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: 2025-10-18 00:46:34 -0400 (Sat, 18 Oct 2025)

EndedAt: 2025-10-18 00:54:59 -0400 (Sat, 18 Oct 2025)

EllapsedTime: 504.9 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_1.7.3.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 7.424  0.244   7.709
readSNVVCF                       6.089  0.067   6.184
readSNVBAM                       6.039  0.026   6.092
selParaPCAUpQuartile             5.907  0.038   5.963
* 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 
 42.119   2.693  45.292

Example timings

RAIDS.Rcheck/RAIDS-Ex.timings

name	user	system	elapsed
add1KG2SampleGDS	0.068	0.024	0.108
addBlockFromDetFile	0.002	0.003	0.006
addBlockInGDSAnnot	0.004	0.004	0.010
addGDS1KGLDBlock	0.002	0.003	0.004
addGDSRef	0.003	0.004	0.007
addGDSStudyPruning	0.001	0.002	0.003
addGeneBlockGDSRefAnnot	1.217	0.130	1.389
addGeneBlockRefAnnot	0.001	0.003	0.004
addRef2GDS1KG	0.006	0.006	0.013
addStudy1Kg	0.012	0.010	0.024
addStudyGDSSample	0.009	0.005	0.014
addUpdateLap	0.002	0.002	0.004
addUpdateSegment	0.001	0.002	0.003
appendGDSRefSample	0.007	0.003	0.012
appendGDSSampleOnly	0.001	0.002	0.003
appendGDSgenotype	0.016	0.015	0.035
appendGDSgenotypeMat	0.001	0.002	0.003
calcAFMLRNA	0.005	0.002	0.007
computeAlleleFraction	0.002	0.000	0.003
computeAllelicFractionDNA	0.160	0.041	0.282
computeAllelicFractionRNA	0.269	0.008	0.279
computeAllelicImbDNAChr	0.009	0.002	0.012
computeAncestryFromSynthetic	0.017	0.006	0.023
computeAncestryFromSyntheticFile	7.424	0.244	7.709
computeKNNRefSample	0.019	0.006	0.025
computeKNNRefSynthetic	2.759	0.118	2.889
computeLOHBlocksDNAChr	0.009	0.002	0.010
computePCAMultiSynthetic	0.007	0.004	0.011
computePCARefRMMulti	0.270	0.006	0.277
computePCARefSample	0.359	0.005	0.365
computePoolSyntheticAncestryGr	0.624	0.017	0.644
computeSyntheticConfMat	0.014	0.005	0.020
computeSyntheticROC	0.050	0.006	0.056
createAUROCGraph	1.072	0.056	1.140
createAccuracyGraph	0.943	0.009	0.961
createProfile	0.066	0.017	0.087
createStudy2GDS1KG	0.069	0.015	0.087
demoKnownSuperPop1KG	1.629	0.041	1.684
demoPCA1KG	0.008	0.005	0.014
demoPCASyntheticProfiles	1.650	0.038	1.695
demoPedigreeEx1	0.021	0.005	0.025
estimateAllelicFraction	0.092	0.006	0.100
extractNucleotide	0.000	0.001	0.001
generateGDS1KG	0.014	0.013	0.029
generateGDS1KGgenotypeFromSNPPileup	0.068	0.015	0.085
generateGDSRefSample	0.005	0.003	0.009
generateGDSSNPinfo	0.004	0.004	0.010
generateGDSgenotype	0.015	0.013	0.030
generateGeneBlock	0.001	0.000	0.001
generateMapSnvSel	0.003	0.002	0.007
generatePhase1KG2GDS	0.014	0.013	0.028
generatePhaseRef	0.013	0.011	0.025
generateProfileGDS	0.066	0.019	0.092
getBlockIDs	0.003	0.002	0.004
getRef1KGPop	0.003	0.002	0.005
getRefSuperPop	0.004	0.001	0.005
getTableSNV	0.014	0.004	0.018
groupChr1KGSNV	0.061	0.096	0.193
identifyRelative	0.010	0.005	0.016
identifyRelativeRef	0.008	0.003	0.011
inferAncestry	0.015	0.002	0.018
inferAncestryDNA	0.015	0.002	0.017
inferAncestryGeneAware	0.016	0.001	0.017
matKNNSynthetic	0.063	0.009	0.072
pedSynthetic	0.048	0.005	0.052
prepPed1KG	0.005	0.002	0.006
prepPedSynthetic1KG	0.005	0.002	0.007
prepSynthetic	0.012	0.005	0.018
processBlockChr	0.003	0.002	0.004
processPileupChrBin	3.575	0.070	3.664
profileAncestry	0.023	0.005	0.028
pruning1KGbyChr	0.004	0.003	0.008
pruningSample	0.048	0.012	0.064
readSNVBAM	6.039	0.026	6.092
readSNVFileGeneric	0.003	0.001	0.005
readSNVPileupFile	0.049	0.001	0.051
readSNVVCF	6.089	0.067	6.184
runExomeAncestry	0.015	0.003	0.018
runIBDKING	0.044	0.005	0.052
runLDPruning	0.021	0.011	0.033
runProfileAncestry	0.019	0.004	0.023
runRNAAncestry	0.016	0.003	0.019
runWrapperAncestry	0.016	0.003	0.019
selParaPCAUpQuartile	5.907	0.038	5.963
select1KGPop	0.006	0.002	0.007
select1KGPopForSynthetic	0.005	0.001	0.006
snpPositionDemo	0.003	0.003	0.006
snvListVCF	0.004	0.002	0.007
splitSelectByPop	0.001	0.000	0.002
syntheticGeno	0.032	0.007	0.039
tableBlockAF	0.023	0.002	0.025
testAlleleFractionChange	0.002	0.001	0.001
testEmptyBox	0.001	0.001	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	0.003	0.002	0.005
validateComputeKNNRefSample	0.003	0.004	0.007
validateComputeKNNRefSynthetic	0.004	0.005	0.010
validateComputePCAMultiSynthetic	0.003	0.002	0.005
validateComputePCARefSample	0.001	0.001	0.002
validateComputePoolSyntheticAncestryGr	0.002	0.001	0.002
validateComputeSyntheticRoc	0.010	0.003	0.012
validateCreateAccuracyGraph	0.002	0.000	0.002
validateCreateStudy2GDS1KG	0.002	0.000	0.003
validateDataRefSynParameter	0.001	0.000	0.001
validateEstimateAllelicFraction	0.004	0.001	0.005
validateGDSClass	0.001	0.001	0.002
validateGenerateGDS1KG	0.001	0.001	0.002
validateLogical	0	0	0
validatePEDStudyParameter	0.001	0.000	0.001
validatePepSynthetic	0.001	0.001	0.002
validatePositiveIntegerVector	0.000	0.000	0.001
validatePrepPed1KG	0.001	0.001	0.002
validateProfileGDSExist	0.001	0.001	0.002
validatePruningSample	0.001	0.001	0.002
validateRunExomeOrRNAAncestry	0.005	0.001	0.006
validateSingleRatio	0	0	0
validateStudyDataFrameParameter	0.000	0.000	0.001
validateSyntheticGeno	0.002	0.001	0.004
validatecreateAUROCGraph	0.001	0.000	0.002
validatecreateProfile	0.002	0.000	0.002
wrapperAncestry	0.017	0.003	0.021