* using log directory ‘/data/gannet/ripley/R/packages/tests-devel/cauphy.Rcheck’
* using R Under development (unstable) (2025-02-14 r87716)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)
    GNU Fortran (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)
* running under: Fedora Linux 40 (Workstation Edition)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘cauphy/DESCRIPTION’ ... OK
* this is package ‘cauphy’ version ‘1.0.3’
* 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 ‘cauphy’ can be installed ... [11s/14s] OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-gcc/cauphy-00install.html' for details.
* used C compiler: ‘gcc (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)’
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [13s/17s] 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [16s/20s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [123s/148s] ERROR
  Running ‘spelling.R’
  Running ‘testthat.R’ [122s/146s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(cauphy)
  Loading required package: ape
  > 
  > test_check("cauphy")
  [ FAIL 20 | WARN 2 | SKIP 0 | PASS 265 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('testAncestralStateReconstruction.R:148:3'): testAncestralFit ──────
  MAP$par (`actual`) not equal to -0.5086788 (`expected`).
  
    `actual`: -1.12
  `expected`: -0.51
  ── Failure ('testCauchyLikelihood.R:258:3'): testLikelihoodFunction ────────────
  ff$disp (`actual`) not equal to 0.06785236 (`expected`).
  
    `actual`: 0.040
  `expected`: 0.068
  ── Failure ('testFitFunctions.R:33:3'): optim ──────────────────────────────────
  ... <= res$logLik is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('testFitFunctions.R:41:3'): optim ──────────────────────────────────
  unname(sqrt(diag(vcov(res)))) (`actual`) not equal to c(0.03243854, 0.0180895) (`expected`).
  
    `actual`: 0.024 0.011
  `expected`: 0.032 0.018
  ── Failure ('testFitFunctions.R:87:3'): optim, random root ─────────────────────
  ... <= res$logLik is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('testFitFunctions.R:100:3'): optim, random root ────────────────────
  reslam$logLik > res$logLik is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('testFitFunctions.R:104:3'): optim, random root ────────────────────
  unname(sqrt(diag(vcov(reslam)))) (`actual`) not equal to c(0.0285, 0.0415) (`expected`).
  
    `actual`: NaN NaN
  `expected`: 0.0 0.0
  ── Failure ('testFitFunctions.R:147:3'): optim, reml ───────────────────────────
  ... <= res$logLik is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('testFitFunctions.R:160:3'): optim, reml ───────────────────────────
  unname(sqrt(diag(vcov(res)))) (`actual`) not equal to c(0.02016588) (`expected`).
  
    `actual`: 0.008
  `expected`: 0.020
  ── Failure ('testFitFunctions.R:164:3'): optim, reml ───────────────────────────
  reslam$logLik > res$logLik is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('testFitFunctions.R:168:3'): optim, reml ───────────────────────────
  unname(sqrt(diag(vcov(reslam)))) (`actual`) not equal to c(0.0283, 0.0574) (`expected`).
  
    `actual`: NaN NaN
  `expected`: 0.0 0.1
  ── Failure ('testFitFunctions.R:324:3'): cauphylm helper functions ─────────────
  logLik(reslmdat) (`actual`) not equal to 13.296526 (`expected`).
  
    `actual`: -Inf
  `expected`: 13.3
  ── Failure ('testFitFunctions.R:325:3'): cauphylm helper functions ─────────────
  AIC(reslmdat) (`actual`) not equal to -20.5930517 (`expected`).
  
    `actual`:   Inf
  `expected`: -20.6
  ── Failure ('testFitFunctions.R:330:3'): cauphylm helper functions ─────────────
  unname(sqrt(diag(vcov(reslmdat)))) (`actual`) not equal to c(0.04988679, 0.065175, 0.18057543) (`expected`).
  
    `actual`: 0.030 0.035 0.303
  `expected`: 0.050 0.065 0.181
  ── Failure ('testFitFunctions.R:390:3'): profile likelihood ────────────────────
  max(pr$lambda$profLogLik) (`actual`) not equal to fit$logLik (`expected`).
  
    `actual`: 12.6
  `expected`: -Inf
  ── Failure ('testFitFunctions.R:391:3'): profile likelihood ────────────────────
  mean(pr$x0$profLogLik) <= fit$logLik is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('testFitFunctions.R:392:3'): profile likelihood ────────────────────
  mean(pr$disp$profLogLik) <= fit$logLik is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('testFitFunctions.R:393:3'): profile likelihood ────────────────────
  mean(pr$lambda$profLogLik) <= fit$logLik is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('testIncrementReconstruction.R:206:3'): testAncestralIncrementFit ──
  MAP$par (`actual`) not equal to 0.2811777 (`expected`).
  
    `actual`: 0.48
  `expected`: 0.28
  ── Failure ('testIncrementReconstruction.R:273:3'): testHDI ────────────────────
  dim(hdi_all[[1]]) (`actual`) not equal to c(2, 2) (`expected`).
  
    `actual`: 1.0 2.0
  `expected`: 2.0 2.0
  
  [ FAIL 20 | WARN 2 | SKIP 0 | PASS 265 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [79s/97s] OK
* checking PDF version of manual ... [9s/12s] 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