Merge branch 'master' into SpectrumList

lgatto · Oct 12, 2018 · 09a3fad · 09a3fad
2 parents 1f18e85 + d2085f8
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diff --git a/NEWS b/NEWS
@@ -1,7 +1,7 @@
 # MSnbase 2.7
 
 Changes in version 2.7.8
-- Add SpectrumList class
+- MGF exporter gets a new `addFields` argument (see PR #362) <2018-10-12 Fri>
 
 Changes in version 2.7.7
 - Fix unit tests (issue #360, wrong MS OBO CV terms for data smoothing
@@ -198,7 +198,7 @@ Changes in version 2.3.10
 - Add msLevel slot to Chromatogram object <2017-08-16 Wed>
 - Add msLevel argument to chromatogram,MSnExp method <2017-08-16 Wed>
 - `calculateFragments` now just calculate fragments for all `n - 1L` bonds
-        (before it incorrectly adds an additional bond; fixes #248) <2017-08-20 Sun>
+	(before it incorrectly adds an additional bond; fixes #248) <2017-08-20 Sun>
 - Add `isEmpty` methods for `Chromatogram` and `Chromatograms` objects
   <2017-09-05 Tue>
 - plot,Chromatogram[s] creates an empty plot and returns a warning if the
@@ -241,7 +241,7 @@ Changes in version 2.3.4
 
 Changes in version 2.3.3
 - Rewrite `getColsFromPattern` and `getRowsFromPattern` and add unit tests
-        <2017-05-11 Thu>.
+	<2017-05-11 Thu>.
 - Add `.filterNA` and rewrite `filterNA` for `matrix` and `MSnSet`
   <2017-05-11 Thu>.
 - Convert main MSnbase-demo vignette to Rmd/html <2017-05-27 Sat>
@@ -503,7 +503,7 @@ Changes in version 1.21.4
  - More MzTab and Spectrum1 unit testing <2016-05-08 Sun>
  - Speed up readMSData (PR #86 by jotsetung) <2016-05-12 Thu>
  - Replace example file URL to use github instead of googlecode
-        <2016-05-12 Thu>
+	<2016-05-12 Thu>
 
 Changes in version 1.21.3
 
@@ -628,7 +628,7 @@ Changes in version 1.19.7
 
  - new sampleNames<- for pSet and MSnExp objects <2015-12-15 Tue>
  - Fix bug preventing to write MS1 to mgf (fixes issue #73 reported by
-        meowcat) <2015-12-18 Fri>
+	meowcat) <2015-12-18 Fri>
 
 Changes in version 1.19.6
 
@@ -797,7 +797,7 @@ Changes in version 1.15.15
 
 Changes in version 1.15.14
   - new msnset data, used in various examples instead of quantifying
-        the itraqdata experiment over and over again [2015-04-01 Wed]
+	the itraqdata experiment over and over again [2015-04-01 Wed]
 
 Changes in version 1.15.13
  - improve nbavg imputation description and add example [2015-03-22 Sun]

diff --git a/NEWS.md b/NEWS.md
@@ -1,7 +1,7 @@
 # MSnbase 2.7
 
 ## Changes in version 2.7.8
-- Add SpectrumList class.
+- MGF exporter gets a new `addFields` argument (see PR [#362](https://github.com/lgatto/MSnbase/issues/362)) <2018-10-12 Fri>
 
 ## Changes in version 2.7.7
 - Fix unit tests (issue [#360](https://github.com/lgatto/MSnbase/issues/360), wrong MS OBO CV terms for data smoothing
@@ -198,7 +198,7 @@
 - Add msLevel slot to Chromatogram object <2017-08-16 Wed>
 - Add msLevel argument to chromatogram,MSnExp method <2017-08-16 Wed>
 - `calculateFragments` now just calculate fragments for all `n - 1L` bonds
-        (before it incorrectly adds an additional bond; fixes [#248](https://github.com/lgatto/MSnbase/issues/248)) <2017-08-20 Sun>
+	(before it incorrectly adds an additional bond; fixes [#248](https://github.com/lgatto/MSnbase/issues/248)) <2017-08-20 Sun>
 - Add `isEmpty` methods for `Chromatogram` and `Chromatograms` objects
   <2017-09-05 Tue>
 - plot,Chromatogram[s] creates an empty plot and returns a warning if the
@@ -241,7 +241,7 @@
 
 ## Changes in version 2.3.3
 - Rewrite `getColsFromPattern` and `getRowsFromPattern` and add unit tests
-        <2017-05-11 Thu>.
+	<2017-05-11 Thu>.
 - Add `.filterNA` and rewrite `filterNA` for `matrix` and `MSnSet`
   <2017-05-11 Thu>.
 - Convert main MSnbase-demo vignette to Rmd/html <2017-05-27 Sat>
@@ -503,7 +503,7 @@
  - More MzTab and Spectrum1 unit testing <2016-05-08 Sun>
  - Speed up readMSData (PR [#86](https://github.com/lgatto/MSnbase/issues/86) by jotsetung) <2016-05-12 Thu>
  - Replace example file URL to use github instead of googlecode
-        <2016-05-12 Thu>
+	<2016-05-12 Thu>
 
 ## Changes in version 1.21.3
 
@@ -628,7 +628,7 @@
 
  - new sampleNames<- for pSet and MSnExp objects <2015-12-15 Tue>
  - Fix bug preventing to write MS1 to mgf (fixes issue [#73](https://github.com/lgatto/MSnbase/issues/73) reported by
-        meowcat) <2015-12-18 Fri>
+	meowcat) <2015-12-18 Fri>
 
 ## Changes in version 1.19.6
 
@@ -797,7 +797,7 @@
 
 ## Changes in version 1.15.14
   - new msnset data, used in various examples instead of quantifying
-        the itraqdata experiment over and over again [2015-04-01 Wed]
+	the itraqdata experiment over and over again [2015-04-01 Wed]
 
 ## Changes in version 1.15.13
  - improve nbavg imputation description and add example [2015-03-22 Sun]

diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/news/index.html b/docs/news/index.html
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -1,4 +1,4 @@
-pandoc: 1.19.2.1
+pandoc: 2.3.1
 pkgdown: 1.1.0
 pkgdown_sha: ~
 articles:

diff --git a/docs/reference/MSmap-class.html b/docs/reference/MSmap-class.html
diff --git a/docs/reference/MSnExp-class.html b/docs/reference/MSnExp-class.html
diff --git a/docs/reference/MSnSet-class.html b/docs/reference/MSnSet-class.html
diff --git a/docs/reference/OnDiskMSnExp-class.html b/docs/reference/OnDiskMSnExp-class.html
diff --git a/docs/reference/bin-methods.html b/docs/reference/bin-methods.html
diff --git a/docs/reference/chromatogram-MSnExp-method-1.png b/docs/reference/chromatogram-MSnExp-method-1.png
diff --git a/docs/reference/chromatogram-MSnExp-method-2.png b/docs/reference/chromatogram-MSnExp-method-2.png
diff --git a/docs/reference/clean-methods.html b/docs/reference/clean-methods.html
diff --git a/docs/reference/combineSpectra-1.png b/docs/reference/combineSpectra-1.png
diff --git a/docs/reference/combineSpectraMovingWindow-1.png b/docs/reference/combineSpectraMovingWindow-1.png
diff --git a/docs/reference/estimateMzResolution-1.png b/docs/reference/estimateMzResolution-1.png
diff --git a/docs/reference/estimateMzScattering-1.png b/docs/reference/estimateMzScattering-1.png