diff --git a/renv.lock b/renv.lock
index 77b2b62..5e0a5bc 100644
--- a/renv.lock
+++ b/renv.lock
@@ -1,6 +1,6 @@
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@@ -29,7 +29,7 @@
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@@ -73,34 +73,31 @@
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@@ -108,7 +105,7 @@
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@@ -122,9 +119,9 @@
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@@ -134,13 +131,12 @@
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@@ -174,23 +169,22 @@
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@@ -200,11 +194,12 @@
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@@ -242,31 +237,32 @@
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@@ -280,9 +276,8 @@
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@@ -296,13 +291,12 @@
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@@ -312,7 +306,7 @@
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@@ -345,9 +339,8 @@
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@@ -355,7 +348,7 @@
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@@ -404,37 +397,36 @@
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@@ -447,16 +439,15 @@
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@@ -475,13 +466,12 @@
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@@ -491,11 +481,11 @@
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@@ -506,7 +496,7 @@
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@@ -527,20 +517,18 @@
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@@ -556,7 +544,7 @@
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@@ -578,6 +566,37 @@
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@@ -616,7 +635,7 @@
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@@ -783,13 +799,13 @@
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@@ -827,7 +842,7 @@
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@@ -1076,11 +1091,11 @@
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     },
     "sessioninfo": {
       "Package": "sessioninfo",
@@ -3560,7 +3575,7 @@
     },
     "shiny": {
       "Package": "shiny",
-      "Version": "1.8.1.1",
+      "Version": "1.8.0",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -3570,6 +3585,7 @@
         "cachem",
         "commonmark",
         "crayon",
+        "ellipsis",
         "fastmap",
         "fontawesome",
         "glue",
@@ -3589,7 +3605,7 @@
         "withr",
         "xtable"
       ],
-      "Hash": "54b26646816af9960a4c64d8ceec75d6"
+      "Hash": "3a1f41807d648a908e3c7f0334bf85e6"
     },
     "sitmo": {
       "Package": "sitmo",
@@ -3625,7 +3641,7 @@
     },
     "sp": {
       "Package": "sp",
-      "Version": "2.1-4",
+      "Version": "2.1-3",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -3638,13 +3654,12 @@
         "stats",
         "utils"
       ],
-      "Hash": "75940133cca2e339afce15a586f85b11"
+      "Hash": "1a0cc0cec2915700e63fd0921085cf6a"
     },
     "sparseMatrixStats": {
       "Package": "sparseMatrixStats",
-      "Version": "1.16.0",
+      "Version": "1.14.0",
       "Source": "Bioconductor",
-      "Repository": "Bioconductor 3.19",
       "Requirements": [
         "Matrix",
         "MatrixGenerics",
@@ -3652,7 +3667,7 @@
         "matrixStats",
         "methods"
       ],
-      "Hash": "7e500a5a527460ca0406473bdcade286"
+      "Hash": "49383d0f6c6152ff7cb594f254c23cc8"
     },
     "stringi": {
       "Package": "stringi",
@@ -3686,7 +3701,7 @@
     },
     "survival": {
       "Package": "survival",
-      "Version": "3.5-8",
+      "Version": "3.5-7",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -3698,7 +3713,7 @@
         "stats",
         "utils"
       ],
-      "Hash": "184d7799bca4ba8c3be72ea396f4b9a3"
+      "Hash": "b8e943d262c3da0b0febd3e04517c197"
     },
     "svglite": {
       "Package": "svglite",
@@ -3721,14 +3736,14 @@
     },
     "systemfonts": {
       "Package": "systemfonts",
-      "Version": "1.0.6",
+      "Version": "1.0.5",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "R",
         "cpp11"
       ],
-      "Hash": "6d538cff441f0f1f36db2209ac7495ac"
+      "Hash": "15b594369e70b975ba9f064295983499"
     },
     "tensorA": {
       "Package": "tensorA",
@@ -3743,7 +3758,7 @@
     },
     "testthat": {
       "Package": "testthat",
-      "Version": "3.2.1.1",
+      "Version": "3.2.1",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -3768,7 +3783,7 @@
         "waldo",
         "withr"
       ],
-      "Hash": "3f6e7e5e2220856ff865e4834766bf2b"
+      "Hash": "4767a686ebe986e6cb01d075b3f09729"
     },
     "textshaping": {
       "Package": "textshaping",
@@ -3826,7 +3841,7 @@
     },
     "tidyselect": {
       "Package": "tidyselect",
-      "Version": "1.2.1",
+      "Version": "1.2.0",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -3838,7 +3853,7 @@
         "vctrs",
         "withr"
       ],
-      "Hash": "829f27b9c4919c16b593794a6344d6c0"
+      "Hash": "79540e5fcd9e0435af547d885f184fd5"
     },
     "tidytree": {
       "Package": "tidytree",
@@ -3864,19 +3879,18 @@
     },
     "tinytex": {
       "Package": "tinytex",
-      "Version": "0.50",
+      "Version": "0.49",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "xfun"
       ],
-      "Hash": "be7a76845222ad20adb761f462eed3ea"
+      "Hash": "5ac22900ae0f386e54f1c307eca7d843"
     },
     "treeio": {
       "Package": "treeio",
-      "Version": "1.28.0",
+      "Version": "1.26.0",
       "Source": "Bioconductor",
-      "Repository": "Bioconductor 3.19",
       "Requirements": [
         "R",
         "ape",
@@ -3888,10 +3902,9 @@
         "stats",
         "tibble",
         "tidytree",
-        "utils",
-        "yulab.utils"
+        "utils"
       ],
-      "Hash": "9e0a0b700763836cd36cb3a49be5a15d"
+      "Hash": "a09203806aa0bc49965563ca7016620e"
     },
     "tzdb": {
       "Package": "tzdb",
@@ -3920,7 +3933,7 @@
     },
     "usethis": {
       "Package": "usethis",
-      "Version": "2.2.3",
+      "Version": "2.2.2",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -3947,7 +3960,7 @@
         "withr",
         "yaml"
       ],
-      "Hash": "d524fd42c517035027f866064417d7e6"
+      "Hash": "60e51f0b94d0324dc19e44110098fa9f"
     },
     "utf8": {
       "Package": "utf8",
@@ -3961,13 +3974,12 @@
     },
     "uwot": {
       "Package": "uwot",
-      "Version": "0.2.2",
+      "Version": "0.1.16",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "FNN",
         "Matrix",
-        "RSpectra",
         "Rcpp",
         "RcppAnnoy",
         "RcppProgress",
@@ -3975,7 +3987,7 @@
         "irlba",
         "methods"
       ],
-      "Hash": "f693a0ca6d34b02eb432326388021805"
+      "Hash": "252deaa1c1d6d3da6946694243781ea3"
     },
     "vctrs": {
       "Package": "vctrs",
@@ -4106,15 +4118,14 @@
     },
     "xfun": {
       "Package": "xfun",
-      "Version": "0.43",
+      "Version": "0.41",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
-        "grDevices",
         "stats",
         "tools"
       ],
-      "Hash": "ab6371d8653ce5f2f9290f4ec7b42a8e"
+      "Hash": "460a5e0fe46a80ef87424ad216028014"
     },
     "xml2": {
       "Package": "xml2",
@@ -4131,14 +4142,14 @@
     },
     "xopen": {
       "Package": "xopen",
-      "Version": "1.0.1",
+      "Version": "1.0.0",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "R",
         "processx"
       ],
-      "Hash": "423df1e86d5533fcb73c6b02b4923b49"
+      "Hash": "6c85f015dee9cc7710ddd20f86881f58"
     },
     "xtable": {
       "Package": "xtable",
@@ -4185,10 +4196,9 @@
     },
     "zlibbioc": {
       "Package": "zlibbioc",
-      "Version": "1.50.0",
+      "Version": "1.48.0",
       "Source": "Bioconductor",
-      "Repository": "Bioconductor 3.19",
-      "Hash": "3db02e3c460e1c852365df117a2b441b"
+      "Hash": "50ad6f7b0baaaccf1a387d2f1ecce911"
     },
     "zoo": {
       "Package": "zoo",
diff --git a/renv/activate.R b/renv/activate.R
index d13f993..cb5401f 100644
--- a/renv/activate.R
+++ b/renv/activate.R
@@ -2,13 +2,11 @@
 local({
 
   # the requested version of renv
-  version <- "1.0.7"
+  version <- "1.0.3"
   attr(version, "sha") <- NULL
 
   # the project directory
-  project <- Sys.getenv("RENV_PROJECT")
-  if (!nzchar(project))
-    project <- getwd()
+  project <- getwd()
 
   # use start-up diagnostics if enabled
   diagnostics <- Sys.getenv("RENV_STARTUP_DIAGNOSTICS", unset = "FALSE")
@@ -33,14 +31,6 @@ local({
     if (!is.null(override))
       return(override)
 
-    # if we're being run in a context where R_LIBS is already set,
-    # don't load -- presumably we're being run as a sub-process and
-    # the parent process has already set up library paths for us
-    rcmd <- Sys.getenv("R_CMD", unset = NA)
-    rlibs <- Sys.getenv("R_LIBS", unset = NA)
-    if (!is.na(rlibs) && !is.na(rcmd))
-      return(FALSE)
-
     # next, check environment variables
     # TODO: prefer using the configuration one in the future
     envvars <- c(
@@ -60,22 +50,9 @@ local({
 
   })
 
-  # bail if we're not enabled
-  if (!enabled) {
-
-    # if we're not enabled, we might still need to manually load
-    # the user profile here
-    profile <- Sys.getenv("R_PROFILE_USER", unset = "~/.Rprofile")
-    if (file.exists(profile)) {
-      cfg <- Sys.getenv("RENV_CONFIG_USER_PROFILE", unset = "TRUE")
-      if (tolower(cfg) %in% c("true", "t", "1"))
-        sys.source(profile, envir = globalenv())
-    }
-
+  if (!enabled)
     return(FALSE)
 
-  }
-
   # avoid recursion
   if (identical(getOption("renv.autoloader.running"), TRUE)) {
     warning("ignoring recursive attempt to run renv autoloader")
@@ -131,21 +108,6 @@ 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
   }
@@ -648,9 +610,6 @@ 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())
   
@@ -842,23 +801,24 @@ local({
   
     # the loaded version of renv doesn't match the requested version;
     # give the user instructions on how to proceed
-    dev <- identical(description[["RemoteType"]], "github")
-    remote <- if (dev)
+    remote <- if (!is.null(description[["RemoteSha"]])) {
       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     = if (dev) description[["RemoteSha"]]
+      sha     = description[["RemoteSha"]]
     )
   
-    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$s into the project library.
-    ")
+    fmt <- paste(
+      "renv %1$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"
+    )
     catf(fmt, friendly, renv_bootstrap_version_friendly(version), remote)
   
     FALSE
@@ -1081,7 +1041,7 @@ local({
     # if jsonlite is loaded, use that instead
     if ("jsonlite" %in% loadedNamespaces()) {
   
-      json <- tryCatch(renv_json_read_jsonlite(file, text), error = identity)
+      json <- catch(renv_json_read_jsonlite(file, text))
       if (!inherits(json, "error"))
         return(json)
   
@@ -1090,7 +1050,7 @@ local({
     }
   
     # otherwise, fall back to the default JSON reader
-    json <- tryCatch(renv_json_read_default(file, text), error = identity)
+    json <- catch(renv_json_read_default(file, text))
     if (!inherits(json, "error"))
       return(json)
   
@@ -1103,14 +1063,14 @@ local({
   }
   
   renv_json_read_jsonlite <- function(file = NULL, text = NULL) {
-    text <- paste(text %||% readLines(file, warn = FALSE), collapse = "\n")
+    text <- paste(text %||% read(file), collapse = "\n")
     jsonlite::fromJSON(txt = text, simplifyVector = FALSE)
   }
   
   renv_json_read_default <- function(file = NULL, text = NULL) {
   
     # find strings in the JSON
-    text <- paste(text %||% readLines(file, warn = FALSE), collapse = "\n")
+    text <- paste(text %||% read(file), collapse = "\n")
     pattern <- '["](?:(?:\\\\.)|(?:[^"\\\\]))*?["]'
     locs <- gregexpr(pattern, text, perl = TRUE)[[1]]
   
@@ -1158,14 +1118,14 @@ local({
     map <- as.list(map)
   
     # remap strings in object
-    remapped <- renv_json_read_remap(json, map)
+    remapped <- renv_json_remap(json, map)
   
     # evaluate
     eval(remapped, envir = baseenv())
   
   }
   
-  renv_json_read_remap <- function(json, map) {
+  renv_json_remap <- function(json, map) {
   
     # fix names
     if (!is.null(names(json))) {
@@ -1192,7 +1152,7 @@ local({
     # recurse
     if (is.recursive(json)) {
       for (i in seq_along(json)) {
-        json[i] <- list(renv_json_read_remap(json[[i]], map))
+        json[i] <- list(renv_json_remap(json[[i]], map))
       }
     }