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This page was generated on 2025-10-15 12:07 -0400 (Wed, 15 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4866
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4653
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4598
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4610
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 1691/2346HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RAIDS 1.7.3  (landing page)
Pascal Belleau
Snapshot Date: 2025-10-14 13:45 -0400 (Tue, 14 Oct 2025)
git_url: https://git.bioconductor.org/packages/RAIDS
git_branch: devel
git_last_commit: 3a182eb
git_last_commit_date: 2025-10-07 16:32:58 -0400 (Tue, 07 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.6 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 taishan

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: 1.7.3
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_1.7.3.tar.gz
StartedAt: 2025-10-14 11:46:46 -0000 (Tue, 14 Oct 2025)
EndedAt: 2025-10-14 11:55:42 -0000 (Tue, 14 Oct 2025)
EllapsedTime: 536.8 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_1.7.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/RAIDS.Rcheck’
* using R version 4.5.0 (2025-04-11)
* 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)
* 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 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                       8.832  0.032   8.891
computeAncestryFromSyntheticFile 8.155  0.064   8.243
selParaPCAUpQuartile             6.882  0.008   6.911
* 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-3.22-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-4.5.0/site-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 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
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: 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 
 48.426   1.747  50.318 

Example timings

RAIDS.Rcheck/RAIDS-Ex.timings

nameusersystemelapsed
add1KG2SampleGDS0.0850.0080.116
addBlockFromDetFile0.0020.0010.006
addBlockInGDSAnnot0.0060.0010.010
addGDS1KGLDBlock0.0010.0000.002
addGDSRef0.0030.0000.005
addGDSStudyPruning0.0000.0010.002
addGeneBlockGDSRefAnnot0.9290.1241.087
addGeneBlockRefAnnot0.0020.0000.002
addRef2GDS1KG0.0050.0000.005
addStudy1Kg0.0130.0000.014
addStudyGDSSample0.0090.0000.011
addUpdateLap0.0020.0000.002
addUpdateSegment0.0010.0000.002
appendGDSRefSample0.0080.0000.009
appendGDSSampleOnly0.0010.0000.002
appendGDSgenotype0.0190.0010.029
appendGDSgenotypeMat0.0010.0000.003
calcAFMLRNA0.0060.0000.007
computeAlleleFraction0.0030.0000.003
computeAllelicFractionDNA0.1950.0030.203
computeAllelicFractionRNA0.3620.0040.371
computeAllelicImbDNAChr0.0060.0030.009
computeAncestryFromSynthetic1.0030.0481.057
computeAncestryFromSyntheticFile8.1550.0648.243
computeKNNRefSample0.0240.0000.024
computeKNNRefSynthetic2.1540.0482.210
computeLOHBlocksDNAChr0.0100.0030.012
computePCAMultiSynthetic0.0050.0060.011
computePCARefRMMulti0.6940.0100.704
computePCARefSample0.7190.0000.721
computePoolSyntheticAncestryGr1.1540.0001.157
computeSyntheticConfMat0.0180.0000.018
computeSyntheticROC0.0490.0040.053
createAUROCGraph1.3380.0161.359
createAccuracyGraph1.2880.0081.300
createProfile0.0710.0000.074
createStudy2GDS1KG0.0660.0000.067
demoKnownSuperPop1KG2.1210.0082.135
demoPCA1KG0.0060.0040.010
demoPCASyntheticProfiles2.1370.0002.144
demoPedigreeEx10.0220.0000.023
estimateAllelicFraction0.1260.0040.130
extractNucleotide0.0010.0000.000
generateGDS1KG0.0190.0000.019
generateGDS1KGgenotypeFromSNPPileup0.0500.0070.059
generateGDSRefSample0.0060.0000.007
generateGDSSNPinfo0.0050.0000.006
generateGDSgenotype0.0180.0010.018
generateGeneBlock0.0020.0000.001
generateMapSnvSel0.0040.0000.005
generatePhase1KG2GDS0.0150.0040.019
generatePhaseRef0.0180.0000.018
generateProfileGDS0.0550.0000.057
getBlockIDs0.0030.0000.003
getRef1KGPop0.0040.0000.005
getRefSuperPop0.0040.0000.003
getTableSNV0.0150.0000.016
groupChr1KGSNV0.0620.0080.074
identifyRelative0.0060.0050.011
identifyRelativeRef0.0080.0000.007
inferAncestry0.020.000.02
inferAncestryDNA0.0200.0000.019
inferAncestryGeneAware0.020.000.02
matKNNSynthetic0.0580.0000.058
pedSynthetic0.0560.0010.058
prepPed1KG0.0050.0010.006
prepPedSynthetic1KG0.0080.0000.008
prepSynthetic0.0170.0000.016
processBlockChr0.0040.0000.004
processPileupChrBin2.9620.0913.061
profileAncestry0.0250.0000.024
pruning1KGbyChr0.0050.0000.005
pruningSample0.0520.0040.057
readSNVBAM4.8560.0364.904
readSNVFileGeneric0.0010.0040.005
readSNVPileupFile0.0400.0000.042
readSNVVCF8.8320.0328.891
runExomeAncestry0.0230.0000.023
runIBDKING0.0560.0000.061
runLDPruning0.0130.0200.035
runProfileAncestry0.0240.0000.024
runRNAAncestry0.0220.0000.022
runWrapperAncestry0.0180.0040.022
selParaPCAUpQuartile6.8820.0086.911
select1KGPop0.0060.0000.006
select1KGPopForSynthetic0.0060.0000.006
snpPositionDemo0.0040.0000.003
snvListVCF0.0050.0000.005
splitSelectByPop0.0020.0000.001
syntheticGeno0.0310.0080.039
tableBlockAF0.0290.0000.029
testAlleleFractionChange0.0020.0000.002
testEmptyBox0.0020.0000.002
validateAccuracyGraphInternal0.0000.0000.001
validateAdd1KG2SampleGDS0.0000.0020.002
validateAddStudy1Kg0.0000.0020.002
validateCharacterString000
validateComputeAncestryFromSyntheticFile0.0020.0000.001
validateComputeKNNRefSample0.0030.0020.005
validateComputeKNNRefSynthetic0.0050.0020.006
validateComputePCAMultiSynthetic0.0040.0000.004
validateComputePCARefSample0.0010.0000.001
validateComputePoolSyntheticAncestryGr0.0000.0010.002
validateComputeSyntheticRoc0.0120.0020.014
validateCreateAccuracyGraph0.0010.0000.001
validateCreateStudy2GDS1KG0.0020.0000.002
validateDataRefSynParameter0.0010.0000.001
validateEstimateAllelicFraction0.0040.0000.004
validateGDSClass0.0000.0010.001
validateGenerateGDS1KG0.0000.0010.001
validateLogical0.0000.0010.000
validatePEDStudyParameter0.0010.0000.001
validatePepSynthetic0.0010.0000.001
validatePositiveIntegerVector000
validatePrepPed1KG0.0010.0000.001
validateProfileGDSExist0.0010.0000.001
validatePruningSample0.0010.0000.001
validateRunExomeOrRNAAncestry0.0050.0000.005
validateSingleRatio000
validateStudyDataFrameParameter0.0010.0000.001
validateSyntheticGeno0.0020.0000.002
validatecreateAUROCGraph0.0020.0000.001
validatecreateProfile0.0030.0000.002
wrapperAncestry0.0230.0000.022