##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SAIGEgds.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings SAIGEgds_2.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.22-bioc/meat/SAIGEgds.Rcheck'
* using R version 4.5.1 (2025-06-13 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'SAIGEgds/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SAIGEgds' version '2.9.0'
* 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 whether package 'SAIGEgds' can be installed ... OK
* used C++ compiler: 'G__~1.EXE (GCC) 14.2.0'
* 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 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 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  seqAssocGLMM_ACAT_O.Rd: seqParallel, seqUnitFilterCond
  seqAssocGLMM_ACAT_V.Rd: seqParallel, seqUnitFilterCond
  seqAssocGLMM_Burden.Rd: seqParallel, seqUnitFilterCond
  seqAssocGLMM_SKAT.Rd: seqParallel, seqUnitFilterCond
  seqAssocGLMM_SPA.Rd: compression.gdsn, seqParallel
  seqseqFitLDpruning.Rd: seqParallel
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 ... INFO
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 for x64 is not available
File 'F:/biocbuild/bbs-3.22-bioc/R/library/SAIGEgds/libs/x64/SAIGEgds.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)

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_O 6.82   0.02    6.83
seqAssocGLMM_ACAT_V 6.17   0.04    6.21
SAIGEgds-package    6.00   0.03    6.03
seqAssocGLMM_Burden 5.67   0.10    5.77
seqAssocGLMM_SPA    5.42   0.06    5.50
seqAssocGLMM_SKAT   5.41   0.00    5.41
glmmHeritability    5.14   0.00    5.14
* 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: 4 NOTEs
See
  'F:/biocbuild/bbs-3.22-bioc/meat/SAIGEgds.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD INSTALL SAIGEgds
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.22-bioc/R/library'
* installing *source* package 'SAIGEgds' ...
** this is package 'SAIGEgds' version '2.9.0'
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 14.2.0'
using C++11
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'F:/biocbuild/bbs-3.22-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/RcppParallel/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -DRCPP_PARALLEL_USE_TBB=1   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c SPATest.cpp -o SPATest.o
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'F:/biocbuild/bbs-3.22-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/RcppParallel/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -DRCPP_PARALLEL_USE_TBB=1   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c saige_fitnull.cpp -o saige_fitnull.o
In file included from F:/biocbuild/bbs-3.22-bioc/R/library/RcppParallel/include/tbb/tbb.h:32,
                 from F:/biocbuild/bbs-3.22-bioc/R/library/RcppParallel/include/RcppParallel/TBB.h:10,
                 from F:/biocbuild/bbs-3.22-bioc/R/library/RcppParallel/include/RcppParallel.h:24,
                 from saige.h:37,
                 from saige_fitnull.cpp:29:
F:/biocbuild/bbs-3.22-bioc/R/library/RcppParallel/include/tbb/atomic.h: In instantiation of 'tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = long unsigned int]':
F:/biocbuild/bbs-3.22-bioc/R/library/RcppParallel/include/tbb/tbb_thread.h:251:29:   required from here
  251 |             return as_atomic(location.my_id).compare_and_swap(value.my_id, comparand.my_id);
      |                    ~~~~~~~~~^~~~~~~~~~~~~~~~
F:/biocbuild/bbs-3.22-bioc/R/library/RcppParallel/include/tbb/atomic.h:544:12: warning: casting 'long unsigned int' to 'tbb::atomic<long unsigned int>&' does not use 'constexpr tbb::atomic<long unsigned int>::atomic(long unsigned int)' [-Wcast-user-defined]
  544 |     return (atomic<T>&)t;
      |            ^~~~~~~~~~~~~
F:/biocbuild/bbs-3.22-bioc/R/library/RcppParallel/include/tbb/atomic.h: In instantiation of 'tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = tbb::interface5::internal::hash_map_base::bucket*]':
F:/biocbuild/bbs-3.22-bioc/R/library/RcppParallel/include/tbb/concurrent_hash_map.h:291:31:   required from here
  291 |                   && as_atomic(my_table[new_seg]).compare_and_swap(is_allocating, NULL) == NULL )
      |                      ~~~~~~~~~^~~~~~~~~~~~~~~~~~~
F:/biocbuild/bbs-3.22-bioc/R/library/RcppParallel/include/tbb/atomic.h:544:12: warning: casting 'tbb::interface5::internal::hash_map_base::bucket*' to 'tbb::atomic<tbb::interface5::internal::hash_map_base::bucket*>&' does not use 'constexpr tbb::atomic<T*>::atomic(T*) [with T = tbb::interface5::internal::hash_map_base::bucket]' [-Wcast-user-defined]
  544 |     return (atomic<T>&)t;
      |            ^~~~~~~~~~~~~
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'F:/biocbuild/bbs-3.22-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/RcppParallel/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -DRCPP_PARALLEL_USE_TBB=1   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c saige_main.cpp -o saige_main.o
In file included from F:/biocbuild/bbs-3.22-bioc/R/library/RcppParallel/include/tbb/tbb.h:32,
                 from F:/biocbuild/bbs-3.22-bioc/R/library/RcppParallel/include/RcppParallel/TBB.h:10,
                 from F:/biocbuild/bbs-3.22-bioc/R/library/RcppParallel/include/RcppParallel.h:24,
                 from saige.h:37,
                 from saige_main.cpp:30:
F:/biocbuild/bbs-3.22-bioc/R/library/RcppParallel/include/tbb/atomic.h: In instantiation of 'tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = long unsigned int]':
F:/biocbuild/bbs-3.22-bioc/R/library/RcppParallel/include/tbb/tbb_thread.h:251:29:   required from here
  251 |             return as_atomic(location.my_id).compare_and_swap(value.my_id, comparand.my_id);
      |                    ~~~~~~~~~^~~~~~~~~~~~~~~~
F:/biocbuild/bbs-3.22-bioc/R/library/RcppParallel/include/tbb/atomic.h:544:12: warning: casting 'long unsigned int' to 'tbb::atomic<long unsigned int>&' does not use 'constexpr tbb::atomic<long unsigned int>::atomic(long unsigned int)' [-Wcast-user-defined]
  544 |     return (atomic<T>&)t;
      |            ^~~~~~~~~~~~~
F:/biocbuild/bbs-3.22-bioc/R/library/RcppParallel/include/tbb/atomic.h: In instantiation of 'tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = tbb::interface5::internal::hash_map_base::bucket*]':
F:/biocbuild/bbs-3.22-bioc/R/library/RcppParallel/include/tbb/concurrent_hash_map.h:291:31:   required from here
  291 |                   && as_atomic(my_table[new_seg]).compare_and_swap(is_allocating, NULL) == NULL )
      |                      ~~~~~~~~~^~~~~~~~~~~~~~~~~~~
F:/biocbuild/bbs-3.22-bioc/R/library/RcppParallel/include/tbb/atomic.h:544:12: warning: casting 'tbb::interface5::internal::hash_map_base::bucket*' to 'tbb::atomic<tbb::interface5::internal::hash_map_base::bucket*>&' does not use 'constexpr tbb::atomic<T*>::atomic(T*) [with T = tbb::interface5::internal::hash_map_base::bucket]' [-Wcast-user-defined]
  544 |     return (atomic<T>&)t;
      |            ^~~~~~~~~~~~~
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'F:/biocbuild/bbs-3.22-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/RcppParallel/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -DRCPP_PARALLEL_USE_TBB=1   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c saige_misc.cpp -o saige_misc.o
In file included from F:/biocbuild/bbs-3.22-bioc/R/library/RcppParallel/include/tbb/tbb.h:32,
                 from F:/biocbuild/bbs-3.22-bioc/R/library/RcppParallel/include/RcppParallel/TBB.h:10,
                 from F:/biocbuild/bbs-3.22-bioc/R/library/RcppParallel/include/RcppParallel.h:24,
                 from saige.h:37,
                 from saige_misc.cpp:25:
F:/biocbuild/bbs-3.22-bioc/R/library/RcppParallel/include/tbb/atomic.h: In instantiation of 'tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = long unsigned int]':
F:/biocbuild/bbs-3.22-bioc/R/library/RcppParallel/include/tbb/tbb_thread.h:251:29:   required from here
  251 |             return as_atomic(location.my_id).compare_and_swap(value.my_id, comparand.my_id);
      |                    ~~~~~~~~~^~~~~~~~~~~~~~~~
F:/biocbuild/bbs-3.22-bioc/R/library/RcppParallel/include/tbb/atomic.h:544:12: warning: casting 'long unsigned int' to 'tbb::atomic<long unsigned int>&' does not use 'constexpr tbb::atomic<long unsigned int>::atomic(long unsigned int)' [-Wcast-user-defined]
  544 |     return (atomic<T>&)t;
      |            ^~~~~~~~~~~~~
F:/biocbuild/bbs-3.22-bioc/R/library/RcppParallel/include/tbb/atomic.h: In instantiation of 'tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = tbb::interface5::internal::hash_map_base::bucket*]':
F:/biocbuild/bbs-3.22-bioc/R/library/RcppParallel/include/tbb/concurrent_hash_map.h:291:31:   required from here
  291 |                   && as_atomic(my_table[new_seg]).compare_and_swap(is_allocating, NULL) == NULL )
      |                      ~~~~~~~~~^~~~~~~~~~~~~~~~~~~
F:/biocbuild/bbs-3.22-bioc/R/library/RcppParallel/include/tbb/atomic.h:544:12: warning: casting 'tbb::interface5::internal::hash_map_base::bucket*' to 'tbb::atomic<tbb::interface5::internal::hash_map_base::bucket*>&' does not use 'constexpr tbb::atomic<T*>::atomic(T*) [with T = tbb::interface5::internal::hash_map_base::bucket]' [-Wcast-user-defined]
  544 |     return (atomic<T>&)t;
      |            ^~~~~~~~~~~~~
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'F:/biocbuild/bbs-3.22-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/RcppParallel/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -DRCPP_PARALLEL_USE_TBB=1   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c vec_ext_avx2.cpp -o vec_ext_avx2.o
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'F:/biocbuild/bbs-3.22-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/RcppParallel/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -DRCPP_PARALLEL_USE_TBB=1   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c vec_ext_avx512bw.cpp -o vec_ext_avx512bw.o
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'F:/biocbuild/bbs-3.22-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/RcppParallel/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -DRCPP_PARALLEL_USE_TBB=1   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c vec_ext_def.cpp -o vec_ext_def.o
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'F:/biocbuild/bbs-3.22-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/RcppParallel/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -DRCPP_PARALLEL_USE_TBB=1   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c vectorization.cpp -o vectorization.o
g++ -shared -s -static-libgcc -o SAIGEgds.dll tmp.def 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 -LF:/biocbuild/bbs-3.22-bioc/R/bin/x64 -lRlapack -LF:/biocbuild/bbs-3.22-bioc/R/bin/x64 -lRblas -lgfortran -lquadmath -LF:/biocbuild/bbs-3.22-bioc/R/library/RcppParallel/libs/x64 -lRcppParallel -LF:/biocbuild/bbs-3.22-bioc/R/library/RcppParallel/lib/x64 -ltbb -ltbbmalloc -lgcc -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.22-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.22-bioc/R/library/00LOCK-SAIGEgds/00new/SAIGEgds/libs/x64
** 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
** 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 4.5.1 (2025-06-13 ucrt) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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 
   0.12    0.14    0.25