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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_2.8.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/SAIGEgds.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* 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-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 ‘2.8.1’
* 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 C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... INFO
  installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
* 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’ ‘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 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: SAIGEgds-package
> ### Title: Scalable Implementation of Generalized mixed models in
> ###   Phenome-Wide Association Studies using GDS files
> ### Aliases: SAIGEgds-package SAIGEgds
> ### Keywords: GDS genetics association
> 
> ### ** Examples
> 
> # open the GDS file
> fn <- system.file("extdata", "grm1k_10k_snp.gds", package="SAIGEgds")
> gdsfile <- seqOpen(fn)
> 
> # load phenotype
> phenofn <- system.file("extdata", "pheno.txt.gz", package="SAIGEgds")
> pheno <- read.table(phenofn, header=TRUE, as.is=TRUE)
> head(pheno)
  sample.id y     yy      x1 x2
1        s1 0 4.5542  1.5118  1
2        s2 0 3.7941  0.3898  1
3        s3 0 5.0411 -0.6212  1
4        s4 0 5.6394 -2.2147  1
5        s5 0 4.2134  1.1249  1
6        s6 0 4.6145 -0.0449  1
> 
> # fit the null model
> glmm <- seqFitNullGLMM_SPA(y ~ x1 + x2, pheno, gdsfile, trait.type="binary")
SAIGE association analysis:
Tue Oct 14 13:45:31 2025
Filtering variants:

[..................................................]  0%, ETC: --- (1/1)    
[==================================================] 100%, used 0s (1/1)    
[==================================================] 100%, complete, 0s    
MAC category for estimating variance ratio:
    MAC[20, Inf):	30+ randomly from 9,650 variants
Fit the null model: y ~ x1 + x2 + var(GRM)
    # of samples: 1,000
    # of variants in GRM: 9,650
    MAF threshold for GRM: >= 0.01
    using 1 thread
Transform on the design matrix with QR decomposition:
    new formula: y ~ x_0 + x_1 + x_2 - 1
Use dense genetic relationship matrix in the file:
    /home/biocbuild/R/R-devel_2025-02-19/site-library/SAIGEgds/extdata/grm1k_10k_snp.gds
Loading SNP genotypes from the GDS file:

[..................................................]  0%, ETC: --- (1/1)    
[==================================================] 100%, used 0s (1/1)        using 2.6M (sparse genotype matrix)

 *** caught segfault ***
address 0x174944e2ac5087, cause 'memory not mapped'

Traceback:
 1: seqFitNullGLMM_SPA(y ~ x1 + x2, pheno, gdsfile, trait.type = "binary")
An irrecoverable exception occurred. R is aborting now ...
* 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, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/SAIGEgds.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL SAIGEgds
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’
* installing *source* package ‘SAIGEgds’ ...
** this is package ‘SAIGEgds’ version ‘2.8.1’
** using staged installation
** libs
using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
using C++11
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-devel_2025-02-19/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++11 -I"/home/biocbuild/R/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppParallel/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c saige_fitnull.cpp -o saige_fitnull.o
In file included from /home/biocbuild/R/R-devel_2025-02-19/site-library/RcppParallel/include/tbb/tbb.h:32,
                 from /home/biocbuild/R/R-devel_2025-02-19/site-library/RcppParallel/include/RcppParallel/TBB.h:10,
                 from /home/biocbuild/R/R-devel_2025-02-19/site-library/RcppParallel/include/RcppParallel.h:24,
                 from saige.h:37,
                 from saige_fitnull.cpp:29:
/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppParallel/include/tbb/atomic.h: In instantiation of ‘tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = long unsigned int]’:
/home/biocbuild/R/R-devel_2025-02-19/site-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);
      |                    ~~~~~~~~~^~~~~~~~~~~~~~~~
/home/biocbuild/R/R-devel_2025-02-19/site-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;
      |            ^~~~~~~~~~~~~
/home/biocbuild/R/R-devel_2025-02-19/site-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*]’:
/home/biocbuild/R/R-devel_2025-02-19/site-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 )
      |                      ~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-devel_2025-02-19/site-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;
      |            ^~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppParallel/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c saige_main.cpp -o saige_main.o
In file included from /home/biocbuild/R/R-devel_2025-02-19/site-library/RcppParallel/include/tbb/tbb.h:32,
                 from /home/biocbuild/R/R-devel_2025-02-19/site-library/RcppParallel/include/RcppParallel/TBB.h:10,
                 from /home/biocbuild/R/R-devel_2025-02-19/site-library/RcppParallel/include/RcppParallel.h:24,
                 from saige.h:37,
                 from saige_main.cpp:30:
/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppParallel/include/tbb/atomic.h: In instantiation of ‘tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = long unsigned int]’:
/home/biocbuild/R/R-devel_2025-02-19/site-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);
      |                    ~~~~~~~~~^~~~~~~~~~~~~~~~
/home/biocbuild/R/R-devel_2025-02-19/site-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;
      |            ^~~~~~~~~~~~~
/home/biocbuild/R/R-devel_2025-02-19/site-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*]’:
/home/biocbuild/R/R-devel_2025-02-19/site-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 )
      |                      ~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-devel_2025-02-19/site-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;
      |            ^~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppParallel/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c saige_misc.cpp -o saige_misc.o
In file included from /home/biocbuild/R/R-devel_2025-02-19/site-library/RcppParallel/include/tbb/tbb.h:32,
                 from /home/biocbuild/R/R-devel_2025-02-19/site-library/RcppParallel/include/RcppParallel/TBB.h:10,
                 from /home/biocbuild/R/R-devel_2025-02-19/site-library/RcppParallel/include/RcppParallel.h:24,
                 from saige.h:37,
                 from saige_misc.cpp:25:
/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppParallel/include/tbb/atomic.h: In instantiation of ‘tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = long unsigned int]’:
/home/biocbuild/R/R-devel_2025-02-19/site-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);
      |                    ~~~~~~~~~^~~~~~~~~~~~~~~~
/home/biocbuild/R/R-devel_2025-02-19/site-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;
      |            ^~~~~~~~~~~~~
/home/biocbuild/R/R-devel_2025-02-19/site-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*]’:
/home/biocbuild/R/R-devel_2025-02-19/site-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 )
      |                      ~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-devel_2025-02-19/site-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;
      |            ^~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-devel_2025-02-19/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++11 -I"/home/biocbuild/R/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-devel_2025-02-19/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++11 -I"/home/biocbuild/R/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-devel_2025-02-19/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++11 -I"/home/biocbuild/R/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-devel_2025-02-19/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++11 -shared -L/home/biocbuild/R/R/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/home/biocbuild/R/R/lib -lRlapack -L/home/biocbuild/R/R/lib -lRblas -lgfortran -lm -lgcc -L/home/biocbuild/R/R/lib -lR
installing to /home/biocbuild/R/R-devel_2025-02-19/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 Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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 
  0.213   0.012   0.370