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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GENESIS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GENESIS_2.41.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/GENESIS.Rcheck’
* using R Under development (unstable) (2025-11-04 r88984)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GENESIS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GENESIS’ version ‘2.41.0’
* 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 ‘GENESIS’ can be installed ... OK
* used C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* used SDK: ‘MacOSX11.3.1.sdk’
* 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 object imported by a ':::' call: ‘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 ... NOTE
checkRd: (-1) sample_annotation_1KG.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sample_annotation_1KG.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sample_annotation_1KG.Rd:16: Lost braces in \itemize; meant \describe ?
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  admixMap.Rd: GenotypeIterator, SeqVarIterator, BiocParallelParam,
    bpparam, BiocParallel
  assocTestAggregate.Rd: SeqVarIterator, SeqVarTools, mcols, GRanges,
    GRangesList, BiocParallelParam, bpparam, BiocParallel,
    GenotypeIterator, SeqVarWindowIterator
  assocTestSingle.Rd: SeqVarIterator, SeqVarTools, GenotypeIterator,
    GWASTools, BiocParallelParam, bpparam, BiocParallel,
    GdsGenotypeReader, MatrixGenotypeReader, NcdfGenotypeReader
  effectAllele.Rd: SeqVarIterator, SeqVarTools, GenotypeIterator,
    GWASTools
  fitNullModel.Rd: AnnotatedDataFrame, SeqVarData, Matrix
  jointScoreTest.Rd: GenotypeData, SeqVarData
  kingToMatrix.Rd: snpgdsIBDKING
  pcair.Rd: snpgdsPCA, MatrixGenotypeReader, GenotypeData,
    GdsGenotypeReader
  pcairPartition.Rd: Matrix
  pcrelate.Rd: SeqVarIterator, SeqVarTools, GenotypeIterator,
    GWASTools, BiocParallelParam, bpparam, BiocParallel
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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... INFO
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
    6.       └─BiocParallel (local) .local(ITER, FUN, ..., BPREDO = BPREDO, BPPARAM = BPPARAM, BPOPTIONS = BPOPTIONS)
    7.         └─BiocParallel:::.bpinit(...)
    8.           ├─BiocParallel::bploop(...)
    9.           └─BiocParallel:::bploop.iterate(...)
   10.             └─BiocParallel:::.bploop_impl(...)
   11.               └─BiocParallel:::.collect_result(manager, reducer, progress, BPPARAM)
   12.                 ├─BiocParallel:::.reducer_add(reducer, njob, value)
   13.                 └─BiocParallel:::.reducer_add(reducer, njob, value)
   14.                   ├─BiocParallel:::.map_index(reducer, idx)
   15.                   └─BiocParallel:::.map_index(reducer, idx)
  
  [ FAIL 1 | WARN 3 | SKIP 0 | PASS 702 ]
  Error:
  ! Test failures.
  Execution halted
* 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
  ‘/Users/biocbuild/bbs-3.23-bioc/meat/GENESIS.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GENESIS
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library’
* installing *source* package ‘GENESIS’ ...
** this is package ‘GENESIS’ version ‘2.41.0’
** using staged installation
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using SDK: ‘MacOSX11.3.1.sdk’
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c fht.c -o fht.o
clang -arch arm64 -std=gnu2x -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o GENESIS.so fht.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/00LOCK-GENESIS/00new/GENESIS/libs
** R
** data
** 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 (GENESIS)

R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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.

> library(testthat)
> library(GENESIS)
> 
> test_check("GENESIS")
Saving _problems/test_assoc_parallel-25.R
# of selected variants: 10
[ FAIL 1 | WARN 3 | SKIP 0 | PASS 702 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_assoc_parallel.R:25:5'): assocTestSingle - GenotypeIterator ────
Error in `if (idx <= length(redo.index)) idx <- redo.index[idx] else idx <- idx - length(redo.index) + reducer$appending.offset`: argument is of length zero
Backtrace:
     ▆
  1. ├─GENESIS::assocTestSingle(...) at test_assoc_parallel.R:25:5
  2. └─GENESIS::assocTestSingle(...)
  3.   └─GENESIS (local) .local(gdsobj, ...)
  4.     ├─BiocParallel::bpiterate(...)
  5.     └─BiocParallel::bpiterate(...)
  6.       └─BiocParallel (local) .local(ITER, FUN, ..., BPREDO = BPREDO, BPPARAM = BPPARAM, BPOPTIONS = BPOPTIONS)
  7.         └─BiocParallel:::.bpinit(...)
  8.           ├─BiocParallel::bploop(...)
  9.           └─BiocParallel:::bploop.iterate(...)
 10.             └─BiocParallel:::.bploop_impl(...)
 11.               └─BiocParallel:::.collect_result(manager, reducer, progress, BPPARAM)
 12.                 ├─BiocParallel:::.reducer_add(reducer, njob, value)
 13.                 └─BiocParallel:::.reducer_add(reducer, njob, value)
 14.                   ├─BiocParallel:::.map_index(reducer, idx)
 15.                   └─BiocParallel:::.map_index(reducer, idx)

[ FAIL 1 | WARN 3 | SKIP 0 | PASS 702 ]
Error:
! Test failures.
Execution halted