* using log directory ‘/data/gannet/ripley/R/packages/tests-ATLAS/galamm.Rcheck’
* using R Under development (unstable) (2025-11-19 r89040)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)
    GNU Fortran (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)
* running under: Fedora Linux 42 (Workstation Edition)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘galamm/DESCRIPTION’ ... OK
* this is package ‘galamm’ version ‘0.2.3’
* 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 ‘galamm’ can be installed ... [110s/147s] OK
* used C++ compiler: ‘g++ (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)’
* checking C++ specification ... 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [23s/31s] 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 ... [30s/44s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [79s/119s]
 [79s/120s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(galamm)
  > 
  > test_check("galamm")
  Saving _problems/test-galamm-semiparametric-139.R
  [ FAIL 1 | WARN 0 | SKIP 14 | PASS 251 ]
  
  ══ Skipped tests (14) ══════════════════════════════════════════════════════════
  • On CRAN (11): 'test-galamm-glmm.R:10:1', 'test-galamm-heteroscedastic.R:1:1',
    'test-galamm-heteroscedastic.R:63:1',
    'test-galamm-latent-covariates-interaction.R:1:1',
    'test-galamm-latent-covariates-interaction.R:52:1', 'test-galamm-lmm.R:11:1',
    'test-galamm-lmm.R:117:1', 'test-galamm-mixed-resp.R:160:1',
    'test-galamm-mixed-resp.R:207:1', 'test-galamm-semiparametric.R:6:1',
    'test-galamm-setup.R:320:1'
  • Skipping extended tests (3): 'test-galamm-lmm.R:317:3',
    'test-parameter-recovery.R:116:3', 'test-parameter-recovery.R:133:5'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-galamm-semiparametric.R:135:3'): galamm reproduces gamm4 ─────
  Expected `c(...)` to equal `mod1$gam$coefficients`.
  Differences:
    `actual[3:6]`: -0.02047 0.39231 -0.49127 -0.94497
  `expected[3:6]`: -0.02047 0.39231 -0.49127  0.94497
  
  
  [ FAIL 1 | WARN 0 | SKIP 14 | PASS 251 ]
  Error:
  ! Test failures.
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [48s/144s] OK
* checking PDF version of manual ... [11s/32s] OK
* checking HTML version of manual ... [9s/24s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 1 ERROR
See
  ‘/data/gannet/ripley/R/packages/tests-ATLAS/galamm.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 10:57.01, 361.42 + 25.25