diff -Nru r-cran-readbrukerflexdata-1.8.2/debian/changelog r-cran-readbrukerflexdata-1.8.3/debian/changelog
--- r-cran-readbrukerflexdata-1.8.2/debian/changelog	2015-07-02 14:41:54.000000000 +0000
+++ r-cran-readbrukerflexdata-1.8.3/debian/changelog	2016-12-12 14:23:25.000000000 +0000
@@ -1,3 +1,24 @@
+r-cran-readbrukerflexdata (1.8.3-1) unstable; urgency=medium
+
+  * Team upload
+
+  [ Sebastian Gibb ]
+  * New upstream release.
+  * debian/control:
+    - Set Standards-Version to 3.9.8.
+    - Use secure canonical URL in Homepage.
+    - Use secure https URLs in Vcs-Git and Vcs-Browser.
+
+  [ Andreas Tille ]
+  * cme fix dpkg-control
+  * Convert to dh-r
+  * Architecture: all
+  * debhelper 10
+  * Update d/copyright
+  * d/watch: version=4
+
+ -- Andreas Tille <tille@debian.org>  Mon, 12 Dec 2016 15:23:25 +0100
+
 r-cran-readbrukerflexdata (1.8.2-1) unstable; urgency=low
 
   * New upstream release.
diff -Nru r-cran-readbrukerflexdata-1.8.2/debian/compat r-cran-readbrukerflexdata-1.8.3/debian/compat
--- r-cran-readbrukerflexdata-1.8.2/debian/compat	2015-07-02 14:41:54.000000000 +0000
+++ r-cran-readbrukerflexdata-1.8.3/debian/compat	2016-12-12 14:23:25.000000000 +0000
@@ -1 +1 @@
-7
+10
diff -Nru r-cran-readbrukerflexdata-1.8.2/debian/control r-cran-readbrukerflexdata-1.8.3/debian/control
--- r-cran-readbrukerflexdata-1.8.2/debian/control	2015-07-02 14:41:54.000000000 +0000
+++ r-cran-readbrukerflexdata-1.8.3/debian/control	2016-12-12 14:23:25.000000000 +0000
@@ -1,18 +1,22 @@
 Source: r-cran-readbrukerflexdata
-Section: gnu-r
-Priority: optional
 Maintainer: The Debichem Group <debichem-devel@lists.alioth.debian.org>
 Uploaders: Filippo Rusconi <lopippo@debian.org>
-Build-Depends: debhelper (>= 9), cdbs, r-base-dev (>= 2.15.0)
-Standards-Version: 3.9.6
-Homepage: http://cran.r-project.org/web/packages/readBrukerFlexData/index.html
-Vcs-Git: git://anonscm.debian.org/debichem/packages/r-cran-readbrukerflexdata.git
-Vcs-Browser: http://anonscm.debian.org/gitweb/?p=debichem/packages/r-cran-readbrukerflexdata.git
+Section: gnu-r
+Priority: optional
+Build-Depends: debhelper (>= 10),
+               dh-r,
+               r-base-dev
+Standards-Version: 3.9.8
+Vcs-Browser: https://anonscm.debian.org/cgit/debichem/packages/r-cran-readbrukerflexdata.git
+Vcs-Git: https://anonscm.debian.org/git/debichem/packages/r-cran-readbrukerflexdata.git
+Homepage: https://cran.r-project.org/package=readBrukerFlexData
 
 Package: r-cran-readbrukerflexdata
-Architecture: any
-Suggests: r-cran-maldiquant
-Depends: ${misc:Depends}, ${R:Depends}
+Architecture: all
+Depends: ${misc:Depends},
+         ${R:Depends}
+Recommends: ${R:Recommends}
+Suggests: ${R:Suggests}
 Description: GNU R package to read Bruker Daltonics *flex format files
  The readBrukerFlexData package reads data files acquired by MALDI-TOF MS on
  Bruker Daltonics machines of the *flex series.
diff -Nru r-cran-readbrukerflexdata-1.8.2/debian/copyright r-cran-readbrukerflexdata-1.8.3/debian/copyright
--- r-cran-readbrukerflexdata-1.8.2/debian/copyright	2015-07-02 14:41:54.000000000 +0000
+++ r-cran-readbrukerflexdata-1.8.3/debian/copyright	2016-12-12 14:23:25.000000000 +0000
@@ -1,14 +1,14 @@
-Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Name: readBrukerFlexData
 Upstream-Contact: Sebastian Gibb <sgibb.debian@gmail.com>
-Source: http://cran.r-project.org/web/packages/readBrukerFlexData/index.html
+Source: https://cran.r-project.org/package=readBrukerFlexData
 
 Files: *
-Copyright: 2011-2015 Sebastian Gibb <sgibb.debian@gmail.com>
+Copyright: 2011-2016 Sebastian Gibb <sgibb.debian@gmail.com>
 License: GPL-3+
 
 Files: debian/*
-Copyright: 2012-2015 Sebastian Gibb <sgibb.debian@gmail.com>
+Copyright: 2012-2016 Sebastian Gibb <sgibb.debian@gmail.com>
 License: GPL-3+
 
 License: GPL-3+
diff -Nru r-cran-readbrukerflexdata-1.8.2/debian/rules r-cran-readbrukerflexdata-1.8.3/debian/rules
--- r-cran-readbrukerflexdata-1.8.2/debian/rules	2015-07-02 14:41:54.000000000 +0000
+++ r-cran-readbrukerflexdata-1.8.3/debian/rules	2016-12-12 14:23:25.000000000 +0000
@@ -1,11 +1,10 @@
 #!/usr/bin/make -f
-# -*- makefile -*-
-# debian/rules file for the Debian/GNU Linux r-cran-readbrukerflex package
-# Copyright 2014 by Sebastian Gibb <sgibb.debian@gmail.com>
-include /usr/share/R/debian/r-cran.mk
 
-DEB_INSTALL_DOCS_ALL :=
-DEB_INSTALL_CHANGELOGS_ALL := NEWS
+%:
+	dh $@ --buildsystem R
+
+override_dh_installchangelogs:
+	dh_installchangelogs NEWS
 
 get-orig-source:
 	## download newest version from CRAN
diff -Nru r-cran-readbrukerflexdata-1.8.2/debian/watch r-cran-readbrukerflexdata-1.8.3/debian/watch
--- r-cran-readbrukerflexdata-1.8.2/debian/watch	2015-07-02 14:41:54.000000000 +0000
+++ r-cran-readbrukerflexdata-1.8.3/debian/watch	2016-12-12 14:23:25.000000000 +0000
@@ -1,3 +1,3 @@
-version=3
+version=4
 http://cran.r-project.org/src/contrib/readBrukerFlexData_([\d\.]*).tar.gz
 
diff -Nru r-cran-readbrukerflexdata-1.8.2/DESCRIPTION r-cran-readbrukerflexdata-1.8.3/DESCRIPTION
--- r-cran-readbrukerflexdata-1.8.2/DESCRIPTION	2014-12-15 23:43:10.000000000 +0000
+++ r-cran-readbrukerflexdata-1.8.3/DESCRIPTION	2016-11-30 13:55:26.000000000 +0000
@@ -1,20 +1,22 @@
 Package: readBrukerFlexData
-Version: 1.8.2
-Date: 2014-12-15
+Version: 1.8.3
+Date: 2016-11-29
 Title: Reads Mass Spectrometry Data in Bruker *flex Format
 Authors@R: person("Sebastian", "Gibb", role=c("aut", "cre"),
     email="mail@sebastiangibb.de")
-Depends: R (>= 2.15.0)
-Description: Reads data files acquired by MALDI-TOF MS on Bruker Daltonics
-    machines of the *flex series.
+Depends: R (>= 3.3.0)
+Description: Reads data files acquired by Bruker Daltonics' matrix-assisted
+    laser desorption/ionization-time-of-flight mass spectrometer of the *flex
+    series.
 License: GPL (>= 3)
 URL: http://strimmerlab.org/software/maldiquant/
         https://github.com/sgibb/readBrukerFlexData/
 BugReports: https://github.com/sgibb/readBrukerFlexData/issues/
 LazyLoad: yes
-Packaged: 2014-12-15 21:40:58 UTC; sebastian
+RoxygenNote: 5.0.1
+NeedsCompilation: no
+Packaged: 2016-11-30 09:58:15 UTC; sebastian
 Author: Sebastian Gibb [aut, cre]
 Maintainer: Sebastian Gibb <mail@sebastiangibb.de>
-NeedsCompilation: no
 Repository: CRAN
-Date/Publication: 2014-12-16 00:43:10
+Date/Publication: 2016-11-30 14:55:26
diff -Nru r-cran-readbrukerflexdata-1.8.2/man/changePrecision.Rd r-cran-readbrukerflexdata-1.8.3/man/changePrecision.Rd
--- r-cran-readbrukerflexdata-1.8.2/man/changePrecision.Rd	2014-12-15 20:56:56.000000000 +0000
+++ r-cran-readbrukerflexdata-1.8.3/man/changePrecision.Rd	2016-11-29 15:03:11.000000000 +0000
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.0): do not edit by hand
+% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/double2singlePrecision-functions.R
 \name{.changePrecision}
 \alias{.changePrecision}
diff -Nru r-cran-readbrukerflexdata-1.8.2/man/cpSpecHpcMzXml.Rd r-cran-readbrukerflexdata-1.8.3/man/cpSpecHpcMzXml.Rd
--- r-cran-readbrukerflexdata-1.8.2/man/cpSpecHpcMzXml.Rd	2014-12-15 20:56:56.000000000 +0000
+++ r-cran-readbrukerflexdata-1.8.3/man/cpSpecHpcMzXml.Rd	2016-11-29 15:03:11.000000000 +0000
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.0): do not edit by hand
+% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/cpSpecHpcMzXml-data.R
 \docType{data}
 \name{cpSpecHpcMzXml}
@@ -13,8 +13,8 @@
 }
 \description{
 This dataset was generated by Bruker Daltonics CompassXport and imported by
-\code{\link[readMzXmlData]{readMzXmlFile}} to R. It is only needed for
-comparison between Bruker Daltonics' HPC and
+\code{\link[readMzXmlData]{readMzXmlFile}} to R. It is only needed for 
+comparison between Bruker Daltonics' HPC and 
 \code{\link[readBrukerFlexData]{.hpc}}.
 }
 \seealso{
diff -Nru r-cran-readbrukerflexdata-1.8.2/man/double2singlePrecision.Rd r-cran-readbrukerflexdata-1.8.3/man/double2singlePrecision.Rd
--- r-cran-readbrukerflexdata-1.8.2/man/double2singlePrecision.Rd	2014-12-15 20:56:56.000000000 +0000
+++ r-cran-readbrukerflexdata-1.8.3/man/double2singlePrecision.Rd	2016-11-29 15:08:42.000000000 +0000
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.0): do not edit by hand
+% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/double2singlePrecision-functions.R
 \name{.double2singlePrecision}
 \alias{.double2singlePrecision}
@@ -42,9 +42,10 @@
 
 ## reset digits option
 options(digits=oldDigits)
+
 }
 \references{
-IEEE 754 standard: \url{http://754r.ucbtest.org/standards/754.pdf}
+IEEE 754 standard: \url{http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=30711&filter=AND(p_Publication_Number:2355)}
 }
 \seealso{
 \code{\link[readBrukerFlexData]{.changePrecision}},
diff -Nru r-cran-readbrukerflexdata-1.8.2/man/extractHPCConstants.Rd r-cran-readbrukerflexdata-1.8.3/man/extractHPCConstants.Rd
--- r-cran-readbrukerflexdata-1.8.2/man/extractHPCConstants.Rd	2014-12-15 20:56:56.000000000 +0000
+++ r-cran-readbrukerflexdata-1.8.3/man/extractHPCConstants.Rd	2016-11-29 15:03:11.000000000 +0000
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.0): do not edit by hand
+% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/hpc-functions.R
 \name{.extractHPCConstants}
 \alias{.extractHPCConstants}
@@ -26,8 +26,8 @@
 a \code{list}:
  \itemize{
    \item{\code{hpcConstants$coefficients}: }{double, vector of coefficents}
-   \item{\code{hpcConstants$calibrationContant0}: }{c0}
-   \item{\code{hpcConstants$calibrationContant2}: }{c2}
+   \item{\code{hpcConstants$calibrationConstant0}: }{c0}
+   \item{\code{hpcConstants$calibrationConstant2}: }{c2}
  }
 }
 \description{
diff -Nru r-cran-readbrukerflexdata-1.8.2/man/grepAcquDoubleValue.Rd r-cran-readbrukerflexdata-1.8.3/man/grepAcquDoubleValue.Rd
--- r-cran-readbrukerflexdata-1.8.2/man/grepAcquDoubleValue.Rd	2014-12-15 20:56:56.000000000 +0000
+++ r-cran-readbrukerflexdata-1.8.3/man/grepAcquDoubleValue.Rd	2016-11-29 15:03:11.000000000 +0000
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.0): do not edit by hand
+% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/grepAcquValue-functions.R
 \name{.grepAcquDoubleValue}
 \alias{.grepAcquDoubleValue}
diff -Nru r-cran-readbrukerflexdata-1.8.2/man/grepAcquValue.Rd r-cran-readbrukerflexdata-1.8.3/man/grepAcquValue.Rd
--- r-cran-readbrukerflexdata-1.8.2/man/grepAcquValue.Rd	2014-12-15 20:56:56.000000000 +0000
+++ r-cran-readbrukerflexdata-1.8.3/man/grepAcquValue.Rd	2016-11-29 15:03:11.000000000 +0000
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.0): do not edit by hand
+% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/grepAcquValue-functions.R
 \name{.grepAcquValue}
 \alias{.grepAcquValue}
diff -Nru r-cran-readbrukerflexdata-1.8.2/man/hpc.Rd r-cran-readbrukerflexdata-1.8.3/man/hpc.Rd
--- r-cran-readbrukerflexdata-1.8.2/man/hpc.Rd	2014-12-15 20:56:56.000000000 +0000
+++ r-cran-readbrukerflexdata-1.8.3/man/hpc.Rd	2016-11-29 15:03:11.000000000 +0000
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.0): do not edit by hand
+% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/hpc-functions.R
 \name{.hpc}
 \alias{.hpc}
@@ -104,6 +104,7 @@
  minMass=noHpcSpec$metaData$hpc$limits["minMass"],
  maxMass=noHpcSpec$metaData$hpc$limits["maxMass"],
  hpcCoefficients=noHpcSpec$metaData$hpc$coefficients)
+
 }
 \references{
 Gobom, J. and Mueller, M. and Egelhofer V. and Theiss, D. and
diff -Nru r-cran-readbrukerflexdata-1.8.2/man/readAcquFile.Rd r-cran-readbrukerflexdata-1.8.3/man/readAcquFile.Rd
--- r-cran-readbrukerflexdata-1.8.2/man/readAcquFile.Rd	2014-12-15 20:56:56.000000000 +0000
+++ r-cran-readbrukerflexdata-1.8.3/man/readAcquFile.Rd	2016-11-29 15:03:11.000000000 +0000
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.0): do not edit by hand
+% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/readAcquFile-functions.R
 \name{.readAcquFile}
 \alias{.readAcquFile}
diff -Nru r-cran-readbrukerflexdata-1.8.2/man/readBrukerFlexData-defunct.Rd r-cran-readbrukerflexdata-1.8.3/man/readBrukerFlexData-defunct.Rd
--- r-cran-readbrukerflexdata-1.8.2/man/readBrukerFlexData-defunct.Rd	2014-12-15 20:56:56.000000000 +0000
+++ r-cran-readbrukerflexdata-1.8.3/man/readBrukerFlexData-defunct.Rd	2016-11-29 15:03:11.000000000 +0000
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.0): do not edit by hand
+% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/package.R
 \name{readBrukerFlexData-defunct}
 \alias{mqReadBrukerFlex}
diff -Nru r-cran-readbrukerflexdata-1.8.2/man/readBrukerFlexData-package.Rd r-cran-readbrukerflexdata-1.8.3/man/readBrukerFlexData-package.Rd
--- r-cran-readbrukerflexdata-1.8.2/man/readBrukerFlexData-package.Rd	2014-12-15 21:03:01.000000000 +0000
+++ r-cran-readbrukerflexdata-1.8.3/man/readBrukerFlexData-package.Rd	2016-11-29 15:54:20.000000000 +0000
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.0): do not edit by hand
+% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/package.R
 \docType{package}
 \name{readBrukerFlexData-package}
@@ -18,9 +18,9 @@
 
 Package: \tab readBrukerFlexData \cr
 
-Version: \tab 1.8.2\cr
+Version: \tab 1.8.3\cr
 
-Date: \tab 2014-12-15\cr
+Date: \tab 2016-11-29\cr
 
 License: \tab GPL (>= 3)\cr
 
diff -Nru r-cran-readbrukerflexdata-1.8.2/man/readBrukerFlexDir.Rd r-cran-readbrukerflexdata-1.8.3/man/readBrukerFlexDir.Rd
--- r-cran-readbrukerflexdata-1.8.2/man/readBrukerFlexDir.Rd	2014-12-15 20:56:56.000000000 +0000
+++ r-cran-readbrukerflexdata-1.8.3/man/readBrukerFlexDir.Rd	2016-11-29 15:03:11.000000000 +0000
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.0): do not edit by hand
+% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/readBrukerFlexDir-functions.R
 \name{readBrukerFlexDir}
 \alias{readBrukerFlexDir}
@@ -73,6 +73,7 @@
 
 ## draw legend
 legend(x="topright", legend=legendStr, col=rainbow(l), lwd=1)
+
 }
 \seealso{
 \code{\link[MALDIquantForeign]{importBrukerFlex}},
diff -Nru r-cran-readbrukerflexdata-1.8.2/man/readBrukerFlexFile.Rd r-cran-readbrukerflexdata-1.8.3/man/readBrukerFlexFile.Rd
--- r-cran-readbrukerflexdata-1.8.2/man/readBrukerFlexFile.Rd	2014-12-15 20:56:56.000000000 +0000
+++ r-cran-readbrukerflexdata-1.8.3/man/readBrukerFlexFile.Rd	2016-11-29 15:03:11.000000000 +0000
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.0): do not edit by hand
+% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/readBrukerFlexFile-functions.R
 \name{readBrukerFlexFile}
 \alias{readBrukerFlexFile}
@@ -12,7 +12,7 @@
 \item{fidFile}{\code{character}, path to \emph{fid} file which should be
 read.}
 
-\item{removeMetaData,}{\code{logical}, to calculate mass data a lot of meta
+\item{removeMetaData, }{\code{logical}, to calculate mass data a lot of meta
 data are needed. To save memory they could be deleted after calculation.}
 
 \item{useHpc}{\code{logical}, should Bruker Daltonics' High Precision
@@ -162,6 +162,7 @@
 
 ## plot spectrum
 plot(spec$spectrum$mass, spec$spectrum$intensity, type="l", col="red")
+
 }
 \seealso{
 \url{https://github.com/sgibb/readBrukerFlexData/wiki},
diff -Nru r-cran-readbrukerflexdata-1.8.2/man/readFidFile.Rd r-cran-readbrukerflexdata-1.8.3/man/readFidFile.Rd
--- r-cran-readbrukerflexdata-1.8.2/man/readFidFile.Rd	2014-12-15 20:56:56.000000000 +0000
+++ r-cran-readbrukerflexdata-1.8.3/man/readFidFile.Rd	2016-11-29 15:03:11.000000000 +0000
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.0): do not edit by hand
+% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/readFidFile-functions.R
 \name{.readFidFile}
 \alias{.readFidFile}
@@ -14,7 +14,7 @@
 (total count; get from acqu file)}
 
 \item{endian}{endianness of the fid file
- (\sQuote{little} or \sQuote{big}; default: \sQuote{little})}
+(\sQuote{little} or \sQuote{big}; default: \sQuote{little})}
 }
 \value{
 A vector of intensity values.
diff -Nru r-cran-readbrukerflexdata-1.8.2/man/sampleName.Rd r-cran-readbrukerflexdata-1.8.3/man/sampleName.Rd
--- r-cran-readbrukerflexdata-1.8.2/man/sampleName.Rd	2014-12-15 20:56:56.000000000 +0000
+++ r-cran-readbrukerflexdata-1.8.3/man/sampleName.Rd	2016-11-29 15:03:11.000000000 +0000
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.0): do not edit by hand
+% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/sampleName-functions.R
 \name{.sampleName}
 \alias{.sampleName}
@@ -8,7 +8,7 @@
 }
 \arguments{
 \item{fidFile}{\code{character}, path to fid file
- (e.g. \sQuote{Pankreas_HB_L_061019_A10/0_a19/1/1SLin/fid})}
+(e.g. \sQuote{Pankreas_HB_L_061019_A10/0_a19/1/1SLin/fid})}
 }
 \value{
 \code{character}, sample name: e.g \sQuote{Pankreas_HB_L_061019_A10}
diff -Nru r-cran-readbrukerflexdata-1.8.2/man/tof2mass.Rd r-cran-readbrukerflexdata-1.8.3/man/tof2mass.Rd
--- r-cran-readbrukerflexdata-1.8.2/man/tof2mass.Rd	2014-12-15 20:56:56.000000000 +0000
+++ r-cran-readbrukerflexdata-1.8.3/man/tof2mass.Rd	2016-11-29 15:03:11.000000000 +0000
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.0): do not edit by hand
+% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/tof2mass-functions.R
 \name{.tof2mass}
 \alias{.tof2mass}
@@ -21,7 +21,7 @@
 \description{
 This function calculates mass from time of flight values
 based on the following article:
- Titulaer, M. K. and Siccama, I. and Dekker, J. L. and
+ Titulaer, M. K. and Siccama, I. and Dekker, J. L. and 
  van Rijswijk, A. L. and Heeren R. M. and Sillevis Smitt, P. A. and
  Luider, T. M. (2006) \cr
  \dQuote{A database application for pre-processing, storage and comparison
@@ -33,7 +33,7 @@
 Arguments are imported from metadata (acqu-file).
 }
 \references{
-Titulaer, M. K. and Siccama, I. and Dekker, J. L. and
+Titulaer, M. K. and Siccama, I. and Dekker, J. L. and 
  van Rijswijk, A. L. and Heeren R. M. and Sillevis Smitt, P. A. and
  Luider, T. M. (2006) \cr
  \dQuote{A database application for pre-processing, storage and comparison
diff -Nru r-cran-readbrukerflexdata-1.8.2/MD5 r-cran-readbrukerflexdata-1.8.3/MD5
--- r-cran-readbrukerflexdata-1.8.2/MD5	2014-12-15 23:43:10.000000000 +0000
+++ r-cran-readbrukerflexdata-1.8.3/MD5	2016-11-30 13:55:26.000000000 +0000
@@ -1,16 +1,16 @@
-e9d67a5387e17e56a770aeec1ac6cdb1 *DESCRIPTION
-c881567c522e436d9be43fe2ba7e6061 *NAMESPACE
-7387c609f0160e11356b9e7fa0700ea2 *NEWS
+dd88855a0eb94809bdbe35790f21ffdd *DESCRIPTION
+e1052c0b606efcbee33069b4e1e739f1 *NAMESPACE
+80ff43b21f38660913e484508f5cb2ec *NEWS
 3af5176f5a2d53bd7e33999b75483b94 *R/cpSpecHpcMzXml-data.R
-45f6ac1c7e92d8d7389aada0cabcb582 *R/double2singlePrecision-functions.R
-508a7700b53501ac07707350afec7298 *R/grepAcquValue-functions.R
-7a028b16b4c9d2eb1efdbd3cdd8c9a5d *R/hpc-functions.R
-aaee9878204b95eb3254f6b311289ca5 *R/package.R
-7c268b0988c34cacdfad0a74f9c6da21 *R/readAcquFile-functions.R
-95fa49784066f583b3766891288795a8 *R/readBrukerFlexDir-functions.R
-fc926b07fac7cdc0fb9107c0e190cc5b *R/readBrukerFlexFile-functions.R
-7ccbabd8c7a3c3f08a80cac327129059 *R/readFidFile-functions.R
-26d54ff3fcaca3ffa55120ed519b1610 *R/sampleName-functions.R
+07db0f76401793b4f9e60c3a495e0950 *R/double2singlePrecision-functions.R
+e38968fc74ec05b1d78052099abf6da7 *R/grepAcquValue-functions.R
+fc9c1306bee5141e30879b861ad7c68b *R/hpc-functions.R
+e6445bdbfe6837f0cbeb3b57b61e7c26 *R/package.R
+9750c47b6cfdd453b736868c906566a3 *R/readAcquFile-functions.R
+55269fed9fc18acabec3c2af24828d1f *R/readBrukerFlexDir-functions.R
+5f37d8ad5dd103f31a779b39848d4c3b *R/readBrukerFlexFile-functions.R
+8320b7e2396fd6cccf7d53b730bbbbf2 *R/readFidFile-functions.R
+17cc7b38eb6cfc708ef3a477ad321a84 *R/sampleName-functions.R
 61f4159d7a248e9d6901bd2781c01fe5 *R/tof2mass-functions.R
 0a984d7b36f80792aaf6170017d7655b *data/cpSpecHpcMzXml.RData
 e5305c9066b13ad272def4dbe36a1d0d *inst/Examples/2010_05_19_Gibb_C8_A1/0_A1/1/1SLin/acqu
@@ -20,18 +20,18 @@
 15eb319eccc8d4253d3bb5e54da98ad3 *inst/Examples/hpc/fid/0_A20/1/1SRef/acqu
 25eec2005318cecd220bff5650de33a5 *inst/Examples/hpc/fid/0_A20/1/1SRef/fid
 4fe5886da4a17568cb4c1a7ed0f2e4fa *inst/Examples/hpc/mzXML/hpc.mzXML
-0f12c2835e3014652fa23773a5d61af2 *man/changePrecision.Rd
-305b48371c35cef52dfc37bbe31b69ac *man/cpSpecHpcMzXml.Rd
-944ef01fee1abfda95e9b132bf8df635 *man/double2singlePrecision.Rd
-4358bd894fb8d5eeae3f1df4a5b28c54 *man/extractHPCConstants.Rd
-cc451e40859f54f3654684ec5566b22e *man/grepAcquDoubleValue.Rd
-dd96d81a2c053bbb84184fd1493b7249 *man/grepAcquValue.Rd
-182558ff70c9807b5905ab7653e27893 *man/hpc.Rd
-384c533e7474435b7d4667484b734287 *man/readAcquFile.Rd
-c97175442f3448fc7a894308c4228cae *man/readBrukerFlexData-defunct.Rd
-f781b4574775b90bc84666aee2cacd70 *man/readBrukerFlexData-package.Rd
-c1d6caf63153fdc6ab4522ada51b5f39 *man/readBrukerFlexDir.Rd
-ce251317bf8bbee18bed8088bfbfc524 *man/readBrukerFlexFile.Rd
-39ef7ce983d88b7c124b9f5e05928309 *man/readFidFile.Rd
-f61df3c4a54ac314cbdb79c78701cacf *man/sampleName.Rd
-8e5680444b54a85469742b16355381eb *man/tof2mass.Rd
+89343b824dc5d3e8ef9bb2b068df09fa *man/changePrecision.Rd
+4448f8bfb5b2903edc8600f6cc16f0b1 *man/cpSpecHpcMzXml.Rd
+57a824cc11bd332cebec0c7c13bb1ece *man/double2singlePrecision.Rd
+ff8a0d4e4f99cdbef5f1b32ce4bf9295 *man/extractHPCConstants.Rd
+420adeb579695de23267915c85008f9b *man/grepAcquDoubleValue.Rd
+8c6f56f952b70625207650620c29dde1 *man/grepAcquValue.Rd
+951f0a71319aeddd814c990c937b5fb3 *man/hpc.Rd
+2227aa1305922c5684f3b5bb878cd855 *man/readAcquFile.Rd
+7adceb7700fcdcc786c932eead46c3b8 *man/readBrukerFlexData-defunct.Rd
+329ea104ced0af8b17b9ad6511cbdceb *man/readBrukerFlexData-package.Rd
+1e9de1bebdffa263c69d7448ef264f71 *man/readBrukerFlexDir.Rd
+eef705454fbe55958da44001180965d3 *man/readBrukerFlexFile.Rd
+b044fb40e0c24d3dd661e90663dcc2b2 *man/readFidFile.Rd
+4cb27f6b23f6382ef1b9ce4985e0b571 *man/sampleName.Rd
+908524857934ecd9c14e0138587554ed *man/tof2mass.Rd
diff -Nru r-cran-readbrukerflexdata-1.8.2/NAMESPACE r-cran-readbrukerflexdata-1.8.3/NAMESPACE
--- r-cran-readbrukerflexdata-1.8.2/NAMESPACE	2014-12-15 20:56:56.000000000 +0000
+++ r-cran-readbrukerflexdata-1.8.3/NAMESPACE	2016-11-29 15:03:11.000000000 +0000
@@ -1,4 +1,4 @@
-# Generated by roxygen2 (4.1.0): do not edit by hand
+# Generated by roxygen2: do not edit by hand
 
 export(readBrukerFlexDir)
 export(readBrukerFlexFile)
diff -Nru r-cran-readbrukerflexdata-1.8.2/NEWS r-cran-readbrukerflexdata-1.8.3/NEWS
--- r-cran-readbrukerflexdata-1.8.2/NEWS	2014-12-15 21:40:19.000000000 +0000
+++ r-cran-readbrukerflexdata-1.8.3/NEWS	2016-11-29 15:52:59.000000000 +0000
@@ -1,6 +1,14 @@
 RELEASE HISTORY OF THE "readBrukerFlexData" PACKAGE
 ===================================================
 
+Version 1.8.3 [2016-11-29]:
+- Fix broken link to IEEE 754 standard in double2singlePrecision manual page.
+- Some acqu files report a greater number of tof/mass values than the number of
+  intensity values in the fid files. Now the last tof/mass values are removed to
+  keep the number of tof/mass/intensity equal and a warning is thrown.
+  Thanks to Frederic Foucault <frederic.foucault@mabritec.com> for reporting
+  this problem.
+
 Version 1.8.2 [2014-12-15]:
 - Fix sampleName for directory structures generated by old versions of the
   Bruker FlexControl software.
diff -Nru r-cran-readbrukerflexdata-1.8.2/R/double2singlePrecision-functions.R r-cran-readbrukerflexdata-1.8.3/R/double2singlePrecision-functions.R
--- r-cran-readbrukerflexdata-1.8.2/R/double2singlePrecision-functions.R	2014-09-27 11:03:54.000000000 +0000
+++ r-cran-readbrukerflexdata-1.8.3/R/double2singlePrecision-functions.R	2016-11-29 15:08:38.000000000 +0000
@@ -38,7 +38,7 @@
 #' @rdname double2singlePrecision
 #' @keywords internal
 #' @references
-#' IEEE 754 standard: \url{http://754r.ucbtest.org/standards/754.pdf}
+#' IEEE 754 standard: \url{http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=30711&filter=AND(p_Publication_Number:2355)}
 #' @examples
 #' ## load library
 #' library("readBrukerFlexData")
@@ -58,7 +58,7 @@
 #'
 .double2singlePrecision <- function(x) {
   stopifnot(is.double(x))
-  return(.changePrecision(x, size=4))
+  .changePrecision(x, size=4L)
 }
 
 #' Change precision.
@@ -84,7 +84,6 @@
   ## size==8 # 64bit, double precision
   virtualCon <- writeBin(object=x, con=virtualCon, size=size)
   ## re-read data
-  x <- readBin(con=virtualCon, what=double(), size=size, n=length(x))
-  return(x)
+  readBin(con=virtualCon, what=double(), size=size, n=length(x))
 }
 
diff -Nru r-cran-readbrukerflexdata-1.8.2/R/grepAcquValue-functions.R r-cran-readbrukerflexdata-1.8.3/R/grepAcquValue-functions.R
--- r-cran-readbrukerflexdata-1.8.2/R/grepAcquValue-functions.R	2014-09-27 11:06:45.000000000 +0000
+++ r-cran-readbrukerflexdata-1.8.3/R/grepAcquValue-functions.R	2016-11-26 20:14:38.000000000 +0000
@@ -19,10 +19,10 @@
 #' Extracts values from acqu file.
 #'
 #' This function is a helper function to extract values from acqu file.
-#' 
+#'
 #' @param patternStr \code{character}, pattern to look for
 #' @param srcStr \code{character} where to look for \code{patternStr}
-#' 
+#'
 #' @return \code{character} vector of the value given in \code{patternStr}
 #'
 #' @seealso
@@ -32,25 +32,23 @@
 #' @keywords internal
 .grepAcquValue <- function(patternStr, srcStr) {
   tmpLine <- grep(pattern=patternStr, x=srcStr, value=TRUE)
-  
+
   ## format e.g.
   ## DATATYPE= CONTINUOUS MASS SPECTRUM
   ## .IONIZATION MODE= LD+
   ## $INSTRUM= <AUTOFLEX>
-  
+
   ## remove front/back pattern environment
-  tmpLine <- gsub(pattern="(^.*= *<?)|(>? *$)", replacement="", x=tmpLine)
-  
-  return(tmpLine)
+  gsub(pattern="(^.*= *<?)|(>? *$)", replacement="", x=tmpLine)
 }
 
 #' Extracts values from acqu file.
 #'
 #' This function is a helper function to extract double values from acqu file.
-#' 
+#'
 #' @param patternStr \code{character}, pattern to look for
 #' @param srcStr \code{character} where to look for \code{patternStr}
-#' 
+#'
 #' @return \code{double} vector of the value given in \code{patternStr}
 #'
 #' @seealso
@@ -60,10 +58,8 @@
 #' @keywords internal
 .grepAcquDoubleValue <- function(patternStr, srcStr) {
   strValue <- .grepAcquValue(patternStr, srcStr)
-  
+
   ## replace comma by dot
-  strValue <- gsub(",", replacement=".", strValue)
-  
-  return(as.double(strValue))
+  as.double(gsub(",", replacement=".", strValue))
 }
- 
+
diff -Nru r-cran-readbrukerflexdata-1.8.2/R/hpc-functions.R r-cran-readbrukerflexdata-1.8.3/R/hpc-functions.R
--- r-cran-readbrukerflexdata-1.8.2/R/hpc-functions.R	2014-09-27 11:06:45.000000000 +0000
+++ r-cran-readbrukerflexdata-1.8.3/R/hpc-functions.R	2016-11-29 15:03:08.000000000 +0000
@@ -40,8 +40,8 @@
 #'  a \code{list}:
 #'  \itemize{
 #'    \item{\code{hpcConstants$coefficients}: }{double, vector of coefficents}
-#'    \item{\code{hpcConstants$calibrationContant0}: }{c0}
-#'    \item{\code{hpcConstants$calibrationContant2}: }{c2}
+#'    \item{\code{hpcConstants$calibrationConstant0}: }{c0}
+#'    \item{\code{hpcConstants$calibrationConstant2}: }{c2}
 #'  }
 #'
 #' @seealso \code{\link[readBrukerFlexData]{.hpc}}
@@ -49,22 +49,15 @@
 #' @keywords internal
 #'
 .extractHPCConstants <- function(hpcStr) {
-  tmpLine <- strsplit(x=hpcStr, split=" ")[[1]]
+  tmpLine <- strsplit(x=hpcStr, split=" ")[[1L]]
   ## remove emtpy elements
-  tmpLine <- tmpLine[tmpLine != ""]
-
-  hpcConstants <- list()
+  tmpLine <- tmpLine[nzchar(tmpLine)]
 
   ## extract only coefficients
-  hpcConstants$coefficients <-
-    as.double(tmpLine[(which(tmpLine == "V1.0VectorDouble") + 2):(which(tmpLine == "c2") - 1)])
-
-  hpcConstants$calibrationConstant2 <-
-    as.double(tmpLine[which(tmpLine == "c2") + 1])
-  hpcConstants$calibrationConstant0 <-
-    as.double(tmpLine[which(tmpLine == "c0") + 1])
-
-  return(hpcConstants)
+  list(coefficients=as.double(tmpLine[(which(tmpLine == "V1.0VectorDouble") + 2L):
+                           (which(tmpLine == "c2") - 1L)]),
+       calibrationConstant0=as.double(tmpLine[which(tmpLine == "c0") + 1L]),
+       calibrationConstant2=as.double(tmpLine[which(tmpLine == "c2") + 1L]))
 }
 
 #' High Precision Calibration
@@ -194,13 +187,13 @@
 
   ## correction=c[0] + c[1]*cal_mass^1 + ... + c[n]*cal_mass^n
   ## mass=cal_mass - correction
-  l <- length(hpcCoefficients) - 1
+  l <- length(hpcCoefficients) - 1L
   m <- sapply(m, function(x) {
-    return(x - sum(hpcCoefficients * x^(0:l)))
+    x - sum(hpcCoefficients * x^(0L:l))
   })
 
   mass[hpcRange] <- m
 
-  return(mass)
+  mass
 }
 
diff -Nru r-cran-readbrukerflexdata-1.8.2/R/package.R r-cran-readbrukerflexdata-1.8.3/R/package.R
--- r-cran-readbrukerflexdata-1.8.2/R/package.R	2014-12-15 21:02:48.000000000 +0000
+++ r-cran-readbrukerflexdata-1.8.3/R/package.R	2016-11-29 15:54:14.000000000 +0000
@@ -30,9 +30,9 @@
 #'
 #' Package: \tab readBrukerFlexData \cr
 #'
-#' Version: \tab 1.8.2\cr
+#' Version: \tab 1.8.3\cr
 #'
-#' Date: \tab 2014-12-15\cr
+#' Date: \tab 2016-11-29\cr
 #'
 #' License: \tab GPL (>= 3)\cr
 #'
diff -Nru r-cran-readbrukerflexdata-1.8.2/R/readAcquFile-functions.R r-cran-readbrukerflexdata-1.8.3/R/readAcquFile-functions.R
--- r-cran-readbrukerflexdata-1.8.2/R/readAcquFile-functions.R	2014-11-05 19:59:52.000000000 +0000
+++ r-cran-readbrukerflexdata-1.8.3/R/readAcquFile-functions.R	2016-11-29 14:59:51.000000000 +0000
@@ -152,7 +152,7 @@
   metaData <- list()
 
   ## endianness
-  isBigEndian <- as.integer(.grepAcquValue("##\\$BYTORDA=", acquLines)) == 1
+  isBigEndian <- as.integer(.grepAcquValue("##\\$BYTORDA=", acquLines)) == 1L
   metaData$byteOrder <- ifelse(isBigEndian, "big", "little")
 
   ## obligate
@@ -174,9 +174,9 @@
 
   ## was HPC involved?  metaData$hpcUse seems to be always true
   isHPCused <- isTRUE(metaData$hpcUse &&
-                      metaData$hpcLimits["maxMass"] > 0 &&
-                      metaData$hpcLimits["minMass"] > 0 &&
-                      metaData$hpcOrder > 0)
+                      metaData$hpcLimits["maxMass"] > 0L &&
+                      metaData$hpcLimits["minMass"] > 0L &&
+                      metaData$hpcOrder > 0L)
 
   if (isHPCused) {
     hpcStr <- .grepAcquValue("##\\$HPCStr=", acquLines)
@@ -273,7 +273,7 @@
 
   metaData$laserShots <- as.double(.grepAcquValue("##\\$NoSHOTS=", acquLines))
 
-  if (metaData$laserShots == 0) {
+  if (metaData$laserShots == 0L) {
     warning("File ", sQuote(fidFile), " seems to be empty because ",
             "no laser shots applied to this sample.")
   }
@@ -284,12 +284,12 @@
   if (length(metaData$patch) &&
       grepl(pattern="(R[0-9]+)?X[0-9]+Y[0-9]+", x=metaData$patch,
             ignore.case=TRUE)) {
-    rx <- gregexpr(pattern="[XY][0-9]+", text=metaData$patch)[[1]]
-    pos <- substring(metaData$patch, rx+1, rx+attr(rx, "match.length")-1)
+    rx <- gregexpr(pattern="[XY][0-9]+", text=metaData$patch)[[1L]]
+    pos <- substring(metaData$patch, rx+1L, rx+attr(rx, "match.length")-1L)
 
-    if (length(pos) == 2) {
+    if (length(pos) == 2L) {
       pos <- as.double(pos)
-      metaData$imaging <- list(pos=c(x=pos[1], y=pos[2]))
+      metaData$imaging <- list(pos=c(x=pos[1L], y=pos[2L]))
     }
   }
 
@@ -319,6 +319,6 @@
   metaData$fullName <- paste(metaData$sampleName, metaData$patch, sep=".")
   metaData$name <- metaData$fullName
 
-  return(metaData)
+  metaData
 }
 
diff -Nru r-cran-readbrukerflexdata-1.8.2/R/readBrukerFlexDir-functions.R r-cran-readbrukerflexdata-1.8.3/R/readBrukerFlexDir-functions.R
--- r-cran-readbrukerflexdata-1.8.2/R/readBrukerFlexDir-functions.R	2014-09-27 11:18:20.000000000 +0000
+++ r-cran-readbrukerflexdata-1.8.3/R/readBrukerFlexDir-functions.R	2016-11-29 15:00:34.000000000 +0000
@@ -102,7 +102,7 @@
   ## remove calibrations scans?
   if (removeCalibrationScans) {
     calibrationScans <- grep(pattern="[Cc]alibration", x=files, value=TRUE)
-    if (length(calibrationScans) > 0) {
+    if (length(calibrationScans)) {
       files <- setdiff(files, calibrationScans)
     }
   }
@@ -112,17 +112,14 @@
   }
 
   ## generate 'path/files'
-  files <- sapply(files, function(x) {
-    x <- file.path(brukerFlexDir, x)
-    return(x)
-  })
+  files <- file.path(brukerFlexDir, files)
 
   ## read fid files
   brukerFlexData <- lapply(X=files, FUN=function(f) {
-    return(readBrukerFlexFile(fidFile=f, removeMetaData=removeMetaData,
-                              useHpc=useHpc,
-                              filterZeroIntensities=filterZeroIntensities,
-                              verbose=verbose))
+    readBrukerFlexFile(fidFile=f, removeMetaData=removeMetaData,
+                       useHpc=useHpc,
+                       filterZeroIntensities=filterZeroIntensities,
+                       verbose=verbose)
   })
 
   if (!removeMetaData & useSpectraNames) {
@@ -142,6 +139,6 @@
     }, USE.NAMES=FALSE)
   }
 
-  return(brukerFlexData)
+  brukerFlexData
 }
 
diff -Nru r-cran-readbrukerflexdata-1.8.2/R/readBrukerFlexFile-functions.R r-cran-readbrukerflexdata-1.8.3/R/readBrukerFlexFile-functions.R
--- r-cran-readbrukerflexdata-1.8.2/R/readBrukerFlexFile-functions.R	2014-11-04 15:26:20.000000000 +0000
+++ r-cran-readbrukerflexdata-1.8.3/R/readBrukerFlexFile-functions.R	2016-11-29 15:23:26.000000000 +0000
@@ -199,6 +199,14 @@
   ## read peak intensities
   intensity <- .readFidFile(fidFile, metaData$number, metaData$byteOrder)
 
+  ## some fid files have less intensity values as reported in acqu
+  if (length(intensity) < metaData$number) {
+    metaData$number <- length(intensity)
+    warning("The number of tof/mass values reported in the acqu file is greater ",
+            "than the number of intensity values in the fid file. ",
+            "The extra tof/mass values are removed.")
+  }
+
   ## calculate tof of metadata
   tof <- as.double(metaData$timeDelay +
                    ((0:(metaData$number-1)) * metaData$timeDelta))
@@ -225,9 +233,9 @@
 
   ## calculate mass of TOFs
   mass <- .tof2mass(tof,
-                    metaData$calibrationConstants[[1]],
-                    metaData$calibrationConstants[[2]],
-                    metaData$calibrationConstants[[3]])
+                    metaData$calibrationConstants[[1L]],
+                    metaData$calibrationConstants[[2L]],
+                    metaData$calibrationConstants[[3L]])
 
   ## TODO: fix equations in .hpc
 
diff -Nru r-cran-readbrukerflexdata-1.8.2/R/readFidFile-functions.R r-cran-readbrukerflexdata-1.8.3/R/readFidFile-functions.R
--- r-cran-readbrukerflexdata-1.8.2/R/readFidFile-functions.R	2014-09-27 11:06:45.000000000 +0000
+++ r-cran-readbrukerflexdata-1.8.3/R/readFidFile-functions.R	2016-11-29 15:01:45.000000000 +0000
@@ -43,9 +43,7 @@
   }
 
   con <- file(fidFile, "rb")
-  intensity <- readBin(con, integer(), n=nIntensities, size=4, endian=endian)
-  close(con)
-
-  return(as.double(intensity))
+  on.exit(close(con))
+  as.double(readBin(con, integer(), n=nIntensities, size=4L, endian=endian))
 }
 
diff -Nru r-cran-readbrukerflexdata-1.8.2/R/sampleName-functions.R r-cran-readbrukerflexdata-1.8.3/R/sampleName-functions.R
--- r-cran-readbrukerflexdata-1.8.2/R/sampleName-functions.R	2014-11-05 20:00:07.000000000 +0000
+++ r-cran-readbrukerflexdata-1.8.3/R/sampleName-functions.R	2016-11-29 15:01:57.000000000 +0000
@@ -58,7 +58,7 @@
   ## 0_L20_1SLin/fid
   ## vs the more recent FlexAnalysis versions use
   ## 0/L20/1SLin/fid
-  isShortPath <- isTRUE(numDirs > 2 &&
+  isShortPath <- isTRUE(numDirs > 2L &&
                         grepl("[0-9]+_[A-z][0-9]+_[0-9][A-z]+$",
                               dirs[numDirs - 1L]))
   if (isShortPath) {
@@ -72,6 +72,6 @@
                        x=sampleName)
   }
 
-  return(sampleName)
+  sampleName
 }