Merge pull request #52 from aberHRML/devel

v2.5.3
aberHRML · Mar 24, 2021 · 2181bda · 2181bda
2 parents 749922e + 259a5c8
commit 2181bda
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diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -63,12 +63,13 @@ jobs:
           do
             eval sudo $cmd
           done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
-          sudo apt install libnetcdf-dev
+          sudo apt install libnetcdf-dev libgit2-dev
 
       - name: Install dependencies
         run: |
           remotes::install_deps(dependencies = TRUE)
           remotes::install_cran(c("rcmdcheck","goodpractice"))
+          metaboData::downloadDataSet('FIE-HRMS','BdistachyonEcotypes',ask = FALSE)
         shell: Rscript {0}
 
       - name: Check

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: binneR
 Title: Spectral Processing for High Resolution Flow Infusion Mass Spectrometry
-Version: 2.5.2
+Version: 2.5.3
 Authors@R: person("Jasen", "Finch", email = "[email protected]", role = c("aut", "cre"))
 Description: A spectral binning approach for high resolution flow infusion mass spectrometry data.
 biocViews: MassSpectrometry, Metabolomics

diff --git a/NEWS.md b/NEWS.md
@@ -1,16 +1,20 @@
-# binneR v2.5.2
+# binneR 2.5.3
+
+* Removed the potential for errors during build of the intensity matrices if identical accurate m/z are retrieved for a bin from multiple samples. 
+
+# binneR 2.5.2
 
 * Fixed I/O issues for sample sets over ~1200.
 
-* Minor alteration to console output
+* Minor alteration to console output.
 
-# binneR v2.5.1
+# binneR 2.5.1
 
 * Performance and memory usage gains through ensuring 0 values are not read from raw files.
 
 * Added console output for processing steps to [`binneR::binneRlyse()`](https://aberhrml.github.io/binneR/reference/binneRlyse.html) and [`binneR::singleSample()](https://aberhrml.github.io/binneR/reference/singleSample.html).
 
-# binneR v2.5.0
+# binneR 2.5.0
 
 * S4 class [`Binalysis`](https://aberhrml.github.io/binneR/reference/Binalysis-class.html) now inherits from S4 class [`BinParameters`](https://aberhrml.github.io/binneR/reference/BinParameters-class.html).
 
@@ -24,15 +28,15 @@
 
 * Added validators for [`Binalysis`](https://aberhrml.github.io/binneR/reference/Binalysis-class.html) S4 class to ensure that sample information contains the correct fields and that the file names in the specified paths match those in the sample information.
 
-# binneR v2.4.2
+# binneR 2.4.2
 
 * Bin measures are now correctly averaged across samples in [`binneR::plotCentrality()`](https://aberHRML.github.io/binneR/reference/plotCentrality.html) and [`binneR::plotPurity()`](https://aberHRML.github.io/binneR/reference/plotPurity.html).
 
-# binneR v2.4.1
+# binneR 2.4.1
 
 * Fixed errors in [`binneR::plotCentrality()`](https://aberHRML.github.io/binneR/reference/plotCentrality.html) and [`binneR::plotPurity()`](https://aberHRML.github.io/binneR/reference/plotPurity.html).
 
-# binneR v2.4.0
+# binneR 2.4.0
 
 * Added a [`NEWS.md`](https://aberHRML.github.io/binneR/news/index.html) file to track changes to the package.
 
@@ -50,7 +54,7 @@
 
 * Updated function documentation examples.
 
-* Parallel processing in `binneR` is now implemented using the [`future`](https://cran.r-project.org/web/packages/future/index.html) package.
+* Parallel processing in `binneR` is now implemented using the [`future`](https://cran.r-project.org/package=future) package.
 Information on how this can now be used is available in the usage vignette.
 
 * `plan()` from the [`future`](https://cran.r-project.org/web/packages/future/index.html) package is now  re-exported.
diff --git a/R/spectralBinning-method.R b/R/spectralBinning-method.R
@@ -83,7 +83,8 @@ setMethod("spectralBinning",
 							filter(intensity == max(intensity)) %>%
 							select(-intensity) %>%
 							mutate(mz = str_c(polarity,mz)) %>%
-							ungroup()
+							ungroup() %>% 
+							distinct()
 
 						if (isTRUE(verbose)) message('Building intensity matrix')
 						binned_data <- binned_data %>%

diff --git a/docs/404.html b/docs/404.html
diff --git a/docs/LICENSE.html b/docs/LICENSE.html
diff --git a/docs/articles/binneR.html b/docs/articles/binneR.html
diff --git a/docs/articles/binneR_files/figure-html/FIEfingerprint-.gif b/docs/articles/binneR_files/figure-html/FIEfingerprint-.gif
diff --git a/docs/articles/index.html b/docs/articles/index.html
diff --git a/docs/authors.html b/docs/authors.html
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
@@ -3,5 +3,5 @@ pkgdown: 1.6.1
 pkgdown_sha: ~
 articles:
   binneR: binneR.html
-last_built: 2021-03-06T01:01Z
+last_built: 2021-03-24T15:42Z
 
diff --git a/docs/reference/BinParameters-class.html b/docs/reference/BinParameters-class.html
diff --git a/docs/reference/Binalysis-class.html b/docs/reference/Binalysis-class.html
diff --git a/docs/reference/binParameters.html b/docs/reference/binParameters.html
diff --git a/docs/reference/binneRlyse.html b/docs/reference/binneRlyse.html
diff --git a/docs/reference/detectInfusionScans.html b/docs/reference/detectInfusionScans.html
diff --git a/docs/reference/detectParameters.html b/docs/reference/detectParameters.html
diff --git a/docs/reference/index.html b/docs/reference/index.html
diff --git a/docs/reference/parameters.html b/docs/reference/parameters.html
diff --git a/docs/reference/plotBin.html b/docs/reference/plotBin.html
diff --git a/docs/reference/plotCentrality.html b/docs/reference/plotCentrality.html
diff --git a/docs/reference/plotChromFromFile.html b/docs/reference/plotChromFromFile.html
diff --git a/docs/reference/plotChromatogram.html b/docs/reference/plotChromatogram.html
diff --git a/docs/reference/plotFingerprint.html b/docs/reference/plotFingerprint.html
diff --git a/docs/reference/plotPurity.html b/docs/reference/plotPurity.html
diff --git a/docs/reference/plotTIC.html b/docs/reference/plotTIC.html
diff --git a/docs/reference/readBinningParameters.html b/docs/reference/readBinningParameters.html