@@ -2,18 +2,18 @@ Package: mzR

 Type: Package

 Title: parser for netCDF, mzXML, mzData and mzML and mzIdentML files

        (mass spectrometry data)

-Version: 2.17.3

+Version: 2.19.1

 Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou, Johannes Rainer

 Maintainer: Steffen Neumann <sneumann@ipb-halle.de>,

 	    Laurent Gatto <lg390@cam.ac.uk>,

 	    Qiang Kou <qkou@umail.iu.edu>

 Description: mzR provides a unified API to the common file formats and

-        parsers available for mass spectrometry data. It comes with a

-        wrapper for the ISB random access parser for mass spectrometry

-        mzXML, mzData and mzML files. The package contains the

-        original code written by the ISB, and a subset of the

-        proteowizard library for mzML and mzIdentML. The netCDF

-        reading code has previously been used in XCMS.

+	parsers available for mass spectrometry data. It comes with a

+	wrapper for the ISB random access parser for mass spectrometry

+	mzXML, mzData and mzML files. The package contains the

+	original code written by the ISB, and a subset of the

+	proteowizard library for mzML and mzIdentML. The netCDF

+	reading code has previously been used in XCMS.

 License: Artistic-2.0

 LazyLoad: yes

 Depends: Rcpp (>= 0.10.1), methods, utils

@@ -26,5 +26,5 @@ SystemRequirements: C++11, GNU make

 URL: https://github.com/sneumann/mzR/

 BugReports: https://github.com/sneumann/mzR/issues/

 biocViews: ImmunoOncology, Infrastructure, DataImport, Proteomics, Metabolomics,

-        MassSpectrometry

+	MassSpectrometry

 RoxygenNote: 6.0.1

@@ -1,3 +1,12 @@

+CHANGES IN VERSION 2.19.1

+-------------------------

+ o Remove analyzer generics, now in ProtGenerics <2019-05-13 Mon>

+

+CHANGES IN VERSION 2.17.4

+-------------------------

+ o Update documentation, pointing to MSnbase rather than directly use

+   low-level classes. <2019-04-17 Wed>

+

 CHANGES IN VERSION 2.17.3

 -------------------------

  o Extract isolation window from mzML files (issue #193): data.frame returned

@@ -14,9 +23,9 @@ CHANGES IN VERSION 2.15.5

 CHANGES IN VERSION 2.15.4

 -------------------------

- o Use new dependency ncdf4 for netCDF reading, 

+ o Use new dependency ncdf4 for netCDF reading,

    removes a lot of build hassles with old libnetcdf-dev linking.

- o specParams returns a numeric scan.number.s. 

+ o specParams returns a numeric scan.number.s.

 CHANGES IN VERSION 2.15.3

 -------------------------

@@ -20,7 +20,6 @@ setGeneric("creationDate", function(object) standardGeneric("creationDate"))

 setGeneric("manufacturer", function(object) standardGeneric("manufacturer"))

 setGeneric("model", function(object) standardGeneric("model"))

 setGeneric("ionisation", function(object) standardGeneric("ionisation"))

-setGeneric("analyzer", function(object) standardGeneric("analyzer"))

 setGeneric("detector", function(object) standardGeneric("detector"))

 setGeneric("isInitialized", function(object) standardGeneric("isInitialized"))

 setGeneric("initializeRamp",

@@ -45,3 +44,4 @@ setGeneric("isolationWindow",

 ## setGeneric("peaks", function(object, ...) standardGeneric("peaks"))

 ## setGeneric("database", function(object, ...) standardGeneric("database"))

 ## setGeneric("modifications", function(object, ...) standardGeneric("modifications"))

+## setGeneric("analyzer", function(object) standardGeneric("analyzer"))

deleted file mode 100644

@@ -1,170 +0,0 @@

-Hi,

-

-after beeing busy in the past weeks, we have now 

-overhauled most of the package. To me the most important 

-change is the possibility to have multiple backends, 

-such as netCDF, Ramp and pwiz to do the actual I/O work.

-

-We also have a patch for XCMS to do the I/O work 

-through mzR, and Laurent also has patches to msnbase 

-to switch to mzR. Both will be applied to BioC SVN

-if we have a few weeks of debugging before the release.

-

-Could you guys please add the Roundup user "lgatto" 

-to the nosy list of this issue ? Thanks in advance.

-

-Yours,

-Steffen

-

-On Mon, 2011-03-07 at 22:27 +0000, herve BioC-Submit wrote:

-herve <hpages@fhcrc.org> added the comment:

-...

-> Detailed review:

-> 

-> 1. Please use a BioC-style version number i.e. x.y.z

->    Note that if you use 0.99.z now, your package will be released as 1.0.0

->    in BioC 2.8 (to be released in April).

-Done.

- 

-> 2. The source tarball you provided is not clean: it contains a lot of object

->    files (i.e. *.o files) in src/boost and src/pwiz. A source

-I've added an mzR/cleanup file

-

-> 3. Please add a biocViews field to your DESCRIPTION file.

-Done. Taken from xcms and affyIO

-

-> 4. It doesn't make sense to have 2 SystemRequirements fields. Please merge

->    them.

-Done. Copy&Paste error :-(

- 

-> 5. Please put the Rcpp package in the Imports field of the DESCRIPTION

->    file. In your NAMESPACE file you import things from Rcpp so you

->    definitely want to reflect this in the Imports field. Keeping

-Done. 

-

->    in the Depends field is up to you but it could be that you don't need

->    this. (Do you want Rcpp to end up in the search path of the user when

->    s/he does library(mzR)? Are there symbols or man pages defined in Rcpp

->    that the end-user of the mzR package might need to access directly?)

-I have placed Rcpp in the dependency (v 0.5.0) and removed import(Rcpp)

-from the NAMESPACE file, to supress a warning about missing '"C++Object"

-unavailable and created in local env' when loading the package.

- 

-> 6. msdata needs to be put in the Suggests field: it's used in the vignette

->    and the unit tests.

-Done.

- 

-> 7. Same thing for RUnit and faahKO: they are used in the unit tests.

-Done.

- 

-> 8. Why call those files AllClass.R and rampMethods.R if the former

->  doesn't

-All of that was more/less rewritten by Laurent, 

-I guess it'll be cleaner now.

-

-> 9. In man/Ramp-class.Rd:

-> 

->      Objects can be created by calls of the form \code{new(Ramp)}

-> 

->    Will the user really create object like this? If yes, then please provide

->    an example on the \examples{} section of the man page.

-There is now a proper constructor (openMSfile, see below) that will read 

-an mass spec file, initialise the Rcpp module and return a proper S4 class.

- 

-> 10. The rampOpenFile() function itself (which is more likely to be *the* way

->     people will create Ramp objects) is not documented. In particular, the

->     documentation is not saying what the supported formats are (only

->     mzXML is used in the example and vignette).

-Done. rampOpenFile() is now called openMSfile() and documented 

-with its own manpage.

- 

-> 11. Overall the documentation is insufficient: there are only 2 small man

->     pages and none of them contains *real* examples. Note that man pages

->     should contain an \examples{} section, not an \section{Example}{} section

->     like you did in man/Ramp-class.Rd, so they are evaluated by 'R CMD check'.

->     The list of C++-style methods provided in man/Ramp-class.Rd gives very

->     little details about what those methods do exactly and it uses some

->     technical jargon that probably only experts in the field will understand:

-> 

->       "suppress RAMP's behavior of creating sparse tables to accomodate

->        unlisted scans"

-> 

->       "obtains minimal info on the msRun contained in the file"

-> 

->       "msLevel", "retentionTime"

-> 

->     If the man page cannot contain a full explanation of those terms, maybe

->     at least it should provide some reference to a document describing them.

-Done.

-

- 

-> 12. One more problem with man/Ramp-class.Rd: the get3DMap method doesn't

->     seem to exist:

-> 

->       > ramp$get3DMap(1)

->       Error in ramp$get3DMap(1) : could not find valid method

-> 

->     But maybe this is just a documentation problem: according to the man

->     page, it takes only 1 argument, when, in fact, 4 args seem to be required.

-all these methods that were called through the Rcpp module are now 

-encapsulated in S4 methods, all of which are documented.

-

-

-> 13. The vignette too is insufficient. It doesn't provide any context, and,

->     in particular, it doesn't provide any explanation about the special nature

->     of the classes that are used here (and the special syntax used to call

->     their methods). Providing some background information about the very

->     special nature of those classes/methods would be more than welcome.

-Done.

-

- 

-> 14. The .onLoad hook contains a setMethod() statement. This is the only

->     explicit use that I see of the S4 class system. That means mzR should

->     import the methods package i.e. have it in the Imports field, and have

->     import(methods) in the NAMESPACE file (generally right after the

->     useDynLib directive).

-Done.

- 

-> 15. I get the 2 following warnings when running 'R CMD check mzR_0.4.tar.gz':

-> 

->       * checking if this is a source package ... WARNING

->       Subdirectory ‘src’ contains:

->         README RcppRamp.hpp cramp.hpp

->       These are unlikely file names for src files.

-README went into inst/doc, and about *.hpp:

-

-Page 14 of http://cran.r-project.org/doc/manuals/R-exts.pdf 

-says "We recommend using ‘.h’ for headers, also for C++",

-with a note about potential not-guaranteed-portability.

-

-However, the *.hpp are valid C++ header files, 

-and it is also used throughout the boost libraries, 

-which is a high quality C++ project, some of which 

-will go into the next C++ standards. 

-

-So complaints about *.hpp is definitely a false positive.

-

-Nevertheless we have changed src/*hpp to src/*h for now.   

-

->     probably something you want to complain about on the R-devel mailing list,

-Will do.

-

->     and

-> 

->       * checking whether the name space can be loaded with stated dependencies

-> ... WARNING

->       Error: .onLoad failed in loadNamespace() for 'mzR', details:

->         call: MS$Ramp

->         error: could not find function "loadMethod"

->       Execution halted

-> 

->       A namespace must be able to be loaded with just the base namespace

->       loaded: otherwise if the namespace gets loaded by a saved object, the

->       session will be unable to start.

-> 

->       Probably some imports need to be declared in the NAMESPACE file.

-> 

->     probably something that will go away by importing the methods package (as

->     mentioned previously).

-Done. Rcpp stuff has been overhauled by Laurent.

-

@@ -75,10 +75,19 @@

   \code{mzRpwiz} are available implementations. \code{mzRramp} uses the

   ISB 'RAMP' random access C/C++ API, and \code{mzRpwiz} uses

   Proteowizard to access the relevant information in \code{mzData},

-  \code{mzXML} and \code{mzML} files. 

+  \code{mzXML} and \code{mzML} files. \code{mzRident} is used as an

+  interface to \code{mzIdentML} files.

+

+  IMPORTANT: New developers that need to access and manipulate raw mass

+  spectrometry data are advised against using this infrastucture

+  directly. They are invited to use the corresponding \code{MSnExp}

+  (with \emph{on disk} mode) from the MSnbase package instead. The

+  latter supports reading multiple files at once and offers access to

+  the spectra data (m/z and intensity) as well as all the spectra

+  metadata using a coherent interface. The MSnbase infrastructure itself

+  used the low level classes in mzR, thus offering fast and efficient

+  access.

-  Additional sub-classes using the proteowizard API and netCDF are

-  planned.

 }

 \section{Objects from the Class}{

@@ -86,10 +95,11 @@

   Objects can be created by calls of the form \code{new("mzRramp",

     ...)}, but more often they will be created with

-  \code{\link{openMSfile}}.  

-  

-  After creating a \code{mzR}, you can write it into a file.

-  mzXML, mzML, mgf formats are supported. 

+  \code{\link{openMSfile}}.

+

+  After creating an \code{mzR} object, one can write it into a new file.

+  mzXML, mzML, mgf formats are supported.

+

 }

 \section{Slots}{

@@ -102,6 +112,7 @@

       from Biobase.}

   }

 }

+

 \section{Extends}{

   Class \code{"\linkS4class{Versioned}"}, directly.

 }

@@ -110,14 +121,14 @@

   For methods to access raw data (spectra and chromatograms), see

   \code{\link{peaks}}.

-  

-  

+

+

   Methods currently implemented for \code{mzR}

   \describe{ \item{fileName}{\code{signature(object = "mzR")}: ... } }

-  

+

   Methods currently implemented for \code{mzRramp}

-  

+

   \describe{

     \item{analyzer}{\code{signature(object = "mzRramp")}: ... }

     \item{close}{\code{signature(con = "mzRramp")}: ... }

@@ -145,7 +156,7 @@

     \item{runInfo}{\code{signature(object = "mzRpwiz")}: ... }

     \item{chromatogramsInfo}{\code{signature(object = "mzRpwiz")}: ... }

   }

-  

+

   Methods currently implemented for \code{mzRident}

   \describe{

     \item{mzidInfo}{\code{signature(object = "mzRident")}: ... }

@@ -175,7 +186,7 @@

  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)

deleted file mode 100644

@@ -1,45 +0,0 @@

-\name{mzR-package}

-\alias{mzR-package}

-\alias{mzR}

-\docType{package}

-\title{

-parser for mzXML, mzData, mzML and mzid files (mass spectrometry data)

-}

-\description{

-  The mzR package is a library purely for accessing mass spectrometry

-  data in a wide range of formats. Several backend libraries are used,

-  such as the ISB random acces parser (RAMP) and ProteoWizard (pwiz) for mass

-  spectrometry mzXML, mzData, mzML and mzid files. The package

-  contains the original RAMP code written by the ISB, and a

-  subset of the proteowizard library for mzML and mzid.

-}

-\details{

-

-

-Further information is available in the following vignette:

-\tabular{ll}{

-\code{mzR} \tab mzR, Ramp, mzXML, mzData, mzML (source, pdf)\cr

-}

-}

-\author{

-Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou

-

-Maintainers: Bernd Fischer <bernd.fischer@embl.de>,

-Steffen Neumann <sneumann@ipb-halle.de>,

-Laurent Gatto <lg390@cam.ac.uk>,

-Qiang Kou <qkou@umail.iu.edu>

-}

-

-\references{

-  Nat Biotechnol. 2012 Oct 10;30(10):918-20. doi: 10.1038/nbt.2377.

-  A cross-platform toolkit for mass spectrometry and proteomics.

-  Chambers MC, Maclean B, Burke R, Amodei D, Ruderman DL, Neumann S,

-  Gatto L, Fischer B, Pratt B, Egertson J, Hoff K, Kessner D, Tasman N,

-  Shulman N, Frewen B, Baker TA, Brusniak MY, Paulse C, Creasy D,

-  Flashner L, Kani K, Moulding C, Seymour SL, Nuwaysir LM, Lefebvre B,

-  Kuhlmann F, Roark J, Rainer P, Detlev S, Hemenway T, Huhmer A,

-  Langridge J, Connolly B, Chadick T, Holly K, Eckels J, Deutsch EW,

-  Moritz RL, Katz JE, Agus DB, Maccoss M, Tabb DL, Mallick P.

-  http://www.ncbi.nlm.nih.gov/pubmed/23051804

-}

-\keyword{package, file}

@@ -1,6 +1,6 @@

 ---

 title: "A parser for raw and identification mass-spectrometry data"

-author: 

+author:

 - name: Bernd Fischer

 - name: Steffen Neumann

 - name: Laurent Gatto

@@ -9,7 +9,7 @@ package: mzR

 output:

   BiocStyle::html_document:

     toc_float: true

-bibliography: mzR.bib 	

+bibliography: mzR.bib

 vignette: >

   %\VignetteEngine{knitr::rmarkdown}

   %\VignetteIndexEntry{Accessin raw mass spectrometry and identification data}

@@ -26,7 +26,7 @@ interface to several mass spectrometry data formats, namely `mzData`

 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 

+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

@@ -55,6 +55,16 @@ The `r BiocStyle::Biocpkg("mzR")` package is in essence a collection of wrappers

 to the C++ code, and benefits from the C++ interface provided through

 the Rcpp package [@Rcpp11].

+**IMPORTANT** New developers that need to access and manipulate raw

+mass spectrometry data are advised against using this infrastucture

+directly. They are invited to use the corresponding `MSnExp` (with *on

+disk* mode) from the`r BiocStyle::Biocpkg("MSnbase")` package instead. The

+latter supports reading multiple files at once and offers access to

+the spectra data (m/z and intensity) as well as all the spectra

+metadata using a coherent interface. The MSnbase infrastructure itself

+used the low level classes in mzR, thus offering fast and efficient

+access.

+

 # Mass spectrometry raw data

@@ -107,17 +117,17 @@ depends on the MS software which converted the data.

 ## `mzXML`/`mzML`/`mzData` files

-A short example sequence to read data from a mass spectrometer. 

+A short example sequence to read data from a mass spectrometer.

 First open the file.

 ```{r openraw}

 library(mzR)

 library(msdata)

-mzxml <- system.file("threonine/threonine_i2_e35_pH_tree.mzXML", 

+mzxml <- system.file("threonine/threonine_i2_e35_pH_tree.mzXML",

                      package = "msdata")

-aa <- openMSfile(mzxml) 

-``` 

+aa <- openMSfile(mzxml)

+```

 We can obtain different kind of header information.

@@ -125,7 +135,7 @@ We can obtain different kind of header information.

 runInfo(aa)

 instrumentInfo(aa)

 header(aa,1)

-``` 

+```

 Read a single spectrum from the file.

@@ -134,14 +144,14 @@ pl <- peaks(aa,10)

 peaksCount(aa,10)

 head(pl)

 plot(pl[,1], pl[,2], type="h", lwd=1)

-``` 

+```

 One should always close the file when not needed any more. This will

 release the memory of cached content.

 ```{r close the file}

 close(aa)

-``` 

+```

 ## `mzIdentML` files

@@ -154,14 +164,14 @@ library(msdata)

 file <- system.file("mzid", "Tandem.mzid.gz", package="msdata")

 x <- openIDfile(file)

-``` 

+```

 `mzidInfo` function will return general information about this

 identification result.

 ```{r metadata}

 mzidInfo(x)

-``` 

+```

 `psms` will return the detailed information on each

 peptide-spectrum-match, include `spectrumID`, `chargeState`,

@@ -196,8 +206,8 @@ colnames(scr)

 Other file formats provided by HUPO, such as `mzQuantML` for

 quantitative data [@Walzer:2013] are also possible in the future.

-# Session information {#sec:sessionInfo} 

+# Session information {#sec:sessionInfo}

 ```{r label=sessioninfo, results='asis', echo=FALSE}

 toLatex(sessionInfo())

-``` 

+```