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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SAIGEgds.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SAIGEgds_1.10.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/SAIGEgds.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SAIGEgds/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SAIGEgds’ version ‘1.10.0’
* 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
* 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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
seqGLMM_GxG_spa        8.360  0.048   8.422
seqAssocGLMM_spaACAT_O 6.910  0.093   7.017
seqAssocGLMM_spaACAT_V 6.779  0.088   6.879
seqAssocGLMM_spaBurden 6.086  0.076   6.170
SAIGEgds-package       5.895  0.074   5.989
seqAssocGLMM_SPA       5.495  0.052   5.562
seqFitNullGLMM_SPA     5.080  0.044   5.129
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.15-bioc/meat/SAIGEgds.Rcheck/00check.log’
for details.