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This page was generated on 2025-08-16 12:05 -0400 (Sat, 16 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" 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: 2025-08-15 13:45 -0400 (Fri, 15 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 lconway

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: 2025-08-15 23:04:53 -0400 (Fri, 15 Aug 2025)
EndedAt: 2025-08-15 23:12:30 -0400 (Fri, 15 Aug 2025)
EllapsedTime: 457.2 seconds
RetCode: 0
Status:   OK  
CheckDir: RAIDS.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### 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 (2025-06-13)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* 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
Examples with CPU (user + system) or elapsed time > 5s
                                  user system elapsed
computeAncestryFromSyntheticFile 7.581  0.155   7.783
selParaPCAUpQuartile             6.155  0.054   6.241
readSNVVCF                       5.871  0.079   5.976
* 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-x86_64/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 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-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
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 
 32.778   2.409  35.515 

Example timings

RAIDS.Rcheck/RAIDS-Ex.timings

nameusersystemelapsed
add1KG2SampleGDS0.0620.0140.085
addBlockFromDetFile0.0030.0030.007
addBlockInGDSAnnot0.0060.0040.012
addGDS1KGLDBlock0.0020.0020.004
addGDSRef0.0020.0020.006
addGDSStudyPruning0.0010.0020.004
addGeneBlockGDSRefAnnot1.0610.1081.194
addGeneBlockRefAnnot0.0020.0020.004
addRef2GDS1KG0.0050.0050.010
addStudy1Kg0.0120.0100.024
addStudyGDSSample0.0090.0050.014
addUpdateLap0.0010.0020.003
addUpdateSegment0.0010.0020.003
appendGDSRefSample0.0080.0050.013
appendGDSSampleOnly0.0010.0020.004
appendGDSgenotype0.0170.0120.033
appendGDSgenotypeMat0.0010.0010.004
calcAFMLRNA0.0050.0020.007
computeAlleleFraction0.0020.0000.003
computeAllelicFractionDNA0.1540.0100.165
computeAllelicFractionRNA0.3960.0100.409
computeAllelicImbDNAChr0.0080.0010.009
computeAncestryFromSynthetic0.0170.0050.022
computeAncestryFromSyntheticFile7.5810.1557.783
computeKNNRefSample0.0190.0070.026
computeKNNRefSynthetic1.6900.0891.789
computeLOHBlocksDNAChr0.0100.0010.011
computePCAMultiSynthetic0.0080.0050.013
computePCARefRMMulti0.2870.0070.297
computePCARefSample0.3440.0030.348
computePoolSyntheticAncestryGr0.5950.0110.610
computeSyntheticConfMat0.0140.0040.017
computeSyntheticROC0.0500.0060.055
createAUROCGraph0.7130.0400.756
createAccuracyGraph0.7320.0100.746
createProfile0.0660.0170.085
createStudy2GDS1KG0.0620.0130.076
demoKnownSuperPop1KG1.5430.0401.591
demoPCA1KG0.0070.0040.011
demoPCASyntheticProfiles1.5600.0271.595
demoPedigreeEx10.0200.0040.024
estimateAllelicFraction0.0910.0060.099
extractNucleotide0.0000.0010.001
generateGDS1KG0.0130.0090.023
generateGDS1KGgenotypeFromSNPPileup0.0590.0120.075
generateGDSRefSample0.0040.0030.008
generateGDSSNPinfo0.0050.0040.010
generateGDSgenotype0.0160.0120.029
generateGeneBlock0.0020.0010.002
generateMapSnvSel0.0030.0030.006
generatePhase1KG2GDS0.0150.0140.031
generatePhaseRef0.0150.0110.028
generateProfileGDS0.0600.0140.077
getBlockIDs0.0020.0010.003
getRef1KGPop0.0030.0010.004
getRefSuperPop0.0030.0010.005
getTableSNV0.0110.0030.015
groupChr1KGSNV0.0600.0940.188
identifyRelative0.0100.0040.015
identifyRelativeRef0.0060.0030.009
inferAncestry0.0150.0020.016
inferAncestryDNA0.0160.0020.019
inferAncestryGeneAware0.0150.0020.017
matKNNSynthetic0.0450.0050.050
pedSynthetic0.0480.0050.054
prepPed1KG0.0050.0010.006
prepPedSynthetic1KG0.0040.0010.007
prepSynthetic0.0130.0050.019
processBlockChr0.0020.0010.003
processPileupChrBin3.2530.0223.294
profileAncestry0.0170.0030.020
pruning1KGbyChr0.0040.0020.006
pruningSample0.0370.0090.047
readSNVBAM0.0010.0000.001
readSNVFileGeneric0.0040.0010.005
readSNVPileupFile0.0510.0010.052
readSNVVCF5.8710.0795.976
runExomeAncestry0.0140.0040.019
runIBDKING0.0440.0040.052
runLDPruning0.0240.0120.037
runProfileAncestry0.0230.0050.029
runRNAAncestry0.0190.0040.023
runWrapperAncestry0.0190.0050.024
selParaPCAUpQuartile6.1550.0546.241
select1KGPop0.0050.0010.007
select1KGPopForSynthetic0.0050.0010.007
snpPositionDemo0.0030.0020.005
snvListVCF0.0050.0020.008
splitSelectByPop0.0010.0010.002
syntheticGeno0.0290.0070.037
tableBlockAF0.0220.0030.025
testAlleleFractionChange0.0010.0000.002
testEmptyBox0.0020.0000.002
validateAdd1KG2SampleGDS0.0020.0010.003
validateAddStudy1Kg0.0020.0020.003
validateCharacterString000
validateComputeAncestryFromSyntheticFile0.0020.0010.004
validateComputeKNNRefSample0.0040.0050.008
validateComputeKNNRefSynthetic0.0050.0050.011
validateComputePCAMultiSynthetic0.0040.0030.007
validateComputePCARefSample0.0020.0010.002
validateComputePoolSyntheticAncestryGr0.0020.0010.003
validateComputeSyntheticRoc0.0100.0030.013
validateCreateAccuracyGraph0.0020.0000.002
validateCreateStudy2GDS1KG0.0020.0010.002
validateDataRefSynParameter0.0000.0000.001
validateEstimateAllelicFraction0.0030.0010.004
validateGDSClass0.0020.0010.002
validateGenerateGDS1KG0.0020.0000.002
validateLogical000
validatePEDStudyParameter0.0010.0000.002
validatePepSynthetic0.0020.0010.003
validatePositiveIntegerVector000
validatePrepPed1KG0.0010.0010.001
validateProfileGDSExist0.0010.0010.001
validatePruningSample0.0020.0010.004
validateRunExomeOrRNAAncestry0.0070.0010.007
validateSingleRatio000
validateStudyDataFrameParameter0.0000.0000.001
validateSyntheticGeno0.0020.0020.003
validatecreateProfile0.0020.0010.003
wrapperAncestry0.0220.0040.025