remove mentions of mzData

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: mzR
 Type: Package
-Title: parser for netCDF, mzXML, mzData and mzML and mzIdentML files
+Title: parser for netCDF, mzXML and mzML and mzIdentML files
        (mass spectrometry data)
-Version: 2.37.1
+Version: 2.37.2
 Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou, Johannes Rainer
 Authors@R: c(
     person("Steffen", "Neumann", email="[email protected]", role=c("aut","cre")),
@@ -12,8 +12,8 @@ Authors@R: c(
     )
 Description: mzR provides a unified API to the common file formats and
         parsers available for mass spectrometry data. It comes with a
-        subset of the proteowizard library for mzXML, mzML and mzIdentML. The netCDF
-        reading code has previously been used in XCMS.
+        subset of the proteowizard library for mzXML, mzML and mzIdentML.
+        The netCDF reading code has previously been used in XCMS.
 License: Artistic-2.0
 LazyLoad: yes
 Depends:

NEWS

@@ -1,3 +1,8 @@
+CHANGES IN VERSION 2.37.2
+-------------------------
+o remove mentions of mzData in the DESCRIPTION, vignette and manual
+  files (support dropped in 2.29.3)
+
 CHANGES IN VERSION 2.37.1
 -------------------------
  o fix compilation on centOS 7 / R-4.3.1 reported in #286

man/mzR-class.Rd

@@ -59,8 +59,7 @@
 
   The sub-classes implement specific APIs to access the underlying data
   and metadata in the files. Currently \code{mzRpwiz} is available.
-  \code{mzRpwiz} uses
-  Proteowizard to access the relevant information in \code{mzData},
+  \code{mzRpwiz} uses Proteowizard to access the relevant information in
   \code{mzXML} and \code{mzML} files. \code{mzRident} is used as an
   interface to \code{mzIdentML} files.
 
@@ -154,7 +153,7 @@
  library(msdata)
  filepath <- system.file("microtofq", package = "msdata")
  file <- list.files(filepath, pattern="MM14.mzML",
-		     full.names=TRUE, recursive = TRUE)
+                     full.names=TRUE, recursive = TRUE)
  mzml <- openMSfile(file)
  close(mzml)
 

man/openMSfile.Rd

@@ -5,20 +5,20 @@
 \alias{openIDfile}
 
 \title{
-  Create and check mzR objects from netCDF, mzXML, mzData or mzML files.
+  Create and check mzR objects from netCDF, mzXML or mzML files.
 }
 \usage{
  openMSfile(filename, backend = NULL, verbose = FALSE)
 
  isInitialized(object)
 
  fileName(object, ...)
- 
+
  openIDfile(filename, verbose = FALSE)
 }
 \arguments{
   \item{filename}{
-    Path name of the netCDF, mzData, mzXML or mzML file to
+    Path name of the netCDF, mzXML or mzML file to
     read/write.
   }
   \item{backend}{
@@ -38,7 +38,7 @@
   \code{mzR} object, open 'filename' file and all header information is
   loaded as a Rcpp module and made accessible through the \code{pwiz}
   slot of the resulting object.
-  
+
   The \code{openIDfile} constructor will create a new format-specifc
   \code{mzR} object, open 'filename' file and all information is
   loaded as a Rcpp module. The mzid format is supported throught
@@ -65,7 +65,7 @@
     mz <- openMSfile(file, backend = "pwiz")
     mz
   }
-  
+
   file <- system.file("mzid", "Tandem.mzid.gz", package="msdata")
   mzid <- openIDfile(file)
   softwareInfo(mzid)

src/RcppIdentModule.cpp

@@ -9,7 +9,7 @@ RCPP_MODULE(Ident)
 
     class_<RcppIdent>( "Ident" )
     .constructor("Initialises a new Rccp ident object.")
-    .method( "open", &RcppIdent::open, "Opens a mass spec file (mzXML, mzData, etc.) and creates a pwiz object" )
+    .method( "open", &RcppIdent::open, "Opens a mass spec file (mzXML, mzML, etc.) and creates a pwiz object" )
     .method( "getIDInfo", &RcppIdent::getIDInfo, "Basic information about this mzid files" )
     .method( "getPsmInfo", &RcppIdent::getPsmInfo, "Basic information about this mzid files" )
     .method( "getModInfo", &RcppIdent::getModInfo, "Modification information about this mzid files" )

src/RcppPwizModule.cpp

@@ -9,9 +9,9 @@ RCPP_MODULE(Pwiz)
 
     class_<RcppPwiz>( "Pwiz" )
     .constructor("Initialises a new Rccp pwiz object.")
-    .method( "open", &RcppPwiz::open, "Opens a mass spec file (mzXML, mzData, etc.) and creates a pwiz object" )
-    .method( "close", &RcppPwiz::close, "Close the connection to a mass spec file (mzXML, mzData, etc.)." )
-    // .method( "writeMSfile", &RcppPwiz::writeMSfile, "Write a pwiz object into files (mzXML, mzData, etc.)" )
+    .method( "open", &RcppPwiz::open, "Opens a mass spec file (mzXML, mzML, etc.) and creates a pwiz object" )
+    .method( "close", &RcppPwiz::close, "Close the connection to a mass spec file (mzXML, mzML, etc.)." )
+    // .method( "writeMSfile", &RcppPwiz::writeMSfile, "Write a pwiz object into files (mzXML, etc.)" )
     .method( "writeSpectrumList", &RcppPwiz::writeSpectrumList, "Write the spectrum list to an mzML file." )
     .method( "copyWriteMSfile", &RcppPwiz::copyWriteMSfile, "Copy general content from the originalting MS file, add the provided spectrum list and write the data to a new mzML file." )
     .method( "getFilename", &RcppPwiz::getFilename, "Returns the mass spec filename.")

vignettes/mzR.Rmd

@@ -13,22 +13,23 @@ bibliography: mzR.bib
 vignette: >
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteIndexEntry{Accessin raw mass spectrometry and identification data}
-  %\VignetteKeywords{mzXML, mzData, netCDF, mzML, mzIdentML, mass spectrometry, proteomics, metabolomics}
+  %\VignetteKeywords{mzXML, netCDF, mzML, mzIdentML, mass spectrometry, proteomics, metabolomics}
   %\VignetteEncoding{UTF-8}
   %\VignettePackage{mzR}
 ---
 
 # Introduction
 
-The `r BiocStyle::Biocpkg("mzR")` package aims at providing a common, low-level
-interface to several mass spectrometry data formats, namely `mzData`
-[@Orchard2007], `mzXML` [@Pedrioli2004], `mzML` [@Martens2010] for raw
-data, and `mzIdentML` [@Jones2012], somewhat similar to the
-Bioconductor package affyio for affymetrix raw data. No processing is
-done in `r BiocStyle::Biocpkg("mzR")`, which is left to packages such as `r
-BiocStyle::Biocpkg("xcms")` [@Smith:2006, Tautenhahn:2008] or
-`r BiocStyle::Biocpkg("MSnbase")` [@Gatto:2012]. These packages also provide more
-convenient, high-level interfaces to raw and identification. data
+The `r BiocStyle::Biocpkg("mzR")` package aims at providing a common,
+low-level interface to several mass spectrometry data formats, namely,
+`mzXML` [@Pedrioli2004], `mzML` [@Martens2010] for raw data, and
+`mzIdentML` [@Jones2012], somewhat similar to the Bioconductor package
+affyio for affymetrix raw data. No processing is done in `r
+BiocStyle::Biocpkg("mzR")`, which is left to packages such as `r
+BiocStyle::Biocpkg("xcms")` [@Smith:2006, Tautenhahn:2008] or `r
+BiocStyle::Biocpkg("MSnbase")` [@Gatto:2012]. These packages also
+provide more convenient, high-level interfaces to raw and
+identification. data
 
 Most importantly, access to the data should be fast and memory
 efficient. This is made possible by allowing on-disk random file
@@ -110,7 +111,7 @@ depends on the MS software which converted the data.
 
 # Example
 
-## `mzXML`/`mzML`/`mzData` files
+## `mzXML`/`mzML` files
 
 A short example sequence to read data from a mass spectrometer.
 First open the file.