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‎.github/workflows/rhub.yaml

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# R-hub's generic GitHub Actions workflow file. It's canonical location is at
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# https://github.com/r-hub/actions/blob/v1/workflows/rhub.yaml
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# You can update this file to a newer version using the rhub2 package:
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#
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# rhub::rhub_setup()
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#
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# It is unlikely that you need to modify this file manually.
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name: R-hub
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run-name: "${{ github.event.inputs.id }}: ${{ github.event.inputs.name || format('Manually run by {0}', github.triggering_actor) }}"
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on:
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workflow_dispatch:
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inputs:
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config:
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description: 'A comma separated list of R-hub platforms to use.'
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type: string
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default: 'linux,windows,macos'
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name:
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description: 'Run name. You can leave this empty now.'
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type: string
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id:
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description: 'Unique ID. You can leave this empty now.'
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type: string
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jobs:
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setup:
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runs-on: ubuntu-latest
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outputs:
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containers: ${{ steps.rhub-setup.outputs.containers }}
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platforms: ${{ steps.rhub-setup.outputs.platforms }}
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steps:
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# NO NEED TO CHECKOUT HERE
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- uses: r-hub/actions/setup@v1
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with:
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config: ${{ github.event.inputs.config }}
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id: rhub-setup
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linux-containers:
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needs: setup
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if: ${{ needs.setup.outputs.containers != '[]' }}
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runs-on: ubuntu-latest
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name: ${{ matrix.config.label }}
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strategy:
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fail-fast: false
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matrix:
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config: ${{ fromJson(needs.setup.outputs.containers) }}
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container:
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image: ${{ matrix.config.container }}
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steps:
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- uses: r-hub/actions/checkout@v1
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- uses: r-hub/actions/platform-info@v1
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with:
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token: ${{ secrets.RHUB_TOKEN }}
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job-config: ${{ matrix.config.job-config }}
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- uses: r-hub/actions/setup-deps@v1
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with:
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token: ${{ secrets.RHUB_TOKEN }}
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job-config: ${{ matrix.config.job-config }}
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- uses: r-hub/actions/run-check@v1
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with:
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token: ${{ secrets.RHUB_TOKEN }}
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job-config: ${{ matrix.config.job-config }}
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other-platforms:
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needs: setup
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if: ${{ needs.setup.outputs.platforms != '[]' }}
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runs-on: ${{ matrix.config.os }}
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name: ${{ matrix.config.label }}
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strategy:
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fail-fast: false
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matrix:
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config: ${{ fromJson(needs.setup.outputs.platforms) }}
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steps:
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- uses: r-hub/actions/checkout@v1
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- uses: r-hub/actions/setup-r@v1
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with:
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job-config: ${{ matrix.config.job-config }}
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token: ${{ secrets.RHUB_TOKEN }}
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- uses: r-hub/actions/platform-info@v1
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with:
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token: ${{ secrets.RHUB_TOKEN }}
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job-config: ${{ matrix.config.job-config }}
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- uses: r-hub/actions/setup-deps@v1
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with:
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job-config: ${{ matrix.config.job-config }}
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token: ${{ secrets.RHUB_TOKEN }}
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- uses: r-hub/actions/run-check@v1
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with:
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job-config: ${{ matrix.config.job-config }}
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token: ${{ secrets.RHUB_TOKEN }}

‎DESCRIPTION

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Package: chromConverter
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Title: Chromatographic File Converter
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Version: 0.6.0
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Version: 0.6.4
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Authors@R: c(
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person(given = "Ethan", family = "Bass", email = "ethanbass@gmail.com",
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role = c("aut", "cre"),
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for parsing 'Agilent' UV files."))
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)
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Maintainer: Ethan Bass <ethanbass@gmail.com>
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Description: Reads chromatograms from binary formats into R objects. Currently supports conversion of 'Agilent ChemStation', 'Agilent MassHunter', and 'ThermoRaw' files as well as various text-based formats. Utilizes file parsers from external libraries, such as 'Aston' <https://github.com/bovee/aston>, 'Entab' <https://github.com/bovee/entab>, 'rainbow' <https://rainbow-api.readthedocs.io/>, and 'ThermoRawFileParser' <https://github.com/compomics/ThermoRawFileParser>.
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Description: Reads chromatograms from binary formats into R objects. Currently supports conversion of 'Agilent ChemStation', 'Agilent MassHunter', 'Shimadzu LabSolutions', 'ThermoRaw' files as well as various text-based formats. Utilizes file parsers from external libraries, such as 'Aston' <https://github.com/bovee/aston>, 'Entab' <https://github.com/bovee/entab>, 'rainbow' <https://rainbow-api.readthedocs.io/>, and 'ThermoRawFileParser' <https://github.com/compomics/ThermoRawFileParser>.
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License: GPL (>= 3)
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URL: https://ethanbass.github.io/chromConverter, https://github.com/ethanbass/chromConverter
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BugReports: https://github.com/ethanbass/chromConverter/issues
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magrittr,
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RaMS,
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tibble,
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xml2
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xml2,
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bit64
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Suggests:
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entab,
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ncdf4,
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Encoding: UTF-8
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Language: en-US
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Roxygen: list(markdown = TRUE)
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RoxygenNote: 7.2.3
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RoxygenNote: 7.3.0
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Additional_repositories: https://ethanbass.github.io/drat/
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Config/testthat/edition: 3

‎NAMESPACE

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export(read_mzml)
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export(read_peaklist)
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export(read_shimadzu)
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export(read_shimadzu_gcd)
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export(read_shimadzu_lcd)
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export(read_sz_lcd_2d)
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export(read_sz_lcd_3d)
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export(read_sz_tic)
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export(read_thermoraw)
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export(read_varian_peaklist)
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export(read_waters_arw)
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import(reticulate)
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import(xml2)
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importFrom(RaMS,grabMSdata)
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importFrom(bit64,as.integer64)
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importFrom(bitops,bitAnd)
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importFrom(bitops,bitShiftL)
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importFrom(purrr,partial)

‎NEWS.md

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## chromConverter 0.6.4
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* Added support for Agilent ChemStation' version 8 (`.ch`) files through `read_chemstation_ch`.
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* Fixed failure to return units in some `Agilent Chemstation` files due to typo.
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* Fixed bug causing "spill-over" of Agilent metadata fields.
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## chromConverter 0.6.3
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* Added parser for total ion chromatogram (TIC) stream in 'Shimadzu' LCD files.
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* Added additional support for extraction of metadata from 'Shimadzu' LCD and GCD files.
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* Updated docs for `read_shimadzu_lcd_2d` to more accurately reflect file structure.
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* Added `scale` argument to `read_chemstation_ch` and `read_shimadzu_lcd` to
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toggle scaling of chromatograms resolving ([#30](https://github.com/ethanbass/chromConverter/issues/30)).
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## chromConverter 0.6.2
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* Updated `read_shimadzu_lcd` function to correctly determine the number of blocks in the "Shimadzu" LCD PDA stream (thanks to [kco-hereon](https://github.com/kco-hereon)).
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* Added preliminary support for 2D data streams from "Shimadzu LCD" files.
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* Added parser for 'Shimadzu GCD' files (from GC-FID).
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## chromConverter 0.6.1
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* Added support for 'Shimadzu' ASCII files with '[LC Chromatogram...]' sub-header.
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* Correct 'Shimadzu' ASCII chromatograms by 'Intensity Multiplier' if it is provided.
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* Fixed bug in logic in `export_cdfs` function to permit conversion of files lacking metadata.
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* Minor, cosmetic changes to documentation.
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## chromConverter 0.6.0
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* Added parser for reading ANDI MS (`.cdf`) files.

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