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"	4902
lconway	macOS 12.7.6 Monterey	x86_64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4692
kjohnson3	macOS 13.7.7 Ventura	arm64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4638
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: 1.8.0

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_1.8.0.tar.gz

StartedAt: 2025-11-03 23:35:14 -0500 (Mon, 03 Nov 2025)

EndedAt: 2025-11-03 23:43:26 -0500 (Mon, 03 Nov 2025)

EllapsedTime: 492.1 seconds

RetCode: 0

Status: OK

CheckDir: RAIDS.Rcheck

Warnings: 0

Command output

##############################################################################
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###
### 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_1.8.0.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 ‘1.8.0’
* 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 7.303  0.232   7.585
readSNVVCF                       6.231  0.055   6.307
selParaPCAUpQuartile             6.064  0.037   6.123
readSNVBAM                       5.768  0.019   5.803
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.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 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 ‘1.8.0’
** 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


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 0 | WARN 0 | SKIP 0 | PASS 478 ]
> 
> proc.time()
   user  system elapsed 
 40.659   2.516  43.634

Example timings

RAIDS.Rcheck/RAIDS-Ex.timings

name	user	system	elapsed
add1KG2SampleGDS	0.056	0.022	0.089
addBlockFromDetFile	0.002	0.004	0.008
addBlockInGDSAnnot	0.006	0.005	0.012
addGDS1KGLDBlock	0.002	0.004	0.006
addGDSRef	0.003	0.004	0.007
addGDSStudyPruning	0.001	0.003	0.003
addGeneBlockGDSRefAnnot	1.173	0.115	1.320
addGeneBlockRefAnnot	0.002	0.003	0.005
addRef2GDS1KG	0.005	0.005	0.011
addStudy1Kg	0.011	0.009	0.022
addStudyGDSSample	0.008	0.005	0.015
addUpdateLap	0.001	0.002	0.004
addUpdateSegment	0.001	0.002	0.003
appendGDSRefSample	0.006	0.004	0.011
appendGDSSampleOnly	0.001	0.002	0.003
appendGDSgenotype	0.016	0.013	0.034
appendGDSgenotypeMat	0.001	0.002	0.004
calcAFMLRNA	0.005	0.003	0.009
computeAlleleFraction	0.003	0.000	0.004
computeAllelicFractionDNA	0.151	0.011	0.165
computeAllelicFractionRNA	0.264	0.007	0.273
computeAllelicImbDNAChr	0.008	0.002	0.010
computeAncestryFromSynthetic	0.016	0.007	0.024
computeAncestryFromSyntheticFile	7.303	0.232	7.585
computeKNNRefSample	0.016	0.005	0.020
computeKNNRefSynthetic	2.696	0.101	2.810
computeLOHBlocksDNAChr	0.013	0.003	0.015
computePCAMultiSynthetic	0.008	0.004	0.012
computePCARefRMMulti	0.253	0.006	0.262
computePCARefSample	0.357	0.003	0.362
computePoolSyntheticAncestryGr	0.589	0.016	0.606
computeSyntheticConfMat	0.013	0.004	0.017
computeSyntheticROC	0.048	0.007	0.054
createAUROCGraph	0.993	0.055	1.054
createAccuracyGraph	0.888	0.008	0.900
createProfile	0.070	0.015	0.087
createStudy2GDS1KG	0.066	0.015	0.083
demoKnownSuperPop1KG	1.573	0.048	1.630
demoPCA1KG	0.006	0.004	0.010
demoPCASyntheticProfiles	1.520	0.041	1.568
demoPedigreeEx1	0.017	0.003	0.022
estimateAllelicFraction	0.089	0.007	0.099
extractNucleotide	0.000	0.001	0.001
generateGDS1KG	0.016	0.012	0.029
generateGDS1KGgenotypeFromSNPPileup	0.057	0.014	0.073
generateGDSRefSample	0.006	0.003	0.010
generateGDSSNPinfo	0.005	0.005	0.011
generateGDSgenotype	0.017	0.012	0.032
generateGeneBlock	0.001	0.001	0.003
generateMapSnvSel	0.003	0.004	0.008
generatePhase1KG2GDS	0.017	0.016	0.035
generatePhaseRef	0.015	0.012	0.029
generateProfileGDS	0.056	0.016	0.075
getBlockIDs	0.002	0.001	0.003
getRef1KGPop	0.003	0.001	0.005
getRefSuperPop	0.003	0.001	0.004
getTableSNV	0.014	0.004	0.019
groupChr1KGSNV	0.085	0.112	0.228
identifyRelative	0.009	0.004	0.013
identifyRelativeRef	0.008	0.004	0.011
inferAncestry	0.012	0.002	0.014
inferAncestryDNA	0.015	0.002	0.017
inferAncestryGeneAware	0.017	0.001	0.019
matKNNSynthetic	0.048	0.007	0.055
pedSynthetic	0.050	0.008	0.059
prepPed1KG	0.005	0.002	0.007
prepPedSynthetic1KG	0.006	0.001	0.008
prepSynthetic	0.011	0.005	0.017
processBlockChr	0.002	0.001	0.004
processPileupChrBin	3.534	0.069	3.625
profileAncestry	0.021	0.005	0.027
pruning1KGbyChr	0.004	0.002	0.006
pruningSample	0.039	0.011	0.050
readSNVBAM	5.768	0.019	5.803
readSNVFileGeneric	0.004	0.001	0.006
readSNVPileupFile	0.047	0.001	0.049
readSNVVCF	6.231	0.055	6.307
runExomeAncestry	0.017	0.003	0.021
runIBDKING	0.042	0.004	0.049
runLDPruning	0.020	0.009	0.029
runProfileAncestry	0.018	0.003	0.021
runRNAAncestry	0.019	0.004	0.022
runWrapperAncestry	0.020	0.005	0.025
selParaPCAUpQuartile	6.064	0.037	6.123
select1KGPop	0.004	0.001	0.006
select1KGPopForSynthetic	0.005	0.001	0.007
snpPositionDemo	0.003	0.002	0.005
snvListVCF	0.004	0.003	0.006
splitSelectByPop	0.002	0.001	0.001
syntheticGeno	0.029	0.006	0.036
tableBlockAF	0.020	0.002	0.022
testAlleleFractionChange	0.001	0.000	0.001
testEmptyBox	0.002	0.000	0.002
validateAccuracyGraphInternal	0	0	0
validateAdd1KG2SampleGDS	0.002	0.001	0.002
validateAddStudy1Kg	0.002	0.001	0.003
validateCharacterString	0.000	0.000	0.001
validateComputeAncestryFromSyntheticFile	0.001	0.002	0.003
validateComputeKNNRefSample	0.003	0.003	0.006
validateComputeKNNRefSynthetic	0.005	0.005	0.010
validateComputePCAMultiSynthetic	0.004	0.003	0.006
validateComputePCARefSample	0.002	0.000	0.002
validateComputePoolSyntheticAncestryGr	0.002	0.001	0.003
validateComputeSyntheticRoc	0.011	0.004	0.015
validateCreateAccuracyGraph	0.002	0.001	0.003
validateCreateStudy2GDS1KG	0.003	0.001	0.004
validateDataRefSynParameter	0.001	0.000	0.001
validateEstimateAllelicFraction	0.004	0.002	0.006
validateGDSClass	0.002	0.001	0.003
validateGenerateGDS1KG	0.002	0.001	0.002
validateLogical	0.000	0.001	0.000
validatePEDStudyParameter	0.001	0.000	0.001
validatePepSynthetic	0.002	0.001	0.002
validatePositiveIntegerVector	0	0	0
validatePrepPed1KG	0.001	0.000	0.002
validateProfileGDSExist	0.001	0.000	0.002
validatePruningSample	0.002	0.001	0.003
validateRunExomeOrRNAAncestry	0.004	0.001	0.005
validateSingleRatio	0	0	0
validateStudyDataFrameParameter	0.001	0.000	0.000
validateSyntheticGeno	0.002	0.002	0.003
validatecreateAUROCGraph	0.002	0.001	0.003
validatecreateProfile	0.003	0.001	0.004
wrapperAncestry	0.018	0.003	0.022