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	R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences"	4777
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences"	4545
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences"	4576
kjohnson3	macOS 13.7.1 Ventura	arm64	R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences"	4528
kunpeng2	Linux (openEuler 24.03 LTS)	aarch64	R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"	4458
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: 1.5.0

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_1.5.0.tar.gz

StartedAt: 2025-03-19 23:21:18 -0400 (Wed, 19 Mar 2025)

EndedAt: 2025-03-19 23:28:59 -0400 (Wed, 19 Mar 2025)

EllapsedTime: 460.9 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_1.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/RAIDS.Rcheck’
* using R Under development (unstable) (2025-03-02 r87868)
* 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 ‘1.5.0’
* 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 ... OK
* 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 8.119  0.163   8.323
readSNVVCF                       6.267  0.060   6.363
selParaPCAUpQuartile             6.053  0.041   6.127
* 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: OK

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 ‘1.5.0’
** 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 Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences"
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
> 
> ## Run all unit tests
> test_check("RAIDS")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 442 ]
> 
> proc.time()
   user  system elapsed 
 32.521   2.507  35.447

Example timings

RAIDS.Rcheck/RAIDS-Ex.timings

name	user	system	elapsed
add1KG2SampleGDS	0.065	0.015	0.085
addBlockFromDetFile	0.002	0.006	0.011
addBlockInGDSAnnot	0.005	0.005	0.011
addGDS1KGLDBlock	0.002	0.003	0.005
addGDSRef	0.004	0.003	0.008
addGDSStudyPruning	0.002	0.002	0.005
addGeneBlockGDSRefAnnot	1.108	0.137	1.298
addGeneBlockRefAnnot	0.002	0.002	0.004
addRef2GDS1KG	0.005	0.004	0.012
addStudy1Kg	0.011	0.009	0.025
addStudyGDSSample	0.009	0.004	0.014
addUpdateLap	0.001	0.002	0.004
addUpdateSegment	0.001	0.002	0.004
appendGDSRefSample	0.008	0.004	0.012
appendGDSSampleOnly	0.001	0.002	0.004
appendGDSgenotype	0.016	0.012	0.032
appendGDSgenotypeMat	0.001	0.001	0.004
calcAFMLRNA	0.004	0.002	0.005
computeAlleleFraction	0.003	0.000	0.002
computeAllelicFractionDNA	0.155	0.009	0.166
computeAllelicFractionRNA	0.268	0.012	0.282
computeAllelicImbDNAChr	0.008	0.002	0.009
computeAncestryFromSynthetic	0.017	0.006	0.024
computeAncestryFromSyntheticFile	8.119	0.163	8.323
computeKNNRefSample	0.018	0.004	0.022
computeKNNRefSynthetic	1.739	0.085	1.837
computeLOHBlocksDNAChr	0.010	0.001	0.013
computePCAMultiSynthetic	0.006	0.003	0.009
computePCARefRMMulti	0.292	0.006	0.299
computePCARefSample	0.318	0.004	0.323
computePoolSyntheticAncestryGr	0.638	0.015	0.658
computeSyntheticConfMat	0.015	0.003	0.018
computeSyntheticROC	0.043	0.004	0.048
createAUROCGraph	0.763	0.043	0.811
createAccuracyGraph	0.728	0.013	0.746
createStudy2GDS1KG	0.067	0.016	0.085
demoKnownSuperPop1KG	1.699	0.038	1.749
demoPCA1KG	0.008	0.004	0.012
demoPCASyntheticProfiles	1.612	0.046	1.670
demoPedigreeEx1	0.017	0.003	0.021
estimateAllelicFraction	0.084	0.005	0.090
generateGDS1KG	0.015	0.013	0.029
generateGDS1KGgenotypeFromSNPPileup	0.053	0.013	0.068
generateGDSRefSample	0.005	0.003	0.009
generateGDSSNPinfo	0.004	0.004	0.010
generateGDSgenotype	0.013	0.010	0.024
generateGeneBlock	0.001	0.001	0.002
generateMapSnvSel	0.003	0.002	0.006
generatePhase1KG2GDS	0.014	0.011	0.026
generatePhaseRef	0.012	0.009	0.023
getBlockIDs	0.003	0.001	0.004
getRef1KGPop	0.003	0.001	0.005
getRefSuperPop	0.003	0.001	0.004
getTableSNV	0.011	0.003	0.014
groupChr1KGSNV	0.065	0.105	0.207
identifyRelative	0.011	0.004	0.015
identifyRelativeRef	0.009	0.003	0.012
inferAncestry	0.017	0.001	0.019
inferAncestryGeneAware	0.017	0.001	0.018
matKNNSynthetic	0.042	0.004	0.047
pedSynthetic	0.042	0.004	0.045
prepPed1KG	0.004	0.002	0.006
prepPedSynthetic1KG	0.004	0.002	0.007
prepSynthetic	0.010	0.004	0.016
processBlockChr	0.003	0.001	0.004
profileAncestry	0.021	0.004	0.026
pruning1KGbyChr	0.004	0.002	0.007
pruningSample	0.064	0.016	0.085
readSNVFileGeneric	0.003	0.001	0.004
readSNVPileupFile	0.050	0.002	0.052
readSNVVCF	6.267	0.060	6.363
runExomeAncestry	0.016	0.004	0.020
runIBDKING	0.037	0.004	0.044
runLDPruning	0.020	0.009	0.030
runProfileAncestry	0.023	0.003	0.027
runRNAAncestry	0.017	0.003	0.021
runWrapperAncestry	0.015	0.003	0.018
selParaPCAUpQuartile	6.053	0.041	6.127
select1KGPop	0.005	0.001	0.007
select1KGPopForSynthetic	0.006	0.001	0.008
snpPositionDemo	0.002	0.002	0.003
snvListVCF	0.004	0.003	0.006
splitSelectByPop	0.002	0.000	0.002
syntheticGeno	0.029	0.006	0.035
tableBlockAF	0.026	0.002	0.027
testAlleleFractionChange	0.001	0.001	0.002
testEmptyBox	0.001	0.001	0.002
validateAdd1KG2SampleGDS	0.001	0.001	0.003
validateAddStudy1Kg	0.002	0.000	0.003
validateCharacterString	0	0	0
validateComputeAncestryFromSyntheticFile	0.001	0.002	0.003
validateComputeKNNRefSample	0.003	0.002	0.005
validateComputeKNNRefSynthetic	0.005	0.003	0.008
validateComputePCAMultiSynthetic	0.003	0.002	0.005
validateComputePCARefSample	0.002	0.001	0.003
validateComputePoolSyntheticAncestryGr	0.002	0.001	0.003
validateComputeSyntheticRoc	0.010	0.003	0.012
validateCreateAccuracyGraph	0.002	0.001	0.002
validateCreateStudy2GDS1KG	0.002	0.001	0.004
validateDataRefSynParameter	0.001	0.000	0.001
validateEstimateAllelicFraction	0.004	0.002	0.005
validateGDSClass	0.001	0.001	0.003
validateGenerateGDS1KG	0.001	0.000	0.001
validateLogical	0.000	0.000	0.001
validatePEDStudyParameter	0.001	0.000	0.001
validatePepSynthetic	0.002	0.001	0.003
validatePositiveIntegerVector	0	0	0
validatePrepPed1KG	0.001	0.001	0.001
validateProfileGDSExist	0.001	0.000	0.002
validatePruningSample	0.002	0.001	0.002
validateRunExomeOrRNAAncestry	0.004	0.001	0.005
validateSingleRatio	0.000	0.000	0.001
validateStudyDataFrameParameter	0.001	0.000	0.001
validateSyntheticGeno	0.002	0.001	0.003
wrapperAncestry	0.019	0.004	0.023