Fix some roxygen annotations

R/leMsmsRaw.R

+## For generating the NAMESPACE
 #' @import mzR
-#' @importClassesFrom mzR
-#' @importMethodsFrom mzR
+# # importClassesFrom mzR ## Causes error 
+# # importMethodsFrom mzR 
+#' @import Rcpp ## Was not in manually written NAMESPACE ?
+#' @import RCurl 
+#' @import XML 
+#' @import methods 
+#' @import mzR 
+#' @import rcdk 
+#' @import rjson 
+#' @import yaml 
 NULL # This is required so that roxygen knows where the first manpage starts
 
 #' Extract MS/MS spectra for specified precursor
@@ -15,7 +24,7 @@ NULL # This is required so that roxygen knows where the first manpage starts
 #' 		is a low-level function which uses the mass directly for lookup and is intended for
 #' 		use as a standalone function in unrelated applications.
 #' 
-#' @Usage findMsMsHR(fileName, cpdID, mode="pH",confirmMode =0, useRtLimit = TRUE,
+#' @usage findMsMsHR(fileName, cpdID, mode="pH",confirmMode =0, useRtLimit = TRUE,
 #' 		ppmFine = getOption("RMassBank")$findMsMsRawSettings$ppmFine,
 #' 		mzCoarse = getOption("RMassBank")$findMsMsRawSettings$mzCoarse,
 #' 		fillPrecursorScan = getOption("RMassBank")$findMsMsRawSettings$fillPrecursorScan,
@@ -700,7 +709,7 @@ addMB <- function(w, cpdID, fileName, mode){
 #' @examples \dontrun{
 #' 		c.msmsWSspecs(w1,w2)
 #' }
-#'export
+#'@export
 c.msmsWSspecs <- function(w1 = NA, w2 = NA){
 
 	if(class(w1) != "msmsWorkspace" || class(w2) != "msmsWorkspace"){
@@ -737,4 +746,4 @@ c.msmsWSspecs <- function(w1 = NA, w2 = NA){
 		}
 	}
 	return(w1)
-}
+}
\ No newline at end of file

man/mbWorkspace-class.Rd

-\docType{class}
-\name{mbWorkspace-class}
-\alias{mbWorkspace-class}
-\alias{show,mbWorkspace-method}
-\title{Workspace for \code{mbWorkflow} data}
-\description{
-  A workspace which stores input and output data for use
-  with \code{mbWorkflow}.
-}
-\details{
-  Slots: \describe{ \item{aggregatedRcSpecs,
-  refilteredRcSpecs}{The corresponding input data from
-  \code{\link{msmsWorkspace-class}}}
-  \item{additionalPeaks}{A list of additional peaks which
-  can be loaded using \code{\link{addPeaks}}.}
-  \item{mbdata, mbdata_archive, mbdata_relisted}{Infolist
-  data: Data for annotation of MassBank records, which can
-  be loaded using \code{\link{loadInfolists}}.}
-  \item{compiled, compiled_ok}{ Compiled tree-structured
-  MassBank records. \code{compiled_ok} contains only the
-  compounds with at least one valid spectrum.}
-  \item{mbfiles}{Compiled MassBank records in text
-  representation.} \item{molfile}{MOL files with the
-  compound structures.} \item{ok,problems}{Index lists for
-  internal use which denote which compounds have valid
-  spectra.} }
-
-  Methods: \describe{ \item{show}{Shows a brief summary of
-  the object. Currently only a stub.} }
-}
-\author{
-  Michael Stravs, Eawag <michael.stravs@eawag.ch>
-}
-\seealso{
-  \code{\link{mbWorkflow}}
-}
-
+% Generated by roxygen2 (4.1.0): do not edit by hand
+% Please edit documentation in R/RmbWorkspace.R
+\docType{class}
+\name{mbWorkspace-class}
+\alias{mbWorkspace-class}
+\alias{show,mbWorkspace-method}
+\title{Workspace for \code{mbWorkflow} data}
+\description{
+A workspace which stores input and output data for use with \code{mbWorkflow}.
+
+
+}
+\details{
+Slots:
+ \describe{
+	\item{aggregatedRcSpecs, refilteredRcSpecs}{The corresponding
+		 input data from \code{\link{msmsWorkspace-class}}}
+ \item{additionalPeaks}{A list of additional peaks which can be loaded
+		using \code{\link{addPeaks}}.}
+ \item{mbdata, mbdata_archive, mbdata_relisted}{Infolist data: Data for
+		annotation of MassBank records, which can be loaded using
+		\code{\link{loadInfolists}}.}
+ \item{compiled, compiled_ok}{
+		Compiled tree-structured MassBank records. \code{compiled_ok} contains
+		only the compounds with at least one valid spectrum.}
+ \item{mbfiles}{Compiled MassBank records in text representation.}
+ \item{molfile}{MOL files with the compound structures.}
+ \item{ok,problems}{Index lists for internal use which denote which compounds
+		have valid spectra.}
+}
+
+Methods:
+\describe{
+		\item{show}{Shows a brief summary of the object. Currently only a stub.}
+}
+}
+\author{
+Michael Stravs, Eawag <michael.stravs@eawag.ch>
+}
+\seealso{
+\code{\link{mbWorkflow}}
+}
+

man/msmsWorkspace-class.Rd

-\docType{class}
-\name{msmsWorkspace-class}
-\alias{msmsWorkspace-class}
-\alias{show,msmsWorkspace-method}
-\title{Workspace for \code{msmsWorkflow} data}
-\description{
-  A workspace which stores input and output data for
-  \code{\link{msmsWorkflow}}.
-}
-\details{
-  Slots:
-
-  \describe{ \item{files}{The input file names}
-  \item{specs}{The spectra extracted from the raw files}
-  \item{analyzedSpecs}{The spectra with annotated peaks
-  after workflow step 2.} \item{aggregatedSpecs}{The
-  \code{analyzedSpec} data regrouped and aggregated, after
-  workflow step 3.} \item{rc, rc.ms1}{The recalibration
-  curves generated in workflow step 4.}
-  \item{recalibratedSpecs}{The spectra from \code{specs}
-  recalibrated with the curves from \code{rc, rc,ms1}.}
-  \item{analyzedRcSpecs}{The recalibrated spectra with
-  annotated peaks after workflow step 5.}
-  \item{aggregatedRcSpecs}{The \code{analyzedRcSpec} data
-  regrouped and aggregated, after workflow step 6.}
-  \item{reanalyzedRcSpecs}{The regrouped and aggregated
-  spectra, with added reanalyzed peaks (after step 7, see
-  \code{\link{reanalyzeFailpeaks}}).}
-  \item{refilteredRcSpecs}{Final data to use for MassBank
-  record creation after multiplicity filtering (step 8).} }
-
-  Methods: \describe{ \item{show}{Shows a brief summary of
-  the object. Currently only the included files.} }
-}
-\author{
-  Michael Stravs, Eawag <michael.stravs@eawag.ch>
-}
-\seealso{
-  \code{\link{msmsWorkflow}}
-}
-
+% Generated by roxygen2 (4.1.0): do not edit by hand
+% Please edit documentation in R/RmbWorkspace.R
+\docType{class}
+\name{msmsWorkspace-class}
+\alias{msmsWorkspace-class}
+\alias{show,msmsWorkspace-method}
+\title{Workspace for \code{msmsWorkflow} data}
+\description{
+A workspace which stores input and output data for \code{\link{msmsWorkflow}}.
+}
+\details{
+Slots:
+
+\describe{
+	\item{files}{The input file names}
+	\item{specs}{The spectra extracted from the raw files}
+ \item{analyzedSpecs}{The spectra with annotated peaks after workflow step 2.}
+ \item{aggregatedSpecs}{The \code{analyzedSpec} data regrouped and aggregated,
+		after workflow step 3.}
+ \item{rc, rc.ms1}{The recalibration curves generated in workflow step 4.}
+ \item{recalibratedSpecs}{The spectra from \code{specs} recalibrated with the curves
+		from \code{rc, rc,ms1}.}
+	\item{analyzedRcSpecs}{The recalibrated spectra with annotated peaks after
+		workflow step 5.}
+	\item{aggregatedRcSpecs}{The \code{analyzedRcSpec} data regrouped and aggregated,
+		after workflow step 6.}
+ \item{reanalyzedRcSpecs}{The regrouped and aggregated spectra, with added reanalyzed
+		peaks (after step 7, see \code{\link{reanalyzeFailpeaks}}).}
+ \item{refilteredRcSpecs}{Final data to use for MassBank record creation after
+		multiplicity filtering (step 8).}
+}
+
+Methods: \describe{
+	\item{show}{Shows a brief summary of the object. Currently only the included files.}
+	}
+}
+\author{
+Michael Stravs, Eawag <michael.stravs@eawag.ch>
+}
+\seealso{
+\code{\link{msmsWorkflow}}
+}
+