From bf70f864101d5abde66dcaf40e185e0cf035f826 Mon Sep 17 00:00:00 2001
From: Vedha Viyash <49812166+vedhav@users.noreply.github.com>
Date: Thu, 23 Jan 2025 17:18:07 +0530
Subject: [PATCH] Use updated BioC package versions (#190)

Changes:

1. Verify the restore works in the CI image using docker and took the
snapshot
2. Remove `teal.logger` from unreleased_packages package list as it is
not released in CRAN.
---
 .github/workflows/deploy.yml |    2 +-
 RNA-seq/renv.lock            | 1035 ++++++++++++++++++++++++----------
 2 files changed, 743 insertions(+), 294 deletions(-)

diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml
index 83e7b32f..3b4243c3 100644
--- a/.github/workflows/deploy.yml
+++ b/.github/workflows/deploy.yml
@@ -132,7 +132,7 @@ jobs:
           lockfile <- renv::lockfile_read()
           pkg_name_structure <- ifelse("${{ matrix.channel }}" == "stable", "%s/%s@*release", "%s/%s")
           unreleased_packages <- c(
-            "osprey", "hermes", "goshawk", "teal.osprey", "teal.logger",
+            "osprey", "hermes", "goshawk", "teal.osprey",
             "teal.modules.hermes", "teal.goshawk", "nestcolor"
           )
           for (package in lockfile$Packages) {
diff --git a/RNA-seq/renv.lock b/RNA-seq/renv.lock
index dfa1101f..e8c51c4c 100644
--- a/RNA-seq/renv.lock
+++ b/RNA-seq/renv.lock
@@ -2,52 +2,8 @@
   "R": {
     "Version": "4.4.1",
     "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": "CRAN",
-        "URL": "https://packagemanager.posit.co/cran/latest"
-      },
-      {
-        "Name": "BioC.BioCsoft",
-        "URL": "https://bioconductor.org/packages/3.19/bioc"
-      },
-      {
-        "Name": "BioC.BioCann",
-        "URL": "https://bioconductor.org/packages/3.19/data/annotation"
-      },
-      {
-        "Name": "BioC.BioCexp",
-        "URL": "https://bioconductor.org/packages/3.19/data/experiment"
-      },
-      {
-        "Name": "BioC.BioCworkflows",
-        "URL": "https://bioconductor.org/packages/3.19/workflows"
-      },
-      {
-        "Name": "BioC.BioCbooks",
-        "URL": "https://bioconductor.org/packages/3.19/books"
-      },
-      {
-        "Name": "BioC.CRAN",
         "URL": "https://cloud.r-project.org"
       }
     ]
@@ -85,17 +41,32 @@
     },
     "Biobase": {
       "Package": "Biobase",
-      "Version": "2.62.0",
+      "Version": "2.64.0",
       "Source": "Bioconductor",
-      "Requirements": ["BiocGenerics", "R", "methods", "utils"],
-      "Hash": "38252a34e82d3ff6bb46b4e2252d2dce"
+      "Repository": "Bioconductor 3.19",
+      "Requirements": [
+        "BiocGenerics",
+        "R",
+        "methods",
+        "utils"
+      ],
+      "Hash": "9bc4cabd3bfda461409172213d932813"
     },
     "BiocBaseUtils": {
       "Package": "BiocBaseUtils",
-      "Version": "1.4.0",
-      "Source": "Bioconductor",
-      "Requirements": ["R", "methods", "utils"],
-      "Hash": "8fdda3c850b2bea92ad4d0877c9549d1"
+      "Version": "1.9.0",
+      "Source": "GitHub",
+      "RemoteType": "github",
+      "RemoteHost": "api.github.com",
+      "RemoteRepo": "BiocBaseUtils",
+      "RemoteUsername": "Bioconductor",
+      "RemoteSha": "d643df4e5d25708002ed5b02e8fc6a04db69d28c",
+      "Requirements": [
+        "R",
+        "methods",
+        "utils"
+      ],
+      "Hash": "77ab4922879e7ebf92610da88f4e89e1"
     },
     "BiocFileCache": {
       "Package": "BiocFileCache",
@@ -119,23 +90,33 @@
     },
     "BiocGenerics": {
       "Package": "BiocGenerics",
-      "Version": "0.48.1",
+      "Version": "0.50.0",
       "Source": "Bioconductor",
-      "Requirements": ["R", "graphics", "methods", "stats", "utils"],
-      "Hash": "e34278c65d7dffcc08f737bf0944ca9a"
+      "Repository": "Bioconductor 3.19",
+      "Requirements": [
+        "R",
+        "graphics",
+        "methods",
+        "stats",
+        "utils"
+      ],
+      "Hash": "ef32d07aafdd12f24c5827374ae3590d"
     },
     "BiocManager": {
       "Package": "BiocManager",
       "Version": "1.30.25",
       "Source": "Repository",
       "Repository": "CRAN",
-      "Requirements": ["utils"],
+      "Requirements": [
+        "utils"
+      ],
       "Hash": "3aec5928ca10897d7a0a1205aae64627"
     },
     "BiocParallel": {
       "Package": "BiocParallel",
-      "Version": "1.36.0",
+      "Version": "1.38.0",
       "Source": "Bioconductor",
+      "Repository": "Bioconductor 3.19",
       "Requirements": [
         "BH",
         "R",
@@ -148,14 +129,17 @@
         "stats",
         "utils"
       ],
-      "Hash": "6d1689ee8b65614ba6ef4012a67b663a"
+      "Hash": "7b6e79f86e3d1c23f62c5e2052e848d4"
     },
     "BiocVersion": {
       "Package": "BiocVersion",
-      "Version": "3.18.1",
+      "Version": "3.19.1",
       "Source": "Bioconductor",
-      "Requirements": ["R"],
-      "Hash": "2ecaed86684f5fae76ed5530f9d29c4a"
+      "Repository": "Bioconductor 3.19",
+      "Requirements": [
+        "R"
+      ],
+      "Hash": "b892e27fc9659a4c8f8787d34c37b8b2"
     },
     "Biostrings": {
       "Package": "Biostrings",
@@ -179,8 +163,9 @@
     },
     "ComplexHeatmap": {
       "Package": "ComplexHeatmap",
-      "Version": "2.18.0",
+      "Version": "2.20.0",
       "Source": "Bioconductor",
+      "Repository": "Bioconductor 3.19",
       "Requirements": [
         "GetoptLong",
         "GlobalOptions",
@@ -202,14 +187,17 @@
         "png",
         "stats"
       ],
-      "Hash": "fd8d03c43e175afce12c1012711a05cc"
+      "Hash": "0308920b8b9315ccfe69bccb66c15485"
     },
     "DBI": {
       "Package": "DBI",
       "Version": "1.2.3",
       "Source": "Repository",
       "Repository": "CRAN",
-      "Requirements": ["R", "methods"],
+      "Requirements": [
+        "R",
+        "methods"
+      ],
       "Hash": "065ae649b05f1ff66bb0c793107508f5"
     },
     "DESeq2": {
@@ -255,8 +243,9 @@
     },
     "DelayedArray": {
       "Package": "DelayedArray",
-      "Version": "0.28.0",
+      "Version": "0.30.1",
       "Source": "Bioconductor",
+      "Repository": "Bioconductor 3.19",
       "Requirements": [
         "BiocGenerics",
         "IRanges",
@@ -270,14 +259,16 @@
         "stats",
         "stats4"
       ],
-      "Hash": "0e5c84e543a3d04ce64c6f60ed46d7eb"
+      "Hash": "395472c65cd9d606a1a345687102f299"
     },
     "Deriv": {
       "Package": "Deriv",
       "Version": "4.1.6",
       "Source": "Repository",
       "Repository": "CRAN",
-      "Requirements": ["methods"],
+      "Requirements": [
+        "methods"
+      ],
       "Hash": "cd52c065c9e687c60c56b51f10f7bcd3"
     },
     "EnvStats": {
@@ -285,7 +276,12 @@
       "Version": "3.0.0",
       "Source": "Repository",
       "Repository": "CRAN",
-      "Requirements": ["MASS", "R", "ggplot2", "nortest"],
+      "Requirements": [
+        "MASS",
+        "R",
+        "ggplot2",
+        "nortest"
+      ],
       "Hash": "08f0337e9a3b03a9027a423a1ae76ed3"
     },
     "Formula": {
@@ -293,7 +289,10 @@
       "Version": "1.2-5",
       "Source": "Repository",
       "Repository": "CRAN",
-      "Requirements": ["R", "stats"],
+      "Requirements": [
+        "R",
+        "stats"
+      ],
       "Hash": "7a29697b75e027767a53fde6c903eca7"
     },
     "GenomeInfoDb": {
@@ -319,7 +318,9 @@
       "Package": "GenomeInfoDbData",
       "Version": "1.2.12",
       "Source": "Bioconductor",
-      "Requirements": ["R"],
+      "Requirements": [
+        "R"
+      ],
       "Hash": "c3c792a7b7f2677be56e8632c5b7543d"
     },
     "GenomicRanges": {
@@ -346,7 +347,13 @@
       "Version": "1.0.5",
       "Source": "Repository",
       "Repository": "CRAN",
-      "Requirements": ["GlobalOptions", "R", "crayon", "methods", "rjson"],
+      "Requirements": [
+        "GlobalOptions",
+        "R",
+        "crayon",
+        "methods",
+        "rjson"
+      ],
       "Hash": "61fac01c73abf03ac72e88dc3952c1e3"
     },
     "GlobalOptions": {
@@ -354,13 +361,18 @@
       "Version": "0.1.2",
       "Source": "Repository",
       "Repository": "CRAN",
-      "Requirements": ["R", "methods", "utils"],
+      "Requirements": [
+        "R",
+        "methods",
+        "utils"
+      ],
       "Hash": "c3f7b221e60c28f5f3533d74c6fef024"
     },
     "IRanges": {
       "Package": "IRanges",
-      "Version": "2.36.0",
+      "Version": "2.38.1",
       "Source": "Bioconductor",
+      "Repository": "Bioconductor 3.19",
       "Requirements": [
         "BiocGenerics",
         "R",
@@ -370,20 +382,27 @@
         "stats4",
         "utils"
       ],
-      "Hash": "f98500eeb93e8a66ad65be955a848595"
+      "Hash": "066f3c5d6b022ed62c91ce49e4d8f619"
     },
     "KEGGREST": {
       "Package": "KEGGREST",
-      "Version": "1.42.0",
+      "Version": "1.44.1",
       "Source": "Bioconductor",
-      "Requirements": ["Biostrings", "R", "httr", "methods", "png"],
-      "Hash": "8d6e9f4dce69aec9c588c27ae79be08e"
+      "Repository": "Bioconductor 3.19",
+      "Requirements": [
+        "Biostrings",
+        "R",
+        "httr",
+        "methods",
+        "png"
+      ],
+      "Hash": "017f19c09477c0473073518db9076ac1"
     },
     "MASS": {
       "Package": "MASS",
-      "Version": "7.3-60.0.1",
+      "Version": "7.3-61",
       "Source": "Repository",
-      "Repository": "RSPM",
+      "Repository": "CRAN",
       "Requirements": [
         "R",
         "grDevices",
@@ -392,13 +411,13 @@
         "stats",
         "utils"
       ],
-      "Hash": "b765b28387acc8ec9e9c1530713cb19c"
+      "Hash": "0cafd6f0500e5deba33be22c46bf6055"
     },
     "Matrix": {
       "Package": "Matrix",
-      "Version": "1.6-5",
+      "Version": "1.7-0",
       "Source": "Repository",
-      "Repository": "RSPM",
+      "Repository": "CRAN",
       "Requirements": [
         "R",
         "grDevices",
@@ -409,27 +428,37 @@
         "stats",
         "utils"
       ],
-      "Hash": "8c7115cd3a0e048bda2a7cd110549f7a"
+      "Hash": "1920b2f11133b12350024297d8a4ff4a"
     },
     "MatrixGenerics": {
       "Package": "MatrixGenerics",
-      "Version": "1.14.0",
+      "Version": "1.16.0",
       "Source": "Bioconductor",
-      "Requirements": ["matrixStats", "methods"],
-      "Hash": "088cd2077b5619fcb7b373b1a45174e7"
+      "Repository": "Bioconductor 3.19",
+      "Requirements": [
+        "matrixStats",
+        "methods"
+      ],
+      "Hash": "152dbbcde6a9a7c7f3beef79b68cd76a"
     },
     "MatrixModels": {
       "Package": "MatrixModels",
       "Version": "0.5-3",
       "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": ["Matrix", "R", "methods", "stats"],
+      "Repository": "CRAN",
+      "Requirements": [
+        "Matrix",
+        "R",
+        "methods",
+        "stats"
+      ],
       "Hash": "0776bf7526869e0286b0463cb72fb211"
     },
     "MultiAssayExperiment": {
       "Package": "MultiAssayExperiment",
-      "Version": "1.28.0",
+      "Version": "1.30.3",
       "Source": "Bioconductor",
+      "Repository": "Bioconductor 3.19",
       "Requirements": [
         "Biobase",
         "BiocBaseUtils",
@@ -441,11 +470,10 @@
         "S4Vectors",
         "SummarizedExperiment",
         "methods",
-        "stats",
         "tidyr",
         "utils"
       ],
-      "Hash": "2c3a92453352cc815a92a9cebc576392"
+      "Hash": "cd68fb46e774cb0924d7af0ce8c69409"
     },
     "R.cache": {
       "Package": "R.cache",
@@ -467,7 +495,10 @@
       "Version": "1.8.2",
       "Source": "Repository",
       "Repository": "CRAN",
-      "Requirements": ["R", "utils"],
+      "Requirements": [
+        "R",
+        "utils"
+      ],
       "Hash": "278c286fd6e9e75d0c2e8f731ea445c8"
     },
     "R.oo": {
@@ -475,7 +506,12 @@
       "Version": "1.27.0",
       "Source": "Repository",
       "Repository": "CRAN",
-      "Requirements": ["R", "R.methodsS3", "methods", "utils"],
+      "Requirements": [
+        "R",
+        "R.methodsS3",
+        "methods",
+        "utils"
+      ],
       "Hash": "6ac79ff194202248cf946fe3a5d6d498"
     },
     "R.utils": {
@@ -483,7 +519,14 @@
       "Version": "2.12.3",
       "Source": "Repository",
       "Repository": "CRAN",
-      "Requirements": ["R", "R.methodsS3", "R.oo", "methods", "tools", "utils"],
+      "Requirements": [
+        "R",
+        "R.methodsS3",
+        "R.oo",
+        "methods",
+        "tools",
+        "utils"
+      ],
       "Hash": "3dc2829b790254bfba21e60965787651"
     },
     "R6": {
@@ -491,7 +534,9 @@
       "Version": "2.5.1",
       "Source": "Repository",
       "Repository": "CRAN",
-      "Requirements": ["R"],
+      "Requirements": [
+        "R"
+      ],
       "Hash": "470851b6d5d0ac559e9d01bb352b4021"
     },
     "RColorBrewer": {
@@ -499,17 +544,11 @@
       "Version": "1.1-3",
       "Source": "Repository",
       "Repository": "CRAN",
-      "Requirements": ["R"],
+      "Requirements": [
+        "R"
+      ],
       "Hash": "45f0398006e83a5b10b72a90663d8d8c"
     },
-    "RCurl": {
-      "Package": "RCurl",
-      "Version": "1.98-1.16",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": ["R", "bitops", "methods"],
-      "Hash": "ddbdf53d15b47be4407ede6914f56fbb"
-    },
     "RSQLite": {
       "Package": "RSQLite",
       "Version": "2.3.9",
@@ -534,7 +573,10 @@
       "Version": "1.0.14",
       "Source": "Repository",
       "Repository": "CRAN",
-      "Requirements": ["methods", "utils"],
+      "Requirements": [
+        "methods",
+        "utils"
+      ],
       "Hash": "e7bdd9ee90e96921ca8a0f1972d66682"
     },
     "RcppArmadillo": {
@@ -542,7 +584,13 @@
       "Version": "14.2.2-1",
       "Source": "Repository",
       "Repository": "CRAN",
-      "Requirements": ["R", "Rcpp", "methods", "stats", "utils"],
+      "Requirements": [
+        "R",
+        "Rcpp",
+        "methods",
+        "stats",
+        "utils"
+      ],
       "Hash": "9da7c242d94a8419d045f6b3a64b9765"
     },
     "RcppEigen": {
@@ -550,7 +598,12 @@
       "Version": "0.3.4.0.2",
       "Source": "Repository",
       "Repository": "CRAN",
-      "Requirements": ["R", "Rcpp", "stats", "utils"],
+      "Requirements": [
+        "R",
+        "Rcpp",
+        "stats",
+        "utils"
+      ],
       "Hash": "4ac8e423216b8b70cb9653d1b3f71eb9"
     },
     "Rdpack": {
@@ -558,7 +611,13 @@
       "Version": "2.6.2",
       "Source": "Repository",
       "Repository": "CRAN",
-      "Requirements": ["R", "methods", "rbibutils", "tools", "utils"],
+      "Requirements": [
+        "R",
+        "methods",
+        "rbibutils",
+        "tools",
+        "utils"
+      ],
       "Hash": "a9e2118c664c2cd694f03de074e8d4b3"
     },
     "S4Arrays": {
@@ -620,13 +679,20 @@
       "Version": "1.84-2",
       "Source": "Repository",
       "Repository": "CRAN",
-      "Requirements": ["R", "graphics", "methods", "stats", "utils"],
+      "Requirements": [
+        "R",
+        "graphics",
+        "methods",
+        "stats",
+        "utils"
+      ],
       "Hash": "e78499cbcbbca98200254bd171379165"
     },
     "SummarizedExperiment": {
       "Package": "SummarizedExperiment",
-      "Version": "1.32.0",
+      "Version": "1.34.0",
       "Source": "Bioconductor",
+      "Repository": "Bioconductor 3.19",
       "Requirements": [
         "Biobase",
         "BiocGenerics",
@@ -644,20 +710,27 @@
         "tools",
         "utils"
       ],
-      "Hash": "caee529bf9710ff6fe1776612fcaa266"
+      "Hash": "2f6c8cc972ed6aee07c96e3dff729d15"
     },
-    "XML": {
-      "Package": "XML",
-      "Version": "3.99-0.18",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": ["R", "methods", "utils"],
-      "Hash": "4a5eca1070ecfe97e68727ed4b9a89fa"
+    "UCSC.utils": {
+      "Package": "UCSC.utils",
+      "Version": "1.0.0",
+      "Source": "Bioconductor",
+      "Repository": "Bioconductor 3.19",
+      "Requirements": [
+        "S4Vectors",
+        "httr",
+        "jsonlite",
+        "methods",
+        "stats"
+      ],
+      "Hash": "83d45b690bffd09d1980c224ef329f5b"
     },
     "XVector": {
       "Package": "XVector",
-      "Version": "0.42.0",
+      "Version": "0.44.0",
       "Source": "Bioconductor",
+      "Repository": "Bioconductor 3.19",
       "Requirements": [
         "BiocGenerics",
         "IRanges",
@@ -668,14 +741,18 @@
         "utils",
         "zlibbioc"
       ],
-      "Hash": "65c0b6bca03f88758f86ef0aa18c4873"
+      "Hash": "4245b9938ac74c0dbddbebbec6036ab4"
     },
     "abind": {
       "Package": "abind",
       "Version": "1.4-8",
       "Source": "Repository",
       "Repository": "CRAN",
-      "Requirements": ["R", "methods", "utils"],
+      "Requirements": [
+        "R",
+        "methods",
+        "utils"
+      ],
       "Hash": "2288423bb0f20a457800d7fc47f6aa54"
     },
     "askpass": {
@@ -683,7 +760,9 @@
       "Version": "1.2.1",
       "Source": "Repository",
       "Repository": "CRAN",
-      "Requirements": ["sys"],
+      "Requirements": [
+        "sys"
+      ],
       "Hash": "c39f4155b3ceb1a9a2799d700fbd4b6a"
     },
     "assertthat": {
@@ -691,7 +770,9 @@
       "Version": "0.2.1",
       "Source": "Repository",
       "Repository": "CRAN",
-      "Requirements": ["tools"],
+      "Requirements": [
+        "tools"
+      ],
       "Hash": "50c838a310445e954bc13f26f26a6ecf"
     },
     "backports": {
@@ -699,7 +780,9 @@
       "Version": "1.5.0",
       "Source": "Repository",
       "Repository": "CRAN",
-      "Requirements": ["R"],
+      "Requirements": [
+        "R"
+      ],
       "Hash": "e1e1b9d75c37401117b636b7ae50827a"
     },
     "base64enc": {
@@ -707,7 +790,9 @@
       "Version": "0.1-3",
       "Source": "Repository",
       "Repository": "CRAN",
-      "Requirements": ["R"],
+      "Requirements": [
+        "R"
+      ],
       "Hash": "543776ae6848fde2f48ff3816d0628bc"
     },
     "biomaRt": {
@@ -734,7 +819,9 @@
       "Version": "4.5.0.1",
       "Source": "Repository",
       "Repository": "CRAN",
-      "Requirements": ["R"],
+      "Requirements": [
+        "R"
+      ],
       "Hash": "f89f074e0e49bf1dbe3eba0a15a91476"
     },
     "bit64": {
@@ -742,22 +829,26 @@
       "Version": "4.6.0-1",
       "Source": "Repository",
       "Repository": "CRAN",
-      "Requirements": ["R", "bit", "graphics", "methods", "stats", "utils"],
+      "Requirements": [
+        "R",
+        "bit",
+        "graphics",
+        "methods",
+        "stats",
+        "utils"
+      ],
       "Hash": "4f572fbc586294afff277db583b9060f"
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+        "utils"
+      ],
       "Hash": "b8acdf8af494d9ec19ccb2481a9b11c2"
     },
     "yaml": {