##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:SAIGEgds.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings SAIGEgds_2.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/SAIGEgds.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 12.3.1 (openEuler 12.3.1-36.oe2403)
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SAIGEgds/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SAIGEgds’ version ‘2.6.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘SAIGEgds’ can be installed ... OK
* used C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... NOTE
  installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
* 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 dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  ‘SeqArray:::.IsForking’ ‘SeqArray:::.McoreParallel’
  ‘SeqArray:::.NumParallel’ ‘SeqArray:::.seqProgForward’
  ‘SeqArray:::.seqProgress’ ‘SeqArray:::process_index’
  ‘survey:::saddle’
  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 is not available
* 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:
Tue Jan 21 10:39:18 2025
Filtering variants:

[..................................................]  0%, ETC: ---    
[==================================================] 100%, completed, 0s
MAC category for estimating variance ratio:
    MAC[20, Inf):	30+ randomly from 9,650 variants
Fit the null model: y ~ x1 + x2 + var(GRM)
    # of samples: 1,000
    # of variants in GRM: 9,650
    MAF threshold for GRM: >= 0.01
    using 1 thread
Transform on the design matrix with QR decomposition:
    new formula: y ~ x_0 + x_1 + x_2 - 1
Use dense genetic relationship matrix in the file:
    /home/biocbuild/R/R-4.4.2/site-library/SAIGEgds/extdata/grm1k_10k_snp.gds
Loading SNP genotypes from the GDS file:

[..................................................]  0%, ETC: ---    
[==================================================] 100%, completed, 1s
    using 2.6M (sparse genotype matrix)

 *** caught segfault ***
address 0x2000000fdf8, cause 'memory not mapped'

Traceback:
 1: seqFitNullGLMM_SPA(y ~ x1 + x2, pheno, gdsfile, trait.type = "binary")
An irrecoverable exception occurred. R is aborting now ...
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/SAIGEgds.Rcheck/00check.log’
for details.