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

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4818
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4553
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4595
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4537
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4535
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: 2025-08-11 13:45 -0400 (Mon, 11 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 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    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 13.7.1 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 nebbiolo2

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: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:RAIDS.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings RAIDS_1.7.2.tar.gz
StartedAt: 2025-08-12 04:37:46 -0400 (Tue, 12 Aug 2025)
EndedAt: 2025-08-12 04:46:11 -0400 (Tue, 12 Aug 2025)
EllapsedTime: 504.8 seconds
RetCode: 0
Status:   OK  
CheckDir: RAIDS.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:RAIDS.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings RAIDS_1.7.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/RAIDS.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 24.04.2 LTS
* using session charset: UTF-8
* 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 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
computeAncestryFromSyntheticFile 5.779  0.243   6.023
readSNVVCF                       4.968  0.048   5.016
* 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-3.22-bioc/meat/RAIDS.Rcheck/00check.log’
for details.


Installation output

RAIDS.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL RAIDS
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-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 (2025-06-13) -- "Great Square Root"
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 445 ]
> 
> proc.time()
   user  system elapsed 
 28.619   1.404  30.027 

Example timings

RAIDS.Rcheck/RAIDS-Ex.timings

nameusersystemelapsed
add1KG2SampleGDS0.0480.0130.077
addBlockFromDetFile0.0020.0020.003
addBlockInGDSAnnot0.0020.0030.011
addGDS1KGLDBlock0.0000.0010.002
addGDSRef0.0030.0000.005
addGDSStudyPruning0.0000.0010.002
addGeneBlockGDSRefAnnot0.7170.0550.776
addGeneBlockRefAnnot0.0020.0000.002
addRef2GDS1KG0.0040.0010.004
addStudy1Kg0.0080.0010.022
addStudyGDSSample0.0070.0000.012
addUpdateLap0.0020.0000.002
addUpdateSegment0.0000.0000.002
appendGDSRefSample0.0050.0000.011
appendGDSSampleOnly0.0010.0000.002
appendGDSgenotype0.0100.0030.022
appendGDSgenotypeMat0.0000.0010.003
calcAFMLRNA0.0040.0010.005
computeAlleleFraction0.0030.0000.002
computeAllelicFractionDNA0.1220.0030.126
computeAllelicFractionRNA0.2090.0010.212
computeAllelicImbDNAChr0.0050.0010.006
computeAncestryFromSynthetic0.0150.0010.016
computeAncestryFromSyntheticFile5.7790.2436.023
computeKNNRefSample0.0150.0020.017
computeKNNRefSynthetic1.4820.0411.523
computeLOHBlocksDNAChr0.0090.0000.009
computePCAMultiSynthetic0.0070.0020.008
computePCARefRMMulti0.1440.0140.158
computePCARefSample0.1820.0000.181
computePoolSyntheticAncestryGr0.4450.0130.458
computeSyntheticConfMat0.0150.0010.015
computeSyntheticROC0.0570.0050.063
createAUROCGraph0.6820.0310.714
createAccuracyGraph0.6840.0050.689
createProfile0.0530.0030.066
createStudy2GDS1KG0.0810.0010.093
demoKnownSuperPop1KG1.5090.0451.555
demoPCA1KG0.0050.0020.008
demoPCASyntheticProfiles1.5000.0021.502
demoPedigreeEx10.0150.0000.016
estimateAllelicFraction0.0800.0020.082
extractNucleotide0.0010.0000.000
generateGDS1KG0.0120.0010.022
generateGDS1KGgenotypeFromSNPPileup0.0410.0040.055
generateGDSRefSample0.0050.0000.008
generateGDSSNPinfo0.0030.0010.009
generateGDSgenotype0.0110.0010.020
generateGeneBlock0.0010.0000.001
generateMapSnvSel0.0010.0010.002
generatePhase1KG2GDS0.0120.0000.021
generatePhaseRef0.0090.0030.020
generateProfileGDS0.0410.0010.051
getBlockIDs0.0020.0000.002
getRef1KGPop0.0010.0020.003
getRefSuperPop0.0020.0000.002
getTableSNV0.0080.0020.010
groupChr1KGSNV0.0450.0060.051
identifyRelative0.0070.0000.009
identifyRelativeRef0.0050.0000.006
inferAncestry0.0110.0000.012
inferAncestryDNA0.0120.0000.012
inferAncestryGeneAware0.0120.0000.011
matKNNSynthetic0.0380.0000.037
pedSynthetic0.0380.0000.038
prepPed1KG0.0040.0000.004
prepPedSynthetic1KG0.0200.0010.021
prepSynthetic0.0080.0020.012
processBlockChr0.0020.0010.003
processPileupChrBin3.2790.0623.342
profileAncestry0.0150.0010.017
pruning1KGbyChr0.0030.0000.004
pruningSample0.0380.0030.042
readSNVBAM0.0010.0000.001
readSNVFileGeneric0.0030.0000.004
readSNVPileupFile0.0330.0000.034
readSNVVCF4.9680.0485.016
runExomeAncestry0.0150.0010.015
runIBDKING0.0510.0040.055
runLDPruning0.0190.0040.023
runProfileAncestry0.0150.0020.016
runRNAAncestry0.0140.0010.014
runWrapperAncestry0.0150.0000.015
selParaPCAUpQuartile4.6110.0314.643
select1KGPop0.0040.0000.004
select1KGPopForSynthetic0.0040.0010.005
snpPositionDemo0.0020.0010.003
snvListVCF0.0040.0000.004
splitSelectByPop0.0010.0000.001
syntheticGeno0.0250.0030.029
tableBlockAF0.020.000.02
testAlleleFractionChange0.0010.0000.001
testEmptyBox0.0000.0000.001
validateAdd1KG2SampleGDS0.0020.0000.001
validateAddStudy1Kg0.0000.0010.001
validateCharacterString000
validateComputeAncestryFromSyntheticFile0.0020.0000.002
validateComputeKNNRefSample0.0030.0020.004
validateComputeKNNRefSynthetic0.0040.0010.005
validateComputePCAMultiSynthetic0.0040.0000.003
validateComputePCARefSample0.0010.0000.001
validateComputePoolSyntheticAncestryGr0.0010.0000.002
validateComputeSyntheticRoc0.0100.0020.012
validateCreateAccuracyGraph0.0010.0000.001
validateCreateStudy2GDS1KG0.0020.0000.002
validateDataRefSynParameter0.0000.0000.001
validateEstimateAllelicFraction0.0030.0000.003
validateGDSClass0.0020.0000.001
validateGenerateGDS1KG0.0020.0000.001
validateLogical000
validatePEDStudyParameter0.0000.0000.001
validatePepSynthetic0.0010.0000.001
validatePositiveIntegerVector000
validatePrepPed1KG0.0010.0000.001
validateProfileGDSExist0.0010.0000.001
validatePruningSample0.0020.0000.001
validateRunExomeOrRNAAncestry0.0040.0010.005
validateSingleRatio000
validateStudyDataFrameParameter0.0000.0000.001
validateSyntheticGeno0.0010.0010.002
validatecreateProfile0.0010.0000.001
wrapperAncestry0.0120.0040.016