diff --git a/.github/workflows/build_packages.yml b/.github/workflows/build_packages.yml
deleted file mode 100644
index 135ef6c2..00000000
--- a/.github/workflows/build_packages.yml
+++ /dev/null
@@ -1,73 +0,0 @@
-name: build_packages
-on: workflow_dispatch
-jobs:
-  build:
-    runs-on: windows-latest
-    strategy:
-      fail-fast: true
-      max-parallel: 1
-      matrix:
-        R: [ 'release', 'oldrel' ]
-    env:
-      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-    name: Build ${{ matrix.R }}
-    steps:
-      - name: Make test artifact
-        run: echo hi from ${{ github.run_id }} > testarti.txt
-      - uses: actions/upload-artifact@v3
-        with:
-            name: testarti
-            path: testarti.txt
-      - name: Test dispatch
-        uses: codex-/return-dispatch@v1
-        id: return_dispatch
-        with:
-            token: ${{ secrets.PAT }}
-            ref: master
-            repo: patRoon
-            owner: rickhelmus
-            workflow: test.yml
-            #workflow_inputs: { "some_input": "value" } # Optional
-            #workflow_timeout_seconds: 120 # Default: 300
-      - name: Await Run ID ${{ steps.return_dispatch.outputs.run_id }}
-        uses: Codex-/await-remote-run@v1.0.0
-        with:
-            token: ${{ secrets.PAT }}
-            repo: patRoon
-            owner: rickhelmus
-            run_id: ${{ steps.return_dispatch.outputs.run_id }}
-            run_timeout_seconds: 300 # Optional
-            poll_interval_ms: 5000 # Optional
-      - uses: actions/checkout@v3
-      - name: Setup R
-        uses: r-lib/actions/setup-r@v2
-        with:
-            r-version: ${{ matrix.R }}
-      - name: Pre-Install R deps
-        run: |
-            if (getRversion() < "4.3") # workaround, see https://support.bioconductor.org/p/9148444/
-                options(BioC_mirror = "http://bioconductor.org")
-            install.packages(c("miniCRAN", "git2r", "devtools", "BiocManager", "rversions"))
-            BiocManager::install(c("Rdisop", "GenomeInfoDbData")) # sometimes needed as dependency may not be picked up...
-            BiocManager::install("ropls") # For KPIC2
-            remotes::install_github("cran/InterpretMSSpectrum@1.3.3") # workaround for https://github.com/cbroeckl/RAMClustR/issues/48
-            BiocManager::install(c("xcms", "qlcMatrix")) # for cliqueMS
-            install.packages("RAMClustR")
-            remotes::install_github(c("blosloos/nontargetData", "blosloos/nontarget"))
-            remotes::install_github("rickhelmus/KPIC2")
-            remotes::install_github("souravc83/fastAdaboost") # For Metaclean, removed from CRAN (9/22)
-            remotes::install_github("KelseyChetnik/MetaClean")
-        shell: Rscript {0}
-      - name: Make repos
-        run: Rscript make_repos.R
-      - name: Push changes
-        env: 
-            CI_COMMIT_MESSAGE: Automated GHA update
-            CI_COMMIT_AUTHOR: GHA
-        run: |
-            git config --global user.name "${{ env.CI_COMMIT_AUTHOR }}"
-            git config --global user.email "notvalid@someemail.com"
-            git add bin/
-            git commit -m "${{ env.CI_COMMIT_MESSAGE }}"
-            git status
-            git push
diff --git a/.github/workflows/make_bundle.yml b/.github/workflows/make_bundle.yml
deleted file mode 100644
index 52063664..00000000
--- a/.github/workflows/make_bundle.yml
+++ /dev/null
@@ -1,32 +0,0 @@
-on: workflow_dispatch
-name: Make R bundle
-jobs:
-  build:
-    name: Make bundle
-    runs-on: windows-latest
-    env:
-      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-    steps:
-      - name: Checkout code
-        uses: actions/checkout@v3
-      - name: Setup R
-        uses: r-lib/actions/setup-r@v2
-        with:
-          r-version: release
-      - name: Pre-Install R deps
-        run: |
-            install.packages("withr")
-        shell: Rscript {0}
-      - name: Run script
-        run: Rscript make_bundle.R
-      - name: Make pre-release
-        uses: andelf/nightly-release@main
-        env:
-            GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        with:
-            tag_name: prerelease
-            name: 'Automated Pre-release $$'
-            prerelease: true
-            body: 'TODO: Add release notes'
-            files: |
-                patRoon-bundle-*.zip
diff --git a/ext/biotransformer-3.0.0.jar b/ext/biotransformer-3.0.0.jar
deleted file mode 100644
index 2bc2f0ff..00000000
Binary files a/ext/biotransformer-3.0.0.jar and /dev/null differ
diff --git a/utils/make_bundle.R b/utils/make_bundle.R
index 507df1be..02df2754 100644
--- a/utils/make_bundle.R
+++ b/utils/make_bundle.R
@@ -1,11 +1,9 @@
-# RExePath <- "../R-win.exe" # on Appveyor
-
 RExePath <- if (Sys.getenv("GITHUB_ACTIONS") == "true")
 {
     sprintf("D:/a/_temp/R-%s-win.exe", getRversion()) # HACK: maybe not very maintainable, let's see...
 } else {
     dl <- tempfile(fileext = ".exe")
-    stopifnot(download.file("https://cloud.r-project.org/bin/windows/base/R-4.3.1-win.exe",
+    stopifnot(download.file("https://cloud.r-project.org/bin/windows/base/R-4.3.2-win.exe",
                             dl, mode = "wb") == 0)
     dl
 }
@@ -24,10 +22,6 @@ stopifnot(system2(file.path(IEDir, "innoextract.exe"), c("-ed", RExtrDir, RExePa
 file.rename(file.path(RExtrDir, "app"), file.path(RExtrDir, "R"))
 file.copy("bundle/Renviron.site", file.path(RExtrDir, "R", "etc"), overwrite = TRUE)
 
-# UNDONE: for now leave the repos as the default, mainly since patRoonInst already deals with setting up the repos
-# cat("\n# Customization of patRoon",
-#     "options(repos = c(CRAN = \"https://cran.rstudio.com/\", patRoonDeps = \"https://rickhelmus.github.io/patRoonDeps/\"))",
-#     sep = "\n", file = file.path(RExtrDir, "R", "etc", "Rprofile.site"), append = TRUE)
 cat("\n# Customization of patRoon",
     "options(repos = c(CRAN = \"https://cran.rstudio.com/\"))",
     sep = "\n", file = file.path(RExtrDir, "R", "etc", "Rprofile.site"), append = TRUE)