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### Running command:
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###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SAIGEgds.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings SAIGEgds_1.9.2.tar.gz
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/SAIGEgds.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'SAIGEgds/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SAIGEgds' version '1.9.2'
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'SAIGEgds' can be installed ... OK
* checking installed package size ... 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 R 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 dependencies in R code ... NOTE
':::' call which should be '::': 'SPAtest:::ScoreTest_wSaddleApprox_NULL_Model'
  See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
  'SPAtest:::ScoreTest_wSaddleApprox_Get_X1' 'SeqArray:::.IsForking'
  'SeqArray:::.NumParallel' 'SeqArray:::.file_split'
  'SeqArray:::.seqGet2bGeno' 'SeqArray:::.seqProgForward'
  'SeqArray:::.seqProgress' 'SeqArray:::process_index'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... 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 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 ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'D:/biocbuild/bbs-3.15-bioc/R/library/SAIGEgds/libs/x64/SAIGEgds.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ... ERROR
Running examples in 'SAIGEgds-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: SAIGEgds-package
> ### Title: Scalable Implementation of Generalized mixed models in
> ###   Phenome-Wide Association Studies using GDS files
> ### Aliases: SAIGEgds-package SAIGEgds
> ### Keywords: GDS genetics association
> 
> ### ** Examples
> 
> # open the GDS file
> fn <- system.file("extdata", "grm1k_10k_snp.gds", package="SAIGEgds")
> gdsfile <- seqOpen(fn)
> 
> # load phenotype
> phenofn <- system.file("extdata", "pheno.txt.gz", package="SAIGEgds")
> pheno <- read.table(phenofn, header=TRUE, as.is=TRUE)
> head(pheno)
  sample.id y     yy      x1 x2
1        s1 0 4.5542  1.5118  1
2        s2 0 3.7941  0.3898  1
3        s3 0 5.0411 -0.6212  1
4        s4 0 5.6394 -2.2147  1
5        s5 0 4.2134  1.1249  1
6        s6 0 4.6145 -0.0449  1
> 
> # fit the null model
> glmm <- seqFitNullGLMM_SPA(y ~ x1 + x2, pheno, gdsfile, trait.type="binary")
SAIGE association analysis:
Thu Mar 17 20:11:47 2022
Filtering variants:

[..................................................]  0%, ETC: ---    
[==================================================] 100%, completed, 0s
# of selected variants: 9,976
Fit the null model: y ~ x1 + x2 + var(GRM)
    # of samples: 1,000
    # of variants: 9,976
    using 1 thread
Transform on the design matrix with QR decomposition:
    new formula: y ~ x_0 + x_1 + x_2 - 1
Start loading SNP genotypes:

[..................................................]  0%, ETC: ---    
[==================================================] 100%, completed, 0s
    using 6.6M (sparse matrix)
Binary outcome: y
       y Number Proportion
       0    902      0.902
       1     98      0.098
Initial fixed-effect coefficients:
         x_0        x_1        x_2
    2.520514 -0.7666948 -0.4557928
Initial variance component estimates, tau:
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'runTests.R'
 ERROR
Running the tests in 'tests/runTests.R' failed.
Last 13 lines of output:
  Transform on the design matrix with QR decomposition:
      new formula: y ~ x_0 + x_1 + x_2 - 1
  Start loading SNP genotypes:
  
  [..................................................]  0%, ETC: ---    
  [==================================================] 100%, completed, 0s
      using 6.6M (sparse matrix)
  Binary outcome: y
         y Number Proportion
         0    902      0.902
         1     98      0.098
  Initial fixed-effect coefficients:
           x_0        x_1        x_2
      2.520514 -0.7666948 -0.4557928
  Initial variance component estimates, tau:
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 3 NOTEs
See
  'D:/biocbuild/bbs-3.15-bioc/meat/SAIGEgds.Rcheck/00check.log'
for details.