diff --git a/renv/activate.R b/renv/activate.R
index 2ebe4034..0eb51088 100644
--- a/renv/activate.R
+++ b/renv/activate.R
@@ -2,7 +2,7 @@
 local({
 
   # the requested version of renv
-  version <- "1.0.8"
+  version <- "1.0.11"
   attr(version, "sha") <- NULL
 
   # the project directory
@@ -368,8 +368,7 @@ local({
       quiet    = TRUE
     )
   
-    if ("headers" %in% names(formals(utils::download.file)))
-    {
+    if ("headers" %in% names(formals(utils::download.file))) {
       headers <- renv_bootstrap_download_custom_headers(url)
       if (length(headers) && is.character(headers))
         args$headers <- headers
@@ -457,9 +456,8 @@ local({
   
         # add custom headers if available -- note that
         # utils::available.packages() will pass this to download.file()
-        if ("headers" %in% names(formals(utils::download.file)))
-        {
-          headers <- renv_bootstrap_download_custom_headers(url)
+        if ("headers" %in% names(formals(utils::download.file))) {
+          headers <- renv_bootstrap_download_custom_headers(repos)
           if (length(headers) && is.character(headers))
             args$headers <- headers
         }
diff --git a/renv/profiles/lesson-requirements/renv.lock b/renv/profiles/lesson-requirements/renv.lock
index e9e9dadf..c8f22c3c 100644
--- a/renv/profiles/lesson-requirements/renv.lock
+++ b/renv/profiles/lesson-requirements/renv.lock
@@ -4,23 +4,23 @@
     "Repositories": [
       {
         "Name": "BioCsoft",
-        "URL": "https://bioconductor.org/packages/3.17/bioc"
+        "URL": "https://bioconductor.org/packages/3.19/bioc"
       },
       {
         "Name": "BioCann",
-        "URL": "https://bioconductor.org/packages/3.17/data/annotation"
+        "URL": "https://bioconductor.org/packages/3.19/data/annotation"
       },
       {
         "Name": "BioCexp",
-        "URL": "https://bioconductor.org/packages/3.17/data/experiment"
+        "URL": "https://bioconductor.org/packages/3.19/data/experiment"
       },
       {
         "Name": "BioCworkflows",
-        "URL": "https://bioconductor.org/packages/3.17/workflows"
+        "URL": "https://bioconductor.org/packages/3.19/workflows"
       },
       {
         "Name": "BioCbooks",
-        "URL": "https://bioconductor.org/packages/3.17/books"
+        "URL": "https://bioconductor.org/packages/3.19/books"
       },
       {
         "Name": "carpentries",
@@ -363,7 +363,7 @@
     },
     "GenomicRanges": {
       "Package": "GenomicRanges",
-      "Version": "1.56.1",
+      "Version": "1.56.2",
       "Source": "Bioconductor",
       "Repository": "Bioconductor 3.19",
       "Requirements": [
@@ -378,7 +378,7 @@
         "stats4",
         "utils"
       ],
-      "Hash": "a3c822ef3c124828e25e7a9611beeb50"
+      "Hash": "fecd026026c4d45e3b57eee97bbbba92"
     },
     "GetoptLong": {
       "Package": "GetoptLong",
@@ -449,7 +449,7 @@
     },
     "MASS": {
       "Package": "MASS",
-      "Version": "7.3-60.2",
+      "Version": "7.3-61",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -460,11 +460,11 @@
         "stats",
         "utils"
       ],
-      "Hash": "2f342c46163b0b54d7b64d1f798e2c78"
+      "Hash": "0cafd6f0500e5deba33be22c46bf6055"
     },
     "Matrix": {
       "Package": "Matrix",
-      "Version": "1.7-0",
+      "Version": "1.7-1",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -477,7 +477,7 @@
         "stats",
         "utils"
       ],
-      "Hash": "1920b2f11133b12350024297d8a4ff4a"
+      "Hash": "5122bb14d8736372411f955e1b16bc8a"
     },
     "MatrixGenerics": {
       "Package": "MatrixGenerics",
@@ -503,7 +503,7 @@
     },
     "R.oo": {
       "Package": "R.oo",
-      "Version": "1.26.0",
+      "Version": "1.27.0",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -512,7 +512,7 @@
         "methods",
         "utils"
       ],
-      "Hash": "4fed809e53ddb5407b3da3d0f572e591"
+      "Hash": "6ac79ff194202248cf946fe3a5d6d498"
     },
     "R.utils": {
       "Package": "R.utils",
@@ -570,14 +570,14 @@
     },
     "Rcpp": {
       "Package": "Rcpp",
-      "Version": "1.0.13",
+      "Version": "1.0.13-1",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "methods",
         "utils"
       ],
-      "Hash": "f27411eb6d9c3dada5edd444b8416675"
+      "Hash": "6b868847b365672d6c1677b1608da9ed"
     },
     "RcppArmadillo": {
       "Package": "RcppArmadillo",
@@ -788,18 +788,6 @@
       ],
       "Hash": "88e77a7f8571a173db7d4f6d9bf46a64"
     },
-    "anytime": {
-      "Package": "anytime",
-      "Version": "0.3.9",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "BH",
-        "R",
-        "Rcpp"
-      ],
-      "Hash": "74a64813f17b492da9c6afda6b128e3d"
-    },
     "ape": {
       "Package": "ape",
       "Version": "5.8",
@@ -856,13 +844,13 @@
     },
     "askpass": {
       "Package": "askpass",
-      "Version": "1.2.0",
+      "Version": "1.2.1",
       "Source": "Repository",
-      "Repository": "RSPM",
+      "Repository": "CRAN",
       "Requirements": [
         "sys"
       ],
-      "Hash": "cad6cf7f1d5f6e906700b9d3e718c796"
+      "Hash": "c39f4155b3ceb1a9a2799d700fbd4b6a"
     },
     "babelgene": {
       "Package": "babelgene",
@@ -929,7 +917,7 @@
     },
     "bit64": {
       "Package": "bit64",
-      "Version": "4.0.5",
+      "Version": "4.5.2",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -939,14 +927,14 @@
         "stats",
         "utils"
       ],
-      "Hash": "9fe98599ca456d6552421db0d6772d8f"
+      "Hash": "e84984bf5f12a18628d9a02322128dfd"
     },
     "bitops": {
       "Package": "bitops",
-      "Version": "1.0-8",
+      "Version": "1.0-9",
       "Source": "Repository",
       "Repository": "CRAN",
-      "Hash": "da69e6b6f8feebec0827205aad3fdbd8"
+      "Hash": "d972ef991d58c19e6efa71b21f5e144b"
     },
     "blob": {
       "Package": "blob",
@@ -1146,10 +1134,10 @@
     },
     "commonmark": {
       "Package": "commonmark",
-      "Version": "1.9.1",
+      "Version": "1.9.2",
       "Source": "Repository",
       "Repository": "CRAN",
-      "Hash": "5d8225445acb167abf7797de48b2ee3c"
+      "Hash": "14eb0596f987c71535d07c3aff814742"
     },
     "cowplot": {
       "Package": "cowplot",
@@ -1215,14 +1203,14 @@
     },
     "data.table": {
       "Package": "data.table",
-      "Version": "1.16.0",
+      "Version": "1.16.2",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "R",
         "methods"
       ],
-      "Hash": "fb24e05d4a91d8b1c7ff8e284bde834a"
+      "Hash": "2e00b378fc3be69c865120d9f313039a"
     },
     "digest": {
       "Package": "digest",
@@ -1332,13 +1320,13 @@
     },
     "evaluate": {
       "Package": "evaluate",
-      "Version": "1.0.0",
+      "Version": "1.0.1",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "R"
       ],
-      "Hash": "6b567375113ceb7d9f800de4dd42218e"
+      "Hash": "3fd29944b231036ad67c3edb32e02201"
     },
     "fansi": {
       "Package": "fansi",
@@ -1435,14 +1423,14 @@
     },
     "fs": {
       "Package": "fs",
-      "Version": "1.6.4",
+      "Version": "1.6.5",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "R",
         "methods"
       ],
-      "Hash": "15aeb8c27f5ea5161f9f6a641fafd93a"
+      "Hash": "7f48af39fa27711ea5fbd183b399920d"
     },
     "futile.logger": {
       "Package": "futile.logger",
@@ -1509,7 +1497,7 @@
     },
     "ggfun": {
       "Package": "ggfun",
-      "Version": "0.1.6",
+      "Version": "0.1.7",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -1522,7 +1510,7 @@
         "utils",
         "yulab.utils"
       ],
-      "Hash": "c56e3463c7358ced17ce79a4cab0fb65"
+      "Hash": "e20ff08a801abd734bf95801ef02adba"
     },
     "ggnewscale": {
       "Package": "ggnewscale",
@@ -1651,18 +1639,18 @@
     },
     "glue": {
       "Package": "glue",
-      "Version": "1.7.0",
+      "Version": "1.8.0",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "R",
         "methods"
       ],
-      "Hash": "e0b3a53876554bd45879e596cdb10a52"
+      "Hash": "5899f1eaa825580172bb56c08266f37c"
     },
     "gplots": {
       "Package": "gplots",
-      "Version": "3.1.3.1",
+      "Version": "3.2.0",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -1673,11 +1661,11 @@
         "methods",
         "stats"
       ],
-      "Hash": "f72b5d1ed587f8905e38ee7295e88d80"
+      "Hash": "d24febf39c58dcb5a6cc6a12bd66d40a"
     },
     "graphlayouts": {
       "Package": "graphlayouts",
-      "Version": "1.1.1",
+      "Version": "1.2.0",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -1686,7 +1674,7 @@
         "RcppArmadillo",
         "igraph"
       ],
-      "Hash": "d329345a6a37666ca3f18f3b3c1347b7"
+      "Hash": "de8fa8478dfcc1913017ff3577d175a2"
     },
     "gridExtra": {
       "Package": "gridExtra",
@@ -1731,7 +1719,7 @@
     },
     "gtable": {
       "Package": "gtable",
-      "Version": "0.3.5",
+      "Version": "0.3.6",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -1740,9 +1728,10 @@
         "glue",
         "grid",
         "lifecycle",
-        "rlang"
+        "rlang",
+        "stats"
       ],
-      "Hash": "e18861963cbc65a27736e02b3cd3c4a0"
+      "Hash": "de949855009e2d4d0e52a844e30617ae"
     },
     "gtools": {
       "Package": "gtools",
@@ -1832,6 +1821,7 @@
       "Version": "1.6.15",
       "Source": "Repository",
       "Repository": "https://carpentries.r-universe.dev",
+      "RemoteType": "repository",
       "RemoteUrl": "https://github.com/rstudio/httpuv",
       "RemoteRef": "v1.6.15",
       "RemoteSha": "19631930c178ee7ffb5e712eefc9b08d94db23f4",
@@ -1843,7 +1833,7 @@
         "promises",
         "utils"
       ],
-      "Hash": "d55aa087c47a63ead0f6fc10f8fa1ee0"
+      "Hash": "c1c6e229019b05f992c00efc8bc7f0ae"
     },
     "httr": {
       "Package": "httr",
@@ -1862,7 +1852,7 @@
     },
     "httr2": {
       "Package": "httr2",
-      "Version": "1.0.4",
+      "Version": "1.0.6",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -1879,7 +1869,7 @@
         "vctrs",
         "withr"
       ],
-      "Hash": "836e9564fbeca3bb390bb429a53cd401"
+      "Hash": "3ef5d07ec78803475a94367d71b40c41"
     },
     "iSEE": {
       "Package": "iSEE",
@@ -1919,7 +1909,7 @@
     },
     "igraph": {
       "Package": "igraph",
-      "Version": "2.0.3",
+      "Version": "2.1.1",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -1938,7 +1928,7 @@
         "utils",
         "vctrs"
       ],
-      "Hash": "c3b7d801d722e26e4cd888e042bf9af5"
+      "Hash": "c03878b48737a0e2da3b772d7b2e22da"
     },
     "isoband": {
       "Package": "isoband",
@@ -2071,7 +2061,7 @@
     },
     "limma": {
       "Package": "limma",
-      "Version": "3.60.4",
+      "Version": "3.60.6",
       "Source": "Bioconductor",
       "Repository": "Bioconductor 3.19",
       "Requirements": [
@@ -2083,7 +2073,7 @@
         "stats",
         "utils"
       ],
-      "Hash": "b75950d7143715041064b21f3120f19e"
+      "Hash": "0eccf07d5db97b84a912922e1d29e130"
     },
     "listviewer": {
       "Package": "listviewer",
@@ -2219,18 +2209,18 @@
     },
     "mvtnorm": {
       "Package": "mvtnorm",
-      "Version": "1.3-1",
+      "Version": "1.3-2",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "R",
         "stats"
       ],
-      "Hash": "77c61d51ce0f36e3c1a76e6b295aab31"
+      "Hash": "9e8405eacb262c0a939e121650247f4b"
     },
     "nlme": {
       "Package": "nlme",
-      "Version": "3.1-164",
+      "Version": "3.1-166",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -2240,7 +2230,7 @@
         "stats",
         "utils"
       ],
-      "Hash": "a623a2239e642806158bc4dc3f51565d"
+      "Hash": "ccbb8846be320b627e6aa2b4616a2ded"
     },
     "numDeriv": {
       "Package": "numDeriv",
@@ -2435,13 +2425,13 @@
     },
     "renv": {
       "Package": "renv",
-      "Version": "1.0.8",
+      "Version": "1.0.11",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "utils"
       ],
-      "Hash": "e082251834fa427514e68bec8afc8fda"
+      "Hash": "47623f66b4e80b3b0587bc5d7b309888"
     },
     "reshape2": {
       "Package": "reshape2",
@@ -2491,7 +2481,7 @@
     },
     "rmarkdown": {
       "Package": "rmarkdown",
-      "Version": "2.28",
+      "Version": "2.29",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -2510,7 +2500,7 @@
         "xfun",
         "yaml"
       ],
-      "Hash": "062470668513dcda416927085ee9bdc7"
+      "Hash": "df99277f63d01c34e95e3d2f06a79736"
     },
     "sass": {
       "Package": "sass",
@@ -2626,7 +2616,7 @@
     },
     "shinyAce": {
       "Package": "shinyAce",
-      "Version": "0.4.2",
+      "Version": "0.4.3",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -2636,16 +2626,15 @@
         "tools",
         "utils"
       ],
-      "Hash": "99b2ee37c4f174539b1b0d920b00d16c"
+      "Hash": "85be5927b81f793a6137bae87d2a67ca"
     },
     "shinyWidgets": {
       "Package": "shinyWidgets",
-      "Version": "0.8.6",
+      "Version": "0.8.7",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "R",
-        "anytime",
         "bslib",
         "grDevices",
         "htmltools",
@@ -2654,7 +2643,7 @@
         "sass",
         "shiny"
       ],
-      "Hash": "bc918b6911c4e928e24a9928295de834"
+      "Hash": "fd8239886f70daa85c36596214958451"
     },
     "shinydashboard": {
       "Package": "shinydashboard",
@@ -2721,6 +2710,7 @@
       "Version": "1.8.4",
       "Source": "Repository",
       "Repository": "https://carpentries.r-universe.dev",
+      "RemoteType": "repository",
       "RemoteUrl": "https://github.com/gagolews/stringi",
       "RemoteRef": "v1.8.4",
       "RemoteSha": "f5a91d1869ec4c757d37519f710ec1fa4f74a1c8",
@@ -2730,7 +2720,7 @@
         "tools",
         "utils"
       ],
-      "Hash": "39e1144fd75428983dc3f63aa53dfa91"
+      "Hash": "83b5725abc57a3f2537ccbc54607b05f"
     },
     "stringr": {
       "Package": "stringr",
@@ -2751,16 +2741,17 @@
     },
     "sys": {
       "Package": "sys",
-      "Version": "3.4.2",
+      "Version": "3.4.3",
       "Source": "Repository",
       "Repository": "CRAN",
-      "Hash": "3a1be13d68d47a8cd0bfd74739ca1555"
+      "Hash": "de342ebfebdbf40477d0758d05426646"
     },
     "systemfonts": {
       "Package": "systemfonts",
       "Version": "1.1.0",
       "Source": "Repository",
       "Repository": "https://carpentries.r-universe.dev",
+      "RemoteType": "repository",
       "RemoteUrl": "https://github.com/r-lib/systemfonts",
       "RemoteRef": "v1.1.0",
       "RemoteSha": "78df90ca6d869feeb6a40c88f72269093505aa22",
@@ -2769,7 +2760,7 @@
         "cpp11",
         "lifecycle"
       ],
-      "Hash": "213b6b8ed5afbf934843e6c3b090d418"
+      "Hash": "a03c27eb829b7acec0b6e18c3edf8788"
     },
     "tibble": {
       "Package": "tibble",
@@ -2876,13 +2867,13 @@
     },
     "tinytex": {
       "Package": "tinytex",
-      "Version": "0.53",
+      "Version": "0.54",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "xfun"
       ],
-      "Hash": "9db859e8aabbb474293dde3097839420"
+      "Hash": "3ec7e3ddcacc2d34a9046941222bf94d"
     },
     "treeio": {
       "Package": "treeio",
@@ -2997,7 +2988,7 @@
     },
     "withr": {
       "Package": "withr",
-      "Version": "3.0.1",
+      "Version": "3.0.2",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -3005,11 +2996,11 @@
         "grDevices",
         "graphics"
       ],
-      "Hash": "07909200e8bbe90426fbfeb73e1e27aa"
+      "Hash": "cc2d62c76458d425210d1eb1478b30b4"
     },
     "xfun": {
       "Package": "xfun",
-      "Version": "0.47",
+      "Version": "0.49",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -3018,7 +3009,7 @@
         "stats",
         "tools"
       ],
-      "Hash": "36ab21660e2d095fef0d83f689e0477c"
+      "Hash": "8687398773806cfff9401a2feca96298"
     },
     "xtable": {
       "Package": "xtable",