repo: update renv, set R to 4.4.1

Author: dshemetov

Diff for: .renvignore

@@ -1,2 +1,3 @@
 tmp.R
 node_modules/*
+local_logs/

Diff for: renv.lock

@@ -1,6 +1,6 @@
 {
   "R": {
-    "Version": "4.4.2",
+    "Version": "4.4.1",
     "Repositories": [
       {
         "Name": "RSPM",
@@ -1702,7 +1702,8 @@
       "URL": "https://gitlab.com/luke-tierney/codetools",
       "License": "GPL",
       "NeedsCompilation": "no",
-      "Repository": "CRAN"
+      "Repository": "RSPM",
+      "Encoding": "UTF-8"
     },
     "collections": {
       "Package": "collections",
@@ -2809,11 +2810,11 @@
       "Author": "Logan Brooks [aut], Dmitry Shemetov [aut], Samuel Gratzl [aut], David Weber [ctb, cre], Nat DeFries [ctb], Alex Reinhart [ctb], Daniel J. McDonald [ctb], Kean Ming Tan [ctb], Will Townes [ctb], George Haff [ctb], Kathryn Mazaitis [ctb]",
       "Maintainer": "David Weber <[email protected]>",
       "RemoteType": "github",
-      "RemoteHost": "api.github.com",
       "RemoteUsername": "cmu-delphi",
       "RemoteRepo": "epidatr",
       "RemoteRef": "dev",
       "RemoteSha": "0026856af0f41f5caf11d53d244e68e31136418f",
+      "RemoteHost": "api.github.com",
       "Remotes": "cmu-delphi/delphidocs"
     },
     "epipredict": {
@@ -2952,11 +2953,11 @@
       "Author": "Jacob Bien [ctb], Logan Brooks [aut, cre], Rafael Catoia [ctb], Nat DeFries [aut], Daniel McDonald [aut], Rachel Lobay [ctb], Ken Mawer [ctb], Chloe You [ctb], Quang Nguyen [ctb], Evan Ray [aut], Dmitry Shemetov [aut], Ryan Tibshirani [aut], David Weber [ctb], Lionel Henry [ctb] (Author of included rlang fragments), Hadley Wickham [ctb] (Author of included rlang fragments), Posit [cph] (Copyright holder of included rlang fragments), Johns Hopkins University Center for Systems Science and Engineering [dtc] (Owner of COVID-19 cases and deaths data from the COVID-19 Data Repository), Johns Hopkins University [cph] (Copyright holder of COVID-19 cases and deaths data from the COVID-19 Data Repository), Carnegie Mellon University Delphi Group [dtc] (Owner of claims-based CLI data from the Delphi Epidata API)",
       "Maintainer": "Logan Brooks <[email protected]>",
       "RemoteType": "github",
+      "RemoteHost": "api.github.com",
       "RemoteUsername": "cmu-delphi",
       "RemoteRepo": "epiprocess",
       "RemoteRef": "dev",
       "RemoteSha": "a699ae8f7c77aabd6a72cdb0209dd34960402047",
-      "RemoteHost": "api.github.com",
       "Remotes": "cmu-delphi/delphidocs, cmu-delphi/epidatasets, cmu-delphi/epidatr, cmu-delphi/epipredict, glmgen/trendfilter, reconverse/outbreaks"
     },
     "evaluate": {
@@ -5228,7 +5229,8 @@
       "NeedsCompilation": "yes",
       "Author": "Deepayan Sarkar [aut, cre] (<https://orcid.org/0000-0003-4107-1553>), Felix Andrews [ctb], Kevin Wright [ctb] (documentation), Neil Klepeis [ctb], Johan Larsson [ctb] (miscellaneous improvements), Zhijian (Jason) Wen [cph] (filled contour code), Paul Murrell [ctb], Stefan Eng [ctb] (violin plot improvements), Achim Zeileis [ctb] (modern colors), Alexandre Courtiol [ctb] (generics for larrows, lpolygon, lrect and lsegments)",
       "Maintainer": "Deepayan Sarkar <[email protected]>",
-      "Repository": "CRAN"
+      "Repository": "RSPM",
+      "Encoding": "UTF-8"
     },
     "lava": {
       "Package": "lava",
@@ -5686,7 +5688,8 @@
       "NeedsCompilation": "no",
       "Author": "Joe Cheng [cre, aut], RStudio [cph]",
       "Maintainer": "Joe Cheng <[email protected]>",
-      "Repository": "CRAN"
+      "Repository": "RSPM",
+      "Encoding": "UTF-8"
     },
     "mirai": {
       "Package": "mirai",
@@ -6541,7 +6544,8 @@
       ],
       "Collate": "'adjective.R' 'adverb.R' 'exclamation.R' 'verb.R' 'rpackage.R' 'package.R'",
       "NeedsCompilation": "no",
-      "Repository": "CRAN"
+      "Repository": "RSPM",
+      "Encoding": "UTF-8"
     },
     "prettyunits": {
       "Package": "prettyunits",
@@ -6955,6 +6959,49 @@
       "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))",
       "Repository": "RSPM"
     },
+    "qs2": {
+      "Package": "qs2",
+      "Version": "0.1.4",
+      "Source": "Repository",
+      "Type": "Package",
+      "Title": "Efficient Serialization of R Objects",
+      "Date": "2024-12-11",
+      "Authors@R": "c( person(\"Travers\", \"Ching\", email = \"[email protected]\", role = c(\"aut\", \"cre\", \"cph\")), person(\"Yann\", \"Collet\", role = c(\"ctb\", \"cph\"), comment = \"Yann Collet is the author of the bundled zstd\"), 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(\"Francesc\", \"Alted\", role = c(\"ctb\", \"cph\"), comment = \"Shuffling routines derived from Blosc library\"))",
+      "Maintainer": "Travers Ching <[email protected]>",
+      "Description": "Streamlines and accelerates the process of saving and loading R objects, improving speed and compression compared to other methods. The package provides two compression formats: the 'qs2' format, which uses R serialization via the C API while optimizing compression and disk I/O, and the 'qdata' format, featuring custom serialization for slightly faster performance and better compression. Additionally, the 'qs2' format can be directly converted to the standard 'RDS' format, ensuring long-term compatibility with future versions of R.",
+      "License": "GPL-3",
+      "LazyData": "true",
+      "Biarch": "true",
+      "Depends": [
+        "R (>= 3.5.0)"
+      ],
+      "Imports": [
+        "Rcpp",
+        "stringfish (>= 0.15.1)"
+      ],
+      "LinkingTo": [
+        "Rcpp",
+        "stringfish",
+        "RcppParallel"
+      ],
+      "Suggests": [
+        "knitr",
+        "rmarkdown",
+        "dplyr",
+        "data.table",
+        "stringi"
+      ],
+      "SystemRequirements": "GNU make",
+      "Encoding": "UTF-8",
+      "RoxygenNote": "7.3.2",
+      "VignetteBuilder": "knitr",
+      "Copyright": "This package includes code from the 'zstd' library owned by Facebook, Inc. and created by Yann Collet; and code derived from the 'Blosc' library created and owned by Francesc Alted.",
+      "URL": "https://github.com/qsbase/qs2",
+      "BugReports": "https://github.com/qsbase/qs2/issues",
+      "NeedsCompilation": "yes",
+      "Author": "Travers Ching [aut, cre, cph], Yann Collet [ctb, cph] (Yann Collet is the author of the bundled zstd), 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), Francesc Alted [ctb, cph] (Shuffling routines derived from Blosc library)",
+      "Repository": "RSPM"
+    },
     "quadprog": {
       "Package": "quadprog",
       "Version": "1.5-8",
@@ -10115,9 +10162,10 @@
         "R (>= 2.10.0)"
       ],
       "License": "GPL (>= 2)",
-      "Repository": "CRAN",
+      "Repository": "RSPM",
       "NeedsCompilation": "no",
-      "Author": "David B. Dahl [aut], David Scott [aut, cre], Charles Roosen [aut], Arni Magnusson [aut], Jonathan Swinton [aut], Ajay Shah [ctb], Arne Henningsen [ctb], Benno Puetz [ctb], Bernhard Pfaff [ctb], Claudio Agostinelli [ctb], Claudius Loehnert [ctb], David Mitchell [ctb], David Whiting [ctb], Fernando da Rosa [ctb], Guido Gay [ctb], Guido Schulz [ctb], Ian Fellows [ctb], Jeff Laake [ctb], John Walker [ctb], Jun Yan [ctb], Liviu Andronic [ctb], Markus Loecher [ctb], Martin Gubri [ctb], Matthieu Stigler [ctb], Robert Castelo [ctb], Seth Falcon [ctb], Stefan Edwards [ctb], Sven Garbade [ctb], Uwe Ligges [ctb]"
+      "Author": "David B. Dahl [aut], David Scott [aut, cre], Charles Roosen [aut], Arni Magnusson [aut], Jonathan Swinton [aut], Ajay Shah [ctb], Arne Henningsen [ctb], Benno Puetz [ctb], Bernhard Pfaff [ctb], Claudio Agostinelli [ctb], Claudius Loehnert [ctb], David Mitchell [ctb], David Whiting [ctb], Fernando da Rosa [ctb], Guido Gay [ctb], Guido Schulz [ctb], Ian Fellows [ctb], Jeff Laake [ctb], John Walker [ctb], Jun Yan [ctb], Liviu Andronic [ctb], Markus Loecher [ctb], Martin Gubri [ctb], Matthieu Stigler [ctb], Robert Castelo [ctb], Seth Falcon [ctb], Stefan Edwards [ctb], Sven Garbade [ctb], Uwe Ligges [ctb]",
+      "Encoding": "UTF-8"
     },
     "yaml": {
       "Package": "yaml",