Update createMSP to use median mz and RT values

.github/workflows/check-bioc.yml

@@ -39,6 +39,7 @@ env:
   run_pkgdown: 'false'
   has_RUnit: 'false'
   cache-version: 'cache-v1'
+  run_docker: 'false'
 
 jobs:
   build-check:
@@ -48,12 +49,14 @@ jobs:
     ## Environment variables unique to this job.
 
     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: 'devel', bioc: '3.17', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
+          - { os: macOS-latest, r: 'devel', bioc: '3.17'}
+          - { os: windows-latest, r: 'devel', 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 }}
@@ -76,51 +79,49 @@ 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
 
       ## 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 }}
 
       ## 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
 
       - 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
+      - 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-
 
       - 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-
 
       - 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 +137,11 @@ 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 tcltk
+          brew install xquartz --cask
 
       - name: Install Windows system dependencies
         if: runner.os == 'Windows'
@@ -153,10 +157,10 @@ jobs:
 
       - 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}
 
-      - name: Install dependencies
+      - name: Install dependencies pass 1
         run: |
           ## Try installing the package dependencies in steps. First the local
           ## dependencies, then any remaining dependencies to avoid the
@@ -165,24 +169,37 @@ 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")
-
+          ## 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()
+
+          ## For running the checks
+          message(paste('****', Sys.time(), 'installing rcmdcheck and 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 = BiocManager::repositories(), build_vignettes = TRUE, upgrade = TRUE)
+          remotes::install_local(dependencies = TRUE, repos = gha_repos, build_vignettes = FALSE, upgrade = TRUE)
+        continue-on-error: true
+        shell: Rscript {0}
 
+      - 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)
-
-          ## For running the checks
-          message(paste('****', Sys.time(), 'installing rcmdcheck and BiocCheck ****'))
-          remotes::install_cran("rcmdcheck")
-          BiocManager::install("BiocCheck")
+          remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = TRUE, upgrade = TRUE, force = TRUE)
         shell: Rscript {0}
 
       - name: Install BiocGenerics
@@ -201,7 +218,13 @@ 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}
+
+      - name: Install suggested packages
+        run: |
+          BiocManager::install(c("MSnbase", "xcms", "BiocStyle", "msPurityData", "CAMERA"))
+          install.packages(c("rmarkdown", "RPostgres", "RMySQL"))
         shell: Rscript {0}
 
       - name: Session info
@@ -214,10 +237,12 @@ 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"
           )
@@ -235,18 +260,14 @@ jobs:
         shell: Rscript {0}
 
       - name: Run BiocCheck
+        env:
+          DISPLAY: 99.0
         run: |
           BiocCheck::BiocCheck(
               dir('check', 'tar.gz$', full.names = TRUE),
               `quit-with-status` = TRUE,
-              `no-check-namespace` =  TRUE,
-              `no-check-pkg-size` = TRUE,
-              `no-check-file-size` = TRUE,
-              `no-check-version-num` = TRUE,
               `no-check-R-ver` = TRUE,
-              `no-check-bioc-help` = TRUE,
-              `no-check-dependencies` = TRUE
-
+              `no-check-bioc-help` = TRUE
           )
         shell: Rscript {0}
 
@@ -260,21 +281,47 @@ jobs:
         if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux'
         run: R CMD INSTALL .
 
-      - 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.
 
+      - 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
+
       - 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
+
+        ## 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

DESCRIPTION

@@ -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: 

R/purityA-create-msp.R

@@ -206,7 +206,7 @@ mspurity_to_msp <- function (pa, msp_file_pth=NULL, metadata=NULL, metadata_cols
 
 
         if (!is.null(av_inter) && nrow(av_inter)>0){
-          write.msp(grpd$mz[1], grpd$rt[1], grpid, NA, av_inter, metadata, metadata_cols, of, method,
+          write.msp(median(grpd$mz), median(grpd$rt), grpid, NA, av_inter, metadata, metadata_cols, of, method,
                     adduct_split, msp_schema, intensity_ra, include_adducts)
         }
 
@@ -230,7 +230,7 @@ mspurity_to_msp <- function (pa, msp_file_pth=NULL, metadata=NULL, metadata_cols
 
 
           if (!is.null(av_intra_j) && nrow(av_intra_j)>0){
-            write.msp(grpd$mz[1], grpd$rt[1], grpid, fileid, av_intra_j, metadata, metadata_cols,
+            write.msp(median(grpd$mz), median(grpd$rt), grpid, fileid, av_intra_j, metadata, metadata_cols,
                       of, method, adduct_split, msp_schema, intensity_ra, include_adducts)
           }
 
@@ -248,7 +248,7 @@ mspurity_to_msp <- function (pa, msp_file_pth=NULL, metadata=NULL, metadata_cols
 
         if (!is.null(av_all) && nrow(av_all)>0){
 
-          write.msp(grpd$mz[1], grpd$rt[1], grpid, NA, av_all, metadata, metadata_cols, of,
+          write.msp(median(grpd$mz), median(grpd$rt), grpid, NA, av_all, metadata, metadata_cols, of,
                     method, adduct_split, msp_schema, intensity_ra, include_adducts)
         }
 

inst/extdata/tests/msp/all.msp

@@ -1 +1,28 @@
-RECORD_TITLE: MZ:150.0581 | RT:63.1 | grpid:187 | file:1 | adduct:[M+H]+MS$FOCUSED_ION: PRECURSOR_M/Z 150.058135986328AC$CHROMATOGRAPHY: RETENTION_TIME 63.078168MS$FOCUSED_ION: PRECURSOR_TYPE [M+H]+AC$MASS_SPECTROMETRY: ION_MODE POSITIVECH$NAME: MethionineXCMS groupid (grpid): 187COMMENT: Exported from msPurity purityA object using function createMSP, using method 'all' msPurity version:1.19.2 PK$NUM_PEAK: 2PK$PEAK: m/z int. rel.int.104.053237915039	16147574	100133.031829833984	10814390	66.97RECORD_TITLE: MZ:150.0582 | RT:62.3 | grpid:187 | file:2 | adduct:[M+H]+MS$FOCUSED_ION: PRECURSOR_M/Z 150.058166503906AC$CHROMATOGRAPHY: RETENTION_TIME 62.3220443725586MS$FOCUSED_ION: PRECURSOR_TYPE [M+H]+AC$MASS_SPECTROMETRY: ION_MODE POSITIVECH$NAME: MethionineXCMS groupid (grpid): 187COMMENT: Exported from msPurity purityA object using function createMSP, using method 'all' msPurity version:1.19.2 PK$NUM_PEAK: 4PK$PEAK: m/z int. rel.int.102.055404663086	4154222.25	29.71104.053276062012	13982832	100133.031875610352	9440187	67.51150.058349609375	1694299.125	12.12
+RECORD_TITLE: MZ:150.0581 | RT:63.1 | grpid:187 | file:1 | adduct:[M+H]+
+MS$FOCUSED_ION: PRECURSOR_M/Z 150.058135986328
+AC$CHROMATOGRAPHY: RETENTION_TIME 63.078168
+MS$FOCUSED_ION: PRECURSOR_TYPE [M+H]+
+AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
+CH$NAME: Methionine
+XCMS groupid (grpid): 187
+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'all' msPurity version:1.21.2 
+PK$NUM_PEAK: 2
+PK$PEAK: m/z int. rel.int.
+104.053237915039	16147574	100
+133.031829833984	10814390	66.97
+
+RECORD_TITLE: MZ:150.0582 | RT:62.3 | grpid:187 | file:2 | adduct:[M+H]+
+MS$FOCUSED_ION: PRECURSOR_M/Z 150.058166503906
+AC$CHROMATOGRAPHY: RETENTION_TIME 62.3220443725586
+MS$FOCUSED_ION: PRECURSOR_TYPE [M+H]+
+AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
+CH$NAME: Methionine
+XCMS groupid (grpid): 187
+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'all' msPurity version:1.21.2 
+PK$NUM_PEAK: 4
+PK$PEAK: m/z int. rel.int.
+102.055404663086	4154222.25	29.71
+104.053276062012	13982832	100
+133.031875610352	9440187	67.51
+150.058349609375	1694299.125	12.12
+