diff --git a/install_tool.R b/install_tool.R
deleted file mode 100644
index 40084d9b..00000000
--- a/install_tool.R
+++ /dev/null
@@ -1,101 +0,0 @@
-installPD <- function(library = getOption("patRoonDeps.library"), ask = TRUE, clean = FALSE, instDE = TRUE,
-                      repos = "https://rickhelmus.github.io/patRoonDeps")
-{
-    checkArg <- function(cond, arg, wh)
-    {
-        if (!cond)
-            stop(sprintf("Please set the '%s' argument %s", arg, wh), call. = FALSE)
-    }
-    
-    checkArg(is.character(library) && nzchar(library), "library", "to a valid path")
-    checkArg(is.logical(ask), "ask", "TRUE/FALSE")
-    checkArg(is.logical(clean), "clean", "as TRUE/FALSE")
-    checkArg(is.logical(instDE), "instDE", "as TRUE/FALSE")
-    checkArg(is.character(repos) && nzchar(repos), "repos", "to the patRoonDeps repository")
-
-    # utils
-    printf <- function(...) cat(sprintf(...), sep = "")
-    yesNo = function(title) !interactive() || !ask || menu(c("Yes", "No"), title = title) == 1
-    # NOTE: force utils:: to avoid using rstudio shims
-    doInstall <- function(pkgs) utils::install.packages(pkgs, lib = library, repos = repos, type = "binary")
-    rmPackages <- function(pkgs) utils::remove.packages(pkgs, lib = library)
-    # Check without loading namespace, from: https://hohenfeld.is/posts/check-if-a-package-is-installed-in-r/
-    isInstalled <- function(pkg, lib.loc = library) nzchar(system.file(package = pkg, lib.loc = lib.loc))
-    
-    pkgList <- read.csv(paste0(repos, "/patRoonDeps.tsv"), sep = "\t", colClasses = "character")
-    
-    if (!file.exists(library))
-    {
-        if (yesNo("The library does not appear to exist. Do you want to initialize it?"))
-        {
-            if (!dir.create(library))
-                stop("Failed to create library directory!", call. = FALSE)
-            doInstall(pkgList$Package)
-        }
-    }
-    else
-    {
-        if (!dir.exists(library))
-            stop(sprintf("The specified library ('%s') does not appear to be a directory", library), call. = FALSE)
-        
-        instPackages <- installed.packages(library, fields = "RemoteSha")[, c("Package", "Version", "RemoteSha")]
-        instPackages <- as.data.frame(instPackages)
-        instPackages$RemoteSha[is.na(instPackages$RemoteSha)] <- "" # normalize with pkgList
-        
-        printf("Comparing the package library with patRoonDeps... ")
-        ignorePkgs <- c("patRoonData", "patRoonExt")
-        checkPkgs <- setdiff(instPackages$Package, ignorePkgs)
-        missingPkgs <- setdiff(pkgList$Package, checkPkgs)
-        otherPkgs <- setdiff(checkPkgs, pkgList$Package)
-        samePkgs <- merge(pkgList, instPackages)$Package
-        changedPkgs <- setdiff(checkPkgs, c(samePkgs, missingPkgs))
-        printf("Done!\n")
-
-        if (length(otherPkgs) > 0)
-        {
-            printf("The following %d packages are not part of patRoonDeps: %s\n", length(otherPkgs),
-                   paste0(otherPkgs, collapse = ", "))
-            if (clean)
-            {
-                printf("Cleaning... ")
-                rmPackages(otherPkgs)
-                printf("Done!\n")
-            }
-            else
-                printf("Re-run with clean=TRUE to remove these packages\n")
-        }
-        
-        if ((length(missingPkgs) > 0 || length(changedPkgs) > 0))
-        {
-            if (length(missingPkgs) > 0)
-                printf("The following %d packages are not yet installed: %s\n\n", length(missingPkgs),
-                       paste0(missingPkgs, collapse = ", "))
-            if (length(changedPkgs) > 0)
-                printf("The following %d packages are with a different version: %s\n", length(changedPkgs),
-                       paste0(changedPkgs, collapse = ", "))
-            
-            if (yesNo("Do you want to synchronize the library by installing or updating packages?"))
-                doInstall(c(missingPkgs, changedPkgs))
-        }
-    }
-    
-    if (instDE)
-    {
-        # UNDONE: install remotes in patRoon library?
-        if (!requireNamespace("remotes", quietly = TRUE))
-        {
-            stop("Please install the remotes package to install patRoonData/patRoonExt ",
-                 "(or set instDE=FALSE to skip the installation", call. = FALSE)
-        }
-        
-        # override .libPaths as install_github() ignores the lib argument when checking if the package already exists
-        lp <- .libPaths()
-        on.exit(.libPaths(lp), add = TRUE)
-        .libPaths(library, include.site = FALSE)
-        
-        printf("Installing/updating patRoonData/patRoonExt (if needed) ...\n")
-        remotes::install_github(c("rickhelmus/patRoonData", "rickhelmus/patRoonExt"), upgrade = "never", lib = library)
-    }
-    
-    printf("All done!\n")
-}
diff --git a/patRoonDeps.lock b/patRoonDeps.lock
deleted file mode 100644
index 8ac538f6..00000000
--- a/patRoonDeps.lock
+++ /dev/null
@@ -1,1988 +0,0 @@
-{
-  "R": {
-    "Version": "4.3.1",
-    "Repositories": [
-      {
-        "Name": "patRoonDeps",
-        "URL": "https://rickhelmus.github.io/patRoonDeps"
-      }
-    ]
-  },
-  "Packages": {
-    "BH": {
-      "Package": "BH",
-      "Version": "1.81.0-1",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "Biobase": {
-      "Package": "Biobase",
-      "Version": "2.60.0",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "BiocBaseUtils": {
-      "Package": "BiocBaseUtils",
-      "Version": "1.2.0",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "BiocGenerics": {
-      "Package": "BiocGenerics",
-      "Version": "0.46.0",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "BiocManager": {
-      "Package": "BiocManager",
-      "Version": "1.30.22",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "BiocParallel": {
-      "Package": "BiocParallel",
-      "Version": "1.34.2",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "BiocStyle": {
-      "Package": "BiocStyle",
-      "Version": "2.28.1",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "CAMERA": {
-      "Package": "CAMERA",
-      "Version": "1.56.0",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "Ckmeans.1d.dp": {
-      "Package": "Ckmeans.1d.dp",
-      "Version": "4.3.5",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "DBI": {
-      "Package": "DBI",
-      "Version": "1.1.3",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "DEoptimR": {
-      "Package": "DEoptimR",
-      "Version": "1.1-2",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "DT": {
-      "Package": "DT",
-      "Version": "0.29",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "DelayedArray": {
-      "Package": "DelayedArray",
-      "Version": "0.26.7",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "Formula": {
-      "Package": "Formula",
-      "Version": "1.2-5",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "GA": {
-      "Package": "GA",
-      "Version": "3.2.3",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "GenomeInfoDb": {
-      "Package": "GenomeInfoDb",
-      "Version": "1.36.3",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "GenomeInfoDbData": {
-      "Package": "GenomeInfoDbData",
-      "Version": "1.2.11",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "patRoonDeps",
-      "RemoteType": "patRoonDeps",
-      "RemoteSha": "f3111730888a3d83e9465ffa2552003de153bbf2",
-      "RemoteUrl": "https://github.com/BioConductor/GenomeInfoDbData",
-      "RemoteRef": "devel",
-      "RemoteUsername": "BioConductor",
-      "RemoteRepo": "GenomeInfoDbData"
-    },
-    "GenomicRanges": {
-      "Package": "GenomicRanges",
-      "Version": "1.52.0",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "GlobalOptions": {
-      "Package": "GlobalOptions",
-      "Version": "0.1.2",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "Hmisc": {
-      "Package": "Hmisc",
-      "Version": "5.1-1",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "IRanges": {
-      "Package": "IRanges",
-      "Version": "2.34.1",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "InterpretMSSpectrum": {
-      "Package": "InterpretMSSpectrum",
-      "Version": "1.3.3",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "patRoonDeps",
-      "RemoteType": "patRoonDeps",
-      "RemoteSha": "0731d92accdf5db2a6d7b03c24b2d324b67b1c72",
-      "RemoteUrl": "https://github.com/cran/InterpretMSSpectrum",
-      "RemoteRef": "1.3.3",
-      "RemoteUsername": "cran",
-      "RemoteRepo": "InterpretMSSpectrum"
-    },
-    "KPIC": {
-      "Package": "KPIC",
-      "Version": "2.4.0",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "patRoonDeps",
-      "RemoteType": "patRoonDeps",
-      "RemoteSha": "dd0dddb0cac9bc7882eb1a420c82c9713a8aa0ce",
-      "RemoteUrl": "https://github.com/rickhelmus/KPIC2",
-      "RemoteRef": "master",
-      "RemoteUsername": "rickhelmus",
-      "RemoteRepo": "KPIC2"
-    },
-    "KernSmooth": {
-      "Package": "KernSmooth",
-      "Version": "2.23-22",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "MALDIquant": {
-      "Package": "MALDIquant",
-      "Version": "1.22.1",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "MASS": {
-      "Package": "MASS",
-      "Version": "7.3-60",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "MLmetrics": {
-      "Package": "MLmetrics",
-      "Version": "1.1.1",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "MSnbase": {
-      "Package": "MSnbase",
-      "Version": "2.26.0",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "MassSpecWavelet": {
-      "Package": "MassSpecWavelet",
-      "Version": "1.66.0",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "Matrix": {
-      "Package": "Matrix",
-      "Version": "1.6-1.1",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "MatrixGenerics": {
-      "Package": "MatrixGenerics",
-      "Version": "1.12.3",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "MetaClean": {
-      "Package": "MetaClean",
-      "Version": "1.0.1",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "patRoonDeps",
-      "RemoteType": "patRoonDeps",
-      "RemoteSha": "d0ce1bc0b2fe4d17e7e047c8c07c75b81c4e5833",
-      "RemoteUrl": "https://github.com/KelseyChetnik/MetaClean",
-      "RemoteRef": "master",
-      "RemoteUsername": "KelseyChetnik",
-      "RemoteRepo": "MetaClean"
-    },
-    "ModelMetrics": {
-      "Package": "ModelMetrics",
-      "Version": "1.2.2.2",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "MsCoreUtils": {
-      "Package": "MsCoreUtils",
-      "Version": "1.12.0",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "MsFeatures": {
-      "Package": "MsFeatures",
-      "Version": "1.8.0",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "MultiAssayExperiment": {
-      "Package": "MultiAssayExperiment",
-      "Version": "1.26.0",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "MultiDataSet": {
-      "Package": "MultiDataSet",
-      "Version": "1.28.0",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "ProtGenerics": {
-      "Package": "ProtGenerics",
-      "Version": "1.32.0",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "R.cache": {
-      "Package": "R.cache",
-      "Version": "0.16.0",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "R.methodsS3": {
-      "Package": "R.methodsS3",
-      "Version": "1.8.2",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "R.oo": {
-      "Package": "R.oo",
-      "Version": "1.25.0",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "R.utils": {
-      "Package": "R.utils",
-      "Version": "2.12.2",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "R6": {
-      "Package": "R6",
-      "Version": "2.5.1",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "RAMClustR": {
-      "Package": "RAMClustR",
-      "Version": "1.3.1",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "patRoonDeps",
-      "RemoteType": "patRoonDeps",
-      "RemoteSha": "e005614d808e0ca93c459ec8cc103b87cd5d11fd",
-      "RemoteUrl": "https://github.com/cbroeckl/RAMClustR",
-      "RemoteRef": "e005614",
-      "RemoteUsername": "cbroeckl",
-      "RemoteRepo": "RAMClustR"
-    },
-    "RANN": {
-      "Package": "RANN",
-      "Version": "2.6.1",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "RBGL": {
-      "Package": "RBGL",
-      "Version": "1.76.0",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "RColorBrewer": {
-      "Package": "RColorBrewer",
-      "Version": "1.1-3",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "RCurl": {
-      "Package": "RCurl",
-      "Version": "1.98-1.12",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "RDCOMClient": {
-      "Package": "RDCOMClient",
-      "Version": "0.95-1",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "patRoonDeps",
-      "RemoteType": "patRoonDeps",
-      "RemoteSha": "1554833f8659461427a93732119756ae1c25bc32",
-      "RemoteUrl": "https://github.com/BSchamberger/RDCOMClient",
-      "RemoteRef": "master",
-      "RemoteUsername": "BSchamberger",
-      "RemoteRepo": "RDCOMClient"
-    },
-    "ROCR": {
-      "Package": "ROCR",
-      "Version": "1.0-11",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "RSQLite": {
-      "Package": "RSQLite",
-      "Version": "2.3.1",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "Rcpp": {
-      "Package": "Rcpp",
-      "Version": "1.0.11",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "RcppArmadillo": {
-      "Package": "RcppArmadillo",
-      "Version": "0.12.6.4.0",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "Rdisop": {
-      "Package": "Rdisop",
-      "Version": "1.60.0",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "Rdpack": {
-      "Package": "Rdpack",
-      "Version": "2.5",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "Rgraphviz": {
-      "Package": "Rgraphviz",
-      "Version": "2.44.0",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "Rhdf5lib": {
-      "Package": "Rhdf5lib",
-      "Version": "1.22.1",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "S4Arrays": {
-      "Package": "S4Arrays",
-      "Version": "1.0.6",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "S4Vectors": {
-      "Package": "S4Vectors",
-      "Version": "0.38.2",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "SQUAREM": {
-      "Package": "SQUAREM",
-      "Version": "2021.1",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "SummarizedExperiment": {
-      "Package": "SummarizedExperiment",
-      "Version": "1.30.2",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "TSP": {
-      "Package": "TSP",
-      "Version": "1.2-4",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "UpSetR": {
-      "Package": "UpSetR",
-      "Version": "1.4.0",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "VennDiagram": {
-      "Package": "VennDiagram",
-      "Version": "1.7.3",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "XML": {
-      "Package": "XML",
-      "Version": "3.99-0.14",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "XVector": {
-      "Package": "XVector",
-      "Version": "0.40.0",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "abind": {
-      "Package": "abind",
-      "Version": "1.4-5",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "affy": {
-      "Package": "affy",
-      "Version": "1.78.2",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "affyio": {
-      "Package": "affyio",
-      "Version": "1.70.0",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "askpass": {
-      "Package": "askpass",
-      "Version": "1.2.0",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "assertthat": {
-      "Package": "assertthat",
-      "Version": "0.2.1",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "backports": {
-      "Package": "backports",
-      "Version": "1.4.1",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "base64enc": {
-      "Package": "base64enc",
-      "Version": "0.1-3",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "bit": {
-      "Package": "bit",
-      "Version": "4.0.5",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "bit64": {
-      "Package": "bit64",
-      "Version": "4.0.5",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
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-      "Package": "survival",
-      "Version": "3.5-7",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "svglite": {
-      "Package": "svglite",
-      "Version": "2.1.1",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "sys": {
-      "Package": "sys",
-      "Version": "3.4.2",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "systemfonts": {
-      "Package": "systemfonts",
-      "Version": "1.0.4",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "textshaping": {
-      "Package": "textshaping",
-      "Version": "0.3.6",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "tibble": {
-      "Package": "tibble",
-      "Version": "3.2.1",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "tidyr": {
-      "Package": "tidyr",
-      "Version": "1.3.0",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "tidyselect": {
-      "Package": "tidyselect",
-      "Version": "1.2.0",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "tidyverse": {
-      "Package": "tidyverse",
-      "Version": "2.0.0",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "timeDate": {
-      "Package": "timeDate",
-      "Version": "4022.108",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "timechange": {
-      "Package": "timechange",
-      "Version": "0.2.0",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "tinytex": {
-      "Package": "tinytex",
-      "Version": "0.46",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "tzdb": {
-      "Package": "tzdb",
-      "Version": "0.4.0",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "utf8": {
-      "Package": "utf8",
-      "Version": "1.2.3",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "uuid": {
-      "Package": "uuid",
-      "Version": "1.1-1",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "vctrs": {
-      "Package": "vctrs",
-      "Version": "0.6.3",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "vegan": {
-      "Package": "vegan",
-      "Version": "2.6-4",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "viridis": {
-      "Package": "viridis",
-      "Version": "0.6.4",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "viridisLite": {
-      "Package": "viridisLite",
-      "Version": "0.4.2",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "visNetwork": {
-      "Package": "visNetwork",
-      "Version": "2.1.2",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "vroom": {
-      "Package": "vroom",
-      "Version": "1.6.3",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "vsn": {
-      "Package": "vsn",
-      "Version": "3.68.0",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "webchem": {
-      "Package": "webchem",
-      "Version": "1.3.0",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "webshot": {
-      "Package": "webshot",
-      "Version": "0.5.5",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "withr": {
-      "Package": "withr",
-      "Version": "2.5.0",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "xcms": {
-      "Package": "xcms",
-      "Version": "3.22.0",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "xfun": {
-      "Package": "xfun",
-      "Version": "0.40",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "xml2": {
-      "Package": "xml2",
-      "Version": "1.3.5",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "xtable": {
-      "Package": "xtable",
-      "Version": "1.8-4",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "yaml": {
-      "Package": "yaml",
-      "Version": "2.3.7",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    },
-    "zlibbioc": {
-      "Package": "zlibbioc",
-      "Version": "1.46.0",
-      "Repository": "https://rickhelmus.github.io/patRoonDeps",
-      "Source": "Repository"
-    }
-  }
-}
diff --git a/patRoonDeps.tsv b/patRoonDeps.tsv
deleted file mode 100644
index 371c44f8..00000000
--- a/patRoonDeps.tsv
+++ /dev/null
@@ -1,317 +0,0 @@
-Package	Version	RemoteSha
-abind	1.4-5	
-affy	1.78.2	
-affyio	1.70.0	
-askpass	1.2.0	
-assertthat	0.2.1	
-backports	1.4.1	
-base64enc	0.1-3	
-BH	1.81.0-1	
-Biobase	2.60.0	
-BiocBaseUtils	1.2.0	
-BiocGenerics	0.46.0	
-BiocManager	1.30.22	
-BiocParallel	1.34.2	
-BiocStyle	2.28.1	
-bit	4.0.5	
-bit64	4.0.5	
-bitops	1.0-7	
-blob	1.2.4	
-bookdown	0.35	
-broom	1.0.5	
-bslib	0.5.1	
-ca	0.71.1	
-cachem	1.0.8	
-calibrate	1.7.7	
-callr	3.7.3	
-CAMERA	1.56.0	
-caret	6.0-94	
-caTools	1.18.2	
-cellranger	1.1.0	
-checkmate	2.2.0	
-circlize	0.4.15	
-Ckmeans.1d.dp	4.3.5	
-class	7.3-22	
-classInt	0.4-10	
-cli	3.6.1	
-clipr	0.8.0	
-cliqueMS	1.7.1	cb569e0b78ce0fa4254f1393874762bed08fa855
-clock	0.7.0	
-clue	0.3-64	
-cluster	2.1.4	
-codetools	0.2-19	
-colorspace	2.1-0	
-combinat	0.0-8	
-commonmark	1.9.0	
-conflicted	1.2.0	
-cpp11	0.4.6	
-crayon	1.5.2	
-crosstalk	1.2.0	
-curl	5.0.2	
-data.table	1.14.8	
-data.tree	1.0.0	
-DBI	1.1.3	
-dbplyr	2.3.3	
-dbscan	1.1-11	
-DelayedArray	0.26.7	
-dendextend	1.17.1	
-DEoptimR	1.1-2	
-diagram	1.6.5	
-digest	0.6.33	
-docopt	0.7.1	
-doParallel	1.0.17	
-dplyr	1.1.3	
-DT	0.29	
-dtplyr	1.3.1	
-dynamicTreeCut	1.63-1	
-e1071	1.7-13	
-egg	0.4.5	
-ellipsis	0.3.2	
-enviPat	2.6	
-enviPick	1.7	d346b23b1f7dc7a226c4e3a45b74fcc617e19c1b
-estimability	1.4.1	
-evaluate	0.21	
-fansi	1.0.4	
-farver	2.1.1	
-fastAdaboost	1.0.0	f331ff8ccfe2e7f318448a29bc72af646dfaf2c1
-fastcluster	1.2.3	
-fastmap	1.1.1	
-ff	4.0.9	
-fingerprint	3.5.7	
-flexdashboard	0.6.2	
-fontawesome	0.5.2	
-forcats	1.0.0	
-foreach	1.5.2	
-foreign	0.8-85	
-formatR	1.14	
-Formula	1.2-5	
-fs	1.6.3	
-fst	0.9.8	
-fstcore	0.9.14	
-futile.logger	1.4.3	
-futile.options	1.0.1	
-future	1.33.0	
-future.apply	1.11.0	
-GA	3.2.3	
-gargle	1.5.2	
-gclus	1.3.2	
-generics	0.1.3	
-GenomeInfoDb	1.36.3	
-GenomeInfoDbData	1.2.11	f3111730888a3d83e9465ffa2552003de153bbf2
-GenomicRanges	1.52.0	
-getPass	0.2-2	
-ggplot2	3.4.3	
-ggrepel	0.9.3	
-GlobalOptions	0.1.2	
-globals	0.16.2	
-glue	1.6.2	
-googledrive	2.1.1	
-googlesheets4	1.1.1	
-gower	1.0.1	
-gplots	3.1.3	
-graph	1.78.0	
-gridExtra	2.3	
-gtable	0.3.4	
-gtools	3.9.4	
-hardhat	1.3.0	
-haven	2.5.3	
-heatmaply	1.4.2	
-highr	0.10	
-Hmisc	5.1-1	
-hms	1.1.3	
-htmlTable	2.4.1	
-htmltools	0.5.6	
-htmlwidgets	1.6.2	
-httpuv	1.6.11	
-httr	1.4.7	
-ids	1.0.1	
-igraph	1.5.1	
-impute	1.74.1	
-InterpretMSSpectrum	1.3.3	0731d92accdf5db2a6d7b03c24b2d324b67b1c72
-ipred	0.9-14	
-IRanges	2.34.1	
-isoband	0.2.7	
-iterators	1.0.14	
-itertools	0.1-3	
-jquerylib	0.1.4	
-jsonlite	1.8.7	
-kableExtra	1.3.4	
-kernlab	0.9-32	
-KernSmooth	2.23-22	
-keys	0.1.1	
-klaR	1.7-2	
-knitr	1.44	
-KPIC	2.4.0	dd0dddb0cac9bc7882eb1a420c82c9713a8aa0ce
-labeling	0.4.3	
-labelled	2.12.0	
-lambda.r	1.2.4	
-later	1.3.1	
-lattice	0.21-8	
-lava	1.7.2.1	
-lazyeval	0.2.2	
-lifecycle	1.0.3	
-limma	3.56.2	
-listenv	0.9.0	
-lubridate	1.9.2	
-magick	2.7.5	
-magrittr	2.0.3	
-MALDIquant	1.22.1	
-MASS	7.3-60	
-MassSpecWavelet	1.66.0	
-Matrix	1.6-1.1	
-MatrixGenerics	1.12.3	
-matrixStats	1.0.0	
-memoise	2.0.1	
-MetaClean	1.0.1	d0ce1bc0b2fe4d17e7e047c8c07c75b81c4e5833
-mgcv	1.9-0	
-mime	0.12	
-miniUI	0.1.1.1	
-MLmetrics	1.1.1	
-ModelMetrics	1.2.2.2	
-modelr	0.1.11	
-MsCoreUtils	1.12.0	
-MsFeatures	1.8.0	
-MSnbase	2.26.0	
-MultiAssayExperiment	1.26.0	
-MultiDataSet	1.28.0	
-multtest	2.56.0	
-munsell	0.5.0	
-mzID	1.38.0	
-mzR	2.34.1	
-ncdf4	1.21	
-nlme	3.1-163	
-nnet	7.3-19	
-nontarget	2.2	e30221585182bc66e1f8e1113b2c1103a0f2cb56
-nontargetData	1.1	75b2a92cd549f72cc71dfe7b86bd42947d62f2c4
-numDeriv	2016.8-1.1	
-openssl	2.1.0	
-parallelly	1.36.0	
-patRoon	2.2.0.9000	88a1da32318b8e45945de6e45bc9f424f372c4f7
-pcaMethods	1.92.0	
-permute	0.9-7	
-pillar	1.9.0	
-pkgconfig	2.0.3	
-plogr	0.2.0	
-plotly	4.10.2	
-plotrix	3.8-2	
-plyr	1.8.8	
-png	0.1-8	
-preprocessCore	1.62.1	
-prettyunits	1.1.1	
-pROC	1.18.4	
-processx	3.8.2	
-prodlim	2023.08.28	
-progress	1.2.2	
-progressr	0.14.0	
-promises	1.2.1	
-ProtGenerics	1.32.0	
-proxy	0.4-27	
-ps	1.7.5	
-purrr	1.0.2	
-qap	0.1-2	
-qlcMatrix	0.9.7	
-qqman	0.1.9	
-questionr	0.7.8	
-R.cache	0.16.0	
-R.methodsS3	1.8.2	
-R.oo	1.25.0	
-R.utils	2.12.2	
-R6	2.5.1	
-ragg	1.2.5	
-RAMClustR	1.3.1	e005614d808e0ca93c459ec8cc103b87cd5d11fd
-randomForest	4.7-1.1	
-RANN	2.6.1	
-rapidjsonr	1.2.0	
-rappdirs	0.3.3	
-RBGL	1.76.0	
-rbibutils	2.2.15	
-rcdk	3.8.1	
-rcdklibs	2.8	
-RColorBrewer	1.1-3	
-Rcpp	1.0.11	
-RcppArmadillo	0.12.6.4.0	
-RCurl	1.98-1.12	
-RDCOMClient	0.95-1	1554833f8659461427a93732119756ae1c25bc32
-Rdisop	1.60.0	
-Rdpack	2.5	
-reactable	0.4.4	
-reactR	0.4.4	
-readMzXmlData	2.8.3	
-readr	2.1.4	
-readxl	1.4.3	
-recipes	1.0.8	
-registry	0.5-1	
-rematch	2.0.0	
-rematch2	2.1.2	
-reprex	2.0.2	
-reshape2	1.4.4	
-Rgraphviz	2.44.0	
-rhandsontable	0.3.8	
-Rhdf5lib	1.22.1	
-rJava	1.0-6	
-rlang	1.1.1	
-rmarkdown	2.25	
-robustbase	0.99-0	
-ROCR	1.0-11	
-ropls	1.32.0	
-rpart	4.1.19	
-rprojroot	2.0.3	
-rsm	2.10.4	
-RSQLite	2.3.1	
-rstudioapi	0.15.0	
-rvest	1.0.3	
-S4Arrays	1.0.6	
-S4Vectors	0.38.2	
-sass	0.4.7	
-scales	1.2.1	
-selectr	0.4-2	
-seriation	1.5.1	
-shape	1.4.6	
-shiny	1.7.5	
-shinyjs	2.1.0	
-slam	0.1-50	
-snow	0.4-4	
-sourcetools	0.1.7-1	
-sparsesvd	0.2-2	
-splashR	0.0.4	174fbf289a0357535f9bacda282b9a2dbb7807cc
-SQUAREM	2021.1	
-stringi	1.7.12	
-stringr	1.5.0	
-styler	1.10.2	
-SummarizedExperiment	1.30.2	
-survival	3.5-7	
-svglite	2.1.1	
-sys	3.4.2	
-systemfonts	1.0.4	
-textshaping	0.3.6	
-tibble	3.2.1	
-tidyr	1.3.0	
-tidyselect	1.2.0	
-tidyverse	2.0.0	
-timechange	0.2.0	
-timeDate	4022.108	
-tinytex	0.46	
-TSP	1.2-4	
-tzdb	0.4.0	
-UpSetR	1.4.0	
-utf8	1.2.3	
-uuid	1.1-1	
-vctrs	0.6.3	
-vegan	2.6-4	
-VennDiagram	1.7.3	
-viridis	0.6.4	
-viridisLite	0.4.2	
-visNetwork	2.1.2	
-vroom	1.6.3	
-vsn	3.68.0	
-webchem	1.3.0	
-webshot	0.5.5	
-withr	2.5.0	
-xcms	3.22.0	
-xfun	0.40	
-XML	3.99-0.14	
-xml2	1.3.5	
-xtable	1.8-4	
-XVector	0.40.0	
-yaml	2.3.7	
-zlibbioc	1.46.0	
diff --git a/utils/make_repos.R b/utils/make_repos.R
index 554ad28d..b6c8fd8a 100644
--- a/utils/make_repos.R
+++ b/utils/make_repos.R
@@ -256,6 +256,7 @@ getAllGHSHAs <- function(pkgs)
 pkgtabSHA <- merge(pkgTab, getAllGHSHAs(dependencies), by = "Package", all = TRUE)
 data.table::fwrite(pkgtabSHA, sprintf("patRoonDeps-%s.tsv", thisRVersion), sep = "\t")
 
+if (FALSE){
 # generate renv.lock file
 pkgLockList <- split(data.table::as.data.table(pkgTab), by = "Package")
 pkgLockList <- lapply(pkgLockList, as.list)
@@ -316,3 +317,5 @@ if (FALSE)
         withr::with_dir(extrp, utils::zip(pkgf, Sys.glob("*")))
     }
 }
+
+}