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This page was generated on 2025-08-20 12:06 -0400 (Wed, 20 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4818
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4596
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4538
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4536
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

Package 1668/2317HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RAIDS 1.7.2  (landing page)
Pascal Belleau
Snapshot Date: 2025-08-19 13:45 -0400 (Tue, 19 Aug 2025)
git_url: https://git.bioconductor.org/packages/RAIDS
git_branch: devel
git_last_commit: b753f2d
git_last_commit_date: 2025-07-31 13:55:01 -0400 (Thu, 31 Jul 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for RAIDS on kjohnson3

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: 1.7.2
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_1.7.2.tar.gz
StartedAt: 2025-08-19 21:07:48 -0400 (Tue, 19 Aug 2025)
EndedAt: 2025-08-19 21:10:25 -0400 (Tue, 19 Aug 2025)
EllapsedTime: 157.1 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_1.7.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/RAIDS.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* 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 13.7.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RAIDS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RAIDS’ version ‘1.7.2’
* 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
* 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 ‘1.7.2’
** 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 (2025-06-14 r88325) -- "Great Square Root"
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 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 445 ]
> 
> proc.time()
   user  system elapsed 
 10.836   0.652  11.578 

Example timings

RAIDS.Rcheck/RAIDS-Ex.timings

nameusersystemelapsed
add1KG2SampleGDS0.0180.0050.027
addBlockFromDetFile0.0010.0010.002
addBlockInGDSAnnot0.0020.0010.004
addGDS1KGLDBlock0.0010.0010.001
addGDSRef0.0010.0010.002
addGDSStudyPruning0.0000.0000.001
addGeneBlockGDSRefAnnot0.3530.0340.388
addGeneBlockRefAnnot0.0000.0000.001
addRef2GDS1KG0.0020.0020.004
addStudy1Kg0.0030.0030.007
addStudyGDSSample0.0020.0010.004
addUpdateLap0.0000.0010.001
addUpdateSegment0.0000.0000.001
appendGDSRefSample0.0020.0010.003
appendGDSSampleOnly0.0010.0000.000
appendGDSgenotype0.0050.0030.008
appendGDSgenotypeMat0.0000.0010.001
calcAFMLRNA0.0020.0010.003
computeAlleleFraction0.0010.0000.001
computeAllelicFractionDNA0.0490.0040.054
computeAllelicFractionRNA0.1400.0030.145
computeAllelicImbDNAChr0.0030.0010.004
computeAncestryFromSynthetic0.0060.0020.008
computeAncestryFromSyntheticFile2.0450.0312.095
computeKNNRefSample0.0050.0030.008
computeKNNRefSynthetic0.4420.0400.501
computeLOHBlocksDNAChr0.0030.0000.004
computePCAMultiSynthetic0.0030.0020.005
computePCARefRMMulti0.0420.0020.045
computePCARefSample0.0500.0020.052
computePoolSyntheticAncestryGr0.1280.0130.141
computeSyntheticConfMat0.0050.0020.008
computeSyntheticROC0.0120.0030.016
createAUROCGraph0.2110.0110.224
createAccuracyGraph0.2080.0010.210
createProfile0.0220.0050.028
createStudy2GDS1KG0.0200.0050.027
demoKnownSuperPop1KG0.4320.0320.469
demoPCA1KG0.0030.0020.004
demoPCASyntheticProfiles0.4390.0470.491
demoPedigreeEx10.0050.0010.006
estimateAllelicFraction0.0230.0020.026
extractNucleotide000
generateGDS1KG0.0040.0040.007
generateGDS1KGgenotypeFromSNPPileup0.0190.0060.025
generateGDSRefSample0.0010.0010.004
generateGDSSNPinfo0.0010.0020.003
generateGDSgenotype0.0040.0040.008
generateGeneBlock0.0000.0000.001
generateMapSnvSel0.0010.0010.002
generatePhase1KG2GDS0.0040.0030.008
generatePhaseRef0.0040.0030.007
generateProfileGDS0.0180.0050.025
getBlockIDs0.0010.0000.001
getRef1KGPop0.0010.0000.002
getRefSuperPop0.0000.0010.001
getTableSNV0.0030.0010.005
groupChr1KGSNV0.0170.0230.041
identifyRelative0.0030.0010.005
identifyRelativeRef0.0020.0010.003
inferAncestry0.0040.0000.004
inferAncestryDNA0.0040.0010.004
inferAncestryGeneAware0.0040.0000.004
matKNNSynthetic0.0130.0020.015
pedSynthetic0.0120.0020.015
prepPed1KG0.0010.0010.002
prepPedSynthetic1KG0.0020.0000.002
prepSynthetic0.0030.0020.006
processBlockChr0.0010.0000.002
processPileupChrBin1.4720.0041.478
profileAncestry0.0060.0020.009
pruning1KGbyChr0.0010.0010.002
pruningSample0.0130.0040.017
readSNVBAM0.0010.0000.001
readSNVFileGeneric0.0010.0010.002
readSNVPileupFile0.0160.0010.016
readSNVVCF1.6010.0361.638
runExomeAncestry0.0050.0010.007
runIBDKING0.0210.0010.022
runLDPruning0.0090.0040.013
runProfileAncestry0.0060.0030.008
runRNAAncestry0.0040.0020.007
runWrapperAncestry0.0050.0010.006
selParaPCAUpQuartile1.4780.0181.498
select1KGPop0.0010.0000.002
select1KGPopForSynthetic0.0010.0000.002
snpPositionDemo0.0000.0000.002
snvListVCF0.0010.0000.002
splitSelectByPop000
syntheticGeno0.0100.0020.012
tableBlockAF0.0060.0010.008
testAlleleFractionChange0.0010.0010.001
testEmptyBox000
validateAdd1KG2SampleGDS0.0010.0000.000
validateAddStudy1Kg0.0010.0010.000
validateCharacterString0.0000.0000.001
validateComputeAncestryFromSyntheticFile0.0000.0000.001
validateComputeKNNRefSample0.0010.0020.003
validateComputeKNNRefSynthetic0.0020.0020.003
validateComputePCAMultiSynthetic0.0010.0020.002
validateComputePCARefSample0.0000.0000.001
validateComputePoolSyntheticAncestryGr0.0000.0000.001
validateComputeSyntheticRoc0.0040.0020.006
validateCreateAccuracyGraph000
validateCreateStudy2GDS1KG0.0010.0000.001
validateDataRefSynParameter0.0000.0010.001
validateEstimateAllelicFraction0.0010.0000.002
validateGDSClass000
validateGenerateGDS1KG0.0000.0010.000
validateLogical000
validatePEDStudyParameter000
validatePepSynthetic0.0000.0000.001
validatePositiveIntegerVector000
validatePrepPed1KG0.0000.0010.000
validateProfileGDSExist000
validatePruningSample0.0010.0000.001
validateRunExomeOrRNAAncestry0.0010.0010.002
validateSingleRatio000
validateStudyDataFrameParameter0.0010.0000.001
validateSyntheticGeno0.0000.0000.001
validatecreateProfile0.0010.0010.001
wrapperAncestry0.0050.0010.006