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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:SAIGEgds.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings SAIGEgds_2.10.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/SAIGEgds.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SAIGEgds/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SAIGEgds’ version ‘2.10.0’
* 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
* used C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
* checking installed package size ... INFO
  installed size is 10.8Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
* 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
Namespace in Imports field not imported from: ‘SKAT’
  All declared Imports should be used.
Unexported objects imported by ':::' calls:
  ‘SeqArray:::.IsForking’ ‘SeqArray:::.McoreParallel’
  ‘SeqArray:::.NumParallel’ ‘SeqArray:::.process_verbose’
  ‘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 ... 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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘SAIGEgds-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: seqFitLDpruning
> ### Title: Linkage disequilibrium pruning
> ### Aliases: seqFitLDpruning
> ### Keywords: GDS genetics association
> 
> ### ** Examples
> 
> library(SeqArray)
> library(SAIGEgds)
> 
> # open a GDS file
> gds_fn <- seqExampleFileName("KG_Phase1")
> 
> seqFitLDpruning(gds_fn, save.gdsfn="grm.gds")
Perform linkage disequilibrium (LD) pruning:
    open ‘/home/biocbuild/R/R-4.5.0/site-library/SeqArray/extdata/1KG_phase1_release_v3_chr22.gds’
SNV pruning based on LD:
Calculating allele counts/frequencies (19773 variants) ...

[..................................................]  0%, ETC: --- (1/1)    
[==================================================] 100%, used 0s (1/1)    
[==================================================] 100%, complete, 0s    
# of selected variants: 7,028
Excluding 12,745 SNVs (monomorphic: TRUE, MAF: 0.01, missing rate: 0.005)
    # of samples: 1,092
    # of SNVs: 7,028
    using 1 thread/core
    sliding window: 500,000 basepairs, Inf SNPs
    |LD| threshold: 0.1
    method: composite
Chrom 22: |====================|====================|
    5.25%, 1,039 / 19,773 (Tue Nov 11 14:18:18 2025)
1,039 markers are selected in total.
Select ultra rare variants ...
MAC categories:
    [0,5.5), [5.5,10.5), [10.5,20.5), [20.5,Inf)

[..................................................]  0%, ETC: --- (1/1)    
[==================================================] 100%, used 0s (1/1)    
[==================================================] 100%, complete, 0s    
    excluding 0 variants according missing rates
    [0,5.5)	random 100 from 8722 variants
    [5.5,10.5)	random 100 from 2008 variants
    [10.5,20.5)	random 100 from 1901 variants
##< 2025-11-11 14:18:18
Export to ‘grm.gds’:
    sample.id (1,092)    [md5: bd2a93b49750ae227793ed23c575b620]
    variant.id (1,339)    [md5: 5dda407f8d859b420345e041f5728add]
    position    [md5: ddb06e7ce0f58e6de76b7d97a825e9ec]
    chromosome    [md5: 15d0c83b3a52ac26a1e3c6a16d1afa93]
    allele    [md5: 13d247e4e61382c424c16b91e71ec5e0]
    genotype    [md5: 217c284cfbbf55694328bdd32a8a774c]
    phase    [md5: b022ab0ff4e49d147d5a5d4698201c4e]
    annotation/id    [md5: 54b9e1d160cdfb913cdcf0785aa8cd50]
    annotation/qual    [md5: ff9bcaaf60ff9cdcc7869cf5b631d93c]
    annotation/filter    [md5: e35b2246d8efcd6f7e58967776771fb7]
Done.  # 2025-11-11 14:18:19
Optimize the access efficiency ...
Clean up the fragments of GDS file:
    open the file 'grm.gds' (193.5K)
    # of fragments: 91
    save to 'grm.gds.tmp'
    rename 'grm.gds.tmp' (193.0K, reduced: 444B)
    # of fragments: 54
##> 2025-11-11 14:18:19
> 
> # delete the temporary file
> unlink("grm.gds", force=TRUE)
> 
> 
> 
> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
> base::cat("seqseqFitLDpruning", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  48.161 0.334 53.423 0 0 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')

 *** caught bus error ***
address 0x31, cause 'invalid alignment'
An irrecoverable exception occurred. R is aborting now ...
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
SAIGEgds-package    12.350  0.020  12.862
seqAssocGLMM_ACAT_V  4.792  0.019   6.007
seqAssocGLMM_ACAT_O  4.258  0.064   5.764
* 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: 1 ERROR, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/SAIGEgds.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL SAIGEgds
###
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* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘SAIGEgds’ ...
** this is package ‘SAIGEgds’ version ‘2.10.0’
** using staged installation
** libs
using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.5.0/site-library/RcppParallel/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c SPATest.cpp -o SPATest.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.5.0/site-library/RcppParallel/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c saige_fitnull.cpp -o saige_fitnull.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.5.0/site-library/RcppParallel/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c saige_main.cpp -o saige_main.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.5.0/site-library/RcppParallel/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c saige_misc.cpp -o saige_misc.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.5.0/site-library/RcppParallel/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c saige_permu.cpp -o saige_permu.o
saige_permu.cpp: In function ‘void SKATExactBin_ComputeProb_Group(arma::uvec&, arma::uvec&, arma::vec&, uint32_t, uint32_t, int, std::vector<double>&)’:
saige_permu.cpp:119:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  119 |         for(int i=0; i < weight.size(); i++)
      |                      ~~^~~~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.5.0/site-library/RcppParallel/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c vec_ext_avx2.cpp -o vec_ext_avx2.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.5.0/site-library/RcppParallel/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c vec_ext_avx512bw.cpp -o vec_ext_avx512bw.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.5.0/site-library/RcppParallel/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c vec_ext_def.cpp -o vec_ext_def.o
vec_ext_def.cpp: In function ‘void vec_init_function()’:
vec_ext_def.cpp:33:27: warning: unused variable ‘VEC_ALGORITHM_AVX2’ [-Wunused-variable]
   33 |         extern const bool VEC_ALGORITHM_AVX2;
      |                           ^~~~~~~~~~~~~~~~~~
vec_ext_def.cpp:34:27: warning: unused variable ‘VEC_ALGORITHM_AVX512BW’ [-Wunused-variable]
   34 |         extern const bool VEC_ALGORITHM_AVX512BW;
      |                           ^~~~~~~~~~~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.5.0/site-library/RcppParallel/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c vectorization.cpp -o vectorization.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.5.0/lib -L/usr/local/lib -o SAIGEgds.so SPATest.o saige_fitnull.o saige_main.o saige_misc.o saige_permu.o vec_ext_avx2.o vec_ext_avx512bw.o vec_ext_def.o vectorization.o -lm -lopenblas -lgfortran -lm -lgcc -L/home/biocbuild/R/R-4.5.0/lib -lR
installing to /home/biocbuild/R/R-4.5.0/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 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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Type 'license()' or 'licence()' for distribution details.

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> # BiocGenerics:::testPackage("SAIGEgds")
> 
> proc.time()
   user  system elapsed 
  0.202   0.016   0.379