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### Running command:
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###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:SAIGEgds.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings SAIGEgds_2.2.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/SAIGEgds.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* 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 ‘2.2.0’
* 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 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 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 ... 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
seqAssocGLMM_ACAT_V 5.729  0.020   5.763
seqAssocGLMM_ACAT_O 5.484  0.016   5.514
seqAssocGLMM_Burden 5.451  0.020   5.488
seqAssocGLMM_SKAT   5.027  0.024   5.071
* 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: 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/SAIGEgds.Rcheck/00check.log’
for details.

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### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL SAIGEgds
###
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* installing to library ‘/home/biocbuild/R/R-4.3.1/site-library’
* installing *source* package ‘SAIGEgds’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 10.3.1’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RcppParallel/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c SPATest.cpp -o SPATest.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RcppParallel/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c saige_fitnull.cpp -o saige_fitnull.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RcppParallel/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c saige_main.cpp -o saige_main.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RcppParallel/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c saige_misc.cpp -o saige_misc.o
saige_misc.cpp: In function ‘SEXPREC* saige_grm_sp_calc_ijx(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
saige_misc.cpp:626:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare]
  626 |  if (SAIGE_NumThread > n_block) SAIGE_NumThread = n_block;
      |      ~~~~~~~~~~~~~~~~^~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RcppParallel/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c vec_ext_avx2.cpp -o vec_ext_avx2.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RcppParallel/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c vec_ext_avx512bw.cpp -o vec_ext_avx512bw.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RcppParallel/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c vec_ext_def.cpp -o vec_ext_def.o
vec_ext_def.cpp: In function ‘void vec_init_function()’:
vec_ext_def.cpp:33:20: warning: unused variable ‘VEC_ALGORITHM_AVX2’ [-Wunused-variable]
   33 |  extern const bool VEC_ALGORITHM_AVX2;
      |                    ^~~~~~~~~~~~~~~~~~
vec_ext_def.cpp:34:20: warning: unused variable ‘VEC_ALGORITHM_AVX512BW’ [-Wunused-variable]
   34 |  extern const bool VEC_ALGORITHM_AVX512BW;
      |                    ^~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RcppParallel/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c vectorization.cpp -o vectorization.o
g++ -std=gnu++11 -shared -L/home/biocbuild/R/R-4.3.1/lib -L/usr/local/lib -o SAIGEgds.so SPATest.o saige_fitnull.o saige_main.o saige_misc.o vec_ext_avx2.o vec_ext_avx512bw.o vec_ext_def.o vectorization.o -lm -llapack -lblas -lgfortran -lm -lgcc -L/home/biocbuild/R/R-4.3.1/lib -lR
installing to /home/biocbuild/R/R-4.3.1/site-library/00LOCK-SAIGEgds/00new/SAIGEgds/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (SAIGEgds)

R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> # BiocGenerics:::testPackage("SAIGEgds")
> 
> proc.time()
   user  system elapsed 
  0.204   0.025   0.214