* using log directory ‘/data/gannet/ripley/R/packages/tests-devel/HLMdiag.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 ‘HLMdiag/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HLMdiag’ version ‘0.5.0’
* 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 ‘HLMdiag’ can be installed ... [129s/146s] OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-gcc/HLMdiag-00install.html' for details.
* used C compiler: ‘gcc (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)’
* used C++ compiler: ‘g++ (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* 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 ... [40s/52s] 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 ... [18s/25s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [187s/232s] ERROR
  Running ‘testthat.R’ [186s/232s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(HLMdiag)
  
  Attaching package: 'HLMdiag'
  
  The following object is masked from 'package:stats':
  
      covratio
  
  > library(lme4)
  Loading required package: Matrix
  > library(nlme)
  
  Attaching package: 'nlme'
  
  The following object is masked from 'package:lme4':
  
      lmList
  
  > 
  > data(sleepstudy, package = 'lme4')
  > 
  > sleepstudy2 <- sleepstudy
  > sleepstudy2[7,1] <- NA
  > sleepstudy2[2,2] <- NA
  > 
  > 
  > test_check("HLMdiag")
  [ FAIL 1 | WARN 970 | SKIP 6 | PASS 423 ]
  
  ══ Skipped tests (6) ═══════════════════════════════════════════════════════════
  • On CRAN (6): 'test-hlm_influence.R:32:3', 'test-hlm_influence.R:56:3',
    'test-hlm_resid.R:90:3', 'test-hlm_resid.R:111:3',
    'test-influence_functions.R:158:3', 'test-influence_functions.R:172:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-case_delete.R:545:3'): Dimenstions of variance components are correct for single case deletion for nlme models ──
  length(sleep.lme.caseD$varcomp.delete) not equal to length(varcomp.lme(sleep.lme)).
  1/1 mismatches
  [1] 3 - 4 == -1
  
  [ FAIL 1 | WARN 970 | SKIP 6 | PASS 423 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [27s/37s] OK
* checking PDF version of manual ... [8s/11s] 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