##############################################################################
##############################################################################
###
### Running command:
###
###   /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_1.99.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/SAIGEgds.Rcheck’
* using R Under development (unstable) (2023-03-16 r83985)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* R was compiled by
    Apple clang version 12.0.0 (clang-1200.0.32.29)
    GNU Fortran (GCC) 8.2.0
* running under: macOS Mojave 10.14.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SAIGEgds/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SAIGEgds’ version ‘1.99.0’
* 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: ‘Apple clang version 11.0.0 (clang-1100.0.33.17)’
* used SDK: ‘’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* 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
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
File ‘/Library/Frameworks/R.framework/Versions/4.3/Resources/library/SAIGEgds/libs/SAIGEgds.so’:
  Found ‘___assert_rtn’, possibly from ‘assert’ (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 nor [v]sprintf. 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
seqAssocGLMM_ACAT_V 6.574  0.109   9.217
seqAssocGLMM_ACAT_O 6.239  0.135   8.718
seqAssocGLMM_Burden 5.759  0.133   7.911
seqseqFitLDpruning  5.223  0.206   7.408
seqAssocGLMM_SKAT   5.181  0.078   7.163
SAIGEgds-package    5.088  0.086   7.313
seqAssocGLMM_SPA    4.889  0.057   6.631
glmmHeritability    4.530  0.034   6.210
seqFitNullGLMM_SPA  4.408  0.031   5.965
* 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.17-bioc/meat/SAIGEgds.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SAIGEgds
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3/Resources/library’
* installing *source* package ‘SAIGEgds’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 11.0.0 (clang-1100.0.33.17)’
using C++11
using SDK: ‘’
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppParallel/include' -I/usr/local/include    -fPIC  -Wall -g -O2  -c SPATest.cpp -o SPATest.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppParallel/include' -I/usr/local/include    -fPIC  -Wall -g -O2  -c saige_fitnull.cpp -o saige_fitnull.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppParallel/include' -I/usr/local/include    -fPIC  -Wall -g -O2  -c saige_main.cpp -o saige_main.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppParallel/include' -I/usr/local/include    -fPIC  -Wall -g -O2  -c saige_misc.cpp -o saige_misc.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppParallel/include' -I/usr/local/include    -fPIC  -Wall -g -O2  -c vec_ext_avx2.cpp -o vec_ext_avx2.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppParallel/include' -I/usr/local/include    -fPIC  -Wall -g -O2  -c vec_ext_avx512bw.cpp -o vec_ext_avx512bw.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppParallel/include' -I/usr/local/include    -fPIC  -Wall -g -O2  -c vec_ext_def.cpp -o vec_ext_def.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppParallel/include' -I/usr/local/include    -fPIC  -Wall -g -O2  -c vectorization.cpp -o vectorization.o
vectorization.cpp:44:13: warning: unused variable 'has_avx512bw' [-Wunused-variable]
        const bool has_avx512bw = __builtin_cpu_supports("avx512f") &&
                   ^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/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 -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.3/Resources/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 Under development (unstable) (2023-03-16 r83985) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 
  0.359   0.082   0.463