Multiple platform build/check report for BioC 3.22 - CHECK results for RAIDS on kjohnson1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"	4882
merida1	macOS 12.7.6 Monterey	x86_64	4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"	4673
kjohnson1	macOS 13.7.5 Ventura	arm64	4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble"	4607
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4671
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 kjohnson1

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: 2025-12-17 18:11:40 -0500 (Wed, 17 Dec 2025)

EndedAt: 2025-12-17 18:24:25 -0500 (Wed, 17 Dec 2025)

EllapsedTime: 764.6 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 4.5.2 Patched (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 ‘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
readSNVBAM                       7.686  0.046  10.980
computeAncestryFromSyntheticFile 7.355  0.202  11.255
selParaPCAUpQuartile             5.627  0.071   8.210
readSNVVCF                       5.308  0.066   7.871
processPileupChrBin              4.622  0.050   6.761
* 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-arm64/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 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble"
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(RAIDS)
Loading required package: gdsfmt
Loading required package: SNPRelate
Loading required package: GENESIS
Loading required package: dplyr

Attaching package: 'dplyr'

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 
 45.984   2.208  71.087

Example timings

RAIDS.Rcheck/RAIDS-Ex.timings

name	user	system	elapsed
add1KG2SampleGDS	0.059	0.021	0.112
addBlockFromDetFile	0.003	0.003	0.008
addBlockInGDSAnnot	0.006	0.004	0.010
addGDS1KGLDBlock	0.002	0.001	0.003
addGDSRef	0.003	0.002	0.006
addGDSStudyPruning	0.001	0.002	0.004
addGeneBlockGDSRefAnnot	1.581	0.107	2.547
addGeneBlockRefAnnot	0.003	0.002	0.005
addRef2GDS1KG	0.005	0.004	0.010
addStudy1Kg	0.010	0.008	0.022
addStudyGDSSample	0.007	0.004	0.012
addUpdateLap	0.002	0.002	0.003
addUpdateSegment	0.001	0.002	0.003
appendGDSRefSample	0.007	0.005	0.013
appendGDSSampleOnly	0.001	0.002	0.003
appendGDSgenotype	0.015	0.011	0.029
appendGDSgenotypeMat	0.002	0.003	0.005
calcAFMLRNA	0.007	0.004	0.020
computeAlleleFraction	0.003	0.000	0.003
computeAllelicFractionDNA	0.173	0.014	0.272
computeAllelicFractionRNA	0.245	0.008	0.340
computeAllelicImbDNAChr	0.009	0.002	0.011
computeAncestryFromSynthetic	0.020	0.008	0.034
computeAncestryFromSyntheticFile	7.355	0.202	11.255
computeKNNRefSample	0.019	0.011	0.047
computeKNNRefSynthetic	2.967	0.078	4.484
computeLOHBlocksDNAChr	0.011	0.001	0.013
computePCAMultiSynthetic	0.011	0.006	0.026
computePCARefRMMulti	0.119	0.008	0.148
computePCARefSample	0.147	0.005	0.191
computePoolSyntheticAncestryGr	0.370	0.017	0.470
computeSyntheticConfMat	0.017	0.007	0.036
computeSyntheticROC	0.045	0.009	0.065
createAUROCGraph	1.007	0.042	1.326
createAccuracyGraph	0.925	0.010	1.234
createProfile	0.073	0.014	0.105
createStudy2GDS1KG	0.068	0.013	0.092
demoKnownSuperPop1KG	1.484	0.043	2.120
demoPCA1KG	0.008	0.007	0.015
demoPCASyntheticProfiles	1.438	0.047	2.162
demoPedigreeEx1	0.016	0.006	0.028
estimateAllelicFraction	0.082	0.006	0.109
extractNucleotide	0.000	0.001	0.001
generateGDS1KG	0.011	0.008	0.021
generateGDS1KGgenotypeFromSNPPileup	0.059	0.018	0.090
generateGDSRefSample	0.005	0.003	0.009
generateGDSSNPinfo	0.005	0.004	0.009
generateGDSgenotype	0.012	0.008	0.021
generateGeneBlock	0.002	0.001	0.002
generateMapSnvSel	0.003	0.002	0.005
generatePhase1KG2GDS	0.011	0.009	0.023
generatePhaseRef	0.011	0.007	0.020
generateProfileGDS	0.095	0.023	0.160
getBlockIDs	0.003	0.001	0.004
getRef1KGPop	0.003	0.001	0.004
getRefSuperPop	0.002	0.001	0.004
getTableSNV	0.013	0.003	0.026
groupChr1KGSNV	0.059	0.072	0.151
identifyRelative	0.011	0.004	0.015
identifyRelativeRef	0.007	0.003	0.012
inferAncestry	0.013	0.001	0.014
inferAncestryDNA	0.014	0.002	0.018
inferAncestryGeneAware	0.014	0.002	0.019
matKNNSynthetic	0.045	0.010	0.076
pedSynthetic	0.042	0.008	0.061
prepPed1KG	0.005	0.001	0.007
prepPedSynthetic1KG	0.005	0.001	0.006
prepSynthetic	0.010	0.004	0.016
processBlockChr	0.003	0.002	0.004
processPileupChrBin	4.622	0.050	6.761
profileAncestry	0.019	0.006	0.026
pruning1KGbyChr	0.005	0.003	0.009
pruningSample	0.043	0.012	0.058
readSNVBAM	7.686	0.046	10.980
readSNVFileGeneric	0.004	0.001	0.007
readSNVPileupFile	0.051	0.002	0.072
readSNVVCF	5.308	0.066	7.871
runExomeAncestry	0.018	0.008	0.034
runIBDKING	0.064	0.004	0.096
runLDPruning	0.031	0.009	0.043
runProfileAncestry	0.023	0.008	0.041
runRNAAncestry	0.018	0.008	0.037
runWrapperAncestry	0.019	0.007	0.040
selParaPCAUpQuartile	5.627	0.071	8.210
select1KGPop	0.006	0.002	0.018
select1KGPopForSynthetic	0.004	0.001	0.006
snpPositionDemo	0.003	0.004	0.007
snvListVCF	0.004	0.002	0.006
splitSelectByPop	0.001	0.000	0.001
syntheticGeno	0.035	0.008	0.066
tableBlockAF	0.022	0.006	0.031
testAlleleFractionChange	0.002	0.001	0.002
testEmptyBox	0.001	0.001	0.002
validateAccuracyGraphInternal	0.000	0.000	0.001
validateAdd1KG2SampleGDS	0.002	0.002	0.003
validateAddStudy1Kg	0.002	0.001	0.003
validateCharacterString	0	0	0
validateComputeAncestryFromSyntheticFile	0.002	0.002	0.006
validateComputeKNNRefSample	0.005	0.008	0.014
validateComputeKNNRefSynthetic	0.007	0.011	0.017
validateComputePCAMultiSynthetic	0.005	0.006	0.011
validateComputePCARefSample	0.001	0.001	0.002
validateComputePoolSyntheticAncestryGr	0.001	0.001	0.002
validateComputeSyntheticRoc	0.015	0.012	0.047
validateCreateAccuracyGraph	0.001	0.001	0.003
validateCreateStudy2GDS1KG	0.002	0.001	0.003
validateDataRefSynParameter	0.001	0.000	0.013
validateEstimateAllelicFraction	0.005	0.001	0.006
validateGDSClass	0.002	0.001	0.018
validateGenerateGDS1KG	0.002	0.000	0.002
validateLogical	0.000	0.000	0.001
validatePEDStudyParameter	0.001	0.000	0.002
validatePepSynthetic	0.002	0.000	0.002
validatePositiveIntegerVector	0.001	0.000	0.001
validatePrepPed1KG	0.001	0.001	0.002
validateProfileGDSExist	0.001	0.000	0.002
validatePruningSample	0.002	0.001	0.003
validateRunExomeOrRNAAncestry	0.005	0.002	0.007
validateSingleRatio	0	0	0
validateStudyDataFrameParameter	0.001	0.000	0.002
validateSyntheticGeno	0.002	0.002	0.003
validatecreateAUROCGraph	0.002	0.001	0.003
validatecreateProfile	0.003	0.001	0.003
wrapperAncestry	0.018	0.006	0.025