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v1.27.1 - createMSP fix to use he median precursor MZ and precursor R…
…T in the MSP file (#101)
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@@ -39,6 +39,7 @@ env: | |
run_pkgdown: 'false' | ||
has_RUnit: 'false' | ||
cache-version: 'cache-v1' | ||
run_docker: 'false' | ||
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jobs: | ||
build-check: | ||
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@@ -48,12 +49,14 @@ jobs: | |
## Environment variables unique to this job. | ||
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||
strategy: | ||
fail-fast: false | ||
fail-fast: false | ||
matrix: | ||
config: | ||
- { os: ubuntu-latest, r: '4.1.3', bioc: '3.14', cont: "bioconductor/bioconductor_docker:RELEASE_3_14", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" } | ||
- { os: macOS-latest, r: '4.1.3', bioc: '3.14'} | ||
- { os: windows-latest, r: '4.1.3', bioc: '3.14'} | ||
- { os: ubuntu-latest, r: 'latest', bioc: '3.17', cont: "bioconductor/bioconductor_docker:latest", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" } | ||
- { os: macOS-latest, r: 'latest', bioc: '3.17'} | ||
- { os: windows-latest, r: 'latest', bioc: '3.17'} | ||
## Check https://github.com/r-lib/actions/tree/master/examples | ||
## for examples using the http-user-agent | ||
env: | ||
R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | ||
RSPM: ${{ matrix.config.rspm }} | ||
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@@ -76,51 +79,50 @@ jobs: | |
## 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 | ||
uses: actions/checkout@v3 | ||
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||
## 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 | ||
uses: r-lib/actions/setup-r@v2 | ||
with: | ||
r-version: ${{ matrix.config.r }} | ||
http-user-agent: ${{ matrix.config.http-user-agent }} | ||
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||
## 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 | ||
uses: r-lib/actions/setup-pandoc@v2 | ||
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||
- name: Query dependencies | ||
run: | | ||
install.packages('remotes') | ||
saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) | ||
shell: Rscript {0} | ||
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||
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- name: Cache R packages | ||
- name: Restore R package cache | ||
if: "!contains(github.event.head_commit.message, '/nocache') && runner.os != 'Linux'" | ||
uses: actions/cache@v2 | ||
uses: actions/cache@v3 | ||
with: | ||
path: ${{ env.R_LIBS_USER }} | ||
key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-r-4.1.3-${{ hashFiles('.github/depends.Rds') }} | ||
restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-r-4.1.3- | ||
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- | ||
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||
- name: Cache R packages on Linux | ||
if: "!contains(github.event.head_commit.message, '/nocache') && runner.os == 'Linux' " | ||
uses: actions/cache@v2 | ||
uses: actions/cache@v3 | ||
with: | ||
path: /home/runner/work/_temp/Library | ||
key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-r-4.1.3-${{ hashFiles('.github/depends.Rds') }} | ||
restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-r-4.1.3 | ||
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- | ||
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||
## Note some specifics here for ncdf4 - depends updated from XCMS github workflow | ||
- name: Install Linux system dependencies | ||
if: runner.os == 'Linux' | ||
## sysreqs=$(Rscript -e 'cat("apt-get update -y && apt-get install -y", paste(gsub("apt-get install -y ", "", remotes::system_requirements("ubuntu", "20.04")), collapse = " "))') | ||
run: | | ||
sysreqs=$(Rscript -e 'cat("apt-get update -y && apt-get install -y libicu-dev pandoc libpq-dev" )') | ||
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' | ||
|
@@ -136,8 +138,21 @@ jobs: | |
## For textshaping, required by ragg, and required by pkgdown | ||
brew install harfbuzz fribidi | ||
## See if this helps get RCurl installed | ||
## brew uninstall curl | ||
## 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' | ||
|
@@ -153,10 +168,11 @@ jobs: | |
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||
- name: Set BiocVersion | ||
run: | | ||
BiocManager::install(version = "${{ matrix.config.bioc }}", ask = FALSE) | ||
BiocManager::install(version = "${{ matrix.config.bioc }}", ask = FALSE, force = TRUE) | ||
shell: Rscript {0} | ||
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- name: Install dependencies | ||
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||
- name: Install dependencies pass 1 | ||
run: | | ||
## Try installing the package dependencies in steps. First the local | ||
## dependencies, then any remaining dependencies to avoid the | ||
|
@@ -165,26 +181,43 @@ jobs: | |
## https://github.com/r-lib/remotes/issues/296 | ||
## Ideally, all dependencies should get installed in the first pass. | ||
## Temporary for now due to https://github.com/ropensci/RefManageR/issues/79 | ||
remotes::install_github("ropensci/bibtex") | ||
remotes::install_github("ropensci/RefManageR") | ||
remotes::install_github("cboettig/knitcitations") | ||
## 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 = TRUE, upgrade = TRUE) | ||
## 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 = TRUE, upgrade = TRUE) | ||
## Set the repos source depending on the OS | ||
## Alternatively use https://storage.googleapis.com/bioconductor_docker/packages/ | ||
## though based on https://bit.ly/bioc2021-package-binaries | ||
## the Azure link will be the main one going forward. | ||
gha_repos <- if( | ||
.Platform$OS.type == "unix" && Sys.info()["sysname"] != "Darwin" | ||
) c( | ||
"AnVIL" = "https://bioconductordocker.blob.core.windows.net/packages/3.17/bioc", | ||
BiocManager::repositories() | ||
) else BiocManager::repositories() | ||
# install suggested packages | ||
BiocManager::install(c("MSnbase", "xcms", "BiocStyle", "msPurityData", "CAMERA")) | ||
install.packages(c("rmarkdown", "RPostgres", "RMySQL")) | ||
## For running the checks | ||
message(paste('****', Sys.time(), 'installing rcmdcheck and BiocCheck ****')) | ||
remotes::install_cran("rcmdcheck") | ||
BiocManager::install("BiocCheck") | ||
install.packages(c("rcmdcheck", "BiocCheck"), repos = gha_repos) | ||
## Pass #1 at installing dependencies | ||
## This pass uses AnVIL-powered fast binaries | ||
## details at https://github.com/nturaga/bioc2021-bioconductor-binaries | ||
## The speed gains only apply to the docker builds. | ||
message(paste('****', Sys.time(), 'pass number 1 at installing dependencies: local dependencies ****')) | ||
remotes::install_local(dependencies = TRUE, repos = gha_repos, build_vignettes = FALSE, upgrade = TRUE) | ||
continue-on-error: true | ||
shell: Rscript {0} | ||
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# - name: Install dependencies pass 2 | ||
# run: | | ||
# ## Pass #2 at installing dependencies | ||
# ## This pass does not use AnVIL and will thus update any packages | ||
# ## that have seen been updated in Bioconductor | ||
# message(paste('****', Sys.time(), 'pass number 2 at installing dependencies: any remaining dependencies ****')) | ||
# remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = TRUE, upgrade = TRUE, force = TRUE) | ||
# shell: Rscript {0} | ||
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- name: Install BiocGenerics | ||
if: env.has_RUnit == 'true' | ||
run: | | ||
|
@@ -201,9 +234,11 @@ jobs: | |
- name: Install pkgdown | ||
if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux' | ||
run: | | ||
remotes::install_cran("pkgdown") | ||
remotes::install_github("r-lib/pkgdown") | ||
shell: Rscript {0} | ||
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- name: Session info | ||
run: | | ||
options(width = 100) | ||
|
@@ -214,10 +249,12 @@ jobs: | |
- name: Run CMD check | ||
env: | ||
_R_CHECK_CRAN_INCOMING_: false | ||
DISPLAY: 99.0 | ||
run: | | ||
options(crayon.enabled = TRUE) | ||
rcmdcheck::rcmdcheck( | ||
args = c("--no-build-vignettes", "--no-manual", "--timings"), | ||
build_args = c("--no-manual", "--no-resave-data"), | ||
args = c("--no-manual", "--no-vignettes", "--timings"), | ||
build_args = c("--no-manual", "--keep-empty-dirs", "--no-resave-data"), | ||
error_on = "warning", | ||
check_dir = "check" | ||
) | ||
|
@@ -235,6 +272,8 @@ jobs: | |
shell: Rscript {0} | ||
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- name: Run BiocCheck | ||
env: | ||
DISPLAY: 99.0 | ||
run: | | ||
BiocCheck::BiocCheck( | ||
dir('check', 'tar.gz$', full.names = TRUE), | ||
|
@@ -246,7 +285,7 @@ jobs: | |
`no-check-R-ver` = TRUE, | ||
`no-check-bioc-help` = TRUE, | ||
`no-check-dependencies` = TRUE | ||
) | ||
shell: Rscript {0} | ||
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||
|
@@ -260,21 +299,47 @@ jobs: | |
if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux' | ||
run: R CMD INSTALL . | ||
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||
- name: Deploy package | ||
- name: Build pkgdown site | ||
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} | ||
run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE) | ||
shell: Rscript {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. | ||
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- name: Install deploy dependencies | ||
if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux' | ||
run: | | ||
apt-get update && apt-get -y install rsync | ||
- name: Deploy pkgdown site to GitHub pages 🚀 | ||
if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux' | ||
uses: JamesIves/github-pages-deploy-action@releases/v4 | ||
with: | ||
clean: false | ||
branch: gh-pages | ||
folder: docs | ||
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- name: Upload check results | ||
if: failure() | ||
uses: actions/upload-artifact@master | ||
with: | ||
name: ${{ runner.os }}-biocversion-r-4.1.3-results | ||
name: ${{ runner.os }}-biocversion-devel-r-devel-results | ||
path: check | ||
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||
## Note that DOCKER_PASSWORD is really a token for your dockerhub | ||
## account, not your actual dockerhub account password. | ||
## This comes from | ||
## https://seandavi.github.io/BuildABiocWorkshop/articles/HOWTO_BUILD_WORKSHOP.html#6-add-secrets-to-github-repo | ||
## Check https://github.com/docker/build-push-action/tree/releases/v1 | ||
## for more details. | ||
- uses: docker/build-push-action@v1 | ||
if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && runner.os == 'Linux' " | ||
with: | ||
username: ${{ secrets.DOCKER_USERNAME }} | ||
password: ${{ secrets.DOCKER_PASSWORD }} | ||
repository: computational-metabolomics/structtoolbox | ||
tag_with_ref: true | ||
tag_with_sha: true | ||
tags: latest |
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|
@@ -2,8 +2,8 @@ Package: msPurity | |
Type: Package | ||
Title: Automated Evaluation of Precursor Ion Purity for Mass Spectrometry Based | ||
Fragmentation in Metabolomics | ||
Version: 1.21.2 | ||
Date: 2022-04-12 | ||
Version: 1.27.1 | ||
Date: 2023-08-30 | ||
Authors@R: c( | ||
person(given = "Thomas N.", family = "Lawson", | ||
email = "[email protected]", role = c("aut", "cre"), | ||
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@@ -61,7 +61,7 @@ Suggests: | |
RPostgres, | ||
RMySQL | ||
VignetteBuilder: knitr | ||
RoxygenNote: 7.1.2 | ||
RoxygenNote: 7.2.3 | ||
Roxygen: list(markdown = TRUE) | ||
biocViews: MassSpectrometry, Metabolomics, Software | ||
Collate: | ||
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