Feature/update pwiz 3 0 21263

.github/.gitignore

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

.github/workflows/check-bioc.yml

@@ -0,0 +1,290 @@
+## 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: '3.15', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
+          - { os: macOS-latest, r: 'devel', bioc: '3.15'}
+          - { os: windows-latest, r: 'devel', bioc: '3.15'}
+    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@master
+        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@master
+
+      - 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" >> $GITHUB_ENV
+
+          ## Required to install magick as noted at
+          ## https://github.com/r-lib/usethis/commit/f1f1e0d10c1ebc75fd4c18fa7e2de4551fd9978f#diff-9bfee71065492f63457918efcd912cf2
+          brew install imagemagick@6
+
+          ## For textshaping, required by ragg, and required by pkgdown
+          brew install harfbuzz fribidi
+
+          ## For installing usethis's dependency gert
+          brew install libgit2
+
+          ## required for ncdf4
+          ## brew install netcdf ## Does not work as it is compiled with gcc
+          ## Use pre-compiled libraries from https://mac.r-project.org/libs-4/
+          curl -O https://mac.r-project.org/libs-4/netcdf-4.7.4-darwin.17-x86_64.tar.gz
+          tar fvxzm netcdf-4.7.4-darwin.17-x86_64.tar.gz -C /
+          rm netcdf-4.7.4-darwin.17-x86_64.tar.gz
+          curl -O https://mac.r-project.org/libs-4/hdf5-1.12.0-darwin.17-x86_64.tar.gz
+          tar fvxzm hdf5-1.12.0-darwin.17-x86_64.tar.gz -C /
+          rm hdf5-1.12.0-darwin.17-x86_64.tar.gz
+          curl -O https://mac.r-project.org/libs-4/szip-2.1.1-darwin.17-x86_64.tar.gz
+          tar fvxzm szip-2.1.1-darwin.17-x86_64.tar.gz -C /
+          rm szip-2.1.1-darwin.17-x86_64.tar.gz
+
+      - name: Install Windows system dependencies
+        if: runner.os == 'Windows'
+        run: |
+          ## Edit below if you have any Windows system dependencies
+        shell: Rscript {0}
+
+      - name: Install BiocManager
+        run: |
+          message(paste('****', Sys.time(), 'installing BiocManager ****'))
+          remotes::install_cran("BiocManager")
+        shell: Rscript {0}
+
+      - name: Set BiocVersion
+        run: |
+          BiocManager::install(version = "${{ 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)
+
+          BiocManager::install(c("rmarkdown", "BiocStyle"))
+        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)
+
+          ## For running the checks
+          message(paste('****', Sys.time(), 'installing rcmdcheck and BiocCheck ****'))
+          remotes::install_cran("rcmdcheck")
+          BiocManager::install(c("BiocCheck", "DBI"))
+        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/master' && env.run_covr == 'true' && runner.os == 'Linux'
+        run: |
+          remotes::install_cran("covr")
+        shell: Rscript {0}
+
+      - name: Install pkgdown
+        if: github.ref == 'refs/heads/master' && 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
+          # Avoid application of UCRT
+          # https://developer.r-project.org/WindowsBuilds/winutf8/ucrt3/howto.html
+          _R_INSTALL_TIME_PATCHES_: 'no'
+
+        run: |
+          rcmdcheck::rcmdcheck(
+              args = c("--no-build-vignettes", "--no-manual", "--timings"),
+              build_args = c("--no-manual", "--no-resave-data"),
+              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/master' && env.run_covr == 'true' && runner.os == 'Linux'
+        run: |
+          covr::codecov()
+        shell: Rscript {0}
+
+      - name: Install package
+        if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux'
+        run: R CMD INSTALL .
+
+      - name: Deploy package
+        if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux'
+        run: |
+          git config --local user.email "[email protected]"
+          git config --local user.name "GitHub Actions"
+          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

@@ -2,11 +2,14 @@ Package: mzR
 Type: Package
 Title: parser for netCDF, mzXML, mzData and mzML and mzIdentML files
        (mass spectrometry data)
-Version: 2.29.2
+Version: 2.29.3
 Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou, Johannes Rainer
-Maintainer: Steffen Neumann <[email protected]>,
-            Laurent Gatto <[email protected]>,
-            Qiakng Kou <[email protected]>
+Authors@R: c(
+    person("Steffen", "Neumann", email="[email protected]", role=c("aut","cre")),
+    person("Laurent", "Gatto", email="[email protected]", role=c("aut")),
+    person("Qiakng", "Kou", email="[email protected]", role=c("aut")),
+    person("David","Rauh",email="[email protected]", role=c("ctb"))
+    )
 Description: mzR provides a unified API to the common file formats and
         parsers available for mass spectrometry data. It comes with a
         wrapper for the ISB random access parser for mass spectrometry
@@ -16,12 +19,30 @@ Description: mzR provides a unified API to the common file formats and
         reading code has previously been used in XCMS.
 License: Artistic-2.0
 LazyLoad: yes
-Depends: Rcpp (>= 0.10.1), methods, utils
-Imports: Biobase, BiocGenerics (>= 0.13.6), ProtGenerics (>= 1.17.3), ncdf4
-Suggests: msdata (>= 0.15.1), RUnit, mzID, BiocStyle (>= 2.5.19), knitr, XML, rmarkdown
+Depends:
+    Rcpp (>= 0.10.1),
+    methods,
+    utils
+Imports:
+    Biobase,
+    BiocGenerics (>= 0.13.6),
+    ProtGenerics (>= 1.17.3),
+    ncdf4
+Suggests:
+    msdata (>= 0.15.1),
+    RUnit,
+    mzID,
+    BiocStyle (>= 2.5.19),
+    knitr,
+    XML,
+    rmarkdown
 VignetteBuilder: knitr
-LinkingTo: Rcpp, zlibbioc, Rhdf5lib (>= 1.1.4)
-RcppModules: Ramp, Pwiz, Ident
+LinkingTo:
+    Rcpp,
+    Rhdf5lib (>= 1.1.4)
+RcppModules:
+    Pwiz,
+    Ident
 SystemRequirements: C++11, GNU make
 URL: https://github.com/sneumann/mzR/
 BugReports: https://github.com/sneumann/mzR/issues/

NAMESPACE

@@ -17,7 +17,6 @@ export(openMSfile,
 
 exportMethods(close,
               isInitialized,
-              initializeRamp,
               runInfo,
               fileName,
               instrumentInfo,
@@ -52,7 +51,6 @@ exportMethods(close,
               writeMSData)
 
 exportClasses("mzR",
-              "mzRramp",
               "mzRnetCDF",
               "mzRpwiz",
               "mzRident")

NEWS

@@ -1,3 +1,9 @@
+CHANGES IN VERSION 2.29.3
+-------------------------
+ o Update to Proteowizard 3_0_21263
+ o Removed RAMP backend, dropping ability to read mzData
+ o header always returns a data.frame even for a single scan.
+
 CHANGES IN VERSION 2.29.2
 -------------------------
  o Cleanup in build files 

R/AllGenerics.R

@@ -21,9 +21,6 @@ setGeneric("model", function(object) standardGeneric("model"))
 setGeneric("ionisation", function(object) standardGeneric("ionisation"))
 setGeneric("detector", function(object) standardGeneric("detector"))
 setGeneric("isInitialized", function(object) standardGeneric("isInitialized"))
-setGeneric("initializeRamp",
-           signature = c("object"),
-           function(object) standardGeneric("initializeRamp"))
 setGeneric("header", function(object, scans, ...) standardGeneric("header"))
 setGeneric("peaksCount",
            function(object, scans, ...) standardGeneric("peaksCount"))