Merge branch 'main' into dependabot/npm_and_yarn/efficacy/tests/follo…

…w-redirects-1.15.6
insightsengineering · Mar 21, 2024 · e06dffd · e06dffd
2 parents f60a58e + 1b3e9f5
commit e06dffd
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Showing 10 changed files with 315 additions and 208 deletions.
diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml
@@ -132,8 +132,8 @@ jobs:
           lockfile <- renv::lockfile_read()
           pkg_name_structure <- ifelse("${{ matrix.channel }}" == "stable", "%s/%s@*release", "%s/%s")
           unreleased_packages <- c(
-            "osprey", "hermes", "goshawk", "teal.modules.general",
-            "teal.osprey", "teal.modules.hermes", "teal.goshawk", "nestcolor"
+            "osprey", "hermes", "goshawk", "teal.osprey",
+            "teal.modules.hermes", "teal.goshawk", "nestcolor"
           )
           for (package in lockfile$Packages) {
               if (package$Source == "GitHub") {

diff --git a/RNA-seq/renv.lock b/RNA-seq/renv.lock
@@ -176,7 +176,7 @@
     },
     "Biostrings": {
       "Package": "Biostrings",
-      "Version": "2.70.2",
+      "Version": "2.70.3",
       "Source": "Bioconductor",
       "Repository": "Bioconductor 3.18",
       "Requirements": [
@@ -193,7 +193,7 @@
         "stats",
         "utils"
       ],
-      "Hash": "b7cc779ab741dce3ad1b419ada1564c9"
+      "Hash": "86ffa781f132f54e9c963a13fd6cf9fc"
     },
     "ComplexHeatmap": {
       "Package": "ComplexHeatmap",
@@ -308,21 +308,22 @@
     },
     "GenomeInfoDb": {
       "Package": "GenomeInfoDb",
-      "Version": "1.38.7",
+      "Version": "1.38.8",
       "Source": "Bioconductor",
       "Repository": "Bioconductor 3.18",
       "Requirements": [
         "BiocGenerics",
         "GenomeInfoDbData",
         "IRanges",
         "R",
+        "RCurl",
         "S4Vectors",
         "methods",
         "stats",
         "stats4",
         "utils"
       ],
-      "Hash": "6ddbcd4f3c7a2c8f73e29cdcc601502a"
+      "Hash": "155053909d2831bfac154a1118151d6b"
     },
     "GenomeInfoDbData": {
       "Package": "GenomeInfoDbData",
@@ -555,6 +556,18 @@
       ],
       "Hash": "45f0398006e83a5b10b72a90663d8d8c"
     },
+    "RCurl": {
+      "Package": "RCurl",
+      "Version": "1.98-1.14",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "bitops",
+        "methods"
+      ],
+      "Hash": "47f648d288079d0c696804ad4e55197e"
+    },
     "RSQLite": {
       "Package": "RSQLite",
       "Version": "2.3.5",
@@ -852,6 +865,13 @@
       ],
       "Hash": "9fe98599ca456d6552421db0d6772d8f"
     },
+    "bitops": {
+      "Package": "bitops",
+      "Version": "1.0-7",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Hash": "b7d8d8ee39869c18d8846a184dd8a1af"
+    },
     "blob": {
       "Package": "blob",
       "Version": "1.2.4",
@@ -1177,9 +1197,9 @@
     },
     "dbplyr": {
       "Package": "dbplyr",
-      "Version": "2.4.0",
+      "Version": "2.5.0",
       "Source": "Repository",
-      "Repository": "RSPM",
+      "Repository": "BioC.CRAN",
       "Requirements": [
         "DBI",
         "R",
@@ -1201,7 +1221,7 @@
         "vctrs",
         "withr"
       ],
-      "Hash": "59351f28a81f0742720b85363c4fdd61"
+      "Hash": "39b2e002522bfd258039ee4e889e0fd1"
     },
     "desc": {
       "Package": "desc",
@@ -2262,9 +2282,9 @@
     },
     "pkgbuild": {
       "Package": "pkgbuild",
-      "Version": "1.4.3",
+      "Version": "1.4.4",
       "Source": "Repository",
-      "Repository": "RSPM",
+      "Repository": "BioC.CRAN",
       "Requirements": [
         "R",
         "R6",
@@ -2273,7 +2293,7 @@
         "desc",
         "processx"
       ],
-      "Hash": "c0143443203205e6a2760ce553dafc24"
+      "Hash": "a29e8e134a460a01e0ca67a4763c595b"
     },
     "pkgconfig": {
       "Package": "pkgconfig",
@@ -2385,16 +2405,16 @@
     },
     "processx": {
       "Package": "processx",
-      "Version": "3.8.3",
+      "Version": "3.8.4",
       "Source": "Repository",
-      "Repository": "RSPM",
+      "Repository": "BioC.CRAN",
       "Requirements": [
         "R",
         "R6",
         "ps",
         "utils"
       ],
-      "Hash": "82d48b1aec56084d9438dbf98087a7e9"
+      "Hash": "0c90a7d71988856bad2a2a45dd871bb9"
     },
     "productplots": {
       "Package": "productplots",
@@ -2607,17 +2627,17 @@
     },
     "sass": {
       "Package": "sass",
-      "Version": "0.4.8",
+      "Version": "0.4.9",
       "Source": "Repository",
-      "Repository": "RSPM",
+      "Repository": "CRAN",
       "Requirements": [
         "R6",
         "fs",
         "htmltools",
         "rappdirs",
         "rlang"
       ],
-      "Hash": "168f9353c76d4c4b0a0bbf72e2c2d035"
+      "Hash": "d53dbfddf695303ea4ad66f86e99b95d"
     },
     "scales": {
       "Package": "scales",
@@ -2763,6 +2783,19 @@
       ],
       "Hash": "88289640c8206dc810ea9cb87bd58ffc"
     },
+    "shinybusy": {
+      "Package": "shinybusy",
+      "Version": "0.3.3",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "htmltools",
+        "htmlwidgets",
+        "jsonlite",
+        "shiny"
+      ],
+      "Hash": "7dc8feb4207741ff581422a04fc8f3ea"
+    },
     "shinycssloaders": {
       "Package": "shinycssloaders",
       "Version": "1.0.0",
@@ -2995,14 +3028,9 @@
     },
     "teal.modules.general": {
       "Package": "teal.modules.general",
-      "Version": "0.3.0.9000",
-      "Source": "GitHub",
-      "RemoteType": "github",
-      "RemoteHost": "api.github.com",
-      "RemoteUsername": "insightsengineering",
-      "RemoteRepo": "teal.modules.general",
-      "RemoteRef": "main",
-      "RemoteSha": "da9dfc285157af93f366896e61895a173357c216",
+      "Version": "0.3.0",
+      "Source": "Repository",
+      "Repository": "RSPM",
       "Requirements": [
         "DT",
         "R",
@@ -3034,18 +3062,18 @@
         "tools",
         "utils"
       ],
-      "Hash": "04c9585b79935e464bf149c35515212e"
+      "Hash": "f54d7bc27cd048cec3a842f980c74e9b"
     },
     "teal.modules.hermes": {
       "Package": "teal.modules.hermes",
-      "Version": "0.1.6.9005",
+      "Version": "0.1.6.9006",
       "Source": "GitHub",
       "RemoteType": "github",
       "RemoteHost": "api.github.com",
       "RemoteUsername": "insightsengineering",
       "RemoteRepo": "teal.modules.hermes",
       "RemoteRef": "main",
-      "RemoteSha": "bcea1efe2c2d90c8066b638bd86dd80c16a69512",
+      "RemoteSha": "d6326b5a776f55628984abc1c6c9873405bd4c29",
       "Requirements": [
         "DT",
         "MultiAssayExperiment",
@@ -3072,11 +3100,11 @@
         "teal.widgets",
         "tern"
       ],
-      "Hash": "7e543d7e024c6dccf1c1d8d53f2350eb"
+      "Hash": "58805365de2dea7e5ed11b9be6cc686b"
     },
     "teal.reporter": {
       "Package": "teal.reporter",
-      "Version": "0.3.0",
+      "Version": "0.3.1",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -3091,10 +3119,11 @@
         "rmarkdown",
         "shiny",
         "shinyWidgets",
+        "shinybusy",
         "yaml",
         "zip"
       ],
-      "Hash": "368a9b64b4e69419f3a3ddb7e3d54d05"
+      "Hash": "b09a5fb625dc8bff3965f58ba69e8fb3"
     },
     "teal.slice": {
       "Package": "teal.slice",
@@ -3309,13 +3338,13 @@
     },
     "tinytex": {
       "Package": "tinytex",
-      "Version": "0.49",
+      "Version": "0.50",
       "Source": "Repository",
-      "Repository": "CRAN",
+      "Repository": "BioC.CRAN",
       "Requirements": [
         "xfun"
       ],
-      "Hash": "5ac22900ae0f386e54f1c307eca7d843"
+      "Hash": "be7a76845222ad20adb761f462eed3ea"
     },
     "triebeard": {
       "Package": "triebeard",
@@ -3467,9 +3496,10 @@
     },
     "zlibbioc": {
       "Package": "zlibbioc",
-      "Version": "1.48.0",
+      "Version": "1.48.2",
       "Source": "Bioconductor",
-      "Hash": "50ad6f7b0baaaccf1a387d2f1ecce911"
+      "Repository": "Bioconductor 3.18",
+      "Hash": "2344be62c2da4d9e9942b5d8db346e59"
     }
   }
 }
diff --git a/basic-teal/renv.lock b/basic-teal/renv.lock
@@ -744,7 +744,7 @@
     },
     "lattice": {
       "Package": "lattice",
-      "Version": "0.22-5",
+      "Version": "0.22-6",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -755,7 +755,7 @@
         "stats",
         "utils"
       ],
-      "Hash": "7c5e89f04e72d6611c77451f6331a091"
+      "Hash": "cc5ac1ba4c238c7ca9fa6a87ca11a7e2"
     },
     "lazyeval": {
       "Package": "lazyeval",
@@ -1076,7 +1076,7 @@
     },
     "sass": {
       "Package": "sass",
-      "Version": "0.4.8",
+      "Version": "0.4.9",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -1086,7 +1086,7 @@
         "rappdirs",
         "rlang"
       ],
-      "Hash": "168f9353c76d4c4b0a0bbf72e2c2d035"
+      "Hash": "d53dbfddf695303ea4ad66f86e99b95d"
     },
     "scales": {
       "Package": "scales",
@@ -1160,6 +1160,19 @@
       ],
       "Hash": "88289640c8206dc810ea9cb87bd58ffc"
     },
+    "shinybusy": {
+      "Package": "shinybusy",
+      "Version": "0.3.3",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "htmltools",
+        "htmlwidgets",
+        "jsonlite",
+        "shiny"
+      ],
+      "Hash": "7dc8feb4207741ff581422a04fc8f3ea"
+    },
     "shinycssloaders": {
       "Package": "shinycssloaders",
       "Version": "1.0.0",
@@ -1340,7 +1353,7 @@
     },
     "teal.reporter": {
       "Package": "teal.reporter",
-      "Version": "0.3.0",
+      "Version": "0.3.1",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -1355,10 +1368,11 @@
         "rmarkdown",
         "shiny",
         "shinyWidgets",
+        "shinybusy",
         "yaml",
         "zip"
       ],
-      "Hash": "368a9b64b4e69419f3a3ddb7e3d54d05"
+      "Hash": "b09a5fb625dc8bff3965f58ba69e8fb3"
     },
     "teal.slice": {
       "Package": "teal.slice",
@@ -1484,13 +1498,13 @@
     },
     "tinytex": {
       "Package": "tinytex",
-      "Version": "0.49",
+      "Version": "0.50",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "xfun"
       ],
-      "Hash": "5ac22900ae0f386e54f1c307eca7d843"
+      "Hash": "be7a76845222ad20adb761f462eed3ea"
     },
     "triebeard": {
       "Package": "triebeard",