##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:SAIGEgds.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings SAIGEgds_2.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/SAIGEgds.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SAIGEgds/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SAIGEgds’ version ‘2.4.0’
* 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: ‘g++ (GCC) 10.3.1’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... NOTE
  installed size is 11.5Mb
  sub-directories of 1Mb or more:
    libs   9.7Mb
* 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’ ‘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 ... NOTE
seqFitLDpruning: no visible global function definition for
  ‘seqParApply’
Undefined global functions or variables:
  seqParApply
* checking Rd files ... NOTE
checkRd: (-1) seqFitSparseGRM.Rd:44: Lost braces; missing escapes or markup?
    44 | $grm_{ij} = avg_l [(g_{il} - 2*p_l)*(g_{jl} - 2*p_l) / 2*p_l*(1 - p_l)]$ for
       |      ^
checkRd: (-1) seqFitSparseGRM.Rd:44: Lost braces; missing escapes or markup?
    44 | $grm_{ij} = avg_l [(g_{il} - 2*p_l)*(g_{jl} - 2*p_l) / 2*p_l*(1 - p_l)]$ for
       |                       ^
checkRd: (-1) seqFitSparseGRM.Rd:44: Lost braces; missing escapes or markup?
    44 | $grm_{ij} = avg_l [(g_{il} - 2*p_l)*(g_{jl} - 2*p_l) / 2*p_l*(1 - p_l)]$ for
       |                                        ^
checkRd: (-1) seqFitSparseGRM.Rd:45: Lost braces; missing escapes or markup?
    45 | individuals i,j and locus l, where $g_{il}$ is 0, 1 or 2, and $p_l$ is the
       |                                       ^
* 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
seqAssocGLMM_ACAT_O 5.926  0.044   5.981
seqAssocGLMM_ACAT_V 5.808  0.008   5.828
seqAssocGLMM_Burden 5.795  0.004   5.811
seqAssocGLMM_SPA    5.578  0.016   5.605
SAIGEgds-package    5.493  0.012   5.515
seqAssocGLMM_SKAT   5.442  0.008   5.462
* 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: 7 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/SAIGEgds.Rcheck/00check.log’
for details.