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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:RAIDS.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings RAIDS_1.7.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/RAIDS.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 ‘RAIDS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RAIDS’ version ‘1.7.2’
* package encoding: UTF-8
* 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 ‘RAIDS’ can be installed ... OK
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* 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 ... NOTE
Documented arguments not in \usage in Rd file 'wrapperAncestry.Rd':
  ‘pathGeno’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                  user system elapsed
computeAncestryFromSyntheticFile 8.616  0.427  13.102
readSNVVCF                       8.132  0.102   9.195
selParaPCAUpQuartile             6.975  0.051   8.489
* 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:
  [7] 0.0881 - 0.0882 == -9.38e-05
  [8] 0.0939 - 0.0940 == -1.55e-04
  ── Failure ('test-gdsWrapper_internal.R:146:5'): runIBDKING() must return expected results ──
  result$kinship not equal to `kinship`.
  6/9 mismatches (average diff: 0.000713)
  [2]  0.01548 -  0.01724 == -0.001756
  [3]  0.00108 -  0.00129 == -0.000214
  [4]  0.01548 -  0.01724 == -0.001756
  [6] -0.01417 - -0.01434 ==  0.000168
  [7]  0.00108 -  0.00129 == -0.000214
  [8] -0.01417 - -0.01434 ==  0.000168
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 443 ]
  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, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/RAIDS.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL RAIDS
###
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* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘RAIDS’ ...
** this is package ‘RAIDS’ version ‘1.7.2’
** using staged installation
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (RAIDS)

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

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(RAIDS)
Loading required package: gdsfmt
Loading required package: SNPRelate
Loading required package: GENESIS
Loading required package: dplyr

Attaching package: 'dplyr'

The following object is masked from 'package:testthat':

    matches

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Loading required package: Rsamtools
Loading required package: Seqinfo
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

The following object is masked from 'package:dplyr':

    explain

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

The following object is masked from 'package:dplyr':

    combine

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:dplyr':

    first, rename

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

The following objects are masked from 'package:dplyr':

    collapse, desc, slice

Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

> 
> ## Run all unit tests
> test_check("RAIDS")

Attaching package: 'Matrix'

The following object is masked from 'package:S4Vectors':

    expand

[ FAIL 2 | WARN 0 | SKIP 0 | PASS 443 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-gdsWrapper_internal.R:145:5'): runIBDKING() must return expected results ──
result$IBS0 not equal to `ibs0`.
6/9 mismatches (average diff: 0.000157)
[2] 0.0799 - 0.0797 ==  2.22e-04
[3] 0.0881 - 0.0882 == -9.38e-05
[4] 0.0799 - 0.0797 ==  2.22e-04
[6] 0.0939 - 0.0940 == -1.55e-04
[7] 0.0881 - 0.0882 == -9.38e-05
[8] 0.0939 - 0.0940 == -1.55e-04
── Failure ('test-gdsWrapper_internal.R:146:5'): runIBDKING() must return expected results ──
result$kinship not equal to `kinship`.
6/9 mismatches (average diff: 0.000713)
[2]  0.01548 -  0.01724 == -0.001756
[3]  0.00108 -  0.00129 == -0.000214
[4]  0.01548 -  0.01724 == -0.001756
[6] -0.01417 - -0.01434 ==  0.000168
[7]  0.00108 -  0.00129 == -0.000214
[8] -0.01417 - -0.01434 ==  0.000168

[ FAIL 2 | WARN 0 | SKIP 0 | PASS 443 ]
Error: Test failures
Execution halted