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 24.04.1 LTS)	x86_64	R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences"	4748
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences"	4459
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"	4349
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: 1.5.0

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_1.5.0.tar.gz

StartedAt: 2024-11-25 04:39:48 -0500 (Mon, 25 Nov 2024)

EndedAt: 2024-11-25 04:50:47 -0500 (Mon, 25 Nov 2024)

EllapsedTime: 658.7 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_1.5.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/RAIDS.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* 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 ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ... 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 5.771  0.270   6.043
readSNVVCF                       5.015  0.125   5.140
* 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: OK

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’ ...
** 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) (2024-10-21 r87258) -- "Unsuffered Consequences"
Copyright (C) 2024 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
> 
> ## Run all unit tests
> test_check("RAIDS")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 442 ]
> 
> proc.time()
   user  system elapsed 
 23.512   1.441  24.949

Example timings

RAIDS.Rcheck/RAIDS-Ex.timings

name	user	system	elapsed
add1KG2SampleGDS	0.049	0.008	0.062
addBlockFromDetFile	0.002	0.001	0.003
addBlockInGDSAnnot	0.004	0.001	0.005
addGDS1KGLDBlock	0.002	0.000	0.002
addGDSRef	0.002	0.001	0.004
addGDSStudyPruning	0.001	0.001	0.001
addGeneBlockGDSRefAnnot	0.662	0.157	0.820
addGeneBlockRefAnnot	0.000	0.001	0.002
addRef2GDS1KG	0.003	0.004	0.006
addStudy1Kg	0.008	0.002	0.009
addStudyGDSSample	0.007	0.000	0.007
addUpdateLap	0.001	0.000	0.002
addUpdateSegment	0.002	0.000	0.001
appendGDSRefSample	0.004	0.002	0.006
appendGDSSampleOnly	0.001	0.000	0.001
appendGDSgenotype	0.011	0.002	0.014
appendGDSgenotypeMat	0.000	0.001	0.001
calcAFMLRNA	0.003	0.001	0.004
computeAlleleFraction	0.003	0.000	0.003
computeAllelicFractionDNA	0.119	0.019	0.140
computeAllelicFractionRNA	0.312	0.014	0.327
computeAllelicImbDNAChr	0.003	0.003	0.007
computeAncestryFromSynthetic	0.013	0.003	0.017
computeAncestryFromSyntheticFile	5.771	0.270	6.043
computeKNNRefSample	0.014	0.003	0.017
computeKNNRefSynthetic	1.429	0.058	1.487
computeLOHBlocksDNAChr	0.009	0.001	0.010
computePCAMultiSynthetic	0.005	0.002	0.009
computePCARefRMMulti	0.136	0.013	0.149
computePCARefSample	0.155	0.002	0.158
computePoolSyntheticAncestryGr	0.423	0.002	0.426
computeSyntheticConfMat	0.011	0.003	0.015
computeSyntheticROC	0.036	0.003	0.040
createAUROCGraph	0.625	0.008	0.635
createAccuracyGraph	0.629	0.002	0.632
createStudy2GDS1KG	0.047	0.004	0.050
demoKnownSuperPop1KG	1.467	0.013	1.481
demoPCA1KG	0.007	0.002	0.009
demoPCASyntheticProfiles	1.462	0.014	1.476
demoPedigreeEx1	0.014	0.003	0.017
estimateAllelicFraction	0.076	0.004	0.080
generateGDS1KG	0.011	0.002	0.013
generateGDS1KGgenotypeFromSNPPileup	0.040	0.001	0.042
generateGDSRefSample	0.004	0.001	0.005
generateGDSSNPinfo	0.004	0.000	0.005
generateGDSgenotype	0.010	0.003	0.013
generateGeneBlock	0.001	0.000	0.002
generateMapSnvSel	0.002	0.001	0.003
generatePhase1KG2GDS	0.010	0.003	0.013
generatePhaseRef	0.011	0.001	0.012
getBlockIDs	0.003	0.000	0.003
getRef1KGPop	0.002	0.001	0.004
getRefSuperPop	0.002	0.002	0.003
getTableSNV	0.011	0.001	0.012
groupChr1KGSNV	0.041	0.015	0.057
identifyRelative	0.006	0.002	0.009
identifyRelativeRef	0.005	0.002	0.006
inferAncestry	0.011	0.002	0.013
inferAncestryGeneAware	0.011	0.002	0.014
matKNNSynthetic	0.035	0.004	0.039
pedSynthetic	0.035	0.004	0.038
prepPed1KG	0.004	0.001	0.005
prepPedSynthetic1KG	0.004	0.002	0.005
prepSynthetic	0.010	0.000	0.011
processBlockChr	0.003	0.000	0.003
profileAncestry	0.015	0.003	0.017
pruning1KGbyChr	0.005	0.000	0.004
pruningSample	0.034	0.010	0.043
readSNVFileGeneric	0.003	0.000	0.004
readSNVPileupFile	0.030	0.001	0.032
readSNVVCF	5.015	0.125	5.140
runExomeAncestry	0.015	0.001	0.016
runIBDKING	0.054	0.002	0.057
runLDPruning	0.020	0.005	0.026
runProfileAncestry	0.017	0.000	0.018
runRNAAncestry	0.011	0.004	0.015
runWrapperAncestry	0.013	0.003	0.016
selParaPCAUpQuartile	4.539	0.006	4.545
select1KGPop	0.002	0.002	0.005
select1KGPopForSynthetic	0.003	0.002	0.004
snpPositionDemo	0.002	0.000	0.003
snvListVCF	0.003	0.001	0.004
splitSelectByPop	0.000	0.002	0.001
syntheticGeno	0.024	0.002	0.027
tableBlockAF	0.016	0.003	0.019
testAlleleFractionChange	0.002	0.000	0.002
testEmptyBox	0.002	0.000	0.002
validateAdd1KG2SampleGDS	0.002	0.000	0.002
validateAddStudy1Kg	0.001	0.001	0.002
validateCharacterString	0.000	0.000	0.001
validateComputeAncestryFromSyntheticFile	0.002	0.001	0.002
validateComputeKNNRefSample	0.003	0.001	0.004
validateComputeKNNRefSynthetic	0.005	0.000	0.006
validateComputePCAMultiSynthetic	0.004	0.001	0.004
validateComputePCARefSample	0.001	0.000	0.002
validateComputePoolSyntheticAncestryGr	0.002	0.001	0.002
validateComputeSyntheticRoc	0.010	0.001	0.011
validateCreateAccuracyGraph	0.001	0.000	0.001
validateCreateStudy2GDS1KG	0.001	0.001	0.002
validateDataRefSynParameter	0.001	0.000	0.001
validateEstimateAllelicFraction	0.003	0.001	0.004
validateGDSClass	0.002	0.000	0.002
validateGenerateGDS1KG	0.000	0.002	0.001
validateLogical	0.000	0.000	0.001
validatePEDStudyParameter	0.001	0.001	0.001
validatePepSynthetic	0.001	0.001	0.002
validatePositiveIntegerVector	0.000	0.000	0.001
validatePrepPed1KG	0.001	0.000	0.001
validateProfileGDSExist	0.000	0.001	0.001
validatePruningSample	0.001	0.001	0.002
validateRunExomeOrRNAAncestry	0.003	0.001	0.004
validateSingleRatio	0.000	0.001	0.000
validateStudyDataFrameParameter	0.000	0.000	0.001
validateSyntheticGeno	0.000	0.002	0.002
wrapperAncestry	0.013	0.002	0.016