Build/check report for BioC 3.23 - CHECK results for RAIDS on nebbiolo1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.3 LTS)	x86_64	R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"	4774
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 nebbiolo1

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: 1.9.0

Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:RAIDS.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings RAIDS_1.9.0.tar.gz

StartedAt: 2025-11-01 02:38:33 -0400 (Sat, 01 Nov 2025)

EndedAt: 2025-11-01 02:47:24 -0400 (Sat, 01 Nov 2025)

EllapsedTime: 531.1 seconds

RetCode: 0

Status: OK

CheckDir: RAIDS.Rcheck

Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:RAIDS.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings RAIDS_1.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/RAIDS.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘RAIDS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RAIDS’ version ‘1.9.0’
* 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 loading without being on the library search path ... 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
readSNVVCF                       5.941  0.065   6.009
readSNVBAM                       5.571  0.104   5.677
computeAncestryFromSyntheticFile 5.410  0.169   5.578
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/RAIDS.Rcheck/00check.log’
for details.

Installation output

RAIDS.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL RAIDS
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘RAIDS’ ...
** this is package ‘RAIDS’ version ‘1.9.0’
** 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 Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 
 35.708   1.947  37.646

Example timings

RAIDS.Rcheck/RAIDS-Ex.timings

name	user	system	elapsed
add1KG2SampleGDS	0.050	0.014	0.072
addBlockFromDetFile	0.003	0.000	0.005
addBlockInGDSAnnot	0.003	0.003	0.006
addGDS1KGLDBlock	0.001	0.001	0.002
addGDSRef	0.002	0.002	0.004
addGDSStudyPruning	0.000	0.000	0.001
addGeneBlockGDSRefAnnot	0.827	0.164	0.992
addGeneBlockRefAnnot	0.002	0.000	0.002
addRef2GDS1KG	0.004	0.002	0.006
addStudy1Kg	0.009	0.001	0.009
addStudyGDSSample	0.007	0.000	0.007
addUpdateLap	0.000	0.001	0.001
addUpdateSegment	0.001	0.000	0.001
appendGDSRefSample	0.006	0.001	0.007
appendGDSSampleOnly	0.002	0.000	0.002
appendGDSgenotype	0.008	0.006	0.015
appendGDSgenotypeMat	0.001	0.000	0.002
calcAFMLRNA	0.004	0.001	0.006
computeAlleleFraction	0.003	0.000	0.002
computeAllelicFractionDNA	0.166	0.026	0.194
computeAllelicFractionRNA	0.229	0.004	0.235
computeAllelicImbDNAChr	0.007	0.001	0.007
computeAncestryFromSynthetic	0.016	0.003	0.020
computeAncestryFromSyntheticFile	5.410	0.169	5.578
computeKNNRefSample	0.015	0.005	0.020
computeKNNRefSynthetic	2.628	0.159	2.787
computeLOHBlocksDNAChr	0.007	0.002	0.009
computePCAMultiSynthetic	0.007	0.004	0.011
computePCARefRMMulti	0.162	0.016	0.179
computePCARefSample	0.184	0.002	0.185
computePoolSyntheticAncestryGr	0.481	0.011	0.492
computeSyntheticConfMat	0.014	0.002	0.016
computeSyntheticROC	0.039	0.004	0.042
createAUROCGraph	0.895	0.051	0.945
createAccuracyGraph	0.828	0.005	0.833
createProfile	0.049	0.001	0.052
createStudy2GDS1KG	0.047	0.003	0.050
demoKnownSuperPop1KG	2.585	0.097	2.682
demoPCA1KG	0.006	0.002	0.009
demoPCASyntheticProfiles	1.473	0.017	1.489
demoPedigreeEx1	0.015	0.001	0.017
estimateAllelicFraction	0.072	0.008	0.082
extractNucleotide	0.001	0.000	0.001
generateGDS1KG	0.009	0.003	0.013
generateGDS1KGgenotypeFromSNPPileup	0.041	0.001	0.044
generateGDSRefSample	0.003	0.002	0.005
generateGDSSNPinfo	0.002	0.002	0.005
generateGDSgenotype	0.011	0.003	0.015
generateGeneBlock	0.002	0.000	0.002
generateMapSnvSel	0.003	0.001	0.003
generatePhase1KG2GDS	0.011	0.001	0.013
generatePhaseRef	0.011	0.003	0.013
generateProfileGDS	0.040	0.003	0.042
getBlockIDs	0.002	0.000	0.002
getRef1KGPop	0.000	0.002	0.004
getRefSuperPop	0.003	0.000	0.004
getTableSNV	0.009	0.003	0.013
groupChr1KGSNV	0.045	0.006	0.051
identifyRelative	0.007	0.002	0.009
identifyRelativeRef	0.006	0.001	0.007
inferAncestry	0.012	0.001	0.013
inferAncestryDNA	0.013	0.000	0.013
inferAncestryGeneAware	0.012	0.001	0.012
matKNNSynthetic	0.033	0.006	0.039
pedSynthetic	0.036	0.004	0.040
prepPed1KG	0.002	0.002	0.005
prepPedSynthetic1KG	0.004	0.002	0.006
prepSynthetic	0.006	0.005	0.011
processBlockChr	0.003	0.000	0.004
processPileupChrBin	3.346	0.084	3.431
profileAncestry	0.015	0.002	0.018
pruning1KGbyChr	0.004	0.001	0.004
pruningSample	0.035	0.010	0.045
readSNVBAM	5.571	0.104	5.677
readSNVFileGeneric	0.003	0.001	0.004
readSNVPileupFile	0.033	0.000	0.033
readSNVVCF	5.941	0.065	6.009
runExomeAncestry	0.012	0.003	0.016
runIBDKING	0.052	0.005	0.058
runLDPruning	0.018	0.007	0.025
runProfileAncestry	0.014	0.004	0.018
runRNAAncestry	0.013	0.003	0.015
runWrapperAncestry	0.016	0.000	0.016
selParaPCAUpQuartile	4.671	0.106	4.777
select1KGPop	0.002	0.002	0.005
select1KGPopForSynthetic	0.003	0.002	0.005
snpPositionDemo	0.002	0.001	0.003
snvListVCF	0.004	0.001	0.004
splitSelectByPop	0.001	0.000	0.001
syntheticGeno	0.026	0.003	0.028
tableBlockAF	0.02	0.00	0.02
testAlleleFractionChange	0.001	0.001	0.002
testEmptyBox	0.002	0.000	0.002
validateAccuracyGraphInternal	0	0	0
validateAdd1KG2SampleGDS	0.001	0.000	0.002
validateAddStudy1Kg	0.002	0.000	0.003
validateCharacterString	0	0	0
validateComputeAncestryFromSyntheticFile	0.002	0.001	0.002
validateComputeKNNRefSample	0.003	0.002	0.005
validateComputeKNNRefSynthetic	0.006	0.001	0.006
validateComputePCAMultiSynthetic	0.003	0.002	0.005
validateComputePCARefSample	0.002	0.000	0.002
validateComputePoolSyntheticAncestryGr	0.001	0.001	0.002
validateComputeSyntheticRoc	0.011	0.001	0.012
validateCreateAccuracyGraph	0.001	0.000	0.002
validateCreateStudy2GDS1KG	0.002	0.000	0.003
validateDataRefSynParameter	0.000	0.000	0.001
validateEstimateAllelicFraction	0.002	0.002	0.004
validateGDSClass	0.001	0.001	0.002
validateGenerateGDS1KG	0.001	0.000	0.001
validateLogical	0.000	0.000	0.001
validatePEDStudyParameter	0.001	0.001	0.001
validatePepSynthetic	0.001	0.001	0.001
validatePositiveIntegerVector	0	0	0
validatePrepPed1KG	0.001	0.000	0.001
validateProfileGDSExist	0.001	0.001	0.001
validatePruningSample	0.001	0.001	0.002
validateRunExomeOrRNAAncestry	0.004	0.001	0.004
validateSingleRatio	0	0	0
validateStudyDataFrameParameter	0.000	0.001	0.000
validateSyntheticGeno	0.001	0.002	0.002
validatecreateAUROCGraph	0.002	0.000	0.002
validatecreateProfile	0.001	0.000	0.002
wrapperAncestry	0.015	0.001	0.016