Check that option and files are not changed during tests

pak.lock

@@ -1,7 +1,7 @@
 {
   "lockfile_version": 1,
   "os": "Ubuntu 22.04.5 LTS",
-  "r_version": "R version 4.4.1 (2024-06-14)",
+  "r_version": "R version 4.4.2 (2024-10-31)",
   "platform": "x86_64-pc-linux-gnu",
   "packages": [
     {
@@ -964,33 +964,35 @@
     {
       "ref": "duckdb",
       "package": "duckdb",
-      "version": "1.1.1",
+      "version": "1.1.2",
       "type": "standard",
       "direct": false,
-      "binary": true,
+      "binary": false,
       "dependencies": "DBI",
       "vignettes": false,
       "metadata": {
         "RemotePkgRef": "duckdb",
         "RemoteType": "standard",
         "RemoteRef": "duckdb",
         "RemoteRepos": "https://packagemanager.posit.co/cran/__linux__/jammy/latest",
-        "RemotePkgPlatform": "x86_64-pc-linux-gnu-ubuntu-22.04",
-        "RemoteSha": "1.1.1"
+        "RemotePkgPlatform": "source",
+        "RemoteSha": "1.1.2"
       },
-      "sources": "https://packagemanager.posit.co/cran/__linux__/jammy/latest/src/contrib/duckdb_1.1.1.tar.gz",
-      "target": "src/contrib/x86_64-pc-linux-gnu-ubuntu-22.04/4.4/duckdb_1.1.1.tar.gz",
-      "platform": "x86_64-pc-linux-gnu-ubuntu-22.04",
-      "rversion": "4.4",
+      "sources": "https://packagemanager.posit.co/cran/__linux__/jammy/latest/src/contrib/duckdb_1.1.2.tar.gz",
+      "target": "src/contrib/duckdb_1.1.2.tar.gz",
+      "platform": "source",
+      "rversion": "*",
       "directpkg": false,
       "license": "MIT + file LICENSE",
       "dep_types": ["Depends", "Imports", "LinkingTo"],
       "params": [],
       "install_args": "",
       "sysreqs": "",
       "sysreqs_packages": {},
-      "needscompilation": false,
-      "repotype": "cranlike"
+      "needscompilation": true,
+      "repotype": "cranlike",
+      "sha256": "1e14e39db3dc1c8b87ddd185c28deb4d11c3b073d3188852ab632339591c1825",
+      "filesize": 5222398
     },
     {
       "ref": "ellipsis",
@@ -1150,7 +1152,7 @@
     {
       "ref": "fs",
       "package": "fs",
-      "version": "1.6.4",
+      "version": "1.6.5",
       "type": "standard",
       "direct": false,
       "binary": true,
@@ -1162,10 +1164,10 @@
         "RemoteRef": "fs",
         "RemoteRepos": "https://packagemanager.posit.co/cran/__linux__/jammy/latest",
         "RemotePkgPlatform": "x86_64-pc-linux-gnu-ubuntu-22.04",
-        "RemoteSha": "1.6.4"
+        "RemoteSha": "1.6.5"
       },
-      "sources": "https://packagemanager.posit.co/cran/__linux__/jammy/latest/src/contrib/fs_1.6.4.tar.gz",
-      "target": "src/contrib/x86_64-pc-linux-gnu-ubuntu-22.04/4.4/fs_1.6.4.tar.gz",
+      "sources": "https://packagemanager.posit.co/cran/__linux__/jammy/latest/src/contrib/fs_1.6.5.tar.gz",
+      "target": "src/contrib/x86_64-pc-linux-gnu-ubuntu-22.04/4.4/fs_1.6.5.tar.gz",
       "platform": "x86_64-pc-linux-gnu-ubuntu-22.04",
       "rversion": "4.4",
       "directpkg": false,
@@ -1616,7 +1618,7 @@
       "repotype": "cranlike"
     },
     {
-      "ref": "installed::/opt/R/4.4.1/lib/R/library/codetools",
+      "ref": "installed::/opt/R/4.4.2/lib/R/library/codetools",
       "package": "codetools",
       "version": "0.2-20",
       "type": "installed",
@@ -1625,15 +1627,15 @@
       "dependencies": [],
       "vignettes": false,
       "metadata": {
-        "RemotePkgRef": "installed::/opt/R/4.4.1/lib/R/library/codetools",
+        "RemotePkgRef": "installed::/opt/R/4.4.2/lib/R/library/codetools",
         "RemoteType": "installed",
         "RemotePkgPlatform": "*",
         "RemoteSha": "0.2-20"
       },
       "sources": [],
       "target": "src/contrib/codetools_0.2-20.tar.gz",
       "platform": "*",
-      "rversion": "R 4.4.1",
+      "rversion": "R 4.4.2",
       "directpkg": false,
       "license": "GPL",
       "dep_types": ["Depends", "Imports", "LinkingTo"],
@@ -1642,10 +1644,10 @@
       "sysreqs_packages": {},
       "needscompilation": false,
       "repotype": "cran",
-      "built": "R 4.4.1; ; 2024-08-22 01:57:26 UTC; unix"
+      "built": "R 4.4.2; ; 2024-10-31 10:06:59 UTC; unix"
     },
     {
-      "ref": "installed::/opt/R/4.4.1/lib/R/library/lattice",
+      "ref": "installed::/opt/R/4.4.2/lib/R/library/lattice",
       "package": "lattice",
       "version": "0.22-6",
       "type": "installed",
@@ -1654,15 +1656,15 @@
       "dependencies": [],
       "vignettes": false,
       "metadata": {
-        "RemotePkgRef": "installed::/opt/R/4.4.1/lib/R/library/lattice",
+        "RemotePkgRef": "installed::/opt/R/4.4.2/lib/R/library/lattice",
         "RemoteType": "installed",
         "RemotePkgPlatform": "x86_64-pc-linux-gnu",
         "RemoteSha": "0.22-6"
       },
       "sources": [],
       "target": "src/contrib/lattice_0.22-6.tar.gz",
       "platform": "x86_64-pc-linux-gnu",
-      "rversion": "R 4.4.1",
+      "rversion": "R 4.4.2",
       "directpkg": false,
       "license": "GPL (>= 2)",
       "dep_types": ["Depends", "Imports", "LinkingTo"],
@@ -1671,27 +1673,27 @@
       "sysreqs_packages": {},
       "needscompilation": true,
       "repotype": "cran",
-      "built": "R 4.4.1; x86_64-pc-linux-gnu; 2024-08-22 01:54:07 UTC; unix"
+      "built": "R 4.4.2; x86_64-pc-linux-gnu; 2024-10-31 10:03:41 UTC; unix"
     },
     {
-      "ref": "installed::/opt/R/4.4.1/lib/R/library/Matrix",
+      "ref": "installed::/opt/R/4.4.2/lib/R/library/Matrix",
       "package": "Matrix",
-      "version": "1.7-0",
+      "version": "1.7-1",
       "type": "installed",
       "direct": false,
       "binary": true,
       "dependencies": "lattice",
       "vignettes": false,
       "metadata": {
-        "RemotePkgRef": "installed::/opt/R/4.4.1/lib/R/library/Matrix",
+        "RemotePkgRef": "installed::/opt/R/4.4.2/lib/R/library/Matrix",
         "RemoteType": "installed",
         "RemotePkgPlatform": "x86_64-pc-linux-gnu",
-        "RemoteSha": "1.7-0"
+        "RemoteSha": "1.7-1"
       },
       "sources": [],
-      "target": "src/contrib/Matrix_1.7-0.tar.gz",
+      "target": "src/contrib/Matrix_1.7-1.tar.gz",
       "platform": "x86_64-pc-linux-gnu",
-      "rversion": "R 4.4.1",
+      "rversion": "R 4.4.2",
       "directpkg": false,
       "license": "GPL (>= 2) | file LICENCE",
       "dep_types": ["Depends", "Imports", "LinkingTo"],
@@ -1700,7 +1702,7 @@
       "sysreqs_packages": {},
       "needscompilation": true,
       "repotype": "cran",
-      "built": "R 4.4.1; x86_64-pc-linux-gnu; 2024-08-22 01:54:16 UTC; unix"
+      "built": "R 4.4.2; x86_64-pc-linux-gnu; 2024-10-31 10:03:50 UTC; unix"
     },
     {
       "ref": "ISOweek",
@@ -2271,7 +2273,7 @@
     {
       "ref": "pkgbuild",
       "package": "pkgbuild",
-      "version": "1.4.4",
+      "version": "1.4.5",
       "type": "standard",
       "direct": false,
       "binary": true,
@@ -2283,10 +2285,10 @@
         "RemoteRef": "pkgbuild",
         "RemoteRepos": "https://packagemanager.posit.co/cran/__linux__/jammy/latest",
         "RemotePkgPlatform": "x86_64-pc-linux-gnu-ubuntu-22.04",
-        "RemoteSha": "1.4.4"
+        "RemoteSha": "1.4.5"
       },
-      "sources": "https://packagemanager.posit.co/cran/__linux__/jammy/latest/src/contrib/pkgbuild_1.4.4.tar.gz",
-      "target": "src/contrib/x86_64-pc-linux-gnu-ubuntu-22.04/4.4/pkgbuild_1.4.4.tar.gz",
+      "sources": "https://packagemanager.posit.co/cran/__linux__/jammy/latest/src/contrib/pkgbuild_1.4.5.tar.gz",
+      "target": "src/contrib/x86_64-pc-linux-gnu-ubuntu-22.04/4.4/pkgbuild_1.4.5.tar.gz",
       "platform": "x86_64-pc-linux-gnu-ubuntu-22.04",
       "rversion": "4.4",
       "directpkg": false,
@@ -2588,7 +2590,7 @@
     {
       "ref": "ps",
       "package": "ps",
-      "version": "1.8.0",
+      "version": "1.8.1",
       "type": "standard",
       "direct": false,
       "binary": true,
@@ -2600,10 +2602,10 @@
         "RemoteRef": "ps",
         "RemoteRepos": "https://packagemanager.posit.co/cran/__linux__/jammy/latest",
         "RemotePkgPlatform": "x86_64-pc-linux-gnu-ubuntu-22.04",
-        "RemoteSha": "1.8.0"
+        "RemoteSha": "1.8.1"
       },
-      "sources": "https://packagemanager.posit.co/cran/__linux__/jammy/latest/src/contrib/ps_1.8.0.tar.gz",
-      "target": "src/contrib/x86_64-pc-linux-gnu-ubuntu-22.04/4.4/ps_1.8.0.tar.gz",
+      "sources": "https://packagemanager.posit.co/cran/__linux__/jammy/latest/src/contrib/ps_1.8.1.tar.gz",
+      "target": "src/contrib/x86_64-pc-linux-gnu-ubuntu-22.04/4.4/ps_1.8.1.tar.gz",
       "platform": "x86_64-pc-linux-gnu-ubuntu-22.04",
       "rversion": "4.4",
       "directpkg": false,
@@ -2799,7 +2801,7 @@
     {
       "ref": "Rcpp",
       "package": "Rcpp",
-      "version": "1.0.13",
+      "version": "1.0.13-1",
       "type": "standard",
       "direct": false,
       "binary": true,
@@ -2811,10 +2813,10 @@
         "RemoteRef": "Rcpp",
         "RemoteRepos": "https://packagemanager.posit.co/cran/__linux__/jammy/latest",
         "RemotePkgPlatform": "x86_64-pc-linux-gnu-ubuntu-22.04",
-        "RemoteSha": "1.0.13"
+        "RemoteSha": "1.0.13-1"
       },
-      "sources": "https://packagemanager.posit.co/cran/__linux__/jammy/latest/src/contrib/Rcpp_1.0.13.tar.gz",
-      "target": "src/contrib/x86_64-pc-linux-gnu-ubuntu-22.04/4.4/Rcpp_1.0.13.tar.gz",
+      "sources": "https://packagemanager.posit.co/cran/__linux__/jammy/latest/src/contrib/Rcpp_1.0.13-1.tar.gz",
+      "target": "src/contrib/x86_64-pc-linux-gnu-ubuntu-22.04/4.4/Rcpp_1.0.13-1.tar.gz",
       "platform": "x86_64-pc-linux-gnu-ubuntu-22.04",
       "rversion": "4.4",
       "directpkg": false,
@@ -3727,7 +3729,7 @@
     {
       "ref": "tinytex",
       "package": "tinytex",
-      "version": "0.53",
+      "version": "0.54",
       "type": "standard",
       "direct": false,
       "binary": true,
@@ -3739,10 +3741,10 @@
         "RemoteRef": "tinytex",
         "RemoteRepos": "https://packagemanager.posit.co/cran/__linux__/jammy/latest",
         "RemotePkgPlatform": "x86_64-pc-linux-gnu-ubuntu-22.04",
-        "RemoteSha": "0.53"
+        "RemoteSha": "0.54"
       },
-      "sources": "https://packagemanager.posit.co/cran/__linux__/jammy/latest/src/contrib/tinytex_0.53.tar.gz",
-      "target": "src/contrib/x86_64-pc-linux-gnu-ubuntu-22.04/4.4/tinytex_0.53.tar.gz",
+      "sources": "https://packagemanager.posit.co/cran/__linux__/jammy/latest/src/contrib/tinytex_0.54.tar.gz",
+      "target": "src/contrib/x86_64-pc-linux-gnu-ubuntu-22.04/4.4/tinytex_0.54.tar.gz",
       "platform": "x86_64-pc-linux-gnu-ubuntu-22.04",
       "rversion": "4.4",
       "directpkg": false,
@@ -4006,7 +4008,7 @@
     {
       "ref": "withr",
       "package": "withr",
-      "version": "3.0.1",
+      "version": "3.0.2",
       "type": "standard",
       "direct": false,
       "binary": true,
@@ -4018,10 +4020,10 @@
         "RemoteRef": "withr",
         "RemoteRepos": "https://packagemanager.posit.co/cran/__linux__/jammy/latest",
         "RemotePkgPlatform": "x86_64-pc-linux-gnu-ubuntu-22.04",
-        "RemoteSha": "3.0.1"
+        "RemoteSha": "3.0.2"
       },
-      "sources": "https://packagemanager.posit.co/cran/__linux__/jammy/latest/src/contrib/withr_3.0.1.tar.gz",
-      "target": "src/contrib/x86_64-pc-linux-gnu-ubuntu-22.04/4.4/withr_3.0.1.tar.gz",
+      "sources": "https://packagemanager.posit.co/cran/__linux__/jammy/latest/src/contrib/withr_3.0.2.tar.gz",
+      "target": "src/contrib/x86_64-pc-linux-gnu-ubuntu-22.04/4.4/withr_3.0.2.tar.gz",
       "platform": "x86_64-pc-linux-gnu-ubuntu-22.04",
       "rversion": "4.4",
       "directpkg": false,
@@ -4037,7 +4039,7 @@
     {
       "ref": "xfun",
       "package": "xfun",
-      "version": "0.48",
+      "version": "0.49",
       "type": "standard",
       "direct": false,
       "binary": true,
@@ -4049,10 +4051,10 @@
         "RemoteRef": "xfun",
         "RemoteRepos": "https://packagemanager.posit.co/cran/__linux__/jammy/latest",
         "RemotePkgPlatform": "x86_64-pc-linux-gnu-ubuntu-22.04",
-        "RemoteSha": "0.48"
+        "RemoteSha": "0.49"
       },
-      "sources": "https://packagemanager.posit.co/cran/__linux__/jammy/latest/src/contrib/xfun_0.48.tar.gz",
-      "target": "src/contrib/x86_64-pc-linux-gnu-ubuntu-22.04/4.4/xfun_0.48.tar.gz",
+      "sources": "https://packagemanager.posit.co/cran/__linux__/jammy/latest/src/contrib/xfun_0.49.tar.gz",
+      "target": "src/contrib/x86_64-pc-linux-gnu-ubuntu-22.04/4.4/xfun_0.49.tar.gz",
       "platform": "x86_64-pc-linux-gnu-ubuntu-22.04",
       "rversion": "4.4",
       "directpkg": false,

tests/testthat/setup.R

@@ -1,3 +1,11 @@
+# Store the current options (for later conservation test -- see test-zzz.R)
+diseasy_opts <- purrr::keep(names(options()), ~ startsWith(., "diseasystore.")) |>
+  purrr::map(options) |>
+  purrr::reduce(c)
+
+# Store the current files (for later conservation test -- see test-zzz.R)
+current_files <- dir(recursive = TRUE)
+
 # Disable logging while testing
 lgr::suspend_logging()
 

tests/testthat/test-zzz.R

@@ -1,2 +1,16 @@
+test_that(r"{options are conserved during testing}", {
+  current_diseasy_opts <- purrr::keep(names(options()), ~ startsWith(., "diseasystore.")) |>
+    purrr::map(options) |>
+    purrr::reduce(c)
+
+  expect_identical(current_diseasy_opts, diseasy_opts)
+})
+
+
+test_that(r"{data is not written locally}", {
+  # CRAN does not allow us to create new files in the package folder
+  expect_setequal(dir(recursive = TRUE), current_files)
+})
+
 # Enable logging after testing
 lgr::unsuspend_logging()