Back to Multiple platform build/check report for BioC 3.22:   simplified   long
ABCDEFGHIJKLMNOPQ[R]STUVWXYZ

This page was generated on 2025-10-03 12:05 -0400 (Fri, 03 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4845
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4632
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4577
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (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

Package 1683/2337HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RAIDS 1.7.2  (landing page)
Pascal Belleau
Snapshot Date: 2025-10-02 13:45 -0400 (Thu, 02 Oct 2025)
git_url: https://git.bioconductor.org/packages/RAIDS
git_branch: devel
git_last_commit: b753f2d
git_last_commit_date: 2025-07-31 13:55:01 -0400 (Thu, 31 Jul 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    ERROR  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    ERROR    OK  
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    ERROR    OK  
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    ERROR  


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: 2025-10-02 23:50:51 -0400 (Thu, 02 Oct 2025)
EndedAt: 2025-10-02 23:58:59 -0400 (Thu, 02 Oct 2025)
EllapsedTime: 488.6 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 7.913  0.229   8.167
selParaPCAUpQuartile             5.967  0.046   6.043
readSNVVCF                       5.589  0.057   5.664
* 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

nameusersystemelapsed
add1KG2SampleGDS0.0690.0230.105
addBlockFromDetFile0.0030.0040.008
addBlockInGDSAnnot0.0050.0050.012
addGDS1KGLDBlock0.0010.0030.004
addGDSRef0.0040.0040.008
addGDSStudyPruning0.0010.0020.004
addGeneBlockGDSRefAnnot1.2730.1331.445
addGeneBlockRefAnnot0.0020.0030.007
addRef2GDS1KG0.0050.0040.011
addStudy1Kg0.0120.0110.026
addStudyGDSSample0.0090.0040.014
addUpdateLap0.0020.0020.003
addUpdateSegment0.0010.0020.003
appendGDSRefSample0.0080.0050.014
appendGDSSampleOnly0.0020.0030.005
appendGDSgenotype0.0180.0150.036
appendGDSgenotypeMat0.0010.0020.004
calcAFMLRNA0.0050.0020.007
computeAlleleFraction0.0020.0000.003
computeAllelicFractionDNA0.1630.0120.177
computeAllelicFractionRNA0.2990.0080.309
computeAllelicImbDNAChr0.0100.0010.012
computeAncestryFromSynthetic0.0230.0060.029
computeAncestryFromSyntheticFile7.9130.2298.167
computeKNNRefSample0.0220.0070.031
computeKNNRefSynthetic2.9970.1053.112
computeLOHBlocksDNAChr0.0110.0010.012
computePCAMultiSynthetic0.0110.0050.015
computePCARefRMMulti0.3280.0050.333
computePCARefSample0.3870.0040.392
computePoolSyntheticAncestryGr0.6550.0120.670
computeSyntheticConfMat0.0140.0040.018
computeSyntheticROC0.0510.0070.057
createAUROCGraph1.2430.0561.307
createAccuracyGraph1.0110.0101.027
createProfile0.0750.0170.094
createStudy2GDS1KG0.0710.0150.087
demoKnownSuperPop1KG1.6490.0611.719
demoPCA1KG0.0070.0040.011
demoPCASyntheticProfiles1.5490.0441.602
demoPedigreeEx10.0190.0040.023
estimateAllelicFraction0.0850.0050.090
extractNucleotide0.0010.0010.001
generateGDS1KG0.0140.0110.027
generateGDS1KGgenotypeFromSNPPileup0.0540.0140.069
generateGDSRefSample0.0050.0030.009
generateGDSSNPinfo0.0050.0040.011
generateGDSgenotype0.0140.0120.028
generateGeneBlock0.0010.0010.002
generateMapSnvSel0.0030.0030.006
generatePhase1KG2GDS0.0150.0100.027
generatePhaseRef0.0140.0110.026
generateProfileGDS0.0580.0160.076
getBlockIDs0.0020.0020.004
getRef1KGPop0.0030.0010.005
getRefSuperPop0.0030.0020.005
getTableSNV0.0130.0040.019
groupChr1KGSNV0.0630.1020.198
identifyRelative0.0110.0040.015
identifyRelativeRef0.0080.0030.011
inferAncestry0.0160.0030.018
inferAncestryDNA0.0160.0020.017
inferAncestryGeneAware0.0130.0020.014
matKNNSynthetic0.0360.0050.040
pedSynthetic0.0490.0050.053
prepPed1KG0.0040.0020.006
prepPedSynthetic1KG0.0040.0020.006
prepSynthetic0.0120.0050.018
processBlockChr0.0030.0020.004
processPileupChrBin3.6250.0573.690
profileAncestry0.0180.0040.023
pruning1KGbyChr0.0030.0030.006
pruningSample0.0480.0090.057
readSNVBAM0.0010.0010.001
readSNVFileGeneric0.0030.0010.005
readSNVPileupFile0.0400.0020.042
readSNVVCF5.5890.0575.664
runExomeAncestry0.0170.0040.022
runIBDKING0.0430.0030.050
runLDPruning0.0200.0100.031
runProfileAncestry0.0190.0030.022
runRNAAncestry0.0180.0040.023
runWrapperAncestry0.0160.0040.020
selParaPCAUpQuartile5.9670.0466.043
select1KGPop0.0050.0020.006
select1KGPopForSynthetic0.0040.0010.005
snpPositionDemo0.0030.0030.006
snvListVCF0.0050.0030.008
splitSelectByPop0.0020.0000.002
syntheticGeno0.0310.0070.040
tableBlockAF0.0250.0030.029
testAlleleFractionChange0.0020.0010.002
testEmptyBox0.0020.0000.002
validateAdd1KG2SampleGDS0.0020.0010.002
validateAddStudy1Kg0.0020.0010.003
validateCharacterString0.0000.0000.001
validateComputeAncestryFromSyntheticFile0.0030.0020.003
validateComputeKNNRefSample0.0040.0040.008
validateComputeKNNRefSynthetic0.0060.0060.011
validateComputePCAMultiSynthetic0.0040.0030.008
validateComputePCARefSample0.0010.0010.002
validateComputePoolSyntheticAncestryGr0.0020.0010.004
validateComputeSyntheticRoc0.0150.0040.019
validateCreateAccuracyGraph0.0010.0010.002
validateCreateStudy2GDS1KG0.0020.0000.003
validateDataRefSynParameter0.0000.0000.001
validateEstimateAllelicFraction0.0030.0020.004
validateGDSClass0.0010.0010.002
validateGenerateGDS1KG0.0010.0010.002
validateLogical0.0010.0000.000
validatePEDStudyParameter0.0010.0000.000
validatePepSynthetic0.0020.0000.003
validatePositiveIntegerVector000
validatePrepPed1KG0.0010.0010.002
validateProfileGDSExist0.0010.0000.002
validatePruningSample0.0020.0010.003
validateRunExomeOrRNAAncestry0.0050.0010.007
validateSingleRatio000
validateStudyDataFrameParameter0.0010.0010.001
validateSyntheticGeno0.0020.0010.004
validatecreateProfile0.0020.0000.003
wrapperAncestry0.0180.0040.023