Running 'testthat.R' [56s/63s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(MAGEE)
  > Sys.setenv(MKL_NUM_THREADS = 1)
  > 
  > test_check("MAGEE")
  Automatic allele flipping enabled...
  Variants matching alt/ref but not ref/alt alleles will also be included, with flipped effects
  Automatic allele flipping enabled...
  Variants matching alt/ref but not ref/alt alleles will also be included, with flipped effects
  Automatic allele flipping enabled...
  Variants matching alt/ref but not ref/alt alleles will also be included, with flipped effects
  Automatic allele flipping enabled...
  Variants matching alt/ref but not ref/alt alleles will also be included, with flipped effects
  Automatic allele flipping enabled...
  Variants matching alt/ref but not ref/alt alleles will also be included, with flipped effects
  Automatic allele flipping enabled...
  Variants matching alt/ref but not ref/alt alleles will also be included, with flipped effects
  Automatic allele flipping enabled...
  Variants matching alt/ref but not ref/alt alleles will also be included, with flipped effects
  Automatic allele flipping enabled...
  Variants matching alt/ref but not ref/alt alleles will also be included, with flipped effects
  Automatic allele flipping enabled...
  Variants matching alt/ref but not ref/alt alleles will also be included, with flipped effects
  Automatic allele flipping enabled...
  Variants matching alt/ref but not ref/alt alleles will also be included, with flipped effects
  Automatic allele flipping enabled...
  Variants matching alt/ref but not ref/alt alleles will also be included, with flipped effects
  Automatic allele flipping enabled...
  Variants matching alt/ref but not ref/alt alleles will also be included, with flipped effects
  Automatic allele flipping enabled...
  Variants matching alt/ref but not ref/alt alleles will also be included, with flipped effects
  Automatic allele flipping enabled...
  Variants matching alt/ref but not ref/alt alleles will also be included, with flipped effects
  [ FAIL 1 | WARN 0 | SKIP 6 | PASS 88 ]
  
  == Skipped tests ===============================================================
  * On CRAN (6)
  
  == Failed tests ================================================================
  -- Error (test_glmm.gei.R:167:3): cross-sectional gaussian ---------------------
  <std::runtime_error/C++Error/error/condition>
  Error in `glmm.gei(null.obj = obj3, interaction = c("sex", "obese"), interaction.covariates = "age", 
      geno.file = bgenfile, bgen.samplefile = samplefile, outfile = obj3.outfile.bgen.cov)`: inv(): matrix is singular
  Backtrace:
      x
   1. \-MAGEE::glmm.gei(...) at test_glmm.gei.R:167:2
  
  [ FAIL 1 | WARN 0 | SKIP 6 | PASS 88 ]
  Error: Test failures
  Execution halted