Merge pull request #53 from aberHRML/devel

v2.6.0
aberHRML · Sep 29, 2021 · 4238c1b · 4238c1b
2 parents 2181bda + 94ea8bf
commit 4238c1b
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diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -1,13 +1,10 @@
-# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
-# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
+# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches:
-      - master
-      - devel
+    branches: [main, master, devel]
   pull_request:
-    branches:
-      - master
+    branches: [main, master]
   schedule:
     - cron: '0 0 * * *'
 
@@ -23,69 +20,47 @@ jobs:
       fail-fast: false
       matrix:
         config:
+          - {os: macOS-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
-          - {os: macOS-latest, r: 'release'}
-          - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
-          - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
 
     env:
-      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
-      RSPM: ${{ matrix.config.rspm }}
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
 
     steps:
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-r@v1
-        with:
-          r-version: ${{ matrix.config.r }}
-
       - uses: r-lib/actions/setup-pandoc@v1
 
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
-        shell: Rscript {0}
-
-      - name: Cache R packages
-        if: runner.os != 'Windows'
-        uses: actions/cache@v2
+      - uses: r-lib/actions/setup-r@v1
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
-
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+      
       - name: Install system dependencies
         if: runner.os == 'Linux'
         run: |
-          while read -r cmd
-          do
-            eval sudo $cmd
-          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
           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}
+      - uses: r-lib/actions/setup-r-dependencies@v1
+        with:
+          extra-packages: rcmdcheck
 
-      - name: Check
-        env:
-          _R_CHECK_CRAN_INCOMING_REMOTE_: false
-        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
-        shell: Rscript {0}
-
-      - name: Good practice
-        run: goodpractice::goodpractice()
-        shell: Rscript {0}
-
+      - uses: r-lib/actions/check-r-package@v1
+
       - name: Test coverage
         run: covr::codecov()
         shell: Rscript {0}
 
+      - name: Show testthat output
+        if: always()
+        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
       - name: Upload check results
         if: failure()
         uses: actions/upload-artifact@main

diff --git a/.gitignore b/.gitignore
@@ -5,3 +5,5 @@ binneR.Rcheck
 inst/doc
 doc
 Meta
+/doc/
+/Meta/
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: binneR
 Title: Spectral Processing for High Resolution Flow Infusion Mass Spectrometry
-Version: 2.5.3
+Version: 2.6.0
 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
@@ -26,25 +26,13 @@ Imports:
     furrr
 License: GPL-3
 Encoding: UTF-8
-RoxygenNote: 7.1.1
-Collate:
-    allGenerics.R
-    allClasses.R
-    binneRlyse.R
-    binParameters.R
-    spectralBinning-method.R
-    show-method.R
-    get.R
-    calc.R
-    readFiles.R
-    binneR.R
-    plot.R
-    detect.R
-    binMeasures.R
-    singleSample.R
-    readBinningParameters.R
-    reexports.R
-    access.R
+RoxygenNote: 7.1.2
+Collate: allGenerics.R allClasses.R binneRlyse.R
+    binParameters.R spectralBinning-method.R 
+    show-method.R get.R calc.R readFiles.R
+    binneR.R plot.R detect.R binMetrics.R
+    singleSample.R readBinningParameters.R
+    reexports.R access.R internals.R
 Suggests: 
     knitr,
     rmarkdown,
@@ -55,6 +43,4 @@ Suggests:
     covr,
     testthat,
     gifski
-LazyData: true
 VignetteBuilder: knitr
-Remotes: aberHRML/metaboData
diff --git a/NAMESPACE b/NAMESPACE
@@ -98,6 +98,7 @@ importFrom(stats,median)
 importFrom(stringr,regex)
 importFrom(stringr,str_c)
 importFrom(stringr,str_detect)
+importFrom(stringr,str_extract)
 importFrom(stringr,str_remove_all)
 importFrom(stringr,str_replace_all)
 importFrom(stringr,str_sub)
@@ -107,6 +108,7 @@ importFrom(tibble,rowid_to_column)
 importFrom(tibble,tibble)
 importFrom(tidyr,gather)
 importFrom(tidyr,spread)
+importFrom(tools,file_path_sans_ext)
 importFrom(utils,capture.output)
 importFrom(utils,packageVersion)
 importFrom(yaml,read_yaml)
diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,19 @@
+# binneR 2.6.0
+
+* Removed the `LazyData` field from the DESCRIPTION file.
+
+* Replaced the `Remotes` field in the DESCRIPTION file with `Additional_repositories` for the installation of the [`metaboData`](https://aberhrml.github.io/metaboData/) dependency.
+
+* The number of decimal places used for spectral binning can now be specified using the `binner_dp` global option or the `BINNER_DP` environment variable.
+
+* The vignette example now uses the `BdistachyonTechnical` data set from [`metaboData`](https://aberhrml.github.io/metaboData/).
+
+* An in-package example data file is now used for documentation examples.
+
+* The vignette chunks that require the [`metaboData`](https://aberhrml.github.io/metaboData/) package are no longer executed to avoid GitHub API rate limit issues.
+
+* The file header gathering iostream error is now fixed for large data sets (> 1000 samples).
+
 # 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. 
@@ -22,7 +38,7 @@
 
 * `version` and `creation_date` slots added to [`Binalysis`](https://aberhrml.github.io/binneR/reference/Binalysis-class.html) S4 class.
 
-* Added additional accessor [methods](file:///home/jasen/Documents/tools/R-package-dev/binneR/docs/reference/results.html) for the [`Binalysis`](https://aberhrml.github.io/binneR/reference/Binalysis-class.html) S4 class.
+* Added additional accessor [methods](https://aberhrml.github.io/binneR/reference/results.html) for the [`Binalysis`](https://aberhrml.github.io/binneR/reference/Binalysis-class.html) S4 class.
 
 * Fixed declaration of generics to ensure they are declared as standard generics.
 
@@ -57,4 +73,4 @@
 * 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.
+* `plan()` from the [`future`](https://cran.r-project.org/package=future) package is now  re-exported.
diff --git a/R/binMeasures.R → R/binMetrics.R b/R/binMeasures.R → R/binMetrics.R
diff --git a/R/binneRlyse.R b/R/binneRlyse.R
@@ -10,13 +10,18 @@
 #' Parallel processing is managed by the \code{future} package. This can 
 #' be specified using the \code{plan() function}. See the example below 
 #' and \code{?future::plan} for details on how this can be specified.
+#' 
+#' By default, spectral binning is performed at the recommended 2 decimal 
+#' places. This can be altered by setting either the global option 
+#' \code{binner_dp} or the environment variable \code{BINNER_DP}.
+#' 
 #' @seealso \code{\link{Binalysis-class}}, \code{\link{binParameters}}, 
 #' \code{\link{sampleInfo}}, \code{\link{binnedData}},  \code{\link{accurateData}}
 #' @examples 
 #' \dontrun{
-#' files <- metaboData::filePaths('FIE-HRMS','BdistachyonEcotypes')
+#' files <- metaboData::filePaths('FIE-HRMS','BdistachyonTechnical')
 #' 
-#' info <- metaboData::runinfo('FIE-HRMS','BdistachyonEcotypes')
+#' info <- metaboData::runinfo('FIE-HRMS','BdistachyonTechnical')
 #' 
 #' parameters <- detectParameters(files)
 #' cls(parameters) <- 'class'
@@ -27,7 +32,7 @@
 #' analysis <- binneRlyse(files, 
 #'                        info, 
 #'                        parameters = parameters)
-#'    }
+#' }
 #' @importFrom dplyr ungroup n
 #' @importFrom magrittr %>%
 #' @importFrom crayon blue red green

diff --git a/R/calc.R b/R/calc.R
@@ -18,8 +18,12 @@ calcBinMeasures <- function(pks,cls){
                               cls,
                               'polarity',
                               'bin')))) %>%
-    summarise(purity = binPurity(mz,intensity),
-              centrality = binCentrality(mz,intensity),
+    summarise(purity = binPurity(mz,
+                                 intensity,
+                                 dp = binnerDP()),
+              centrality = binCentrality(mz,
+                                         intensity,
+                                         dp = binnerDP()),
               .groups = 'drop')
 
   return(binMeasures)

diff --git a/R/detect.R b/R/detect.R
@@ -6,11 +6,9 @@
 #' @return Numeric vector of detected infusion scans.
 #' @seealso \code{\link{detectParameters}}
 #' @examples 
-#' if (requireNamespace("metaboData", quietly = TRUE)) {
-#'    detectInfusionScans(
-#'       metaboData::filePaths('FIE-HRMS',
-#'                             'BdistachyonEcotypes')[1])
-#' }
+#' file_paths <- system.file('example-data/1.mzML.gz',package = 'binneR')
+#' 
+#' detectInfusionScans(file_paths)
 #' @importFrom mzR openMSfile header
 #' @importFrom dplyr group_by summarise
 #' @export
@@ -70,8 +68,8 @@ detectInfusionScans <- function(files,
 #' @param files character vector of file paths
 #' @return S4 object of class BinParameters
 #' @examples 
-#' files <- metaboData::filePaths('FIE-HRMS','BdistachyonEcotypes')
-#' parameters <- detectParameters(files[1])
+#' file_paths <-system.file('example-data/1.mzML.gz',package = 'binneR')
+#' parameters <- detectParameters(file_paths)
 #' @seealso \code{\link{BinParameters-class}}, \code{\link{binParameters}}
 #' @export