Multiple platform build/check report for BioC 3.22 - CHECK results for RAIDS on lconway

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"	4853
lconway	macOS 12.7.1 Monterey	x86_64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4640
kjohnson3	macOS 13.7.7 Ventura	arm64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4585
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4576
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

CHECK results for RAIDS on lconway

To the developers/maintainers of the RAIDS package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RAIDS.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: RAIDS

Version: 1.7.2

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RAIDS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RAIDS_1.7.2.tar.gz

StartedAt: 2025-10-05 23:54:54 -0400 (Sun, 05 Oct 2025)

EndedAt: 2025-10-06 00:02:55 -0400 (Mon, 06 Oct 2025)

EllapsedTime: 480.8 seconds

RetCode: 1

Status: ERROR

CheckDir: RAIDS.Rcheck

Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RAIDS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RAIDS_1.7.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/RAIDS.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* 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 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 7.585  0.234   7.860
readSNVVCF                       6.399  0.072   6.495
selParaPCAUpQuartile             5.795  0.033   5.845
* 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
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/RAIDS.Rcheck/00check.log’
for details.

Installation output

RAIDS.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL RAIDS
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/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)

Tests output

RAIDS.Rcheck/tests/testthat.Rout.fail


R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-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(RAIDS)
Loading required package: gdsfmt
Loading required package: SNPRelate
SNPRelate -- supported by Streaming SIMD Extensions 2 (SSE2)
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

Example timings

RAIDS.Rcheck/RAIDS-Ex.timings

name	user	system	elapsed
add1KG2SampleGDS	0.065	0.023	0.102
addBlockFromDetFile	0.003	0.004	0.008
addBlockInGDSAnnot	0.004	0.004	0.011
addGDS1KGLDBlock	0.001	0.002	0.004
addGDSRef	0.003	0.003	0.007
addGDSStudyPruning	0.001	0.001	0.003
addGeneBlockGDSRefAnnot	1.166	0.109	1.297
addGeneBlockRefAnnot	0.001	0.001	0.003
addRef2GDS1KG	0.005	0.005	0.012
addStudy1Kg	0.012	0.009	0.023
addStudyGDSSample	0.007	0.004	0.012
addUpdateLap	0.001	0.002	0.004
addUpdateSegment	0.001	0.002	0.003
appendGDSRefSample	0.008	0.005	0.013
appendGDSSampleOnly	0.002	0.002	0.004
appendGDSgenotype	0.017	0.013	0.033
appendGDSgenotypeMat	0.001	0.002	0.004
calcAFMLRNA	0.004	0.003	0.007
computeAlleleFraction	0.003	0.000	0.003
computeAllelicFractionDNA	0.142	0.010	0.153
computeAllelicFractionRNA	0.271	0.008	0.282
computeAllelicImbDNAChr	0.008	0.002	0.009
computeAncestryFromSynthetic	0.019	0.006	0.025
computeAncestryFromSyntheticFile	7.585	0.234	7.860
computeKNNRefSample	0.019	0.005	0.024
computeKNNRefSynthetic	2.906	0.102	3.027
computeLOHBlocksDNAChr	0.012	0.002	0.014
computePCAMultiSynthetic	0.008	0.005	0.013
computePCARefRMMulti	0.304	0.008	0.315
computePCARefSample	0.359	0.006	0.366
computePoolSyntheticAncestryGr	0.594	0.016	0.613
computeSyntheticConfMat	0.016	0.004	0.020
computeSyntheticROC	0.053	0.007	0.060
createAUROCGraph	1.224	0.057	1.289
createAccuracyGraph	1.046	0.010	1.061
createProfile	0.081	0.018	0.102
createStudy2GDS1KG	0.080	0.015	0.099
demoKnownSuperPop1KG	1.738	0.045	1.792
demoPCA1KG	0.007	0.003	0.009
demoPCASyntheticProfiles	1.619	0.054	1.676
demoPedigreeEx1	0.020	0.004	0.024
estimateAllelicFraction	0.088	0.005	0.094
extractNucleotide	0.001	0.001	0.000
generateGDS1KG	0.015	0.010	0.026
generateGDS1KGgenotypeFromSNPPileup	0.060	0.013	0.075
generateGDSRefSample	0.005	0.003	0.008
generateGDSSNPinfo	0.005	0.004	0.010
generateGDSgenotype	0.016	0.014	0.034
generateGeneBlock	0.002	0.000	0.002
generateMapSnvSel	0.003	0.002	0.007
generatePhase1KG2GDS	0.016	0.013	0.030
generatePhaseRef	0.016	0.013	0.030
generateProfileGDS	0.051	0.012	0.066
getBlockIDs	0.003	0.001	0.004
getRef1KGPop	0.004	0.002	0.005
getRefSuperPop	0.003	0.001	0.005
getTableSNV	0.013	0.003	0.018
groupChr1KGSNV	0.062	0.095	0.191
identifyRelative	0.010	0.003	0.014
identifyRelativeRef	0.008	0.003	0.012
inferAncestry	0.015	0.001	0.016
inferAncestryDNA	0.015	0.001	0.017
inferAncestryGeneAware	0.015	0.001	0.017
matKNNSynthetic	0.050	0.005	0.056
pedSynthetic	0.043	0.005	0.049
prepPed1KG	0.006	0.002	0.007
prepPedSynthetic1KG	0.006	0.002	0.007
prepSynthetic	0.014	0.005	0.020
processBlockChr	0.003	0.001	0.005
processPileupChrBin	3.616	0.058	3.685
profileAncestry	0.021	0.004	0.025
pruning1KGbyChr	0.004	0.003	0.007
pruningSample	0.044	0.010	0.056
readSNVBAM	0.002	0.000	0.002
readSNVFileGeneric	0.004	0.002	0.005
readSNVPileupFile	0.051	0.002	0.054
readSNVVCF	6.399	0.072	6.495
runExomeAncestry	0.015	0.003	0.019
runIBDKING	0.040	0.007	0.050
runLDPruning	0.021	0.010	0.031
runProfileAncestry	0.016	0.004	0.021
runRNAAncestry	0.020	0.004	0.024
runWrapperAncestry	0.018	0.004	0.023
selParaPCAUpQuartile	5.795	0.033	5.845
select1KGPop	0.006	0.001	0.007
select1KGPopForSynthetic	0.006	0.002	0.008
snpPositionDemo	0.003	0.002	0.004
snvListVCF	0.004	0.003	0.008
splitSelectByPop	0.001	0.001	0.002
syntheticGeno	0.031	0.007	0.040
tableBlockAF	0.020	0.002	0.023
testAlleleFractionChange	0.001	0.000	0.002
testEmptyBox	0.001	0.000	0.002
validateAdd1KG2SampleGDS	0.002	0.001	0.002
validateAddStudy1Kg	0.003	0.001	0.003
validateCharacterString	0.001	0.000	0.001
validateComputeAncestryFromSyntheticFile	0.003	0.002	0.004
validateComputeKNNRefSample	0.004	0.005	0.008
validateComputeKNNRefSynthetic	0.004	0.004	0.008
validateComputePCAMultiSynthetic	0.003	0.002	0.005
validateComputePCARefSample	0.001	0.000	0.002
validateComputePoolSyntheticAncestryGr	0.001	0.000	0.002
validateComputeSyntheticRoc	0.009	0.003	0.012
validateCreateAccuracyGraph	0.001	0.000	0.001
validateCreateStudy2GDS1KG	0.002	0.000	0.003
validateDataRefSynParameter	0.001	0.000	0.001
validateEstimateAllelicFraction	0.004	0.002	0.005
validateGDSClass	0.001	0.001	0.002
validateGenerateGDS1KG	0.001	0.001	0.002
validateLogical	0.000	0.001	0.001
validatePEDStudyParameter	0.001	0.000	0.001
validatePepSynthetic	0.002	0.001	0.003
validatePositiveIntegerVector	0	0	0
validatePrepPed1KG	0.001	0.000	0.002
validateProfileGDSExist	0.000	0.000	0.001
validatePruningSample	0.001	0.001	0.002
validateRunExomeOrRNAAncestry	0.004	0.001	0.005
validateSingleRatio	0	0	0
validateStudyDataFrameParameter	0.001	0.001	0.001
validateSyntheticGeno	0.002	0.001	0.003
validatecreateProfile	0.003	0.001	0.003
wrapperAncestry	0.015	0.003	0.019