* using log directory ‘/data/gannet/ripley/R/packages/tests-clang/partR2.Rcheck’
* using R Under development (unstable) (2025-02-28 r87848)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    clang version 20.1.0-rc3
    flang version 20.1.0-rc3
* running under: Fedora Linux 40 (Workstation Edition)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘partR2/DESCRIPTION’ ... OK
* this is package ‘partR2’ version ‘0.9.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘partR2’ can be installed ... OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-clang/partR2-00install.html' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [10s/12s] OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [17s/20s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [44s/54s] ERROR
  Running ‘testthat.R’ [44s/53s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(partR2)
  > test_check("partR2")
  [ FAIL 11 | WARN 141 | SKIP 0 | PASS 81 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_combinations.R:63:3'): partbatch without partvars works ──────
  R2_BMc$R2$estimate not equal to c(0.600551, 0.3910285).
  2/2 mismatches (average diff: 0.0345)
  [1] 0.559 - 0.601 == -0.0420
  [2] 0.364 - 0.391 == -0.0269
  ── Failure ('test_partR2.R:22:3'): partR2 works for some special cases ─────────
  r2_1$R2$estimate not equal to c(0.599, 0.0125, 0, 0.0124).
  3/4 mismatches (average diff: 0.0146)
  [1] 0.5573 - 0.5990 == -0.04172
  [2] 0.0114 - 0.0125 == -0.00115
  [4] 0.0113 - 0.0124 == -0.00107
  ── Failure ('test_r2.R:25:3'): R2 marginal and conditional are correct ─────────
  r2_marg$R2 not equal to 0.2.
  1/1 mismatches
  [1] 0.164 - 0.2 == -0.0362
  ── Failure ('test_r2.R:26:3'): R2 marginal and conditional are correct ─────────
  r2_cond$R2 not equal to 0.229.
  1/1 mismatches
  [1] 0.406 - 0.229 == 0.177
  ── Failure ('test_r2.R:123:3'): part R2s are correct with part_R2s() ───────────
  r2_6$estimate not equal to c(0.219, 0.02).
  2/2 mismatches (average diff: 0.0202)
  [1] 0.1814 - 0.219 == -0.03761
  [2] 0.0172 - 0.020 == -0.00282
  ── Failure ('test_r2.R:131:3'): part R2s are correct with part_R2s() ───────────
  r2_8[r2_8$term == "Year+SpeciesDiversity:I(Temperature^2)", "estimate"][[1]] not equal to 0.0210613.
  1/1 mismatches
  [1] 0.0177 - 0.0211 == -0.00336
  ── Failure ('test_varcomps.R:88:3'): Gaussian variance components are correct ──
  var_comps1$var_ran not equal to 0.2272901.
  1/1 mismatches
  [1] 0.306 - 0.227 == 0.0785
  ── Failure ('test_varcomps.R:89:3'): Gaussian variance components are correct ──
  var_comps1$var_res not equal to 0.7646179.
  1/1 mismatches
  [1] 0.749 - 0.765 == -0.016
  ── Failure ('test_varcomps.R:92:3'): Gaussian variance components are correct ──
  var_comps2$var_fix not equal to 0.4129966.
  1/1 mismatches
  [1] 0.414 - 0.413 == 0.00124
  ── Failure ('test_varcomps.R:93:3'): Gaussian variance components are correct ──
  var_comps2$var_ran not equal to 0.2048629.
  1/1 mismatches
  [1] 0.156 - 0.205 == -0.0487
  ── Failure ('test_varcomps.R:94:3'): Gaussian variance components are correct ──
  var_comps2$var_res not equal to 0.3723833.
  1/1 mismatches
  [1] 0.382 - 0.372 == 0.00999
  
  [ FAIL 11 | WARN 141 | SKIP 0 | PASS 81 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [137s/165s] OK
* checking PDF version of manual ... [9s/14s] OK
* checking HTML version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 ERROR, 1 NOTE