From ff9587dd0663e877be126ab942b89582f530535d Mon Sep 17 00:00:00 2001
From: csmagnano <chrismagnano@gmail.com>
Date: Mon, 20 May 2024 14:59:54 -0400
Subject: [PATCH] Updated to R version 4.4.0 and Bioc version 3.19

Currently successfully builds locally.
---
 renv/activate.R                             |  43 +-
 renv/profiles/lesson-requirements/renv.lock | 771 ++++++++++----------
 2 files changed, 406 insertions(+), 408 deletions(-)

diff --git a/renv/activate.R b/renv/activate.R
index 9b2e7f1..d13f993 100644
--- a/renv/activate.R
+++ b/renv/activate.R
@@ -2,11 +2,13 @@
 local({
 
   # the requested version of renv
-  version <- "1.0.5"
+  version <- "1.0.7"
   attr(version, "sha") <- NULL
 
   # the project directory
-  project <- getwd()
+  project <- Sys.getenv("RENV_PROJECT")
+  if (!nzchar(project))
+    project <- getwd()
 
   # use start-up diagnostics if enabled
   diagnostics <- Sys.getenv("RENV_STARTUP_DIAGNOSTICS", unset = "FALSE")
@@ -129,6 +131,21 @@ local({
   
   }
   
+  heredoc <- function(text, leave = 0) {
+  
+    # remove leading, trailing whitespace
+    trimmed <- gsub("^\\s*\\n|\\n\\s*$", "", text)
+  
+    # split into lines
+    lines <- strsplit(trimmed, "\n", fixed = TRUE)[[1L]]
+  
+    # compute common indent
+    indent <- regexpr("[^[:space:]]", lines)
+    common <- min(setdiff(indent, -1L)) - leave
+    paste(substring(lines, common), collapse = "\n")
+  
+  }
+  
   startswith <- function(string, prefix) {
     substring(string, 1, nchar(prefix)) == prefix
   }
@@ -631,6 +648,9 @@ local({
   
     # if the user has requested an automatic prefix, generate it
     auto <- Sys.getenv("RENV_PATHS_PREFIX_AUTO", unset = NA)
+    if (is.na(auto) && getRversion() >= "4.4.0")
+      auto <- "TRUE"
+  
     if (auto %in% c("TRUE", "True", "true", "1"))
       return(renv_bootstrap_platform_prefix_auto())
   
@@ -822,24 +842,23 @@ local({
   
     # the loaded version of renv doesn't match the requested version;
     # give the user instructions on how to proceed
-    remote <- if (!is.null(description[["RemoteSha"]])) {
+    dev <- identical(description[["RemoteType"]], "github")
+    remote <- if (dev)
       paste("rstudio/renv", description[["RemoteSha"]], sep = "@")
-    } else {
+    else
       paste("renv", description[["Version"]], sep = "@")
-    }
   
     # display both loaded version + sha if available
     friendly <- renv_bootstrap_version_friendly(
       version = description[["Version"]],
-      sha     = description[["RemoteSha"]]
+      sha     = if (dev) description[["RemoteSha"]]
     )
   
-    fmt <- paste(
-      "renv %1$s was loaded from project library, but this project is configured to use renv %2$s.",
-      "- Use `renv::record(\"%3$s\")` to record renv %1$s in the lockfile.",
-      "- Use `renv::restore(packages = \"renv\")` to install renv %2$s into the project library.",
-      sep = "\n"
-    )
+    fmt <- heredoc("
+      renv %1$s was loaded from project library, but this project is configured to use renv %2$s.
+      - Use `renv::record(\"%3$s\")` to record renv %1$s in the lockfile.
+      - Use `renv::restore(packages = \"renv\")` to install renv %2$s into the project library.
+    ")
     catf(fmt, friendly, renv_bootstrap_version_friendly(version), remote)
   
     FALSE
diff --git a/renv/profiles/lesson-requirements/renv.lock b/renv/profiles/lesson-requirements/renv.lock
index 59eb583..43537ea 100644
--- a/renv/profiles/lesson-requirements/renv.lock
+++ b/renv/profiles/lesson-requirements/renv.lock
@@ -1,27 +1,7 @@
 {
   "R": {
-    "Version": "4.3.2",
+    "Version": "4.4.0",
     "Repositories": [
-      {
-        "Name": "BioCsoft",
-        "URL": "https://bioconductor.org/packages/3.18/bioc"
-      },
-      {
-        "Name": "BioCann",
-        "URL": "https://bioconductor.org/packages/3.18/data/annotation"
-      },
-      {
-        "Name": "BioCexp",
-        "URL": "https://bioconductor.org/packages/3.18/data/experiment"
-      },
-      {
-        "Name": "BioCworkflows",
-        "URL": "https://bioconductor.org/packages/3.18/workflows"
-      },
-      {
-        "Name": "BioCbooks",
-        "URL": "https://bioconductor.org/packages/3.18/books"
-      },
       {
         "Name": "carpentries",
         "URL": "https://carpentries.r-universe.dev"
@@ -37,13 +17,14 @@
     ]
   },
   "Bioconductor": {
-    "Version": "3.18"
+    "Version": "3.19"
   },
   "Packages": {
     "AUCell": {
       "Package": "AUCell",
-      "Version": "1.24.0",
+      "Version": "1.26.0",
       "Source": "Bioconductor",
+      "Repository": "Bioconductor 3.19",
       "Requirements": [
         "BiocGenerics",
         "DelayedArray",
@@ -57,16 +38,16 @@
         "graphics",
         "methods",
         "mixtools",
-        "shiny",
         "stats",
         "utils"
       ],
-      "Hash": "ce7561b7d55ab86b1046ad9d3435355d"
+      "Hash": "40f8fe9c663d117a1486e7716f148891"
     },
     "AnnotationDbi": {
       "Package": "AnnotationDbi",
-      "Version": "1.64.1",
+      "Version": "1.66.0",
       "Source": "Bioconductor",
+      "Repository": "Bioconductor 3.19",
       "Requirements": [
         "Biobase",
         "BiocGenerics",
@@ -80,12 +61,13 @@
         "stats",
         "stats4"
       ],
-      "Hash": "27587689922e22f60ec9ad0182a0a825"
+      "Hash": "b7df9c597fb5533fc8248d73b8c703ac"
     },
     "AnnotationFilter": {
       "Package": "AnnotationFilter",
-      "Version": "1.26.0",
-      "Source": "Bioconductor",
+      "Version": "1.28.0",
+      "Source": "Repository",
+      "Repository": "https://bioconductor.org/packages/3.19/bioc",
       "Requirements": [
         "GenomicRanges",
         "R",
@@ -93,12 +75,13 @@
         "methods",
         "utils"
       ],
-      "Hash": "759acec0b1522c1a85c6ba703d4c0ec5"
+      "Hash": "24e809470aef6d81b25003d775b2fb56"
     },
     "AnnotationHub": {
       "Package": "AnnotationHub",
-      "Version": "3.10.0",
+      "Version": "3.12.0",
       "Source": "Bioconductor",
+      "Repository": "Bioconductor 3.19",
       "Requirements": [
         "AnnotationDbi",
         "BiocFileCache",
@@ -111,13 +94,12 @@
         "dplyr",
         "grDevices",
         "httr",
-        "interactiveDisplayBase",
         "methods",
         "rappdirs",
         "utils",
         "yaml"
       ],
-      "Hash": "a25fbabd5d4c7bf62d7149443b21a35d"
+      "Hash": "346ca347b61989d1da5f655d7bac6a8c"
     },
     "BH": {
       "Package": "BH",
@@ -128,20 +110,22 @@
     },
     "Biobase": {
       "Package": "Biobase",
-      "Version": "2.62.0",
+      "Version": "2.64.0",
       "Source": "Bioconductor",
+      "Repository": "Bioconductor 3.19",
       "Requirements": [
         "BiocGenerics",
         "R",
         "methods",
         "utils"
       ],
-      "Hash": "38252a34e82d3ff6bb46b4e2252d2dce"
+      "Hash": "9bc4cabd3bfda461409172213d932813"
     },
     "BiocFileCache": {
       "Package": "BiocFileCache",
-      "Version": "2.10.1",
+      "Version": "2.12.0",
       "Source": "Bioconductor",
+      "Repository": "Bioconductor 3.19",
       "Requirements": [
         "DBI",
         "R",
@@ -155,12 +139,13 @@
         "stats",
         "utils"
       ],
-      "Hash": "ac2a12468b948654220ed90ae94e9d08"
+      "Hash": "9c3414bcfae204d56080dd0f0a220136"
     },
     "BiocGenerics": {
       "Package": "BiocGenerics",
-      "Version": "0.48.1",
+      "Version": "0.50.0",
       "Source": "Bioconductor",
+      "Repository": "Bioconductor 3.19",
       "Requirements": [
         "R",
         "graphics",
@@ -168,12 +153,13 @@
         "stats",
         "utils"
       ],
-      "Hash": "e34278c65d7dffcc08f737bf0944ca9a"
+      "Hash": "ef32d07aafdd12f24c5827374ae3590d"
     },
     "BiocIO": {
       "Package": "BiocIO",
-      "Version": "1.12.0",
+      "Version": "1.14.0",
       "Source": "Bioconductor",
+      "Repository": "Bioconductor 3.19",
       "Requirements": [
         "BiocGenerics",
         "R",
@@ -181,23 +167,23 @@
         "methods",
         "tools"
       ],
-      "Hash": "aa543468283543c9a8dad23a4897be96"
+      "Hash": "f97a7ef01d364cf20d1946d43a3d526f"
     },
     "BiocManager": {
       "Package": "BiocManager",
-      "Version": "1.30.22",
+      "Version": "1.30.23",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "utils"
       ],
-      "Hash": "d57e43105a1aa9cb54fdb4629725acb1"
+      "Hash": "47e968dfe563c1b22c2e20a067ec21d5"
     },
     "BiocNeighbors": {
       "Package": "BiocNeighbors",
-      "Version": "1.20.2",
+      "Version": "1.22.0",
       "Source": "Bioconductor",
-      "Repository": "Bioconductor 3.18",
+      "Repository": "Bioconductor 3.19",
       "Requirements": [
         "BiocParallel",
         "Matrix",
@@ -207,12 +193,13 @@
         "methods",
         "stats"
       ],
-      "Hash": "c5c8ade5852fd3b25c66ec28873d00f1"
+      "Hash": "da9f332c88453734623406dcca13ee03"
     },
     "BiocParallel": {
       "Package": "BiocParallel",
-      "Version": "1.36.0",
+      "Version": "1.38.0",
       "Source": "Bioconductor",
+      "Repository": "Bioconductor 3.19",
       "Requirements": [
         "BH",
         "R",
@@ -225,12 +212,13 @@
         "stats",
         "utils"
       ],
-      "Hash": "6d1689ee8b65614ba6ef4012a67b663a"
+      "Hash": "7b6e79f86e3d1c23f62c5e2052e848d4"
     },
     "BiocSingular": {
       "Package": "BiocSingular",
-      "Version": "1.18.0",
+      "Version": "1.20.0",
       "Source": "Bioconductor",
+      "Repository": "Bioconductor 3.19",
       "Requirements": [
         "BiocGenerics",
         "BiocParallel",
@@ -245,12 +233,13 @@
         "rsvd",
         "utils"
       ],
-      "Hash": "bed2b7ea3b0b0b31387d1d80286abb97"
+      "Hash": "9d2e9fbd803f4eddfeb307b1ee376aad"
     },
     "BiocStyle": {
       "Package": "BiocStyle",
-      "Version": "2.30.0",
+      "Version": "2.32.0",
       "Source": "Bioconductor",
+      "Repository": "Bioconductor 3.19",
       "Requirements": [
         "BiocManager",
         "bookdown",
@@ -260,22 +249,23 @@
         "utils",
         "yaml"
       ],
-      "Hash": "1e22f9ad3acac55ff3069c5292d858cd"
+      "Hash": "d93773e50f3776f134734d8320bec61f"
     },
     "BiocVersion": {
       "Package": "BiocVersion",
-      "Version": "3.18.1",
+      "Version": "3.19.1",
       "Source": "Bioconductor",
+      "Repository": "Bioconductor 3.19",
       "Requirements": [
         "R"
       ],
-      "Hash": "2ecaed86684f5fae76ed5530f9d29c4a"
+      "Hash": "b892e27fc9659a4c8f8787d34c37b8b2"
     },
     "Biostrings": {
       "Package": "Biostrings",
-      "Version": "2.70.3",
+      "Version": "2.72.0",
       "Source": "Bioconductor",
-      "Repository": "Bioconductor 3.18",
+      "Repository": "Bioconductor 3.19",
       "Requirements": [
         "BiocGenerics",
         "GenomeInfoDb",
@@ -285,17 +275,17 @@
         "XVector",
         "crayon",
         "grDevices",
-        "graphics",
         "methods",
         "stats",
         "utils"
       ],
-      "Hash": "86ffa781f132f54e9c963a13fd6cf9fc"
+      "Hash": "48618c7c7b90b503837824ebcfee6363"
     },
     "BumpyMatrix": {
       "Package": "BumpyMatrix",
-      "Version": "1.10.0",
+      "Version": "1.12.0",
       "Source": "Bioconductor",
+      "Repository": "Bioconductor 3.19",
       "Requirements": [
         "IRanges",
         "Matrix",
@@ -303,7 +293,7 @@
         "methods",
         "utils"
       ],
-      "Hash": "746b6ebb83983ce7ecdee26c613fd588"
+      "Hash": "3b8df7cee39a58edeb161fededd5086c"
     },
     "Cairo": {
       "Package": "Cairo",
@@ -317,6 +307,39 @@
       ],
       "Hash": "3918e6b40d27984ca4a99c73b92406c3"
     },
+    "CuratedAtlasQueryR": {
+      "Package": "CuratedAtlasQueryR",
+      "Version": "1.2.0",
+      "Source": "Bioconductor",
+      "Repository": "Bioconductor 3.19",
+      "Requirements": [
+        "BiocGenerics",
+        "DBI",
+        "HDF5Array",
+        "R",
+        "S4Vectors",
+        "Seurat",
+        "SeuratObject",
+        "SingleCellExperiment",
+        "SummarizedExperiment",
+        "assertthat",
+        "cli",
+        "dbplyr",
+        "dplyr",
+        "duckdb",
+        "glue",
+        "httr",
+        "methods",
+        "purrr",
+        "rlang",
+        "stats",
+        "stringr",
+        "tibble",
+        "tools",
+        "utils"
+      ],
+      "Hash": "534696c0023f797cf38c578c7c8d027e"
+    },
     "DBI": {
       "Package": "DBI",
       "Version": "1.2.2",
@@ -328,27 +351,11 @@
       ],
       "Hash": "164809cd72e1d5160b4cb3aa57f510fe"
     },
-    "DT": {
-      "Package": "DT",
-      "Version": "0.32",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "crosstalk",
-        "htmltools",
-        "htmlwidgets",
-        "httpuv",
-        "jquerylib",
-        "jsonlite",
-        "magrittr",
-        "promises"
-      ],
-      "Hash": "0d3ab8abbb0c3e3daa47d4dc8e17bbae"
-    },
     "DelayedArray": {
       "Package": "DelayedArray",
-      "Version": "0.28.0",
+      "Version": "0.30.1",
       "Source": "Bioconductor",
+      "Repository": "Bioconductor 3.19",
       "Requirements": [
         "BiocGenerics",
         "IRanges",
@@ -362,12 +369,13 @@
         "stats",
         "stats4"
       ],
-      "Hash": "0e5c84e543a3d04ce64c6f60ed46d7eb"
+      "Hash": "395472c65cd9d606a1a345687102f299"
     },
     "DelayedMatrixStats": {
       "Package": "DelayedMatrixStats",
-      "Version": "1.24.0",
+      "Version": "1.26.0",
       "Source": "Bioconductor",
+      "Repository": "Bioconductor 3.19",
       "Requirements": [
         "DelayedArray",
         "IRanges",
@@ -377,12 +385,13 @@
         "methods",
         "sparseMatrixStats"
       ],
-      "Hash": "71c2d178d33f9d91999f67dc2d53b747"
+      "Hash": "5d9536664ccddb0eaa68a90afe4ee76e"
     },
     "DropletUtils": {
       "Package": "DropletUtils",
-      "Version": "1.22.0",
+      "Version": "1.24.0",
       "Source": "Bioconductor",
+      "Repository": "Bioconductor 3.19",
       "Requirements": [
         "BH",
         "BiocGenerics",
@@ -408,12 +417,13 @@
         "stats",
         "utils"
       ],
-      "Hash": "be3893d30c97591f1d3ec6f053830c3a"
+      "Hash": "77f762ad74d48a0ef578fc81deded039"
     },
     "EnsDb.Mmusculus.v79": {
       "Package": "EnsDb.Mmusculus.v79",
       "Version": "2.99.0",
-      "Source": "Bioconductor",
+      "Source": "Repository",
+      "Repository": "https://bioconductor.org/packages/3.19/data/annotation",
       "Requirements": [
         "ensembldb"
       ],
@@ -421,8 +431,9 @@
     },
     "ExperimentHub": {
       "Package": "ExperimentHub",
-      "Version": "2.10.0",
+      "Version": "2.12.0",
       "Source": "Bioconductor",
+      "Repository": "Bioconductor 3.19",
       "Requirements": [
         "AnnotationHub",
         "BiocFileCache",
@@ -433,7 +444,7 @@
         "rappdirs",
         "utils"
       ],
-      "Hash": "fb43ec028a58aa8a8539d79ea936d39f"
+      "Hash": "988693270e5886a33c536dda6b3c9f98"
     },
     "FNN": {
       "Package": "FNN",
@@ -447,8 +458,9 @@
     },
     "GSEABase": {
       "Package": "GSEABase",
-      "Version": "1.64.0",
+      "Version": "1.66.0",
       "Source": "Bioconductor",
+      "Repository": "Bioconductor 3.19",
       "Requirements": [
         "AnnotationDbi",
         "Biobase",
@@ -459,41 +471,41 @@
         "graph",
         "methods"
       ],
-      "Hash": "96e2adf800dc97758f8c5a36b98d8fef"
+      "Hash": "b55026a2047cdc8fbadac8670eb6fd8b"
     },
     "GenomeInfoDb": {
       "Package": "GenomeInfoDb",
-      "Version": "1.38.8",
+      "Version": "1.40.0",
       "Source": "Bioconductor",
-      "Repository": "Bioconductor 3.18",
+      "Repository": "Bioconductor 3.19",
       "Requirements": [
         "BiocGenerics",
         "GenomeInfoDbData",
         "IRanges",
         "R",
-        "RCurl",
         "S4Vectors",
+        "UCSC.utils",
         "methods",
         "stats",
         "stats4",
         "utils"
       ],
-      "Hash": "155053909d2831bfac154a1118151d6b"
+      "Hash": "614124bc9fb80d222cfa0d2e3e76c339"
     },
     "GenomeInfoDbData": {
       "Package": "GenomeInfoDbData",
-      "Version": "1.2.11",
+      "Version": "1.2.12",
       "Source": "Bioconductor",
       "Requirements": [
         "R"
       ],
-      "Hash": "10f32956181d1d46bd8402c93ac193e8"
+      "Hash": "c3c792a7b7f2677be56e8632c5b7543d"
     },
     "GenomicAlignments": {
       "Package": "GenomicAlignments",
-      "Version": "1.38.2",
+      "Version": "1.40.0",
       "Source": "Bioconductor",
-      "Repository": "Bioconductor 3.18",
+      "Repository": "Bioconductor 3.19",
       "Requirements": [
         "BiocGenerics",
         "BiocParallel",
@@ -509,42 +521,36 @@
         "stats",
         "utils"
       ],
-      "Hash": "3447de036330c8c2ae54f064c8f4e299"
+      "Hash": "e539709764587c581b31e446dc84d7b8"
     },
     "GenomicFeatures": {
       "Package": "GenomicFeatures",
-      "Version": "1.54.4",
-      "Source": "Bioconductor",
-      "Repository": "Bioconductor 3.18",
+      "Version": "1.56.0",
+      "Source": "Repository",
+      "Repository": "https://bioconductor.org/packages/3.19/bioc",
       "Requirements": [
         "AnnotationDbi",
-        "Biobase",
         "BiocGenerics",
-        "BiocIO",
         "Biostrings",
         "DBI",
         "GenomeInfoDb",
         "GenomicRanges",
         "IRanges",
         "R",
-        "RSQLite",
         "S4Vectors",
         "XVector",
-        "biomaRt",
-        "httr",
         "methods",
-        "rjson",
         "rtracklayer",
         "stats",
-        "tools",
         "utils"
       ],
-      "Hash": "28667ac05b72cf841adf792154f387de"
+      "Hash": "0d19619d13b06b9dea85993ce7f09c52"
     },
     "GenomicRanges": {
       "Package": "GenomicRanges",
-      "Version": "1.54.1",
+      "Version": "1.56.0",
       "Source": "Bioconductor",
+      "Repository": "Bioconductor 3.19",
       "Requirements": [
         "BiocGenerics",
         "GenomeInfoDb",
@@ -557,13 +563,13 @@
         "stats4",
         "utils"
       ],
-      "Hash": "7e0c1399af35369312d9c399454374e8"
+      "Hash": "0fab423e3f49e207681eb404d9182a1e"
     },
     "HDF5Array": {
       "Package": "HDF5Array",
-      "Version": "1.30.1",
+      "Version": "1.32.0",
       "Source": "Bioconductor",
-      "Repository": "Bioconductor 3.18",
+      "Repository": "Bioconductor 3.19",
       "Requirements": [
         "BiocGenerics",
         "DelayedArray",
@@ -580,12 +586,13 @@
         "tools",
         "utils"
       ],
-      "Hash": "9b8deb4fd34fa439c16c829457d1968f"
+      "Hash": "b10ddb24baf506cf7b4bc868ae65b984"
     },
     "IRanges": {
       "Package": "IRanges",
-      "Version": "2.36.0",
+      "Version": "2.38.0",
       "Source": "Bioconductor",
+      "Repository": "Bioconductor 3.19",
       "Requirements": [
         "BiocGenerics",
         "R",
@@ -595,12 +602,13 @@
         "stats4",
         "utils"
       ],
-      "Hash": "f98500eeb93e8a66ad65be955a848595"
+      "Hash": "836770692f7c8401090519228b93af32"
     },
     "KEGGREST": {
       "Package": "KEGGREST",
-      "Version": "1.42.0",
+      "Version": "1.44.0",
       "Source": "Bioconductor",
+      "Repository": "Bioconductor 3.19",
       "Requirements": [
         "Biostrings",
         "R",
@@ -608,22 +616,22 @@
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@@ -3571,14 +3560,15 @@
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@@ -3659,13 +3649,13 @@
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@@ -3679,12 +3669,13 @@
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@@ -3692,7 +3683,7 @@
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@@ -3757,7 +3748,7 @@
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@@ -3765,7 +3756,7 @@
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@@ -3781,19 +3772,6 @@
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@@ -3815,8 +3793,9 @@
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@@ -3829,14 +3808,14 @@
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