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

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"	4831
palomino7	Windows Server 2022 Datacenter	x64	4.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six"	4573
lconway	macOS 12.7.1 Monterey	x86_64	4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"	4599
kjohnson3	macOS 13.7.1 Ventura	arm64	4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"	4553
kunpeng2	Linux (openEuler 24.03 LTS)	aarch64	R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"	4570
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 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: 1.6.1

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_1.6.1.tar.gz

StartedAt: 2025-04-21 22:53:06 -0400 (Mon, 21 Apr 2025)

EndedAt: 2025-04-21 23:00:47 -0400 (Mon, 21 Apr 2025)

EllapsedTime: 461.5 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_1.6.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/RAIDS.Rcheck’
* using R version 4.5.0 RC (2025-04-04 r88126)
* 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 ‘1.6.1’
* 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 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 7.462  0.153   7.652
readSNVVCF                       5.873  0.092   5.994
selParaPCAUpQuartile             5.580  0.046   5.650
* 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-3.21-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 ‘1.6.1’
** 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 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"
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: 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 
 34.296   2.451  37.337

Example timings

RAIDS.Rcheck/RAIDS-Ex.timings

name	user	system	elapsed
add1KG2SampleGDS	0.067	0.016	0.093
addBlockFromDetFile	0.002	0.003	0.007
addBlockInGDSAnnot	0.004	0.004	0.011
addGDS1KGLDBlock	0.001	0.003	0.004
addGDSRef	0.003	0.003	0.006
addGDSStudyPruning	0.001	0.002	0.003
addGeneBlockGDSRefAnnot	1.061	0.112	1.199
addGeneBlockRefAnnot	0.002	0.003	0.005
addRef2GDS1KG	0.005	0.006	0.012
addStudy1Kg	0.011	0.008	0.022
addStudyGDSSample	0.007	0.003	0.012
addUpdateLap	0.002	0.002	0.003
addUpdateSegment	0.001	0.002	0.003
appendGDSRefSample	0.007	0.004	0.012
appendGDSSampleOnly	0.002	0.002	0.004
appendGDSgenotype	0.017	0.013	0.033
appendGDSgenotypeMat	0.002	0.002	0.004
calcAFMLRNA	0.005	0.002	0.007
computeAlleleFraction	0.002	0.001	0.003
computeAllelicFractionDNA	0.146	0.010	0.158
computeAllelicFractionRNA	0.397	0.022	0.423
computeAllelicImbDNAChr	0.009	0.002	0.010
computeAncestryFromSynthetic	0.017	0.007	0.023
computeAncestryFromSyntheticFile	7.462	0.153	7.652
computeKNNRefSample	0.015	0.005	0.020
computeKNNRefSynthetic	1.607	0.082	1.708
computeLOHBlocksDNAChr	0.011	0.001	0.013
computePCAMultiSynthetic	0.008	0.004	0.012
computePCARefRMMulti	0.268	0.007	0.277
computePCARefSample	0.332	0.005	0.338
computePoolSyntheticAncestryGr	0.609	0.014	0.628
computeSyntheticConfMat	0.016	0.005	0.021
computeSyntheticROC	0.051	0.006	0.057
createAUROCGraph	0.799	0.050	0.856
createAccuracyGraph	0.801	0.009	0.814
createProfile	0.067	0.016	0.086
createStudy2GDS1KG	0.070	0.014	0.087
demoKnownSuperPop1KG	2.710	0.053	2.778
demoPCA1KG	0.006	0.003	0.009
demoPCASyntheticProfiles	1.550	0.059	1.618
demoPedigreeEx1	0.015	0.003	0.018
estimateAllelicFraction	0.076	0.004	0.081
extractNucleotide	0.001	0.000	0.000
generateGDS1KG	0.013	0.011	0.026
generateGDS1KGgenotypeFromSNPPileup	0.057	0.012	0.073
generateGDSRefSample	0.005	0.003	0.009
generateGDSSNPinfo	0.005	0.004	0.010
generateGDSgenotype	0.013	0.010	0.024
generateGeneBlock	0.001	0.001	0.002
generateMapSnvSel	0.003	0.003	0.007
generatePhase1KG2GDS	0.014	0.013	0.030
generatePhaseRef	0.015	0.012	0.030
generateProfileGDS	0.063	0.014	0.080
getBlockIDs	0.003	0.002	0.004
getRef1KGPop	0.004	0.002	0.006
getRefSuperPop	0.003	0.001	0.004
getTableSNV	0.013	0.003	0.017
groupChr1KGSNV	0.060	0.100	0.192
identifyRelative	0.011	0.004	0.016
identifyRelativeRef	0.005	0.003	0.009
inferAncestry	0.017	0.001	0.019
inferAncestryDNA	0.011	0.001	0.012
inferAncestryGeneAware	0.012	0.002	0.014
matKNNSynthetic	0.049	0.005	0.055
pedSynthetic	0.048	0.005	0.053
prepPed1KG	0.005	0.001	0.007
prepPedSynthetic1KG	0.004	0.001	0.006
prepSynthetic	0.012	0.005	0.018
processBlockChr	0.003	0.002	0.004
processPileupChrBin	3.339	0.019	3.375
profileAncestry	0.022	0.005	0.027
pruning1KGbyChr	0.004	0.002	0.006
pruningSample	0.043	0.009	0.053
readSNVBAM	0.001	0.001	0.001
readSNVFileGeneric	0.003	0.001	0.005
readSNVPileupFile	0.042	0.001	0.044
readSNVVCF	5.873	0.092	5.994
runExomeAncestry	0.018	0.002	0.020
runIBDKING	0.037	0.004	0.044
runLDPruning	0.020	0.010	0.031
runProfileAncestry	0.024	0.004	0.028
runRNAAncestry	0.019	0.003	0.023
runWrapperAncestry	0.016	0.003	0.020
selParaPCAUpQuartile	5.580	0.046	5.650
select1KGPop	0.004	0.001	0.006
select1KGPopForSynthetic	0.004	0.001	0.005
snpPositionDemo	0.003	0.002	0.004
snvListVCF	0.004	0.002	0.006
splitSelectByPop	0.002	0.000	0.002
syntheticGeno	0.032	0.007	0.040
tableBlockAF	0.021	0.003	0.024
testAlleleFractionChange	0.001	0.001	0.001
testEmptyBox	0.001	0.001	0.002
validateAdd1KG2SampleGDS	0.001	0.001	0.003
validateAddStudy1Kg	0.001	0.000	0.002
validateCharacterString	0.000	0.000	0.001
validateComputeAncestryFromSyntheticFile	0.002	0.002	0.003
validateComputeKNNRefSample	0.003	0.003	0.006
validateComputeKNNRefSynthetic	0.004	0.004	0.009
validateComputePCAMultiSynthetic	0.004	0.003	0.006
validateComputePCARefSample	0.001	0.002	0.002
validateComputePoolSyntheticAncestryGr	0.002	0.001	0.002
validateComputeSyntheticRoc	0.013	0.004	0.017
validateCreateAccuracyGraph	0.001	0.001	0.001
validateCreateStudy2GDS1KG	0.002	0.001	0.003
validateDataRefSynParameter	0.000	0.001	0.001
validateEstimateAllelicFraction	0.005	0.002	0.007
validateGDSClass	0.001	0.001	0.002
validateGenerateGDS1KG	0.001	0.001	0.003
validateLogical	0	0	0
validatePEDStudyParameter	0.001	0.001	0.001
validatePepSynthetic	0.002	0.001	0.003
validatePositiveIntegerVector	0.000	0.001	0.001
validatePrepPed1KG	0.000	0.000	0.001
validateProfileGDSExist	0.001	0.000	0.001
validatePruningSample	0.002	0.001	0.003
validateRunExomeOrRNAAncestry	0.005	0.001	0.006
validateSingleRatio	0.000	0.000	0.001
validateStudyDataFrameParameter	0.001	0.000	0.001
validateSyntheticGeno	0.002	0.001	0.003
validatecreateProfile	0.002	0.000	0.003
wrapperAncestry	0.020	0.004	0.024