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"	4887
lconway	macOS 12.7.6 Monterey	x86_64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4677
kjohnson3	macOS 13.7.7 Ventura	arm64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4622
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4632
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: 1.7.3

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_1.7.3.tar.gz

StartedAt: 2025-10-20 00:57:51 -0400 (Mon, 20 Oct 2025)

EndedAt: 2025-10-20 01:06:15 -0400 (Mon, 20 Oct 2025)

EllapsedTime: 504.8 seconds

RetCode: 0

Status: OK

CheckDir: RAIDS.Rcheck

Warnings: 0

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_1.7.3.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 ‘1.7.3’
* 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 7.552  0.248   7.845
selParaPCAUpQuartile             6.356  0.035   6.410
readSNVVCF                       5.997  0.063   6.084
readSNVBAM                       5.853  0.025   5.900
* 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 ‘1.7.3’
** 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 
 42.627   2.673  45.794

Example timings

RAIDS.Rcheck/RAIDS-Ex.timings

name	user	system	elapsed
add1KG2SampleGDS	0.078	0.030	0.123
addBlockFromDetFile	0.002	0.004	0.008
addBlockInGDSAnnot	0.005	0.005	0.013
addGDS1KGLDBlock	0.001	0.003	0.006
addGDSRef	0.004	0.003	0.008
addGDSStudyPruning	0.002	0.002	0.004
addGeneBlockGDSRefAnnot	1.240	0.134	1.412
addGeneBlockRefAnnot	0.003	0.003	0.006
addRef2GDS1KG	0.006	0.007	0.014
addStudy1Kg	0.014	0.013	0.034
addStudyGDSSample	0.009	0.005	0.016
addUpdateLap	0.001	0.002	0.004
addUpdateSegment	0.002	0.002	0.004
appendGDSRefSample	0.008	0.004	0.015
appendGDSSampleOnly	0.001	0.002	0.003
appendGDSgenotype	0.017	0.015	0.037
appendGDSgenotypeMat	0.001	0.002	0.003
calcAFMLRNA	0.006	0.003	0.010
computeAlleleFraction	0.003	0.001	0.004
computeAllelicFractionDNA	0.169	0.035	0.276
computeAllelicFractionRNA	0.265	0.007	0.276
computeAllelicImbDNAChr	0.008	0.001	0.008
computeAncestryFromSynthetic	0.020	0.005	0.026
computeAncestryFromSyntheticFile	7.552	0.248	7.845
computeKNNRefSample	0.015	0.005	0.020
computeKNNRefSynthetic	2.765	0.105	2.885
computeLOHBlocksDNAChr	0.012	0.002	0.013
computePCAMultiSynthetic	0.008	0.005	0.013
computePCARefRMMulti	0.344	0.005	0.351
computePCARefSample	0.368	0.003	0.373
computePoolSyntheticAncestryGr	0.629	0.014	0.648
computeSyntheticConfMat	0.022	0.006	0.028
computeSyntheticROC	0.047	0.006	0.053
createAUROCGraph	0.980	0.052	1.039
createAccuracyGraph	0.885	0.007	0.895
createProfile	0.068	0.017	0.088
createStudy2GDS1KG	0.066	0.016	0.087
demoKnownSuperPop1KG	1.594	0.052	1.656
demoPCA1KG	0.007	0.004	0.013
demoPCASyntheticProfiles	1.610	0.045	1.693
demoPedigreeEx1	0.016	0.004	0.019
estimateAllelicFraction	0.081	0.006	0.088
extractNucleotide	0.001	0.001	0.000
generateGDS1KG	0.015	0.015	0.033
generateGDS1KGgenotypeFromSNPPileup	0.062	0.017	0.083
generateGDSRefSample	0.006	0.003	0.010
generateGDSSNPinfo	0.005	0.003	0.009
generateGDSgenotype	0.015	0.012	0.029
generateGeneBlock	0.002	0.001	0.002
generateMapSnvSel	0.004	0.003	0.007
generatePhase1KG2GDS	0.016	0.012	0.030
generatePhaseRef	0.014	0.013	0.030
generateProfileGDS	0.060	0.015	0.078
getBlockIDs	0.003	0.002	0.004
getRef1KGPop	0.004	0.001	0.005
getRefSuperPop	0.003	0.001	0.003
getTableSNV	0.013	0.003	0.016
groupChr1KGSNV	0.057	0.101	0.190
identifyRelative	0.010	0.004	0.014
identifyRelativeRef	0.007	0.003	0.011
inferAncestry	0.013	0.001	0.015
inferAncestryDNA	0.013	0.001	0.015
inferAncestryGeneAware	0.011	0.001	0.012
matKNNSynthetic	0.068	0.008	0.076
pedSynthetic	0.048	0.005	0.052
prepPed1KG	0.004	0.002	0.006
prepPedSynthetic1KG	0.004	0.001	0.007
prepSynthetic	0.013	0.004	0.018
processBlockChr	0.003	0.001	0.005
processPileupChrBin	3.534	0.060	3.613
profileAncestry	0.020	0.004	0.024
pruning1KGbyChr	0.003	0.001	0.005
pruningSample	0.040	0.010	0.051
readSNVBAM	5.853	0.025	5.900
readSNVFileGeneric	0.005	0.001	0.006
readSNVPileupFile	0.048	0.002	0.049
readSNVVCF	5.997	0.063	6.084
runExomeAncestry	0.018	0.004	0.023
runIBDKING	0.047	0.006	0.056
runLDPruning	0.024	0.011	0.034
runProfileAncestry	0.022	0.006	0.028
runRNAAncestry	0.021	0.005	0.025
runWrapperAncestry	0.016	0.004	0.020
selParaPCAUpQuartile	6.356	0.035	6.410
select1KGPop	0.004	0.002	0.007
select1KGPopForSynthetic	0.004	0.002	0.006
snpPositionDemo	0.003	0.003	0.005
snvListVCF	0.003	0.003	0.007
splitSelectByPop	0.002	0.001	0.002
syntheticGeno	0.033	0.008	0.042
tableBlockAF	0.022	0.003	0.025
testAlleleFractionChange	0.002	0.001	0.002
testEmptyBox	0.001	0.001	0.002
validateAccuracyGraphInternal	0	0	0
validateAdd1KG2SampleGDS	0.002	0.001	0.002
validateAddStudy1Kg	0.002	0.001	0.004
validateCharacterString	0	0	0
validateComputeAncestryFromSyntheticFile	0.002	0.002	0.004
validateComputeKNNRefSample	0.004	0.005	0.008
validateComputeKNNRefSynthetic	0.005	0.005	0.011
validateComputePCAMultiSynthetic	0.003	0.002	0.006
validateComputePCARefSample	0.002	0.001	0.003
validateComputePoolSyntheticAncestryGr	0.002	0.001	0.003
validateComputeSyntheticRoc	0.015	0.004	0.019
validateCreateAccuracyGraph	0.001	0.001	0.002
validateCreateStudy2GDS1KG	0.002	0.001	0.004
validateDataRefSynParameter	0.001	0.000	0.001
validateEstimateAllelicFraction	0.004	0.001	0.005
validateGDSClass	0.002	0.001	0.003
validateGenerateGDS1KG	0.001	0.000	0.001
validateLogical	0.000	0.000	0.001
validatePEDStudyParameter	0.001	0.001	0.001
validatePepSynthetic	0.002	0.001	0.003
validatePositiveIntegerVector	0.001	0.001	0.001
validatePrepPed1KG	0.001	0.000	0.002
validateProfileGDSExist	0.001	0.001	0.002
validatePruningSample	0.002	0.001	0.004
validateRunExomeOrRNAAncestry	0.006	0.001	0.007
validateSingleRatio	0.001	0.000	0.000
validateStudyDataFrameParameter	0.001	0.001	0.001
validateSyntheticGeno	0.001	0.001	0.003
validatecreateAUROCGraph	0.002	0.000	0.003
validatecreateProfile	0.002	0.000	0.003
wrapperAncestry	0.020	0.004	0.025