Updated README to explain renv better and added a line about renv::st…

…atus()
idem-lab · Jun 27, 2024 · 92327ff · 92327ff
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diff --git a/README.Rmd b/README.Rmd
@@ -57,7 +57,7 @@ To run this analysis pipeline, you would need to be familiar with the `targets`
 
 First, download the zip file of this analysis pipeline from our [Zenodo repository](https://zenodo.org/records/11365943). Open the project in a new RStudio session.
 
-Once you've opened the project in a new RStudio session, you will be prompted to run `renv::restore()`. Run `renv::restore()` to install the packages used in this analysis to your workspace.
+Once you've opened the project in a new RStudio session, you will be prompted to run `renv::restore()`. Run `renv::restore()` to install the packages used in this analysis to your workspace. If you then come across issues, run `renv::status()`. Also run `?renv::status()` for advice on resolving these issues.
 
 Open the `_targets.R` file, and run all lines of code under the **Set-up** section to load the R packages required for this pipeline. You can then run `tar_make()` to run the entire pipeline.
 

diff --git a/README.md b/README.md
@@ -83,7 +83,9 @@ new RStudio session.
 
 Once you’ve opened the project in a new RStudio session, you will be
 prompted to run `renv::restore()`. Run `renv::restore()` to install the
-packages used in this analysis to your workspace.
+packages used in this analysis to your workspace. If you then come
+across issues, run `renv::status()`. Also run `?renv::status()` for
+advice on resolving these issues.
 
 Open the `_targets.R` file, and run all lines of code under the
 **Set-up** section to load the R packages required for this pipeline.

diff --git a/renv.lock b/renv.lock
@@ -1,6 +1,6 @@
 {
   "R": {
-    "Version": "4.3.3",
+    "Version": "4.4.1",
     "Repositories": [
       {
         "Name": "CRAN",
@@ -19,7 +19,7 @@
   "Packages": {
     "MASS": {
       "Package": "MASS",
-      "Version": "7.3-60.0.1",
+      "Version": "7.3-61",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -30,11 +30,11 @@
         "stats",
         "utils"
       ],
-      "Hash": "b765b28387acc8ec9e9c1530713cb19c"
+      "Hash": "0cafd6f0500e5deba33be22c46bf6055"
     },
     "Matrix": {
       "Package": "Matrix",
-      "Version": "1.6-5",
+      "Version": "1.7-0",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -47,7 +47,7 @@
         "stats",
         "utils"
       ],
-      "Hash": "8c7115cd3a0e048bda2a7cd110549f7a"
+      "Hash": "1920b2f11133b12350024297d8a4ff4a"
     },
     "R6": {
       "Package": "R6",
@@ -238,13 +238,8 @@
     "conmat": {
       "Package": "conmat",
       "Version": "0.0.2.9000",
-      "Source": "GitHub",
-      "RemoteType": "github",
-      "RemoteHost": "api.github.com",
-      "RemoteUsername": "idem-lab",
-      "RemoteRepo": "conmat",
-      "RemoteRef": "master",
-      "RemoteSha": "419c9baf90d48923d49d95a11ff7f40142f5d29e",
+      "Source": "Repository",
+      "Repository": "IDEM",
       "Requirements": [
         "R",
         "cli",
@@ -268,7 +263,7 @@
         "vctrs",
         "waldo"
       ],
-      "Hash": "b1683fea455b88b7cb4c5110ced1abe9"
+      "Hash": "f2b3e4dd940242926c48add8e0476d48"
     },
     "countrycode": {
       "Package": "countrycode",
@@ -340,14 +335,14 @@
     },
     "digest": {
       "Package": "digest",
-      "Version": "0.6.35",
+      "Version": "0.6.36",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "R",
         "utils"
       ],
-      "Hash": "698ece7ba5a4fa4559e3d537e7ec3d31"
+      "Hash": "fd6824ad91ede64151e93af67df6376b"
     },
     "dotCall64": {
       "Package": "dotCall64",
@@ -414,10 +409,10 @@
     },
     "farver": {
       "Package": "farver",
-      "Version": "2.1.1",
+      "Version": "2.1.2",
       "Source": "Repository",
       "Repository": "CRAN",
-      "Hash": "8106d78941f34855c440ddb946b8f7a5"
+      "Hash": "680887028577f3fa2a81e410ed0d6e42"
     },
     "fastmap": {
       "Package": "fastmap",
@@ -507,9 +502,9 @@
     },
     "ggplot2": {
       "Package": "ggplot2",
-      "Version": "3.4.4",
+      "Version": "3.5.1",
       "Source": "Repository",
-      "Repository": "https://packagemanager.posit.co/cran/2023-12-06",
+      "Repository": "CRAN",
       "Requirements": [
         "MASS",
         "R",
@@ -528,7 +523,7 @@
         "vctrs",
         "withr"
       ],
-      "Hash": "313d31eff2274ecf4c1d3581db7241f9"
+      "Hash": "44c6a2f8202d5b7e878ea274b1092426"
     },
     "globals": {
       "Package": "globals",
@@ -554,7 +549,7 @@
     },
     "gtable": {
       "Package": "gtable",
-      "Version": "0.3.4",
+      "Version": "0.3.5",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -565,7 +560,7 @@
         "lifecycle",
         "rlang"
       ],
-      "Hash": "b29cf3031f49b04ab9c852c912547eef"
+      "Hash": "e18861963cbc65a27736e02b3cd3c4a0"
     },
     "highr": {
       "Package": "highr",
@@ -817,14 +812,14 @@
     },
     "munsell": {
       "Package": "munsell",
-      "Version": "0.5.0",
+      "Version": "0.5.1",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "colorspace",
         "methods"
       ],
-      "Hash": "6dfe8bf774944bd5595785e3229d8771"
+      "Hash": "4fd8900853b746af55b81fda99da7695"
     },
     "nlme": {
       "Package": "nlme",
@@ -878,9 +873,9 @@
     },
     "patchwork": {
       "Package": "patchwork",
-      "Version": "1.1.3",
+      "Version": "1.2.0",
       "Source": "Repository",
-      "Repository": "https://packagemanager.posit.co/cran/2023-12-06",
+      "Repository": "CRAN",
       "Requirements": [
         "cli",
         "ggplot2",
@@ -892,7 +887,7 @@
         "stats",
         "utils"
       ],
-      "Hash": "c5754106c02e8e019941100c81149431"
+      "Hash": "9c8ab14c00ac07e9e04d1664c0b74486"
     },
     "pillar": {
       "Package": "pillar",
@@ -1061,9 +1056,9 @@
     },
     "rmarkdown": {
       "Package": "rmarkdown",
-      "Version": "2.25",
+      "Version": "2.27",
       "Source": "Repository",
-      "Repository": "https://packagemanager.posit.co/cran/2023-12-06",
+      "Repository": "CRAN",
       "Requirements": [
         "R",
         "bslib",
@@ -1074,14 +1069,13 @@
         "jsonlite",
         "knitr",
         "methods",
-        "stringr",
         "tinytex",
         "tools",
         "utils",
         "xfun",
         "yaml"
       ],
-      "Hash": "d65e35823c817f09f4de424fcdfa812a"
+      "Hash": "27f9502e1cdbfa195f94e03b0f517484"
     },
     "sass": {
       "Package": "sass",
@@ -1129,14 +1123,9 @@
     },
     "socialmixr": {
       "Package": "socialmixr",
-      "Version": "0.3.2.9000",
-      "Source": "GitHub",
-      "RemoteType": "github",
-      "RemoteUsername": "epiforecasts",
-      "RemoteRepo": "socialmixr",
-      "RemoteRef": "HEAD",
-      "RemoteSha": "753bef4f60890ebde5c62d2a95fe91e91beba3de",
-      "RemoteHost": "api.github.com",
+      "Version": "0.3.2",
+      "Source": "Repository",
+      "Repository": "CRAN",
       "Requirements": [
         "R",
         "countrycode",
@@ -1152,7 +1141,7 @@
         "wpp2017",
         "xml2"
       ],
-      "Hash": "e5c1bfa7e7ba72f1f58176597bc4140a"
+      "Hash": "45662d7e3ca41647455b89c74eb28abf"
     },
     "spam": {
       "Package": "spam",
@@ -1275,9 +1264,9 @@
     },
     "tidyr": {
       "Package": "tidyr",
-      "Version": "1.3.0",
+      "Version": "1.3.1",
       "Source": "Repository",
-      "Repository": "https://packagemanager.posit.co/cran/2023-12-06",
+      "Repository": "CRAN",
       "Requirements": [
         "R",
         "cli",
@@ -1294,7 +1283,7 @@
         "utils",
         "vctrs"
       ],
-      "Hash": "e47debdc7ce599b070c8e78e8ac0cfcf"
+      "Hash": "915fb7ce036c22a6a33b5a8adb712eb1"
     },
     "tidyselect": {
       "Package": "tidyselect",