Update renv to reduce GH package use

Dockerfile

@@ -91,7 +91,6 @@ RUN --mount=type=secret,id=GITHUB_TOKEN,env=GITHUB_PAT,required=false \
 # Some challenges with multi-arch builds and Bioconductor binaries mean we
 # want to be sure to set up repos manually here, lest the ones recorded in the
 # renv.lock file cause failures.
-arch <- R.version[['arch']]
 # set up repos for both BioC and CRAN
 repos <- c(
     BioCsoft = 'https://bioconductor.org/packages/3.22/bioc',

renv.lock

@@ -306,8 +306,8 @@
     },
     "Banksy": {
       "Package": "Banksy",
-      "Version": "1.9.1",
-      "Source": "GitHub",
+      "Version": "1.6.0",
+      "Source": "Bioconductor",
       "Title": "Spatial transcriptomic clustering",
       "Authors@R": "c( person(given = \"Vipul\", family = \"Singhal\", role = c(\"aut\")), person(given = \"Joseph\", family = \"Lee\", role = c(\"aut\", \"cre\"), email = \"joseph.lee@u.nus.edu\", comment = c(ORCID=\"0000-0002-4983-4714\")) )",
       "Description": "Banksy is an R package that incorporates spatial information to  cluster cells in a feature space (e.g. gene expression). To incorporate  spatial information, BANKSY computes the mean neighborhood expression and  azimuthal Gabor filters that capture gene expression gradients. These  features are combined with the cell's own expression to embed cells in a  neighbor-augmented product space which can then be clustered, allowing for accurate and spatially-aware cell typing and tissue domain segmentation.",
@@ -359,14 +359,14 @@
       "VignetteBuilder": "knitr",
       "Config/testthat/edition": "3",
       "biocViews": "Clustering, Spatial, SingleCell, GeneExpression, DimensionReduction",
+      "git_url": "https://git.bioconductor.org/packages/Banksy",
+      "git_branch": "RELEASE_3_22",
+      "git_last_commit": "6847ab5",
+      "git_last_commit_date": "2025-10-29",
+      "Repository": "Bioconductor 3.22",
+      "NeedsCompilation": "no",
       "Author": "Vipul Singhal [aut], Joseph Lee [aut, cre] (ORCID: <https://orcid.org/0000-0002-4983-4714>)",
-      "Maintainer": "Joseph Lee <joseph.lee@u.nus.edu>",
-      "RemoteType": "github",
-      "RemoteHost": "api.github.com",
-      "RemoteUsername": "bioc",
-      "RemoteRepo": "Banksy",
-      "RemoteRef": "devel",
-      "RemoteSha": "5157d9cf8020ec49c99f18d833b143b69a496762"
+      "Maintainer": "Joseph Lee <joseph.lee@u.nus.edu>"
     },
     "Biobase": {
       "Package": "Biobase",
@@ -617,7 +617,7 @@
       "NeedsCompilation": "no",
       "Author": "Martin Morgan [aut] (ORCID: <https://orcid.org/0000-0002-5874-8148>), Marcel Ramos [aut, cre] (ORCID: <https://orcid.org/0000-0002-3242-0582>)",
       "Maintainer": "Marcel Ramos <marcel.ramos@sph.cuny.edu>",
-      "Repository": "CRAN"
+      "Repository": "https://p3m.dev/cran/latest"
     },
     "BiocNeighbors": {
       "Package": "BiocNeighbors",
@@ -9398,12 +9398,6 @@
       "biocViews": "Alignment, Annotation, Clustering, DataImport, MultipleSequenceAlignment, Phylogenetics, ReproducibleResearch, Software, Visualization",
       "RoxygenNote": "7.3.3",
       "Roxygen": "list(markdown = TRUE)",
-      "git_url": "https://git.bioconductor.org/packages/ggtree",
-      "git_branch": "RELEASE_3_22",
-      "git_last_commit": "8e25254",
-      "git_last_commit_date": "2026-01-04",
-      "Repository": "Bioconductor 3.22",
-      "NeedsCompilation": "no",
       "Author": "Guangchuang Yu [aut, cre, cph] (ORCID: <https://orcid.org/0000-0002-6485-8781>), Tommy Tsan-Yuk Lam [aut, ths], Shuangbin Xu [aut] (ORCID: <https://orcid.org/0000-0003-3513-5362>), Lin Li [ctb], Bradley Jones [ctb], Justin Silverman [ctb], Watal M. Iwasaki [ctb], Yonghe Xia [ctb], Ruizhu Huang [ctb]",
       "RemoteType": "bioconductor",
       "RemoteUrl": "https://github.com/bioc/ggtree",
@@ -11050,7 +11044,7 @@
     },
     "leidenAlg": {
       "Package": "leidenAlg",
-      "Version": "1.1.7",
+      "Version": "1.1.8",
       "Source": "Repository",
       "Type": "Package",
       "Title": "Implements the Leiden Algorithm via an R Interface",
@@ -12965,10 +12959,10 @@
     "qs": {
       "Package": "qs",
       "Version": "0.27.3",
-      "Source": "GitHub",
+      "Source": "Repository",
       "Type": "Package",
       "Title": "Quick Serialization of R Objects",
-      "Date": "2025-3-6",
+      "Date": "2025-3-7",
       "Authors@R": "c( person(\"Travers\", \"Ching\", email = \"traversc@gmail.com\", role = c(\"aut\", \"cre\", \"cph\")), person(\"Yann\", \"Collet\", role = c(\"ctb\", \"cph\"), comment = \"Yann Collet is the author of the bundled zstd, lz4 and xxHash code\"), person(\"Facebook, Inc.\", role = \"cph\", comment = \"Facebook is the copyright holder of the bundled zstd code\"), person(\"Reichardt\", \"Tino\", role = c(\"ctb\", \"cph\"), comment = \"Contributor/copyright holder of zstd bundled code\"), person(\"Skibinski\", \"Przemyslaw\", role = c(\"ctb\", \"cph\"), comment = \"Contributor/copyright holder of zstd bundled code\"), person(\"Mori\", \"Yuta\", role = c(\"ctb\", \"cph\"), comment = \"Contributor/copyright holder of zstd bundled code\"), person(\"Romain\", \"Francois\", role = c(\"ctb\", \"cph\"), comment = \"Derived example/tutorials for ALTREP structures\"), person(\"Francesc\", \"Alted\", role = c(\"ctb\", \"cph\"), comment = \"Shuffling routines derived from Blosc library\"), person(\"Bryce\", \"Chamberlain\", email = \"superchordate@gmail.com\", role = c(\"ctb\"), comment = \"qsavem and qload functions\"), person(\"Salim\", \"Brüggemann\", email = \"salim-b@pm.me\", role = c(\"ctb\"), comment = \"Contributing to documentation (ORCID:0000-0002-5329-5987)\"))",
       "Maintainer": "Travers Ching <traversc@gmail.com>",
       "Description": "Provides functions for quickly writing and reading any R object to and from disk.",
@@ -12990,7 +12984,6 @@
         "BH"
       ],
       "Encoding": "UTF-8",
-      "Roxygen": "list(markdown = TRUE)",
       "RoxygenNote": "7.3.2",
       "Suggests": [
         "knitr",
@@ -13003,13 +12996,9 @@
       "Copyright": "This package includes code from the 'zstd' library owned by Facebook, Inc. and created by Yann Collet; the 'lz4' library created and owned by Yann Collet; xxHash library created and owned by Yann Collet; and code derived from the 'Blosc' library created and owned by Francesc Alted.",
       "URL": "https://github.com/qsbase/qs",
       "BugReports": "https://github.com/qsbase/qs/issues",
+      "NeedsCompilation": "yes",
       "Author": "Travers Ching [aut, cre, cph], Yann Collet [ctb, cph] (Yann Collet is the author of the bundled zstd, lz4 and xxHash code), Facebook, Inc. [cph] (Facebook is the copyright holder of the bundled zstd code), Reichardt Tino [ctb, cph] (Contributor/copyright holder of zstd bundled code), Skibinski Przemyslaw [ctb, cph] (Contributor/copyright holder of zstd bundled code), Mori Yuta [ctb, cph] (Contributor/copyright holder of zstd bundled code), Romain Francois [ctb, cph] (Derived example/tutorials for ALTREP structures), Francesc Alted [ctb, cph] (Shuffling routines derived from Blosc library), Bryce Chamberlain [ctb] (qsavem and qload functions), Salim Brüggemann [ctb] (Contributing to documentation (ORCID:0000-0002-5329-5987))",
-      "RemoteType": "github",
-      "RemoteHost": "api.github.com",
-      "RemoteUsername": "qsbase",
-      "RemoteRepo": "qs",
-      "RemoteRef": "master",
-      "RemoteSha": "eca241e1bc5f65fcec28b516ed3e4e9ccb05487f"
+      "Repository": "RSPM"
     },
     "quadprog": {
       "Package": "quadprog",
@@ -13386,7 +13375,7 @@
     },
     "renv": {
       "Package": "renv",
-      "Version": "1.1.7",
+      "Version": "1.2.3",
       "Source": "Repository",
       "Type": "Package",
       "Title": "Project Environments",
@@ -13437,7 +13426,7 @@
       "NeedsCompilation": "no",
       "Author": "Kevin Ushey [aut, cre] (ORCID: <https://orcid.org/0000-0003-2880-7407>), Hadley Wickham [aut] (ORCID: <https://orcid.org/0000-0003-4757-117X>), Posit Software, PBC [cph, fnd]",
       "Maintainer": "Kevin Ushey <kevin@rstudio.com>",
-      "Repository": "CRAN"
+      "Repository": "https://p3m.dev/cran/latest"
     },
     "reprex": {
       "Package": "reprex",
@@ -15554,10 +15543,10 @@
     },
     "stringfish": {
       "Package": "stringfish",
-      "Version": "0.17.0",
-      "Source": "GitHub",
+      "Version": "0.19.0",
+      "Source": "Repository",
       "Title": "Alt String Implementation",
-      "Date": "2025-07-12",
+      "Date": "2026-04-18",
       "Authors@R": "c( person(\"Travers\", \"Ching\", email = \"traversc@gmail.com\", role = c(\"aut\", \"cre\", \"cph\")), person(\"Phillip\", \"Hazel\", role = c(\"ctb\"), comment = \"Bundled PCRE2 code\"), person(\"Zoltan\", \"Herczeg\", role = c(\"ctb\", \"cph\"), comment = \"Bundled PCRE2 code\"), person(\"University of Cambridge\", role = c(\"cph\"), comment = \"Bundled PCRE2 code\"), person(\"Tilera Corporation\", role = c(\"cph\"), comment = \"Stack-less Just-In-Time compiler bundled with PCRE2\"), person(\"Yann\", \"Collet\", role = c(\"ctb\", \"cph\"), comment = \"Yann Collet is the author of the bundled xxHash code\"))",
       "Maintainer": "Travers Ching <traversc@gmail.com>",
       "Description": "Provides an extendable, performant and multithreaded 'alt-string' implementation backed by 'C++' vectors and strings.",
@@ -15567,7 +15556,7 @@
       "Depends": [
         "R (>= 3.6.0)"
       ],
-      "SystemRequirements": "GNU make",
+      "SystemRequirements": "GNU make, C++17",
       "LinkingTo": [
         "Rcpp (>= 0.12.18.3)",
         "RcppParallel (>= 5.1.4)"
@@ -15577,27 +15566,17 @@
         "RcppParallel"
       ],
       "Suggests": [
-        "qs2",
-        "qs",
         "knitr",
-        "rmarkdown",
-        "usethis",
-        "dplyr",
-        "stringr",
-        "rlang"
+        "rmarkdown"
       ],
       "VignetteBuilder": "knitr",
-      "RoxygenNote": "7.3.2",
-      "Copyright": "Copyright for the bundled 'PCRE2' library is held by University of Cambridge, Zoltan Herczeg and Tilera Coporation (Stack-less Just-In-Time compiler); Copyright for the bundled 'xxHash' code is held by Yann Collet.",
+      "RoxygenNote": "7.3.3",
+      "Copyright": "Copyright for the bundled 'PCRE2' library is held by University of Cambridge, Zoltan Herczeg and Tilera Corporation (Stack-less Just-In-Time compiler); Copyright for the bundled 'xxHash' code is held by Yann Collet.",
       "URL": "https://github.com/traversc/stringfish",
       "BugReports": "https://github.com/traversc/stringfish/issues",
+      "NeedsCompilation": "yes",
       "Author": "Travers Ching [aut, cre, cph], Phillip Hazel [ctb] (Bundled PCRE2 code), Zoltan Herczeg [ctb, cph] (Bundled PCRE2 code), University of Cambridge [cph] (Bundled PCRE2 code), Tilera Corporation [cph] (Stack-less Just-In-Time compiler bundled with PCRE2), Yann Collet [ctb, cph] (Yann Collet is the author of the bundled xxHash code)",
-      "RemoteType": "github",
-      "RemoteHost": "api.github.com",
-      "RemoteUsername": "traversc",
-      "RemoteRepo": "stringfish",
-      "RemoteRef": "f3a44d26d77b4980c829481363bc3aa6d2a2bc3f",
-      "RemoteSha": "f3a44d26d77b4980c829481363bc3aa6d2a2bc3f"
+      "Repository": "CRAN"
     },
     "stringi": {
       "Package": "stringi",

renv/activate.R

@@ -2,8 +2,8 @@
 local({
 
   # the requested version of renv
-  version <- "1.1.7"
-  attr(version, "md5") <- "dd5d60f155dadff4c88c2fc6680504b4"
+  version <- "1.2.3"
+  attr(version, "md5") <- "1bd9f58e1cfe27ce035933937c6f03de"
   attr(version, "sha") <- NULL
 
   # the project directory
@@ -226,13 +226,17 @@ local({
     section <- header(sprintf("Bootstrapping renv %s", friendly))
     catf(section)
 
+    # ensure the target library path exists; required for file.copy(..., recursive = TRUE)
+    dir.create(library, showWarnings = FALSE, recursive = TRUE)
+
     # try to install renv from cache
     md5 <- attr(version, "md5", exact = TRUE)
     if (length(md5)) {
       pkgpath <- renv_bootstrap_find(version)
       if (length(pkgpath) && file.exists(pkgpath)) {
-        file.copy(pkgpath, library, recursive = TRUE)
-        return(invisible())
+        ok <- file.copy(pkgpath, library, recursive = TRUE)
+        if (isTRUE(ok))
+          return(invisible())
       }
     }
 
@@ -1231,6 +1235,21 @@ local({
   }
 
   renv_bootstrap_run <- function(project, libpath, version) {
+    tryCatch(
+      renv_bootstrap_run_impl(project, libpath, version),
+      error = function(e) {
+        msg <- paste(
+          "failed to bootstrap renv: the project will not be loaded.",
+          paste("Reason:", conditionMessage(e)),
+          "Use `renv::activate()` to re-initialize the project.",
+          sep = "\n"
+        )
+        warning(msg, call. = FALSE)
+      }
+    )
+  }
+
+  renv_bootstrap_run_impl <- function(project, libpath, version) {
 
     # perform bootstrap
     bootstrap(version, libpath)