[actions] update 14 packages

carpentries-incubator · Jun 4, 2024 · 6da9f91 · 6da9f91
1 parent 9b877f3
commit 6da9f91
Showing 1 changed file with 59 additions and 39 deletions.
diff --git a/renv/profiles/lesson-requirements/renv.lock b/renv/profiles/lesson-requirements/renv.lock
@@ -2,6 +2,26 @@
   "R": {
     "Version": "4.4.0",
     "Repositories": [
+      {
+        "Name": "BioCsoft",
+        "URL": "https://bioconductor.org/packages/3.19/bioc"
+      },
+      {
+        "Name": "BioCann",
+        "URL": "https://bioconductor.org/packages/3.19/data/annotation"
+      },
+      {
+        "Name": "BioCexp",
+        "URL": "https://bioconductor.org/packages/3.19/data/experiment"
+      },
+      {
+        "Name": "BioCworkflows",
+        "URL": "https://bioconductor.org/packages/3.19/workflows"
+      },
+      {
+        "Name": "BioCbooks",
+        "URL": "https://bioconductor.org/packages/3.19/books"
+      },
       {
         "Name": "carpentries",
         "URL": "https://carpentries.r-universe.dev"
@@ -66,8 +86,8 @@
     "AnnotationFilter": {
       "Package": "AnnotationFilter",
       "Version": "1.28.0",
-      "Source": "Repository",
-      "Repository": "https://bioconductor.org/packages/3.19/bioc",
+      "Source": "Bioconductor",
+      "Repository": "Bioconductor 3.19",
       "Requirements": [
         "GenomicRanges",
         "R",
@@ -263,7 +283,7 @@
     },
     "Biostrings": {
       "Package": "Biostrings",
-      "Version": "2.72.0",
+      "Version": "2.72.1",
       "Source": "Bioconductor",
       "Repository": "Bioconductor 3.19",
       "Requirements": [
@@ -279,7 +299,7 @@
         "stats",
         "utils"
       ],
-      "Hash": "48618c7c7b90b503837824ebcfee6363"
+      "Hash": "886ff0ed958d6f839ed2e0d01f6853b3"
     },
     "BumpyMatrix": {
       "Package": "BumpyMatrix",
@@ -342,14 +362,14 @@
     },
     "DBI": {
       "Package": "DBI",
-      "Version": "1.2.2",
+      "Version": "1.2.3",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "R",
         "methods"
       ],
-      "Hash": "164809cd72e1d5160b4cb3aa57f510fe"
+      "Hash": "065ae649b05f1ff66bb0c793107508f5"
     },
     "DelayedArray": {
       "Package": "DelayedArray",
@@ -422,8 +442,7 @@
     "EnsDb.Mmusculus.v79": {
       "Package": "EnsDb.Mmusculus.v79",
       "Version": "2.99.0",
-      "Source": "Repository",
-      "Repository": "https://bioconductor.org/packages/3.19/data/annotation",
+      "Source": "Bioconductor",
       "Requirements": [
         "ensembldb"
       ],
@@ -475,7 +494,7 @@
     },
     "GenomeInfoDb": {
       "Package": "GenomeInfoDb",
-      "Version": "1.40.0",
+      "Version": "1.40.1",
       "Source": "Bioconductor",
       "Repository": "Bioconductor 3.19",
       "Requirements": [
@@ -490,7 +509,7 @@
         "stats4",
         "utils"
       ],
-      "Hash": "614124bc9fb80d222cfa0d2e3e76c339"
+      "Hash": "171e9becd9bb948b9e64eb3759208c94"
     },
     "GenomeInfoDbData": {
       "Package": "GenomeInfoDbData",
@@ -526,8 +545,8 @@
     "GenomicFeatures": {
       "Package": "GenomicFeatures",
       "Version": "1.56.0",
-      "Source": "Repository",
-      "Repository": "https://bioconductor.org/packages/3.19/bioc",
+      "Source": "Bioconductor",
+      "Repository": "Bioconductor 3.19",
       "Requirements": [
         "AnnotationDbi",
         "BiocGenerics",
@@ -693,8 +712,8 @@
     "ProtGenerics": {
       "Package": "ProtGenerics",
       "Version": "1.36.0",
-      "Source": "Repository",
-      "Repository": "https://bioconductor.org/packages/3.19/bioc",
+      "Source": "Bioconductor",
+      "Repository": "Bioconductor 3.19",
       "Requirements": [
         "methods"
       ],
@@ -795,7 +814,7 @@
     },
     "RSQLite": {
       "Package": "RSQLite",
-      "Version": "2.3.6",
+      "Version": "2.3.7",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -810,7 +829,7 @@
         "plogr",
         "rlang"
       ],
-      "Hash": "ae4a925e0f6bb1b7e5fa96b739c5221a"
+      "Hash": "46b45a4dd7bb0e0f4e3fc22245817240"
     },
     "RSpectra": {
       "Package": "RSpectra",
@@ -850,7 +869,7 @@
     },
     "RcppArmadillo": {
       "Package": "RcppArmadillo",
-      "Version": "0.12.8.3.0",
+      "Version": "0.12.8.4.0",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -860,7 +879,7 @@
         "stats",
         "utils"
       ],
-      "Hash": "1eb4a0603478b5557b77d75534251371"
+      "Hash": "a535dd90aa8ec9a2e63a8f79b4a1bf43"
     },
     "RcppEigen": {
       "Package": "RcppEigen",
@@ -921,8 +940,8 @@
     "ResidualMatrix": {
       "Package": "ResidualMatrix",
       "Version": "1.14.0",
-      "Source": "Repository",
-      "Repository": "https://bioconductor.org/packages/3.19/bioc",
+      "Source": "Bioconductor",
+      "Repository": "Bioconductor 3.19",
       "Requirements": [
         "DelayedArray",
         "Matrix",
@@ -989,7 +1008,7 @@
     },
     "S4Arrays": {
       "Package": "S4Arrays",
-      "Version": "1.4.0",
+      "Version": "1.4.1",
       "Source": "Bioconductor",
       "Repository": "Bioconductor 3.19",
       "Requirements": [
@@ -1003,7 +1022,7 @@
         "methods",
         "stats"
       ],
-      "Hash": "665d1f150ce8a6e7614375eafdbad645"
+      "Hash": "deeed4802c5132e88f24a432a1caf5e0"
     },
     "S4Vectors": {
       "Package": "S4Vectors",
@@ -1169,7 +1188,7 @@
     },
     "SparseArray": {
       "Package": "SparseArray",
-      "Version": "1.4.3",
+      "Version": "1.4.8",
       "Source": "Bioconductor",
       "Repository": "Bioconductor 3.19",
       "Requirements": [
@@ -1186,7 +1205,7 @@
         "stats",
         "utils"
       ],
-      "Hash": "97e01fd020665f2b0c6bd182b0ab68c2"
+      "Hash": "97f70ff11c14edd379ee2429228cbb60"
     },
     "SpatialExperiment": {
       "Package": "SpatialExperiment",
@@ -1381,8 +1400,8 @@
     "batchelor": {
       "Package": "batchelor",
       "Version": "1.20.0",
-      "Source": "Repository",
-      "Repository": "https://bioconductor.org/packages/3.19/bioc",
+      "Source": "Bioconductor",
+      "Repository": "Bioconductor 3.19",
       "Requirements": [
         "BiocGenerics",
         "BiocNeighbors",
@@ -1783,7 +1802,7 @@
     },
     "dqrng": {
       "Package": "dqrng",
-      "Version": "0.4.0",
+      "Version": "0.4.1",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -1792,7 +1811,7 @@
         "Rcpp",
         "sitmo"
       ],
-      "Hash": "b31198e6268008976689b196bf9d883f"
+      "Hash": "6d7b942d8f615705f89a7883998fc839"
     },
     "duckdb": {
       "Package": "duckdb",
@@ -1827,8 +1846,8 @@
     "ensembldb": {
       "Package": "ensembldb",
       "Version": "2.28.0",
-      "Source": "Repository",
-      "Repository": "https://bioconductor.org/packages/3.19/bioc",
+      "Source": "Bioconductor",
+      "Repository": "Bioconductor 3.19",
       "Requirements": [
         "AnnotationDbi",
         "AnnotationFilter",
@@ -2224,14 +2243,14 @@
     },
     "highr": {
       "Package": "highr",
-      "Version": "0.10",
+      "Version": "0.11",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "R",
         "xfun"
       ],
-      "Hash": "06230136b2d2b9ba5805e1963fa6e890"
+      "Hash": "d65ba49117ca223614f71b60d85b8ab7"
     },
     "htmltools": {
       "Package": "htmltools",
@@ -2384,7 +2403,7 @@
     },
     "knitr": {
       "Package": "knitr",
-      "Version": "1.46",
+      "Version": "1.47",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -2396,7 +2415,7 @@
         "xfun",
         "yaml"
       ],
-      "Hash": "6e008ab1d696a5283c79765fa7b56b47"
+      "Hash": "7c99b2d55584b982717fcc0950378612"
     },
     "labeling": {
       "Package": "labeling",
@@ -2936,7 +2955,7 @@
     },
     "reticulate": {
       "Package": "reticulate",
-      "Version": "1.36.1",
+      "Version": "1.37.0",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -2954,7 +2973,7 @@
         "utils",
         "withr"
       ],
-      "Hash": "e037fb5dc364efdaf616eb6bc05aaca2"
+      "Hash": "9465d3bc6ec44eeaa52527ac2cba4020"
     },
     "rhdf5": {
       "Package": "rhdf5",
@@ -3579,15 +3598,16 @@
     },
     "textshaping": {
       "Package": "textshaping",
-      "Version": "0.3.7",
+      "Version": "0.4.0",
       "Source": "Repository",
-      "Repository": "CRAN",
+      "Repository": "carpentries",
       "Requirements": [
         "R",
         "cpp11",
+        "lifecycle",
         "systemfonts"
       ],
-      "Hash": "997aac9ad649e0ef3b97f96cddd5622b"
+      "Hash": "5142f8bc78ed3d819d26461b641627ce"
     },
     "tibble": {
       "Package": "tibble",