Multiple platform build/check report for BioC 3.21 - CHECK results for RAIDS on nebbiolo1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4824
merida1	macOS 12.7.5 Monterey	x86_64	4.5.1 RC (2025-06-05 r88288) -- "Great Square Root"	4604
kjohnson1	macOS 13.6.6 Ventura	arm64	4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"	4545
kunpeng2	Linux (openEuler 24.03 LTS)	aarch64	R 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*

CHECK results for RAIDS on nebbiolo1

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: 1.6.1

Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:RAIDS.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings RAIDS_1.6.1.tar.gz

StartedAt: 2025-08-21 01:48:43 -0400 (Thu, 21 Aug 2025)

EndedAt: 2025-08-21 01:57:01 -0400 (Thu, 21 Aug 2025)

EllapsedTime: 498.1 seconds

RetCode: 0

Status: OK

CheckDir: RAIDS.Rcheck

Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:RAIDS.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings RAIDS_1.6.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-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 24.04.3 LTS
* using session charset: UTF-8
* 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 6.180  0.532   6.712
readSNVVCF                       4.952  0.122   5.076
* 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-3.21-bioc/meat/RAIDS.Rcheck/00check.log’
for details.

Installation output

RAIDS.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL RAIDS
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/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 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: 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 
 27.955   1.633  29.579

Example timings

RAIDS.Rcheck/RAIDS-Ex.timings

name	user	system	elapsed
add1KG2SampleGDS	0.055	0.014	0.072
addBlockFromDetFile	0.004	0.000	0.004
addBlockInGDSAnnot	0.006	0.000	0.005
addGDS1KGLDBlock	0.002	0.000	0.002
addGDSRef	0.003	0.000	0.003
addGDSStudyPruning	0.001	0.000	0.001
addGeneBlockGDSRefAnnot	0.785	0.205	0.998
addGeneBlockRefAnnot	0.002	0.000	0.002
addRef2GDS1KG	0.006	0.001	0.006
addStudy1Kg	0.009	0.000	0.009
addStudyGDSSample	0.006	0.001	0.007
addUpdateLap	0.000	0.001	0.002
addUpdateSegment	0.001	0.000	0.001
appendGDSRefSample	0.006	0.001	0.007
appendGDSSampleOnly	0.000	0.001	0.002
appendGDSgenotype	0.012	0.004	0.017
appendGDSgenotypeMat	0.002	0.000	0.002
calcAFMLRNA	0.005	0.002	0.006
computeAlleleFraction	0.002	0.001	0.003
computeAllelicFractionDNA	0.136	0.020	0.156
computeAllelicFractionRNA	0.227	0.018	0.246
computeAllelicImbDNAChr	0.007	0.001	0.007
computeAncestryFromSynthetic	0.016	0.003	0.019
computeAncestryFromSyntheticFile	6.180	0.532	6.712
computeKNNRefSample	0.017	0.002	0.019
computeKNNRefSynthetic	1.466	0.108	1.573
computeLOHBlocksDNAChr	0.008	0.002	0.011
computePCAMultiSynthetic	0.008	0.003	0.012
computePCARefRMMulti	0.154	0.017	0.171
computePCARefSample	0.167	0.001	0.167
computePoolSyntheticAncestryGr	0.442	0.011	0.453
computeSyntheticConfMat	0.014	0.001	0.016
computeSyntheticROC	0.035	0.005	0.041
createAUROCGraph	0.651	0.049	0.702
createAccuracyGraph	0.680	0.027	0.707
createProfile	0.045	0.005	0.051
createStudy2GDS1KG	0.046	0.004	0.050
demoKnownSuperPop1KG	1.409	0.008	1.417
demoPCA1KG	0.006	0.003	0.009
demoPCASyntheticProfiles	1.431	0.072	1.502
demoPedigreeEx1	0.015	0.002	0.017
estimateAllelicFraction	0.075	0.002	0.077
extractNucleotide	0	0	0
generateGDS1KG	0.012	0.000	0.013
generateGDS1KGgenotypeFromSNPPileup	0.040	0.003	0.043
generateGDSRefSample	0.003	0.002	0.004
generateGDSSNPinfo	0.003	0.002	0.005
generateGDSgenotype	0.012	0.002	0.014
generateGeneBlock	0.000	0.002	0.002
generateMapSnvSel	0.002	0.001	0.004
generatePhase1KG2GDS	0.011	0.004	0.015
generatePhaseRef	0.010	0.003	0.013
generateProfileGDS	0.039	0.004	0.043
getBlockIDs	0.002	0.001	0.003
getRef1KGPop	0.002	0.002	0.004
getRefSuperPop	0.003	0.001	0.003
getTableSNV	0.010	0.004	0.013
groupChr1KGSNV	0.048	0.008	0.054
identifyRelative	0.007	0.003	0.010
identifyRelativeRef	0.006	0.001	0.006
inferAncestry	0.010	0.004	0.014
inferAncestryDNA	0.012	0.002	0.014
inferAncestryGeneAware	0.012	0.002	0.014
matKNNSynthetic	0.058	0.001	0.059
pedSynthetic	0.040	0.001	0.040
prepPed1KG	0.004	0.001	0.005
prepPedSynthetic1KG	0.004	0.001	0.006
prepSynthetic	0.011	0.000	0.011
processBlockChr	0.003	0.001	0.004
processPileupChrBin	3.049	0.284	3.333
profileAncestry	0.015	0.003	0.017
pruning1KGbyChr	0.002	0.002	0.005
pruningSample	0.036	0.009	0.045
readSNVBAM	0.002	0.000	0.001
readSNVFileGeneric	0.002	0.002	0.004
readSNVPileupFile	0.032	0.000	0.033
readSNVVCF	4.952	0.122	5.076
runExomeAncestry	0.013	0.004	0.017
runIBDKING	0.053	0.004	0.058
runLDPruning	0.022	0.003	0.026
runProfileAncestry	0.016	0.002	0.020
runRNAAncestry	0.015	0.001	0.017
runWrapperAncestry	0.016	0.001	0.017
selParaPCAUpQuartile	4.588	0.060	4.652
select1KGPop	0.006	0.000	0.006
select1KGPopForSynthetic	0.005	0.001	0.005
snpPositionDemo	0.003	0.001	0.003
snvListVCF	0.001	0.003	0.005
splitSelectByPop	0.000	0.001	0.002
syntheticGeno	0.026	0.008	0.034
tableBlockAF	0.019	0.002	0.021
testAlleleFractionChange	0.000	0.001	0.002
testEmptyBox	0.001	0.000	0.002
validateAdd1KG2SampleGDS	0.002	0.000	0.002
validateAddStudy1Kg	0.002	0.001	0.002
validateCharacterString	0	0	0
validateComputeAncestryFromSyntheticFile	0.002	0.001	0.003
validateComputeKNNRefSample	0.004	0.001	0.005
validateComputeKNNRefSynthetic	0.004	0.003	0.006
validateComputePCAMultiSynthetic	0.003	0.002	0.004
validateComputePCARefSample	0.001	0.000	0.002
validateComputePoolSyntheticAncestryGr	0.002	0.000	0.002
validateComputeSyntheticRoc	0.009	0.003	0.012
validateCreateAccuracyGraph	0.001	0.000	0.002
validateCreateStudy2GDS1KG	0.000	0.002	0.003
validateDataRefSynParameter	0.001	0.000	0.001
validateEstimateAllelicFraction	0.002	0.003	0.005
validateGDSClass	0.002	0.000	0.001
validateGenerateGDS1KG	0.001	0.001	0.001
validateLogical	0.001	0.000	0.000
validatePEDStudyParameter	0.001	0.000	0.000
validatePepSynthetic	0.001	0.001	0.002
validatePositiveIntegerVector	0	0	0
validatePrepPed1KG	0.001	0.001	0.001
validateProfileGDSExist	0.001	0.000	0.001
validatePruningSample	0.000	0.002	0.002
validateRunExomeOrRNAAncestry	0.003	0.002	0.004
validateSingleRatio	0	0	0
validateStudyDataFrameParameter	0.001	0.000	0.001
validateSyntheticGeno	0.001	0.002	0.003
validatecreateProfile	0.003	0.001	0.004
wrapperAncestry	0.024	0.006	0.029