Define the class versions.
+ versions <- list(Spectrum = getClassVersionString("Spectrum"),
+ Spectrum1 = getClassVersionString("Spectrum1"))
  res <- .Call("Spectrum1_constructor",
  1L, peaksCount, rt, acquisitionNum, scanIndex, tic, mz,
  intensity, fromFile, centroided, smoothed, polarity, TRUE,
- PACKAGE = "MSnbase")
+ lapply(versions, .versionToNum), PACKAGE = "MSnbase")
  return(res)
 }
 
+############################################################
+## .versionToNum
+## Simple helper function to convert a character version string into an
+## integer vector.
+.versionToNum <- function(z) {
+ return(as.integer(unlist(strsplit(z, split = ".", fixed = TRUE))))
+}
+
 ############################################################
 ## Constructor for Spectrum1 that ensures ordering of M/Z-intensity
 ## pairs by M/Z value (increasing).
+## It calls the "versioned" constructor in C that adds also the class version(s)
+## (see issue #163).
 Spectrum1_mz_sorted <- function(peaksCount = length(mz), rt = numeric(),
  acquisitionNum = NA_integer_,
  scanIndex = integer(), tic = 0,
@@ -56,103 +71,22 @@ Spectrum1_mz_sorted <- function(peaksCount = length(mz), rt = numeric(),
  if (!is.logical(centroided)) centroided <- as.logical(centroided)
  if (!is.logical(smoothed)) smoothed <- as.logical(smoothed)
  if (!is.integer(polarity)) polarity <- as.integer(polarity)
+ ## Define the class versions.
+ versions <- list(Spectrum = getClassVersionString("Spectrum"),
+ Spectrum1 = getClassVersionString("Spectrum1"))
  res <- .Call("Spectrum1_constructor_mz_sorted",
  1L, peaksCount, rt, acquisitionNum, scanIndex, tic, mz,
  intensity, fromFile, centroided, smoothed, polarity, TRUE,
- PACKAGE="MSnbase")
+ lapply(versions, .versionToNum), PACKAGE="MSnbase")
  return(res)
 }
 
-############################################################
-## This one does not ensure M/Z ordering is correct!
-Spectra1 <- function(peaksCount = NULL, rt = numeric(),
- acquisitionNum = NA_integer_,
- scanIndex = integer(), tic = 0, mz = numeric(),
- intensity = numeric(), fromFile = integer(),
- centroided = NA, smoothed = NA,
- polarity = NA_integer_, nvalues = integer()) {
- if (length(mz) == 0 | length(intensity) == 0 | length(nvalues) == 0){
- stop("Arguments 'mz', 'intensity' and 'nvalues' are required!")
- } else {
- if (length(mz) != length(intensity))
- stop("Lengths of 'mz' and 'intensity' do not match!")
- }
- nvals <- length(nvalues)
- ## Now match all of the lengths to the length of nvalues.
- if (length(peaksCount) == 0)
- peaksCount <- nvalues
- ## rt
- if (length(rt) == 0){
- rt <- rep(NA_integer_, nvals)
- } else {
- if (length(rt) != nvals)
- stop("Length of 'rt' has to match the length of 'nvalues'!")
- }
- ## acquisitionNum
- if (length(acquisitionNum) == 1) {
- acquisitionNum <- rep(acquisitionNum, nvals)
- } else {
- if (length(acquisitionNum) != nvals)
- stop("Length of 'acquisitionNum' has to match the length of 'nvalues'!")
- }
- ## scanIndex
- if (length(scanIndex) == 0){
- scanIndex <- rep(NA_integer_, nvals)
- } else {
- if (length(scanIndex) != nvals)
- stop("Length of 'scanIndex' has to match the length of 'nvalues'!")
- }
- ## tic
- if (length(tic) == 1){
- tic <- rep(tic, nvals)
- } else {
- if (length(tic) != nvals)
- stop("Length of 'tic' has to match the length of 'nvalues'!")
- }
- ## fromFile
- if (length(fromFile) == 0){
- fromFile <- rep(NA_integer_, nvals)
- } else {
- if (length(fromFile) != nvals)
- stop("Length of 'fromFile' has to match the length of 'nvalues'!")
- }
- ## polarity
- if (length(polarity) == 1){
- polarity <- rep(polarity, nvals)
- } else {
- if (length(polarity) != nvals)
- stop("Length of 'polarity' has to match the length of 'nvalues'!")
- }
- ## Ensure the arguments are in correct format
- if (!is.integer(peaksCount)) peaksCount <- as.integer(peaksCount)
- if (!is.double(rt)) rt <- as.double(rt)
- if (!is.integer(acquisitionNum)) acquisitionNum <- as.integer(acquisitionNum)
- if (!is.integer(scanIndex)) scanIndex <- as.integer(scanIndex)
- if (!is.double(tic)) tic <- as.double(tic)
- if (!is.double(mz)) mz <- as.double(mz)
- if (!is.double(intensity)) intensity <- as.double(intensity)
- if (!is.integer(fromFile)) fromFile <- as.integer(fromFile)
- if (!is.logical(centroided)) centroided <- as.logical(centroided)
- if (!is.logical(smoothed)) smoothed <- as.logical(smoothed)
- if (!is.integer(polarity)) polarity <- as.integer(polarity)
- ## OK, now let's call C.
- res <- .Call("Multi_Spectrum1_constructor", 1L, as.integer(peaksCount),
- rt,
- acquisitionNum,
- scanIndex,
- tic, mz, intensity,
- fromFile,
- centroided,
- smoothed,
- polarity,
- as.integer(nvalues), TRUE,
- PACKAGE = "MSnbase")
- return(res)
-}
 
 ############################################################
 ## Constructor to create multiple Spectrum1 objects ensuring that
 ## M/Z-intensity pairs are ordered by M/Z.
+## It calls the "versioned" constructor in C that adds also the class version(s)
+## (see issue #163).
 Spectra1_mz_sorted <- function(peaksCount = NULL, rt = numeric(),
  acquisitionNum = NA_integer_,
  scanIndex = integer(), tic = 0, mz = numeric(),
@@ -236,6 +170,9 @@ Spectra1_mz_sorted <- function(peaksCount = NULL, rt = numeric(),
  if (!is.logical(centroided)) centroided <- as.logical(centroided)
  if (!is.logical(smoothed)) smoothed <- as.logical(smoothed)
  if (!is.integer(polarity)) polarity <- as.integer(polarity)
+ ## Define the class versions.
+ versions <- list(Spectrum = getClassVersionString("Spectrum"),
+ Spectrum1 = getClassVersionString("Spectrum1"))
  ## OK, now let's call C.
  res <- .Call("Multi_Spectrum1_constructor_mz_sorted",
  1L,
@@ -249,6 +186,7 @@ Spectra1_mz_sorted <- function(peaksCount = NULL, rt = numeric(),
  smoothed,
  polarity,
  as.integer(nvalues), TRUE,
+ lapply(versions, .versionToNum),
  PACKAGE = "MSnbase")
  return(res)
 }