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"	4767
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences"	4487
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"	4450
kjohnson3	macOS 13.7.1 Ventura	arm64	R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"	4405
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"	4398
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: 2025-01-14 01:18:44 -0500 (Tue, 14 Jan 2025)

EndedAt: 2025-01-14 01:26:53 -0500 (Tue, 14 Jan 2025)

EllapsedTime: 489.0 seconds

RetCode: 0

Status: OK

CheckDir: RAIDS.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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
###
##############################################################################
##############################################################################


* 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 ... 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 6.228  0.516   6.745
readSNVVCF                       4.996  0.183   5.180
* 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 
 28.458   1.690  30.147

Example timings

RAIDS.Rcheck/RAIDS-Ex.timings

name	user	system	elapsed
add1KG2SampleGDS	0.100	0.050	0.162
addBlockFromDetFile	0.002	0.000	0.003
addBlockInGDSAnnot	0.005	0.001	0.007
addGDS1KGLDBlock	0.000	0.001	0.002
addGDSRef	0.002	0.001	0.003
addGDSStudyPruning	0.001	0.000	0.001
addGeneBlockGDSRefAnnot	0.944	0.254	1.198
addGeneBlockRefAnnot	0.001	0.001	0.002
addRef2GDS1KG	0.003	0.004	0.006
addStudy1Kg	0.008	0.003	0.011
addStudyGDSSample	0.008	0.001	0.008
addUpdateLap	0.000	0.002	0.002
addUpdateSegment	0.000	0.001	0.001
appendGDSRefSample	0.005	0.002	0.007
appendGDSSampleOnly	0.002	0.000	0.001
appendGDSgenotype	0.014	0.004	0.017
appendGDSgenotypeMat	0.001	0.000	0.002
calcAFMLRNA	0.005	0.000	0.005
computeAlleleFraction	0.000	0.002	0.003
computeAllelicFractionDNA	0.142	0.039	0.182
computeAllelicFractionRNA	0.233	0.037	0.271
computeAllelicImbDNAChr	0.004	0.004	0.008
computeAncestryFromSynthetic	0.014	0.005	0.019
computeAncestryFromSyntheticFile	6.228	0.516	6.745
computeKNNRefSample	0.015	0.002	0.016
computeKNNRefSynthetic	1.415	0.061	1.476
computeLOHBlocksDNAChr	0.008	0.002	0.010
computePCAMultiSynthetic	0.005	0.004	0.009
computePCARefRMMulti	0.182	0.017	0.199
computePCARefSample	0.273	0.012	0.284
computePoolSyntheticAncestryGr	0.550	0.031	0.584
computeSyntheticConfMat	0.013	0.002	0.015
computeSyntheticROC	0.039	0.003	0.043
createAUROCGraph	0.677	0.071	0.753
createAccuracyGraph	0.648	0.012	0.660
createStudy2GDS1KG	0.054	0.005	0.059
demoKnownSuperPop1KG	1.433	0.054	1.487
demoPCA1KG	0.005	0.004	0.009
demoPCASyntheticProfiles	1.436	0.040	1.476
demoPedigreeEx1	0.013	0.003	0.016
estimateAllelicFraction	0.076	0.009	0.085
generateGDS1KG	0.011	0.003	0.014
generateGDS1KGgenotypeFromSNPPileup	0.040	0.005	0.045
generateGDSRefSample	0.002	0.002	0.005
generateGDSSNPinfo	0.003	0.001	0.005
generateGDSgenotype	0.011	0.003	0.013
generateGeneBlock	0.001	0.001	0.001
generateMapSnvSel	0.003	0.000	0.003
generatePhase1KG2GDS	0.013	0.001	0.014
generatePhaseRef	0.011	0.002	0.013
getBlockIDs	0.002	0.001	0.003
getRef1KGPop	0.003	0.001	0.003
getRefSuperPop	0.002	0.001	0.003
getTableSNV	0.010	0.003	0.013
groupChr1KGSNV	0.042	0.012	0.055
identifyRelative	0.008	0.002	0.010
identifyRelativeRef	0.005	0.001	0.007
inferAncestry	0.011	0.004	0.014
inferAncestryGeneAware	0.011	0.004	0.015
matKNNSynthetic	0.039	0.004	0.044
pedSynthetic	0.061	0.007	0.068
prepPed1KG	0.003	0.002	0.005
prepPedSynthetic1KG	0.002	0.003	0.006
prepSynthetic	0.010	0.001	0.011
processBlockChr	0.002	0.001	0.003
profileAncestry	0.018	0.000	0.017
pruning1KGbyChr	0.004	0.001	0.004
pruningSample	0.033	0.012	0.045
readSNVFileGeneric	0.002	0.001	0.004
readSNVPileupFile	0.032	0.000	0.033
readSNVVCF	4.996	0.183	5.180
runExomeAncestry	0.014	0.003	0.016
runIBDKING	0.052	0.005	0.058
runLDPruning	0.023	0.003	0.026
runProfileAncestry	0.014	0.003	0.017
runRNAAncestry	0.015	0.000	0.016
runWrapperAncestry	0.015	0.001	0.016
selParaPCAUpQuartile	4.896	0.096	4.992
select1KGPop	0.003	0.002	0.005
select1KGPopForSynthetic	0.004	0.001	0.006
snpPositionDemo	0.002	0.001	0.003
snvListVCF	0.003	0.001	0.005
splitSelectByPop	0.001	0.000	0.002
syntheticGeno	0.025	0.004	0.030
tableBlockAF	0.02	0.00	0.02
testAlleleFractionChange	0.001	0.001	0.002
testEmptyBox	0.001	0.001	0.001
validateAdd1KG2SampleGDS	0.002	0.001	0.002
validateAddStudy1Kg	0.002	0.000	0.002
validateCharacterString	0	0	0
validateComputeAncestryFromSyntheticFile	0.003	0.000	0.002
validateComputeKNNRefSample	0.002	0.002	0.004
validateComputeKNNRefSynthetic	0.003	0.002	0.006
validateComputePCAMultiSynthetic	0.004	0.000	0.005
validateComputePCARefSample	0.002	0.000	0.002
validateComputePoolSyntheticAncestryGr	0.001	0.001	0.001
validateComputeSyntheticRoc	0.007	0.004	0.012
validateCreateAccuracyGraph	0.002	0.000	0.002
validateCreateStudy2GDS1KG	0.002	0.001	0.003
validateDataRefSynParameter	0.001	0.000	0.000
validateEstimateAllelicFraction	0.002	0.002	0.004
validateGDSClass	0.002	0.000	0.002
validateGenerateGDS1KG	0.001	0.002	0.001
validateLogical	0	0	0
validatePEDStudyParameter	0.000	0.000	0.001
validatePepSynthetic	0.000	0.001	0.002
validatePositiveIntegerVector	0	0	0
validatePrepPed1KG	0.001	0.000	0.001
validateProfileGDSExist	0.001	0.001	0.001
validatePruningSample	0.001	0.001	0.002
validateRunExomeOrRNAAncestry	0.003	0.001	0.004
validateSingleRatio	0	0	0
validateStudyDataFrameParameter	0.001	0.000	0.000
validateSyntheticGeno	0.000	0.002	0.002
wrapperAncestry	0.015	0.002	0.016