diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 580aec0..3345a45 100644 --- 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 index e3ebcfe..882cfbb 100644 --- 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 = "jsf9@aber.ac.uk", 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 index 93f09cd..739276e 100644 --- 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 index 758affa..c1d9f8a 100644 --- 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 index bf4f208..ee151c8 100644 --- a/docs/404.html +++ b/docs/404.html @@ -71,7 +71,7 @@ binneR - 2.5.2 + 2.5.3 diff --git a/docs/LICENSE.html b/docs/LICENSE.html index 470260c..0612f6a 100644 --- a/docs/LICENSE.html +++ b/docs/LICENSE.html @@ -71,7 +71,7 @@ binneR - 2.5.2 + 2.5.3 diff --git a/docs/articles/binneR.html b/docs/articles/binneR.html index d929464..160e30c 100644 --- a/docs/articles/binneR.html +++ b/docs/articles/binneR.html @@ -31,7 +31,7 @@ binneR - 2.5.2 + 2.5.3 @@ -232,7 +232,7 @@

Spectral binning can then be performed with the following.

 analysis <- binneRlyse(files,info,parameters)
-
## binneR v2.5.2 Sat Mar  6 01:02:44 2021
+
## binneR v2.5.3 Wed Mar 24 15:43:53 2021
## ________________________________________________________________________________
## Scans: 5:13 
 ## Class: class
@@ -246,10 +246,10 @@ 

## Building intensity matrix
## Gathering file headers
##
-
## Completed! [1M 1.7S]
+
## Completed! [1M 11.2S]
## 
-## binneR v2.5.2
-## Sat Mar  6 01:02:44 2021
+## binneR v2.5.3
+## Wed Mar 24 15:43:53 2021
 ## Samples: 68
 ## n: 7828 features
 ## p: 9406 features
diff --git a/docs/articles/binneR_files/figure-html/FIEfingerprint-.gif b/docs/articles/binneR_files/figure-html/FIEfingerprint-.gif
index 15d25ff..2f0da89 100644
Binary files a/docs/articles/binneR_files/figure-html/FIEfingerprint-.gif and b/docs/articles/binneR_files/figure-html/FIEfingerprint-.gif differ
diff --git a/docs/articles/index.html b/docs/articles/index.html
index 674e04c..137544d 100644
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -71,7 +71,7 @@
       
       
         binneR
-        2.5.2
+        2.5.3
       
     
 
diff --git a/docs/authors.html b/docs/authors.html
index fa9d7da..1e52267 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -71,7 +71,7 @@
       
       
         binneR
-        2.5.2
+        2.5.3
       
     
 
diff --git a/docs/index.html b/docs/index.html
index 46d42a1..4f15e8a 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -31,7 +31,7 @@
       
       
         binneR
-        2.5.2
+        2.5.3
       
     
 
diff --git a/docs/news/index.html b/docs/news/index.html
index 0e46387..2897839 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -71,7 +71,7 @@
       
       
         binneR
-        2.5.2
+        2.5.3
       
     
 
@@ -117,27 +117,35 @@ 
Changelog 

       Source: NEWS.md
     
 
-    

+    

+

+binneR 2.5.3 Unreleased 
+

+
    
+
  • 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 v2.5.2 Unreleased 
+binneR 2.5.2 Unreleased 
 

 
    
 
  • Fixed I/O issues for sample sets over ~1200.
    • 
-
  • Minor alteration to console output
    • 
+
  • Minor alteration to console output.
    • 
 

 

-    

+    

 

-binneR v2.5.1 Unreleased 
+binneR 2.5.1 Unreleased 
 

 
 

-    

+    

 

-binneR v2.5.0 Unreleased 
+binneR 2.5.0 Unreleased 
 

 
    
 
  • S4 class Binalysis now inherits from S4 class BinParameters.
    • 
@@ -148,25 +156,25 @@ 
    
 
  • Added validators for Binalysis 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 Unreleased 
+binneR 2.4.2 Unreleased 
 

 
 

-    

+    

 

-binneR v2.4.1 Unreleased 
+binneR 2.4.1 Unreleased 
 

 
 

-    

+    

 

-binneR v2.4.0 Unreleased 
+binneR 2.4.0 Unreleased 
 

 
    
 
  • Added a NEWS.md file to track changes to the package.
    • 
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index cacb0ab..e4c2cfd 100644
--- 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
index 33b0d8d..75aada8 100644
--- a/docs/reference/BinParameters-class.html
+++ b/docs/reference/BinParameters-class.html
@@ -72,7 +72,7 @@
       
       
         binneR
-        2.5.2
+        2.5.3
       
     

 
diff --git a/docs/reference/Binalysis-class.html b/docs/reference/Binalysis-class.html
index f8a734d..f483430 100644
--- a/docs/reference/Binalysis-class.html
+++ b/docs/reference/Binalysis-class.html
@@ -73,7 +73,7 @@
       
       
         binneR
-        2.5.2
+        2.5.3
       
     

 
diff --git a/docs/reference/binParameters.html b/docs/reference/binParameters.html
index 32ed3ac..9a858d7 100644
--- a/docs/reference/binParameters.html
+++ b/docs/reference/binParameters.html
@@ -72,7 +72,7 @@
       
       
         binneR
-        2.5.2
+        2.5.3
       
     

 
diff --git a/docs/reference/binneRlyse.html b/docs/reference/binneRlyse.html
index 9aa92ad..3417ae5 100644
--- a/docs/reference/binneRlyse.html
+++ b/docs/reference/binneRlyse.html
@@ -72,7 +72,7 @@
       
       
         binneR
-        2.5.2
+        2.5.3
       
     

 
diff --git a/docs/reference/detectInfusionScans.html b/docs/reference/detectInfusionScans.html
index c39828b..f199417 100644
--- a/docs/reference/detectInfusionScans.html
+++ b/docs/reference/detectInfusionScans.html
@@ -72,7 +72,7 @@
       
       
         binneR
-        2.5.2
+        2.5.3
       
     

 
diff --git a/docs/reference/detectParameters.html b/docs/reference/detectParameters.html
index b99dbf0..af96740 100644
--- a/docs/reference/detectParameters.html
+++ b/docs/reference/detectParameters.html
@@ -72,7 +72,7 @@
       
       
         binneR
-        2.5.2
+        2.5.3
       
     

 
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 768f39c..08fb989 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -71,7 +71,7 @@
       
       
         binneR
-        2.5.2
+        2.5.3
       
     

 
diff --git a/docs/reference/parameters.html b/docs/reference/parameters.html
index 6fe230e..cbd3f45 100644
--- a/docs/reference/parameters.html
+++ b/docs/reference/parameters.html
@@ -72,7 +72,7 @@
       
       
         binneR
-        2.5.2
+        2.5.3
       
     
 
diff --git a/docs/reference/plotBin.html b/docs/reference/plotBin.html
index afb0b33..a2d925b 100644
--- a/docs/reference/plotBin.html
+++ b/docs/reference/plotBin.html
@@ -72,7 +72,7 @@
       
       
         binneR
-        2.5.2
+        2.5.3
       
     
 
diff --git a/docs/reference/plotCentrality.html b/docs/reference/plotCentrality.html
index c2fe81a..4a5082b 100644
--- a/docs/reference/plotCentrality.html
+++ b/docs/reference/plotCentrality.html
@@ -72,7 +72,7 @@
       
       
         binneR
-        2.5.2
+        2.5.3
       
     
 
diff --git a/docs/reference/plotChromFromFile.html b/docs/reference/plotChromFromFile.html
index 003bbf4..204b45c 100644
--- a/docs/reference/plotChromFromFile.html
+++ b/docs/reference/plotChromFromFile.html
@@ -73,7 +73,7 @@
       
       
         binneR
-        2.5.2
+        2.5.3
       
     
 
diff --git a/docs/reference/plotChromatogram.html b/docs/reference/plotChromatogram.html
index 1b5bea6..ae1c781 100644
--- a/docs/reference/plotChromatogram.html
+++ b/docs/reference/plotChromatogram.html
@@ -73,7 +73,7 @@
       
       
         binneR
-        2.5.2
+        2.5.3
       
     
 
diff --git a/docs/reference/plotFingerprint.html b/docs/reference/plotFingerprint.html
index e7803e0..3cb41ca 100644
--- a/docs/reference/plotFingerprint.html
+++ b/docs/reference/plotFingerprint.html
@@ -72,7 +72,7 @@
       
       
         binneR
-        2.5.2
+        2.5.3
       
     
 
diff --git a/docs/reference/plotPurity.html b/docs/reference/plotPurity.html
index 46b1ff3..675a972 100644
--- a/docs/reference/plotPurity.html
+++ b/docs/reference/plotPurity.html
@@ -72,7 +72,7 @@
       
       
         binneR
-        2.5.2
+        2.5.3
       
     
 
diff --git a/docs/reference/plotTIC.html b/docs/reference/plotTIC.html
index e81f5b1..0824b7b 100644
--- a/docs/reference/plotTIC.html
+++ b/docs/reference/plotTIC.html
@@ -72,7 +72,7 @@
       
       
         binneR
-        2.5.2
+        2.5.3
       
     
 
diff --git a/docs/reference/readBinningParameters.html b/docs/reference/readBinningParameters.html
index 20ba21e..a3e7b3b 100644
--- a/docs/reference/readBinningParameters.html
+++ b/docs/reference/readBinningParameters.html
@@ -72,7 +72,7 @@
       
       
         binneR
-        2.5.2
+        2.5.3
       
     
 
diff --git a/docs/reference/readFiles.html b/docs/reference/readFiles.html
index d1ad952..7c20d87 100644
--- a/docs/reference/readFiles.html
+++ b/docs/reference/readFiles.html
@@ -72,7 +72,7 @@
       
       
         binneR
-        2.5.2
+        2.5.3
       
     
 
diff --git a/docs/reference/reexports.html b/docs/reference/reexports.html
index 15dc3ea..c84618e 100644
--- a/docs/reference/reexports.html
+++ b/docs/reference/reexports.html
@@ -79,7 +79,7 @@
       
       
         binneR
-        2.5.2
+        2.5.3
       
     
 
diff --git a/docs/reference/results.html b/docs/reference/results.html
index e194ca6..34e7f1a 100644
--- a/docs/reference/results.html
+++ b/docs/reference/results.html
@@ -72,7 +72,7 @@
       
       
         binneR
-        2.5.2
+        2.5.3
       
     
 
diff --git a/docs/reference/show.html b/docs/reference/show.html
index 3779633..3fda837 100644
--- a/docs/reference/show.html
+++ b/docs/reference/show.html
@@ -72,7 +72,7 @@
       
       
         binneR
-        2.5.2
+        2.5.3
       
     
 
diff --git a/docs/reference/singleSample.html b/docs/reference/singleSample.html
index 2cdf1c8..92a01eb 100644
--- a/docs/reference/singleSample.html
+++ b/docs/reference/singleSample.html
@@ -72,7 +72,7 @@
       
       
         binneR
-        2.5.2
+        2.5.3
       
     
 
@@ -161,7 +161,7 @@ 
Examp
 # plan(future::multisession,workers = 2)
 
 bd <- singleSample(file_path)
-
#> binneR v2.5.2 Sat Mar  6 01:01:39 2021
#> ________________________________________________________________________________
#> Scans: 5:13 
#> ________________________________________________________________________________
#> Reading raw data
#> Calculating bins
#> Removing single scan events
#> Calculating intensity totals
#> Calculating bin measures
#> Calculating accurate m/z
#> Building intensity matrix
#> 
#> Completed! [1.8S]
+
#> binneR v2.5.3 Wed Mar 24 15:42:44 2021
#> ________________________________________________________________________________
#> Scans: 5:13
#> ________________________________________________________________________________
#> Reading raw data
#> Calculating bins
#> Removing single scan events
#> Calculating intensity totals
#> Calculating bin measures
#> Calculating accurate m/z
#> Building intensity matrix
#>
#> Completed! [2S]