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This page was generated on 2025-09-04 12:05 -0400 (Thu, 04 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4822
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4617
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4564
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4541
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 1671/2321HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RAIDS 1.7.2  (landing page)
Pascal Belleau
Snapshot Date: 2025-09-03 13:45 -0400 (Wed, 03 Sep 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: 2025-09-03 23:07:40 -0400 (Wed, 03 Sep 2025)
EndedAt: 2025-09-03 23:15:21 -0400 (Wed, 03 Sep 2025)
EllapsedTime: 461.4 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 (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 7.824  0.158   8.022
readSNVVCF                       5.780  0.106   5.918
selParaPCAUpQuartile             5.678  0.049   5.756
* 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 
 33.409   2.364  36.244 

Example timings

RAIDS.Rcheck/RAIDS-Ex.timings

nameusersystemelapsed
add1KG2SampleGDS0.0690.0170.097
addBlockFromDetFile0.0020.0040.008
addBlockInGDSAnnot0.0050.0040.012
addGDS1KGLDBlock0.0020.0020.004
addGDSRef0.0030.0030.007
addGDSStudyPruning0.0010.0020.004
addGeneBlockGDSRefAnnot1.1450.1051.275
addGeneBlockRefAnnot0.0030.0030.005
addRef2GDS1KG0.0060.0060.013
addStudy1Kg0.0140.0100.029
addStudyGDSSample0.0110.0060.017
addUpdateLap0.0020.0030.004
addUpdateSegment0.0010.0020.004
appendGDSRefSample0.0080.0050.014
appendGDSSampleOnly0.0020.0020.004
appendGDSgenotype0.0200.0160.040
appendGDSgenotypeMat0.0020.0020.004
calcAFMLRNA0.0060.0030.010
computeAlleleFraction0.0040.0000.004
computeAllelicFractionDNA0.1920.0150.212
computeAllelicFractionRNA0.4460.0100.461
computeAllelicImbDNAChr0.0100.0010.013
computeAncestryFromSynthetic0.0190.0050.024
computeAncestryFromSyntheticFile7.8240.1588.022
computeKNNRefSample0.0160.0050.022
computeKNNRefSynthetic1.7540.0801.842
computeLOHBlocksDNAChr0.0080.0010.009
computePCAMultiSynthetic0.0070.0040.011
computePCARefRMMulti0.2920.0060.299
computePCARefSample0.3990.0050.407
computePoolSyntheticAncestryGr0.6620.0180.682
computeSyntheticConfMat0.0190.0050.025
computeSyntheticROC0.0450.0060.051
createAUROCGraph0.7690.0390.813
createAccuracyGraph0.7900.0060.801
createProfile0.0650.0150.083
createStudy2GDS1KG0.0730.0170.093
demoKnownSuperPop1KG1.7480.0421.796
demoPCA1KG0.0070.0050.012
demoPCASyntheticProfiles1.7400.0291.782
demoPedigreeEx10.0190.0040.024
estimateAllelicFraction0.0910.0050.097
extractNucleotide0.0000.0000.001
generateGDS1KG0.0160.0150.035
generateGDS1KGgenotypeFromSNPPileup0.0620.0150.080
generateGDSRefSample0.0050.0030.009
generateGDSSNPinfo0.0040.0040.010
generateGDSgenotype0.0140.0130.028
generateGeneBlock0.0020.0010.002
generateMapSnvSel0.0030.0030.006
generatePhase1KG2GDS0.0160.0140.034
generatePhaseRef0.0130.0110.025
generateProfileGDS0.0560.0130.071
getBlockIDs0.0020.0010.004
getRef1KGPop0.0030.0020.004
getRefSuperPop0.0040.0010.005
getTableSNV0.0140.0040.018
groupChr1KGSNV0.0610.1020.199
identifyRelative0.0100.0030.014
identifyRelativeRef0.0070.0030.010
inferAncestry0.0140.0010.016
inferAncestryDNA0.0140.0010.016
inferAncestryGeneAware0.0150.0010.017
matKNNSynthetic0.0490.0050.055
pedSynthetic0.0520.0050.058
prepPed1KG0.0050.0020.007
prepPedSynthetic1KG0.0050.0020.008
prepSynthetic0.0120.0050.018
processBlockChr0.0020.0010.004
processPileupChrBin3.4080.0223.444
profileAncestry0.0250.0040.029
pruning1KGbyChr0.0040.0020.007
pruningSample0.0350.0080.045
readSNVBAM0.0010.0000.001
readSNVFileGeneric0.0040.0010.006
readSNVPileupFile0.0460.0020.048
readSNVVCF5.7800.1065.918
runExomeAncestry0.0180.0030.020
runIBDKING0.0430.0050.051
runLDPruning0.0190.0100.029
runProfileAncestry0.0220.0050.027
runRNAAncestry0.0160.0050.020
runWrapperAncestry0.0150.0030.018
selParaPCAUpQuartile5.6780.0495.756
select1KGPop0.0040.0010.005
select1KGPopForSynthetic0.0040.0000.005
snpPositionDemo0.0020.0010.004
snvListVCF0.0030.0020.005
splitSelectByPop0.0000.0010.001
syntheticGeno0.0320.0060.040
tableBlockAF0.0200.0020.023
testAlleleFractionChange0.0020.0000.003
testEmptyBox0.0020.0000.002
validateAdd1KG2SampleGDS0.0020.0010.003
validateAddStudy1Kg0.0020.0010.003
validateCharacterString000
validateComputeAncestryFromSyntheticFile0.0020.0020.004
validateComputeKNNRefSample0.0030.0030.006
validateComputeKNNRefSynthetic0.0040.0030.007
validateComputePCAMultiSynthetic0.0030.0020.006
validateComputePCARefSample0.0010.0010.003
validateComputePoolSyntheticAncestryGr0.0020.0010.003
validateComputeSyntheticRoc0.0130.0040.017
validateCreateAccuracyGraph0.0010.0010.002
validateCreateStudy2GDS1KG0.0020.0010.003
validateDataRefSynParameter0.0010.0010.001
validateEstimateAllelicFraction0.0030.0010.004
validateGDSClass0.0010.0010.003
validateGenerateGDS1KG0.0010.0000.002
validateLogical000
validatePEDStudyParameter0.0010.0000.001
validatePepSynthetic0.0020.0010.002
validatePositiveIntegerVector000
validatePrepPed1KG0.0000.0000.002
validateProfileGDSExist0.0010.0010.001
validatePruningSample0.0010.0010.002
validateRunExomeOrRNAAncestry0.0040.0010.005
validateSingleRatio0.0000.0010.000
validateStudyDataFrameParameter0.0000.0000.001
validateSyntheticGeno0.0010.0010.003
validatecreateProfile0.0020.0000.002
wrapperAncestry0.0150.0030.018