Back to Multiple platform build/check report for BioC 3.21:   simplified   long
ABCDEFGHIJKLMNOPQ[R]STUVWXYZ

This page was generated on 2025-08-21 11:42 -0400 (Thu, 21 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4604
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4545
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4579
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 1685/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RAIDS 1.6.1  (landing page)
Pascal Belleau
Snapshot Date: 2025-08-18 13:40 -0400 (Mon, 18 Aug 2025)
git_url: https://git.bioconductor.org/packages/RAIDS
git_branch: RELEASE_3_21
git_last_commit: cf24404
git_last_commit_date: 2025-04-15 22:57:27 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for RAIDS on kunpeng2

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: RAIDS
Version: 1.6.1
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:RAIDS.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings RAIDS_1.6.1.tar.gz
StartedAt: 2025-08-19 12:55:07 -0000 (Tue, 19 Aug 2025)
EndedAt: 2025-08-19 13:04:18 -0000 (Tue, 19 Aug 2025)
EllapsedTime: 550.7 seconds
RetCode: 0
Status:   OK  
CheckDir: RAIDS.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:RAIDS.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings RAIDS_1.6.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/RAIDS.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RAIDS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RAIDS’ version ‘1.6.1’
* 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 10.599  0.203  10.826
readSNVVCF                        8.068  0.220   8.313
selParaPCAUpQuartile              7.073  0.052   7.144
* 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
  ‘/home/biocbuild/bbs-3.21-bioc/meat/RAIDS.Rcheck/00check.log’
for details.


Installation output

RAIDS.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL RAIDS
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’
* installing *source* package ‘RAIDS’ ...
** this is package ‘RAIDS’ version ‘1.6.1’
** 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) (2025-02-19 r87757) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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
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: GenomeInfoDb
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: S4Vectors
Loading required package: stats4

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: GenomicRanges
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 
 46.245   2.069  48.418 

Example timings

RAIDS.Rcheck/RAIDS-Ex.timings

nameusersystemelapsed
add1KG2SampleGDS0.0760.0040.098
addBlockFromDetFile0.0030.0000.005
addBlockInGDSAnnot0.0060.0000.008
addGDS1KGLDBlock0.0010.0010.002
addGDSRef0.0010.0030.005
addGDSStudyPruning0.0010.0000.001
addGeneBlockGDSRefAnnot1.0210.0681.114
addGeneBlockRefAnnot0.0020.0000.002
addRef2GDS1KG0.0060.0000.006
addStudy1Kg0.0130.0000.014
addStudyGDSSample0.010.000.01
addUpdateLap0.0010.0000.002
addUpdateSegment0.0010.0000.002
appendGDSRefSample0.0050.0040.009
appendGDSSampleOnly0.0010.0000.002
appendGDSgenotype0.0150.0030.024
appendGDSgenotypeMat0.0010.0010.002
calcAFMLRNA0.0060.0000.007
computeAlleleFraction0.0030.0000.003
computeAllelicFractionDNA0.1930.0080.204
computeAllelicFractionRNA0.4820.0220.508
computeAllelicImbDNAChr0.0080.0000.008
computeAncestryFromSynthetic0.0170.0040.023
computeAncestryFromSyntheticFile10.599 0.20310.826
computeKNNRefSample0.0240.0000.025
computeKNNRefSynthetic2.2030.0362.245
computeLOHBlocksDNAChr0.0120.0000.012
computePCAMultiSynthetic0.0230.0080.031
computePCARefRMMulti1.6720.0081.683
computePCARefSample2.0370.0082.049
computePoolSyntheticAncestryGr2.1430.0482.195
computeSyntheticConfMat0.0180.0000.018
computeSyntheticROC0.0540.0040.058
createAUROCGraph1.0370.0361.076
createAccuracyGraph0.9930.0321.027
createProfile0.0730.0000.075
createStudy2GDS1KG0.0720.0000.073
demoKnownSuperPop1KG3.5190.1363.663
demoPCA1KG0.0080.0000.009
demoPCASyntheticProfiles2.1180.0162.138
demoPedigreeEx10.0230.0000.023
estimateAllelicFraction0.1520.0000.153
extractNucleotide000
generateGDS1KG0.0180.0000.019
generateGDS1KGgenotypeFromSNPPileup0.0620.0000.063
generateGDSRefSample0.0050.0000.007
generateGDSSNPinfo0.0020.0030.006
generateGDSgenotype0.0160.0000.016
generateGeneBlock0.0020.0000.001
generateMapSnvSel0.0040.0000.004
generatePhase1KG2GDS0.0130.0040.018
generatePhaseRef0.0120.0040.016
generateProfileGDS0.0550.0040.059
getBlockIDs0.0030.0000.003
getRef1KGPop0.0030.0000.004
getRefSuperPop0.0030.0000.003
getTableSNV0.0150.0000.015
groupChr1KGSNV0.0590.0120.073
identifyRelative0.010.000.01
identifyRelativeRef0.0070.0000.007
inferAncestry0.0180.0000.018
inferAncestryDNA0.0190.0000.019
inferAncestryGeneAware0.0190.0000.019
matKNNSynthetic0.0540.0000.054
pedSynthetic0.0550.0000.056
prepPed1KG0.0060.0000.006
prepPedSynthetic1KG0.0070.0000.007
prepSynthetic0.0110.0030.015
processBlockChr0.0000.0030.004
processPileupChrBin3.9090.0793.994
profileAncestry0.0240.0000.024
pruning1KGbyChr0.0050.0000.004
pruningSample0.0590.0000.060
readSNVBAM0.0010.0000.001
readSNVFileGeneric0.0040.0000.005
readSNVPileupFile0.0390.0030.044
readSNVVCF8.0680.2208.313
runExomeAncestry0.0220.0000.022
runIBDKING0.0670.0000.071
runLDPruning0.0340.0000.035
runProfileAncestry0.0240.0000.025
runRNAAncestry0.0230.0000.022
runWrapperAncestry0.0190.0040.022
selParaPCAUpQuartile7.0730.0527.144
select1KGPop0.0060.0000.006
select1KGPopForSynthetic0.0060.0000.007
snpPositionDemo0.0020.0010.004
snvListVCF0.0030.0020.004
splitSelectByPop0.0010.0000.001
syntheticGeno0.0410.0000.042
tableBlockAF0.030.000.03
testAlleleFractionChange0.0020.0000.002
testEmptyBox0.0020.0000.002
validateAdd1KG2SampleGDS0.0010.0000.002
validateAddStudy1Kg0.0020.0000.002
validateCharacterString000
validateComputeAncestryFromSyntheticFile0.0020.0000.002
validateComputeKNNRefSample0.0040.0000.004
validateComputeKNNRefSynthetic0.0010.0040.005
validateComputePCAMultiSynthetic0.0010.0030.004
validateComputePCARefSample0.0010.0000.002
validateComputePoolSyntheticAncestryGr0.0010.0000.002
validateComputeSyntheticRoc0.0130.0000.014
validateCreateAccuracyGraph0.0000.0010.002
validateCreateStudy2GDS1KG0.0000.0030.003
validateDataRefSynParameter0.0000.0010.001
validateEstimateAllelicFraction0.0020.0020.004
validateGDSClass0.0010.0000.002
validateGenerateGDS1KG0.0010.0000.001
validateLogical000
validatePEDStudyParameter0.0010.0000.001
validatePepSynthetic0.0020.0000.002
validatePositiveIntegerVector000
validatePrepPed1KG0.0000.0010.001
validateProfileGDSExist0.0000.0010.001
validatePruningSample0.0010.0010.001
validateRunExomeOrRNAAncestry0.0050.0000.005
validateSingleRatio000
validateStudyDataFrameParameter0.0010.0000.001
validateSyntheticGeno0.0010.0000.003
validatecreateProfile0.0020.0000.003
wrapperAncestry0.0220.0000.022