Suggested updates and fixes for PlainTextParam

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.github/workflows/check-bioc.yml

@@ -0,0 +1,292 @@
+## Read more about GitHub actions the features of this GitHub Actions workflow
+## at https://lcolladotor.github.io/biocthis/articles/biocthis.html#use_bioc_github_action
+##
+## For more details, check the biocthis developer notes vignette at
+## https://lcolladotor.github.io/biocthis/articles/biocthis_dev_notes.html
+##
+## You can add this workflow to other packages using:
+## > biocthis::use_bioc_github_action()
+##
+## Using GitHub Actions exposes you to many details about how R packages are
+## compiled and installed in several operating system.s
+### If you need help, please follow the steps listed at
+## https://github.com/r-lib/actions#where-to-find-help
+##
+## If you found an issue specific to biocthis's GHA workflow, please report it
+## with the information that will make it easier for others to help you.
+## Thank you!
+
+## Acronyms:
+## * GHA: GitHub Action
+## * OS: operating system
+
+on:
+  push:
+  pull_request:
+
+name: R-CMD-check-bioc
+
+## These environment variables control whether to run GHA code later on that is
+## specific to testthat, covr, and pkgdown.
+##
+## If you need to clear the cache of packages, update the number inside
+## cache-version as discussed at https://github.com/r-lib/actions/issues/86.
+## Note that you can always run a GHA test without the cache by using the word
+## "/nocache" in the commit message.
+env:
+  has_testthat: 'true'
+  run_covr: 'true'
+  run_pkgdown: 'true'
+  has_RUnit: 'false'
+  has_BiocCheck: 'false'
+  cache-version: 'cache-v1'
+
+jobs:
+  build-check:
+    runs-on: ${{ matrix.config.os }}
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+    container: ${{ matrix.config.cont }}
+    ## Environment variables unique to this job.
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - { os: ubuntu-latest, r: 'devel', bioc: 'devel', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
+          - { os: macOS-latest, r: 'devel', bioc: '3.20'}
+          - { os: windows-latest, r: 'devel', bioc: '3.20'}
+    env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      RSPM: ${{ matrix.config.rspm }}
+      NOT_CRAN: true
+      TZ: UTC
+      GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+
+      ## Set the R library to the directory matching the
+      ## R packages cache step further below when running on Docker (Linux).
+      - name: Set R Library home on Linux
+        if: runner.os == 'Linux'
+        run: |
+          mkdir /__w/_temp/Library
+          echo ".libPaths('/__w/_temp/Library')" > ~/.Rprofile
+
+      ## Most of these steps are the same as the ones in
+      ## https://github.com/r-lib/actions/blob/master/examples/check-standard.yaml
+      ## If they update their steps, we will also need to update ours.
+      - name: Checkout Repository
+        uses: actions/checkout@v2
+
+      ## R is already included in the Bioconductor docker images
+      - name: Setup R from r-lib
+        if: runner.os != 'Linux'
+        uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+
+      ## pandoc is already included in the Bioconductor docker images
+      - name: Setup pandoc from r-lib
+        if: runner.os != 'Linux'
+        uses: r-lib/actions/setup-pandoc@v2
+
+      - name: Query dependencies
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+        shell: Rscript {0}
+
+      - name: Cache R packages
+        if: "!contains(github.event.head_commit.message, '/nocache') && runner.os != 'Linux'"
+        uses: actions/cache@v2
+        with:
+          path: ${{ env.R_LIBS_USER }}
+          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-devel-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-devel-
+
+      - name: Cache R packages on Linux
+        if: "!contains(github.event.head_commit.message, '/nocache') && runner.os == 'Linux' "
+        uses: actions/cache@v2
+        with:
+          path: /home/runner/work/_temp/Library
+          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-devel-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-devel-
+
+      - name: Install Linux system dependencies
+        if: runner.os == 'Linux'
+        run: |
+          sysreqs=$(Rscript -e 'cat("apt-get update -y && apt-get install -y", paste(gsub("apt-get install -y ", "", remotes::system_requirements("ubuntu", "20.04")), collapse = " "))')
+          echo $sysreqs
+          sudo -s eval "$sysreqs"
+
+      - name: Install macOS system dependencies
+        if: matrix.config.os == 'macOS-latest'
+        run: |
+          ## Enable installing XML from source if needed
+          brew install libxml2
+          echo "XML_CONFIG=/usr/local/opt/libxml2/bin/xml2-config" >> $GITHUB_ENV
+
+          ## Required to install magick as noted at
+          ## https://github.com/r-lib/usethis/commit/f1f1e0d10c1ebc75fd4c18fa7e2de4551fd9978f#diff-9bfee71065492f63457918efcd912cf2
+          brew install imagemagick@6
+
+          ## For textshaping, required by ragg, and required by pkgdown
+          brew install harfbuzz fribidi
+
+          ## For installing usethis's dependency gert
+          brew install libgit2
+
+          ## required for ncdf4 - can not use the homebrew one because that uses GCC
+          ## Use pre-compiled libraries from https://mac.r-project.org/libs-4/
+          curl -O https://mac.r-project.org/libs-4/netcdf-4.7.4-darwin.17-x86_64.tar.gz
+          tar fvxzm netcdf-4.7.4-darwin.17-x86_64.tar.gz -C /
+          rm netcdf-4.7.4-darwin.17-x86_64.tar.gz
+          curl -O https://mac.r-project.org/libs-4/hdf5-1.12.0-darwin.17-x86_64.tar.gz
+          tar fvxzm hdf5-1.12.0-darwin.17-x86_64.tar.gz -C /
+          rm hdf5-1.12.0-darwin.17-x86_64.tar.gz
+          curl -O https://mac.r-project.org/libs-4/szip-2.1.1-darwin.17-x86_64.tar.gz
+          tar fvxzm szip-2.1.1-darwin.17-x86_64.tar.gz -C /
+          rm szip-2.1.1-darwin.17-x86_64.tar.gz
+
+      - name: Install Windows system dependencies
+        if: runner.os == 'Windows'
+        run: |
+          ## Edit below if you have any Windows system dependencies
+        shell: Rscript {0}
+
+      - name: Install BiocManager
+        run: |
+          message(paste('****', Sys.time(), 'installing BiocManager ****'))
+          remotes::install_cran("BiocManager")
+        shell: Rscript {0}
+
+      - name: Set BiocVersion
+        run: |
+          BiocManager::install(version = "${{ matrix.config.bioc }}", ask = FALSE)
+        shell: Rscript {0}
+
+      - name: Install dependencies pass 1
+        run: |
+          ## Try installing the package dependencies in steps. First the local
+          ## dependencies, then any remaining dependencies to avoid the
+          ## issues described at
+          ## https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016675.html
+          ## https://github.com/r-lib/remotes/issues/296
+          ## Ideally, all dependencies should get installed in the first pass.
+
+          ## Pass #1 at installing dependencies
+          message(paste('****', Sys.time(), 'pass number 1 at installing dependencies: local dependencies ****'))
+          remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = FALSE, upgrade = TRUE)
+        continue-on-error: true
+        shell: Rscript {0}
+
+      - name: Install dependencies pass 2
+        run: |
+          ## Pass #2 at installing dependencies
+          message(paste('****', Sys.time(), 'pass number 2 at installing dependencies: any remaining dependencies ****'))
+          remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = FALSE, upgrade = TRUE)
+
+          ## Manually install required packages
+          BiocManager::install('rhdf5', dependencies = TRUE, ask = FALSE, update = FALSE, INSTALL_opts = '--force-biarch')
+          BiocManager::install("mzR", dependencies = TRUE, ask = FALSE, update = FALSE)
+          BiocManager::install("msdata")
+
+          message(paste('****', Sys.time(), 'force installation of selected packages ****'))
+          BiocManager::install(c("BiocStyle", "rmarkdown", "magick", "Spectra"))
+
+          ## For running the checks
+          message(paste('****', Sys.time(), 'installing rcmdcheck and BiocCheck ****'))
+          remotes::install_cran("rcmdcheck")
+          BiocManager::install("BiocCheck")
+        shell: Rscript {0}
+
+      - name: Install BiocGenerics
+        if:  env.has_RUnit == 'true'
+        run: |
+          ## Install BiocGenerics
+          BiocManager::install("BiocGenerics")
+        shell: Rscript {0}
+
+      - name: Install covr
+        if: github.ref == 'refs/heads/main' && env.run_covr == 'true' && runner.os == 'Linux'
+        run: |
+          remotes::install_cran("covr")
+        shell: Rscript {0}
+
+      - name: Install pkgdown
+        if: github.ref == 'refs/heads/main' && env.run_pkgdown == 'true' && runner.os == 'Linux'
+        run: |
+          remotes::install_github("r-lib/pkgdown")
+        shell: Rscript {0}
+
+      - name: Session info
+        run: |
+          options(width = 100)
+          pkgs <- installed.packages()[, "Package"]
+          sessioninfo::session_info(pkgs, include_base = TRUE)
+        shell: Rscript {0}
+
+      - name: Run CMD check
+        env:
+          _R_CHECK_CRAN_INCOMING_: false
+        run: |
+          rcmdcheck::rcmdcheck(
+              args = c("--no-build-vignettes", "--no-manual", "--timings"),
+              build_args = c("--no-manual", "--no-resave-data"),
+              error_on = "warning",
+              check_dir = "check"
+          )
+        shell: Rscript {0}
+
+      ## Might need an to add this to the if:  && runner.os == 'Linux'
+      - name: Reveal testthat details
+        if:  env.has_testthat == 'true'
+        run: find . -name testthat.Rout -exec cat '{}' ';'
+
+      - name: Run RUnit tests
+        if:  env.has_RUnit == 'true'
+        run: |
+          BiocGenerics:::testPackage()
+        shell: Rscript {0}
+
+      - name: Run BiocCheck
+        if:  env.has_BiocCheck == 'true'
+        run: |
+          BiocCheck::BiocCheck(
+              dir('check', 'tar.gz$', full.names = TRUE),
+              `quit-with-status` = TRUE,
+              `no-check-R-ver` = TRUE,
+              `no-check-bioc-help` = TRUE
+          )
+        shell: Rscript {0}
+
+      - name: Test coverage
+        if: github.ref == 'refs/heads/main' && env.run_covr == 'true' && runner.os == 'Linux'
+        run: |
+          covr::codecov()
+        shell: Rscript {0}
+
+      - name: Install package
+        if: github.ref == 'refs/heads/main' && env.run_pkgdown == 'true' && runner.os == 'Linux'
+        run: R CMD INSTALL .
+
+      - name: Deploy package
+        if: github.ref == 'refs/heads/main' && env.run_pkgdown == 'true' && runner.os == 'Linux'
+        run: |
+          git config --global user.email "[email protected]"
+          git config --global user.name "GitHub Actions"
+          git config --global --add safe.directory /__w/MsIO/MsIO
+          Rscript -e "pkgdown::deploy_to_branch(new_process = FALSE)"
+        shell: bash {0}
+        ## Note that you need to run pkgdown::deploy_to_branch(new_process = FALSE)
+        ## at least one locally before this will work. This creates the gh-pages
+        ## branch (erasing anything you haven't version controlled!) and
+        ## makes the git history recognizable by pkgdown.
+
+      - name: Upload check results
+        if: failure()
+        uses: actions/upload-artifact@master
+        with:
+          name: ${{ runner.os }}-biocversion-devel-r-devel-results
+          path: check

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: MsIO
 Title: Serializing and restoring/importing mass spectrometry data objects
-Version: 0.0.1
+Version: 0.0.2
 Authors@R:
     c(person(given = "Johannes", family = "Rainer",
              email = "[email protected]",
@@ -38,7 +38,7 @@ Suggests:
     rmarkdown,
     roxygen2,
     Spectra,
-    testthat, 
+    testthat,
     xcms
 License: Artistic-2.0
 Encoding: UTF-8
@@ -48,7 +48,7 @@ URL: https://github.com/RforMassSpectrometry/MsIO
 biocViews: Infrastructure, MassSpectrometry, Metabolomics, DataImport, Proteomics
 Roxygen: list(markdown=TRUE)
 RoxygenNote: 7.3.2
-Collate: 
+Collate:
     'AllGenerics.R'
     'MsBackend.R'
     'PlainTextParam.R'

NAMESPACE

@@ -17,8 +17,10 @@ importFrom(jsonlite,write_json)
 importFrom(methods,as)
 importFrom(methods,callNextMethod)
 importFrom(methods,existsMethod)
+importFrom(methods,getFunction)
 importFrom(methods,new)
 importFrom(methods,validObject)
 importFrom(stats,setNames)
 importFrom(utils,read.table)
 importFrom(utils,write.table)
+importMethodsFrom(S4Vectors,"mcols<-")

NEWS.md

@@ -0,0 +1,5 @@
+# Version 0.0
+
+## Changes in 0.0.2
+
+- Refactor code for text-based import and export of MS data objects.

R/MsBackendMzR.R

@@ -24,27 +24,28 @@ setMethod("saveMsObject", signature(object = "MsBackendMzR",
                          recursive = TRUE,
                          showWarnings = FALSE)
               object <-  Spectra::dropNaSpectraVariables(object)
-              fl <- file.path(param@path, "backend_data.txt")
+              fl <- file.path(param@path, "ms_backend_data.txt")
               if (file.exists(fl))
-                  warning("Overwriting already present 'backend_data.txt' file")
+                  warning("Overwriting already present ",
+                          "'ms_backend_data.txt' file")
               writeLines(paste0("# ", class(object)[1L]), con = fl)
               if (nrow(object@spectraData))
                   suppressWarnings(
                       write.table(object@spectraData,
                                   file = fl, sep = "\t", quote = TRUE,
-                                  append = TRUE, row.names = FALSE))
+                                  append = TRUE))
           })
 
 #' @rdname PlainTextParam
 setMethod("readMsObject", signature(object = "MsBackendMzR",
                                    param = "PlainTextParam"),
           function(object, param, spectraPath = character()) {
-              fl <- file.path(param@path, "backend_data.txt")
+              fl <- file.path(param@path, "ms_backend_data.txt")
               if (!file.exists(fl))
                   stop("No 'backend_data.txt' file found in the provided path.")
               l2 <- readLines(fl, n = 2)
               if (l2[1] != "# MsBackendMzR")
-                  stop("Invalid class in 'backend_data.txt' file.",
+                  stop("Invalid class in 'ms_backend_data.txt' file.",
                   "Should run with object = ", l2[1])
               if (length(l2) > 1L) {
                   data <- read.table(file = fl, sep = "\t", header = TRUE)
@@ -53,8 +54,8 @@ setMethod("readMsObject", signature(object = "MsBackendMzR",
                   if (length(spectraPath) > 0) {
                       old <- common_path(dataStorage(object))
                       dataStoragePaths <- dataStorage(object)
-                      normalizedDataStoragePaths <- normalizePath(dataStoragePaths,
-                                                                  winslash = "/")
+                      normalizedDataStoragePaths <- normalizePath(
+                          dataStoragePaths, winslash = "/", mustWork = FALSE)
                       dataStorage(object) <- sub(old, spectraPath,
                                                  normalizedDataStoragePaths)
                   }