* 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 $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK * checking pragmas in C/C++ headers and code ... OK * checking compilation flags used ... OK * checking compiled code ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [16s/20s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [123s/148s] ERROR Running ‘spelling.R’ Running ‘testthat.R’ [122s/146s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(cauphy) Loading required package: ape > > test_check("cauphy") [ FAIL 20 | WARN 2 | SKIP 0 | PASS 265 ] â•â• Failed tests â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â• ── Failure ('testAncestralStateReconstruction.R:148:3'): testAncestralFit ────── MAP$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