* using log directory ‘/data/gannet/ripley/R/packages/tests-Suggests/GMMAT.Rcheck’
* using R Under development (unstable) (2024-04-19 r86451)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc-13 (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Fedora Linux 36 (Workstation Edition)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘GMMAT/DESCRIPTION’ ... OK
* this is package ‘GMMAT’ version ‘1.4.2’
* 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 ‘GMMAT’ can be installed ... [105s/203s] OK
* used C compiler: ‘gcc-13 (GCC) 13.2.0’
* used C++ compiler: ‘g++-13 (GCC) 13.2.0’
* 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 ... [44s/62s] 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 data for ASCII and uncompressed saves ... OK
* checking line endings in shell scripts ... 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(GMMAT)
  > Sys.setenv(MKL_NUM_THREADS = 1)
  > 
  > test_check("GMMAT")
  The following SNPs have been removed due to inconsistent alleles across studies:
  [1] "L10" "L12" "L15"
  [ FAIL 1 | WARN 0 | SKIP 30 | PASS 3 ]
  
  ══ Skipped tests (30) ══════════════════════════════════════════════════════════
  • On CRAN (28): 'test_SMMAT.R:56:2', 'test_SMMAT.R:103:2',
    'test_SMMAT.R:149:2', 'test_SMMAT.R:196:2', 'test_SMMAT.R:236:2',
    'test_SMMAT.R:276:2', 'test_SMMAT.meta.R:45:2', 'test_SMMAT.meta.R:77:2',
    'test_SMMAT.meta.R:108:2', 'test_SMMAT.meta.R:140:2',
    'test_SMMAT.meta.R:165:2', 'test_glmm.score.R:317:2',
    'test_glmm.score.R:616:2', 'test_glmm.score.R:914:2',
    'test_glmm.score.R:1213:2', 'test_glmm.score.R:1505:2',
    'test_glmm.score.R:1797:2', 'test_glmm.wald.R:2:2', 'test_glmm.wald.R:805:2',
    'test_glmm.wald.R:1609:2', 'test_glmm.wald.R:1761:2', 'test_glmmkin.R:2:2',
    'test_glmmkin.R:82:2', 'test_glmmkin.R:163:2', 'test_glmmkin.R:245:2',
    'test_glmmkin.R:328:2', 'test_glmmkin.R:362:2', 'test_glmmkin.R:396:2'
  • SeqArray cannot be loaded (2): 'test_SMMAT.R:2:9', 'test_SMMAT.meta.R:2:2'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_glmm.score.R:37:2'): cross-sectional id le 400 binomial ────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'doMC'
  Backtrace:
      ▆
   1. ├─GMMAT::glmm.score(...) at test_glmm.score.R:37:9
   2. └─base::loadNamespace(x)
   3.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   4.     └─base (local) withOneRestart(expr, restarts[[1L]])
   5.       └─base (local) doWithOneRestart(return(expr), restart)
  
  [ FAIL 1 | WARN 0 | SKIP 30 | PASS 3 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [246s/344s] OK
* checking PDF version of manual ... [11s/15s] 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
See
  ‘/data/gannet/ripley/R/packages/tests-Suggests/GMMAT.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 12:56.75, 480.15 + 31.12