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easystats
Fix all new failing checks
Multiple checks are currently failing. They should be fixed before the next CRAN submission
── Test failures ───────────────────────────────────────────────── testthat ────
> # Generate snapshots only on Windows to avoid having to generate snapshot variant
> # corresponding to each OS (#312).
> #
> # This is especially important for Bayesian models where the results can be different
> # across OS, and there is no way to specify a threshold when it comes to snapshots
> # since the values included are of character type.
> if (tolower(Sys.info()[["sysname"]]) == "windows") {
+ library(testthat)
+
+ test_check("report")
+ }
Loading required package: report
Start sampling
boundary (singular) fit: see help('isSingular')
[ FAIL 3 | WARN 1 | SKIP 3 | PASS 226 ]
══ Skipped tests (3) ═══════════════════════════════════════════════════════════
• Skipping because of a .01 decimal difference in snapshots (3):
'test-report.brmsfit.R:34:3', 'test-report.lm.R:6:3',
'test-report_performance.R:124:3'
══ Warnings ════════════════════════════════════════════════════════════════════
── Warning ('test-report.brmsfit.R:3:1'): report.brms ──────────────────────────
Global state has changed:
names(before[[4]])[122:127] vs names(after[[4]])[122:129]
"PHPROOT"
"PIPX_BIN_DIR"
"PIPX_HOME"
"PKGCACHE_HTTP_VERSION"
+ "PKG_CPPFLAGS"
+ "PKG_LIBS"
"POWERSHELL_DISTRIBUTION_CHANNEL"
"POWERSHELL_UPDATECHECK"
"PROCESSOR_ARCHITECTURE"
names(before[[4]])[207:212] vs names(after[[4]])[209:215]
"USERDOMAIN"
"USERDOMAIN_ROAMINGPROFILE"
"USERNAME"
"USERPROFILE"
+ "USE_CXX17"
"VCPKG_INSTALLATION_ROOT"
"WIX"
"_R_CHECK_BROWSER_NONINTERACTIVE_"
before[[4]][110:116] vs after[[4]][110:116]
NOT_CRAN"true"
NUMBER_OF_PROCESSORS"4"
OS"Windows_NT"
- PATH"C:\\rtools44/x86_64-w64-mingw32.static.posix/bin;C:\\rtools44/usr/bin;C:\\rtools44/x86_64-w64-mingw32.static.posix/bin;C:\\rtools44/usr/bin;C:\\rtools44/x86_64-w64-mingw32.static.posix/bin;C:\\rtools44/usr/bin;C:\\rtools44/x86_64-w64-mingw32.static.posix/bin;C:\\rtools44/usr/bin;C:\\R\\bin/x64;C:\\rtools44/x86_64-w64-mingw32.static.posix/bin;C:\\rtools44/usr/bin;C:\\rtools44/x86_64-w64-mingw32.static.posix/bin;C:\\rtools44/usr/bin;c:\\program files\\gs\\gs10.03.0\\bin;C:\\rtools44\\x86_64-w64-mingw32.static.posix\\bin;C:\\rtools44\\usr\\bin;C:\\R\\bin;C:\\hostedtoolcache\\windows\\pandoc\\3.2.1\\x64\\pandoc-3.2.1;C:\\Program Files\\MongoDB\\Server\\5.0\\bin;C:\\aliyun-cli;C:\\vcpkg;C:\\Program Files (x86)\\NSIS\\;C:\\tools\\zstd;C:\\Program Files\\Mercurial\\;C:\\hostedtoolcache\\windows\\stack\\2.15.7\\x64;C:\\cabal\\bin;C:\\\\ghcup\\bin;C:\\mingw64\\bin;C:\\Program Files\\dotnet;C:\\Program Files\\MySQL\\MySQL Server 8.0\\bin;C:\\Program Files\\R\\R-4.4.1\\bin\\x64;C:\\SeleniumWebDrivers\\GeckoDriver;C:\\SeleniumWebDrivers\\EdgeDriver\\;C:\\SeleniumWebDrivers\\ChromeDriver;C:\\Program Files (x86)\\sbt\\bin;C:\\Program Files (x86)\\GitHub CLI;C:\\Program Files\\Git\\bin;C:\\Program Files (x86)\\pipx_bin;C:\\npm\\prefix;C:\\hostedtoolcache\\windows\\go\\1.21.11\\x64\\bin;C:\\hostedtoolcache\\windows\\Python\\3.9.13\\x64\\Scripts;C:\\hostedtoolcache\\windows\\Python\\3.9.13\\x64;C:\\hostedtoolcache\\windows\\Ruby\\3.0.7\\x64\\bin;C:\\Program Files\\OpenSSL\\bin;C:\\tools\\kotlinc\\bin;C:\\hostedtoolcache\\windows\\Java_Temurin-Hotspot_jdk\\8.0.412-8\\x64\\bin;C:\\Program Files\\ImageMagick-7.1.1-Q16-HDRI;C:\\Program Files\\Microsoft SDKs\\Azure\\CLI2\\wbin;C:\\ProgramData\\kind;C:\\ProgramData\\docker-compose;C:\\ProgramData\\Chocolatey\\bin;C:\\Windows\\system32;C:\\Windows;C:\\Windows\\System32\\Wbem;C:\\Windows\\System32\\WindowsPowerShell\\v1.0\\;C:\\Windows\\System32\\OpenSSH\\;C:\\Program Files\\dotnet\\;C:\\Program Files\\PowerShell\\7\\;C:\\Program Files\\Microsoft\\Web Platform Installer\\;C:\\Program Files\\TortoiseSVN\\bin;C:\\Program Files\\Microsoft SQL Server\\Client SDK\\ODBC\\170\\Tools\\Binn\\;C:\\Program Files\\Microsoft SQL Server\\150\\Tools\\Binn\\;C:\\Program Files (x86)\\Windows Kits\\10\\Windows Performance Toolkit\\;C:\\Program Files (x86)\\WiX Toolset v3.14\\bin;C:\\Program Files\\Microsoft SQL Server\\130\\DTS\\Binn\\;C:\\Program Files\\Microsoft SQL Server\\140\\DTS\\Binn\\;C:\\Program Files\\Microsoft SQL Server\\150\\DTS\\Binn\\;C:\\Program Files\\Microsoft SQL Server\\[160](https://github.com/easystats/report/actions/runs/9745581166/job/26893883963#step:6:162)\\DTS\\Binn\\;C:\\Strawberry\\c\\bin;C:\\Strawberry\\perl\\site\\bin;C:\\Strawberry\\perl\\bin;C:\\ProgramData\\chocolatey\\lib\\pulumi\\tools\\Pulumi\\bin;C:\\Program Files\\CMake\\bin;C:\\ProgramData\\chocolatey\\lib\\maven\\apache-maven-3.8.7\\bin;C:\\Program Files\\Microsoft Service Fabric\\bin\\Fabric\\Fabric.Code;C:\\Program Files\\Microsoft SDKs\\Service Fabric\\Tools\\ServiceFabricLocalClusterManager;C:\\Program Files\\nodejs\\;C:\\Program Files\\Git\\cmd;C:\\Program Files\\Git\\mingw64\\bin;C:\\Program Files\\Git\\usr\\bin;C:\\Program Files\\GitHub CLI\\;c:\\tools\\php;C:\\Program Files (x86)\\sbt\\bin;C:\\Program Files\\Amazon\\AWSCLIV2\\;C:\\Program Files\\Amazon\\SessionManagerPlugin\\bin\\;C:\\Program Files\\Amazon\\AWSSAMCLI\\bin\\;C:\\Program Files\\Microsoft SQL Server\\130\\Tools\\Binn\\;C:\\Program Files\\LLVM\\bin;C:\\Users\\runneradmin\\.dotnet\\tools;C:\\Users\\runneradmin\\.cargo\\bin;C:\\Users\\runneradmin\\AppData\\Local\\Microsoft\\WindowsApps//"
+ PATH"C:\\rtools44\\x86_64-w64-mingw32.static.posix\\bin;C:\\rtools44\\usr\\bin;C:\\rtools44\\x86_64-w64-mingw32.static.posix\\bin;C:\\rtools44\\usr\\bin;C:\\rtools44\\x86_64-w64-mingw32.static.posix\\bin;C:\\rtools44\\usr\\bin;C:\\rtools44\\x86_64-w64-mingw32.static.posix\\bin;C:\\rtools44\\usr\\bin;C:\\R\\bin\\x64;C:\\rtools44\\x86_64-w64-mingw32.static.posix\\bin;C:\\rtools44\\usr\\bin;C:\\rtools44\\x86_64-w64-mingw32.static.posix\\bin;C:\\rtools44\\usr\\bin;C:\\Program Files\\gs\\gs10.03.0\\bin;C:\\rtools44\\x86_64-w64-mingw32.static.posix\\bin;C:\\rtools44\\usr\\bin;C:\\R\\bin;C:\\hostedtoolcache\\windows\\pandoc\\3.2.1\\x64\\pandoc-3.2.1;C:\\Program Files\\MongoDB\\Server\\5.0\\bin;C:\\aliyun-cli;C:\\vcpkg;C:\\Program Files (x86)\\NSIS;C:\\tools\\zstd;C:\\Program Files\\Mercurial;C:\\hostedtoolcache\\windows\\stack\\2.15.7\\x64;C:\\cabal\\bin;C:\\ghcup\\bin;C:\\mingw64\\bin;C:\\Program Files\\dotnet;C:\\Program Files\\MySQL\\MySQL Server 8.0\\bin;C:\\Program Files\\R\\R-4.4.1\\bin\\x64;C:\\SeleniumWebDrivers\\GeckoDriver;C:\\SeleniumWebDrivers\\EdgeDriver;C:\\SeleniumWebDrivers\\ChromeDriver;C:\\Program Files (x86)\\sbt\\bin;C:\\Program Files (x86)\\GitHub CLI;C:\\Program Files\\Git\\bin;C:\\Program Files (x86)\\pipx_bin;C:\\npm\\prefix;C:\\hostedtoolcache\\windows\\go\\1.21.11\\x64\\bin;C:\\hostedtoolcache\\windows\\Python\\3.9.13\\x64\\Scripts;C:\\hostedtoolcache\\windows\\Python\\3.9.13\\x64;C:\\hostedtoolcache\\windows\\Ruby\\3.0.7\\x64\\bin;C:\\Program Files\\OpenSSL\\bin;C:\\tools\\kotlinc\\bin;C:\\hostedtoolcache\\windows\\Java_Temurin-Hotspot_jdk\\8.0.412-8\\x64\\bin;C:\\Program Files\\ImageMagick-7.1.1-Q16-HDRI;C:\\Program Files\\Microsoft SDKs\\Azure\\CLI2\\wbin;C:\\ProgramData\\kind;C:\\ProgramData\\docker-compose;C:\\ProgramData\\chocolatey\\bin;C:\\Windows\\System32;C:\\Windows;C:\\Windows\\System32\\wbem;C:\\Windows\\System32\\WindowsPowerShell\\v1.0;C:\\Windows\\System32\\OpenSSH;C:\\Program Files\\dotnet;C:\\Program Files\\PowerShell\\7;C:\\Program Files\\Microsoft\\Web Platform Installer;C:\\Program Files\\TortoiseSVN\\bin;C:\\Program Files\\Microsoft SQL Server\\Client SDK\\ODBC\\[170](https://github.com/easystats/report/actions/runs/9745581166/job/26893883963#step:6:172)\\Tools\\Binn;C:\\Program Files\\Microsoft SQL Server\\150\\Tools\\Binn;C:\\Program Files (x86)\\Windows Kits\\10\\Windows Performance Toolkit;C:\\Program Files (x86)\\WiX Toolset v3.14\\bin;C:\\Program Files\\Microsoft SQL Server\\130\\DTS\\Binn;C:\\Program Files\\Microsoft SQL Server\\140\\DTS\\Binn\\;C:\\Program Files\\Microsoft SQL Server\\150\\DTS\\Binn\\;C:\\Program Files\\Microsoft SQL Server\\160\\DTS\\Binn\\;C:\\Strawberry\\c\\bin;C:\\Strawberry\\perl\\site\\bin;C:\\Strawberry\\perl\\bin;C:\\ProgramData\\chocolatey\\lib\\pulumi\\tools\\pulumi\\bin;C:\\Program Files\\CMake\\bin;C:\\ProgramData\\chocolatey\\lib\\maven\\apache-maven-3.8.7\\bin;C:\\Program Files\\Microsoft Service Fabric\\bin\\Fabric\\Fabric.Code;C:\\Program Files\\Microsoft SDKs\\Service Fabric\\Tools\\ServiceFabricLocalClusterManager;C:\\Program Files\\nodejs;C:\\Program Files\\Git\\cmd;C:\\Program Files\\Git\\mingw64\\bin;C:\\Program Files\\Git\\usr\\bin;C:\\Program Files\\GitHub CLI;C:\\tools\\php;C:\\Program Files (x86)\\sbt\\bin;C:\\Program Files\\Amazon\\AWSCLIV2;C:\\Program Files\\Amazon\\SessionManagerPlugin\\bin;C:\\Program Files\\Amazon\\AWSSAMCLI\\bin;C:\\Program Files\\Microsoft SQL Server\\130\\Tools\\Binn;C:\\Program Files\\LLVM\\bin;C:\\Users\\runneradmin\\.dotnet\\tools;C:\\Users\\runneradmin\\.cargo\\bin;C:\\Users\\runneradmin\\AppData\\Local\\Microsoft\\WindowsApps"
PATHEXT".COM;.EXE;.BAT;.CMD;.VBS;.VBE;.JS;.JSE;.WSF;.WSH;.MSC"
PERFLOG_LOCATION_SETTING"RUNNER_PERFLOG"
PGBIN"C:\\Program Files\\PostgreSQL\\14\\bin"
before[[4]][122:127] vs after[[4]][122:129]
PHPROOT"c:\\tools\\php"
PIPX_BIN_DIR"C:\\Program Files (x86)\\pipx_bin"
PIPX_HOME"C:\\Program Files (x86)\\pipx"
PKGCACHE_HTTP_VERSION"2"
+ PKG_CPPFLAGS" -I\"D:/a/_temp/Library/Rcpp/include/\" -I\"C:/Users/runneradmin/AppData/Local/Temp/Rtmp8YSs4Z/RLIBS_89845fc253f/RcppEigen/include/\" -I\"C:/Users/runneradmin/AppData/Local/Temp/Rtmp8YSs4Z/RLIBS_89845fc253f/RcppEigen/include/unsupported\" -I\"C:/Users/runneradmin/AppData/Local/Temp/Rtmp8YSs4Z/RLIBS_89845fc253f/BH/include\" -I\"D:/a/_temp/Library/StanHeaders/include/src/\" -I\"D:/a/_temp/Library/StanHeaders/include/\" -I\"D:/a/_temp/Library/RcppParallel/include/\" -DRCPP_PARALLEL_USE_TBB=1 -I\"D:/a/_temp/Library/rstan/include\" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DUSE_STANC3 -DSTRICT_R_HEADERS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -include \"D:/a/_temp/Library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp\" -std=c++1y"
+ PKG_LIBS" \"D:/a/_temp/Library/rstan/lib/x64/libStanServices.a\" -L\"D:/a/_temp/Library/StanHeaders/libs/x64\" -lStanHeaders -L\"D:/a/_temp/Library/RcppParallel/lib/x64\" -ltbb -LD:/a/_temp/Library/RcppParallel/lib/x64 -ltbb -ltbbmalloc"
POWERSHELL_DISTRIBUTION_CHANNEL"GitHub-Actions-win22"
POWERSHELL_UPDATECHECK"Off"
PROCESSOR_ARCHITECTURE"AMD64"
before[[4]][207:212] vs after[[4]][209:215]
USERDOMAIN"fv-az980-277"
USERDOMAIN_ROAMINGPROFILE"fv-az980-277"
USERNAME"runneradmin"
USERPROFILE"C:\\Users\\runneradmin"
+ USE_CXX17"1"
VCPKG_INSTALLATION_ROOT"C:\\vcpkg"
WIX"C:\\Program Files (x86)\\WiX Toolset v3.14\\"
_R_CHECK_BROWSER_NONINTERACTIVE_"true"
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-report.htest-chi2.R:12:3'): report.htest-chi2 report ───────────
Error in `interpret.effectsize_table(structure(list(Cramers_v_adjusted = 0.100919982784409,
CI = 0.95, CI_low = 0.0657027540669358, CI_high = 1), row.names = c(NA,
-1L), ci = 0.95, ci_method = list(method = "ncp", distribution = "chisq"), alternative = "greater", class = c("effectsize_table",
"see_effectsize_table", "data.frame"), approximate = FALSE),
rules = "funder2019", rules = "funder2019")`: formal argument "rules" matched by multiple actual arguments
Backtrace:
▆
1. └─testthat::expect_snapshot(variant = "windows", report(x, rules = "funder2019")) at test-report.htest-chi2.R:12:3
2. └─rlang::cnd_signal(state$error)
── Error ('test-report.htest-t-test.R:86:3'): report.htest-t-test ──────────────
Error in `interpret.effectsize_table(structure(list(Cohens_d = -1.69603248205151,
CI = 0.95, CI_low = -2.54800792461072, CI_high = -0.8[185](https://github.com/easystats/report/actions/runs/9745581166/job/26893883963#step:6:187)82847644837), row.names = "difference in means between group 0 and group 1", class = c("effectsize_difference",
"effectsize_table", "see_effectsize_table", "data.frame"), paired = FALSE, pooled_sd = FALSE, mu = c(`difference in means between group 0 and group 1` = 0), ci = 0.95, ci_method = list(
method = "ncp", distribution = "t"), alternative = "two.sided", adjust = FALSE, approximate = FALSE),
rules = "cohen[198](https://github.com/easystats/report/actions/runs/9745581166/job/26893883963#step:6:200)8", rules = "cohen1988")`: formal argument "rules" matched by multiple actual arguments
Backtrace:
▆
1. └─testthat::expect_snapshot(...) at test-report.htest-t-test.R:86:3
2. └─rlang::cnd_signal(state$error)
── Failure ('test-report.lmer.R:22:3'): report-lmer ────────────────────────────
Snapshot of code has changed (variant 'windows'):
old[2:13] vs new[2:19]
Code
report(m2)
Message
boundary (singular) fit: see help('isSingular')
+ boundary (singular) fit: see help('isSingular')
Output
Random effect variances not available. Returned R2 does not account for random effects.
Message
+ boundary (singular) fit: see help('isSingular')
+ boundary (singular) fit: see help('isSingular')
boundary (singular) fit: see help('isSingular')
Output
Random effect variances not available. Returned R2 does not account for random effects.
+ Message
+ boundary (singular) fit: see help('isSingular')
+ Output
We fitted a linear mixed model (estimated using REML and nloptwrap optimizer)
to predict Reaction with Days (formula: Reaction ~ Days). The model included
mysubgrp as random effects (formula: list(~1 | mysubgrp:mygrp, ~1 | mygrp, ~1 |
* Run `testthat::snapshot_accept('windows/report.lmer')` to accept the change.
* Run `testthat::snapshot_review('windows/report.lmer')` to interactively review the change.
[ FAIL 3 | WARN 1 | SKIP 3 | PASS 226 ]
Error: Error: Test failures
Execution halted
The check-test-warnings workflow is failing because test-report.brmsfit generates a warning,
Global state has changed