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This page was generated on 2025-03-19 11:41 -0400 (Wed, 19 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences" 4742
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" 4545
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4576
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4528
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4459
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

Package 1668/2313HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RAIDS 1.5.0  (landing page)
Pascal Belleau
Snapshot Date: 2025-03-18 13:40 -0400 (Tue, 18 Mar 2025)
git_url: https://git.bioconductor.org/packages/RAIDS
git_branch: devel
git_last_commit: bb243c9
git_last_commit_date: 2024-10-29 11:24:12 -0400 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  YES
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


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: 2025-03-19 01:28:27 -0400 (Wed, 19 Mar 2025)
EndedAt: 2025-03-19 01:36:31 -0400 (Wed, 19 Mar 2025)
EllapsedTime: 484.0 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
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/RAIDS.Rcheck’
* using R Under development (unstable) (2025-03-13 r87965)
* 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 24.04.2 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 6.056  0.244   6.301
* 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’ ...
** 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) (2025-03-13 r87965) -- "Unsuffered Consequences"
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
> 
> ## Run all unit tests
> test_check("RAIDS")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 442 ]
> 
> proc.time()
   user  system elapsed 
 27.464   1.646  29.099 

Example timings

RAIDS.Rcheck/RAIDS-Ex.timings

nameusersystemelapsed
add1KG2SampleGDS0.0480.0100.068
addBlockFromDetFile0.0000.0030.003
addBlockInGDSAnnot0.0050.0010.007
addGDS1KGLDBlock0.0000.0010.002
addGDSRef0.0020.0010.003
addGDSStudyPruning0.0020.0000.001
addGeneBlockGDSRefAnnot0.7750.1550.951
addGeneBlockRefAnnot0.0020.0010.002
addRef2GDS1KG0.0040.0020.005
addStudy1Kg0.0080.0020.009
addStudyGDSSample0.0060.0010.007
addUpdateLap0.0010.0000.001
addUpdateSegment0.0010.0000.001
appendGDSRefSample0.0040.0020.006
appendGDSSampleOnly0.0000.0010.001
appendGDSgenotype0.0120.0020.015
appendGDSgenotypeMat0.0010.0010.002
calcAFMLRNA0.0050.0000.005
computeAlleleFraction0.0030.0000.003
computeAllelicFractionDNA0.1340.0200.155
computeAllelicFractionRNA0.2060.0240.231
computeAllelicImbDNAChr0.0050.0020.007
computeAncestryFromSynthetic0.0140.0040.018
computeAncestryFromSyntheticFile6.0560.2446.301
computeKNNRefSample0.0130.0040.017
computeKNNRefSynthetic1.4240.0401.465
computeLOHBlocksDNAChr0.0060.0030.010
computePCAMultiSynthetic0.0050.0040.010
computePCARefRMMulti0.1800.0120.193
computePCARefSample0.2070.0090.216
computePoolSyntheticAncestryGr0.4710.0150.485
computeSyntheticConfMat0.0110.0040.015
computeSyntheticROC0.0380.0020.041
createAUROCGraph0.6560.0430.700
createAccuracyGraph0.6510.0060.658
createStudy2GDS1KG0.0460.0050.051
demoKnownSuperPop1KG1.5150.0531.568
demoPCA1KG0.0060.0030.008
demoPCASyntheticProfiles1.4250.0041.429
demoPedigreeEx10.0140.0030.016
estimateAllelicFraction0.0730.0030.076
generateGDS1KG0.0100.0020.013
generateGDS1KGgenotypeFromSNPPileup0.0380.0040.043
generateGDSRefSample0.0040.0000.005
generateGDSSNPinfo0.0040.0000.004
generateGDSgenotype0.0110.0010.012
generateGeneBlock0.0010.0000.002
generateMapSnvSel0.0010.0020.003
generatePhase1KG2GDS0.0100.0020.012
generatePhaseRef0.0100.0020.011
getBlockIDs0.0020.0010.003
getRef1KGPop0.0020.0010.004
getRefSuperPop0.0030.0000.003
getTableSNV0.0100.0010.011
groupChr1KGSNV0.0410.0110.051
identifyRelative0.0080.0010.009
identifyRelativeRef0.0060.0010.007
inferAncestry0.0100.0020.013
inferAncestryGeneAware0.0110.0020.012
matKNNSynthetic0.0350.0030.038
pedSynthetic0.0350.0030.038
prepPed1KG0.0020.0020.005
prepPedSynthetic1KG0.0030.0030.006
prepSynthetic0.0080.0020.010
processBlockChr0.0020.0010.003
profileAncestry0.0120.0050.017
pruning1KGbyChr0.0040.0010.005
pruningSample0.0320.0130.044
readSNVFileGeneric0.0020.0010.004
readSNVPileupFile0.0310.0000.032
readSNVVCF4.8890.0364.926
runExomeAncestry0.0160.0020.017
runIBDKING0.0560.0020.060
runLDPruning0.0180.0060.024
runProfileAncestry0.0160.0020.018
runRNAAncestry0.0100.0060.015
runWrapperAncestry0.0150.0010.016
selParaPCAUpQuartile4.6710.0164.687
select1KGPop0.0040.0010.005
select1KGPopForSynthetic0.0050.0000.005
snpPositionDemo0.0030.0010.003
snvListVCF0.0010.0030.004
splitSelectByPop0.0010.0000.002
syntheticGeno0.0270.0050.032
tableBlockAF0.0190.0030.022
testAlleleFractionChange0.0020.0000.002
testEmptyBox0.0000.0010.001
validateAdd1KG2SampleGDS0.0010.0010.002
validateAddStudy1Kg0.0010.0010.002
validateCharacterString0.0000.0010.000
validateComputeAncestryFromSyntheticFile0.0000.0020.002
validateComputeKNNRefSample0.0020.0030.004
validateComputeKNNRefSynthetic0.0050.0010.006
validateComputePCAMultiSynthetic0.0020.0030.005
validateComputePCARefSample0.0020.0000.002
validateComputePoolSyntheticAncestryGr0.0020.0000.001
validateComputeSyntheticRoc0.0090.0030.012
validateCreateAccuracyGraph0.0020.0000.002
validateCreateStudy2GDS1KG0.0030.0000.003
validateDataRefSynParameter0.0010.0010.001
validateEstimateAllelicFraction0.0020.0020.005
validateGDSClass0.0020.0000.002
validateGenerateGDS1KG0.0010.0000.002
validateLogical000
validatePEDStudyParameter0.0010.0000.001
validatePepSynthetic0.0020.0000.002
validatePositiveIntegerVector0.0010.0000.001
validatePrepPed1KG0.0000.0010.001
validateProfileGDSExist0.0010.0000.002
validatePruningSample0.0000.0020.002
validateRunExomeOrRNAAncestry0.0020.0020.004
validateSingleRatio0.0000.0000.001
validateStudyDataFrameParameter0.0000.0000.001
validateSyntheticGeno0.0020.0010.003
wrapperAncestry0.0150.0010.017