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This page was generated on 2024-12-23 12:08 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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 1654/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RAIDS 1.4.0  (landing page)
Pascal Belleau
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/RAIDS
git_branch: RELEASE_3_20
git_last_commit: 6b32a2c
git_last_commit_date: 2024-10-29 11:24:12 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for RAIDS on kjohnson1

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: 1.4.0
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_1.4.0.tar.gz
StartedAt: 2024-12-21 05:56:13 -0500 (Sat, 21 Dec 2024)
EndedAt: 2024-12-21 06:03:37 -0500 (Sat, 21 Dec 2024)
EllapsedTime: 444.2 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_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/RAIDS.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RAIDS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RAIDS’ version ‘1.4.0’
* 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 5.368  0.101   5.473
readSNVVCF                       5.027  0.046   5.081
* 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/4.4-arm64/Resources/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 version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-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
Loading required package: GENESIS
> 
> ## Run all unit tests
> test_check("RAIDS")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 442 ]
> 
> proc.time()
   user  system elapsed 
 32.354   1.802  34.304 

Example timings

RAIDS.Rcheck/RAIDS-Ex.timings

nameusersystemelapsed
add1KG2SampleGDS0.0240.0140.044
addBlockFromDetFile0.0010.0010.002
addBlockInGDSAnnot0.0050.0030.008
addGDS1KGLDBlock0.0010.0010.002
addGDSRef0.0020.0010.004
addGDSStudyPruning0.0000.0020.002
addGeneBlockGDSRefAnnot1.1590.0811.267
addGeneBlockRefAnnot0.0020.0010.003
addRef2GDS1KG0.0050.0040.009
addStudy1Kg0.0120.0080.024
addStudyGDSSample0.0070.0030.012
addUpdateLap0.0010.0020.005
addUpdateSegment0.0010.0020.003
appendGDSRefSample0.0060.0030.010
appendGDSSampleOnly0.0010.0010.003
appendGDSgenotype0.0140.0100.028
appendGDSgenotypeMat0.0010.0020.003
calcAFMLRNA0.0060.0020.008
computeAlleleFraction0.0030.0010.004
computeAllelicFractionDNA0.2060.0130.218
computeAllelicFractionRNA0.2200.0070.227
computeAllelicImbDNAChr0.0080.0020.010
computeAncestryFromSynthetic0.0180.0060.023
computeAncestryFromSyntheticFile5.3680.1015.473
computeKNNRefSample0.0160.0040.021
computeKNNRefSynthetic2.7920.1132.914
computeLOHBlocksDNAChr0.0110.0020.012
computePCAMultiSynthetic0.0100.0050.015
computePCARefRMMulti0.1310.0070.138
computePCARefSample0.1500.0040.159
computePoolSyntheticAncestryGr0.3810.0110.396
computeSyntheticConfMat0.0160.0050.021
computeSyntheticROC0.0690.0070.075
createAUROCGraph0.6960.0270.726
createAccuracyGraph0.660.020.68
createStudy2GDS1KG0.0700.0120.086
demoKnownSuperPop1KG1.3560.0681.427
demoPCA1KG0.0090.0050.013
demoPCASyntheticProfiles1.3780.0741.452
demoPedigreeEx10.0160.0040.019
estimateAllelicFraction0.0780.0050.084
generateGDS1KG0.0110.0070.021
generateGDS1KGgenotypeFromSNPPileup0.0570.0120.073
generateGDSRefSample0.0040.0020.008
generateGDSSNPinfo0.0040.0030.009
generateGDSgenotype0.0110.0070.022
generateGeneBlock0.0020.0010.002
generateMapSnvSel0.0030.0020.006
generatePhase1KG2GDS0.0130.0090.025
generatePhaseRef0.0120.0060.019
getBlockIDs0.0030.0010.004
getRef1KGPop0.0030.0020.005
getRefSuperPop0.0030.0010.004
getTableSNV0.0110.0040.015
groupChr1KGSNV0.0590.0600.128
identifyRelative0.0110.0030.014
identifyRelativeRef0.0070.0020.010
inferAncestry0.0130.0020.014
inferAncestryGeneAware0.0130.0010.014
matKNNSynthetic0.0420.0050.047
pedSynthetic0.0410.0060.047
prepPed1KG0.0050.0020.007
prepPedSynthetic1KG0.0050.0020.008
prepSynthetic0.0120.0060.018
processBlockChr0.0040.0020.006
profileAncestry0.0210.0050.025
pruning1KGbyChr0.0050.0020.007
pruningSample0.0400.0100.049
readSNVFileGeneric0.0040.0010.005
readSNVPileupFile0.0470.0020.050
readSNVVCF5.0270.0465.081
runExomeAncestry0.0160.0040.020
runIBDKING0.0640.0030.067
runLDPruning0.0290.0090.038
runProfileAncestry0.0200.0040.025
runRNAAncestry0.0160.0040.026
runWrapperAncestry0.0160.0030.020
selParaPCAUpQuartile4.7520.0414.851
select1KGPop0.0040.0010.005
select1KGPopForSynthetic0.0040.0010.005
snpPositionDemo0.0030.0020.005
snvListVCF0.0040.0020.006
splitSelectByPop0.0010.0000.001
syntheticGeno0.0300.0070.037
tableBlockAF0.0200.0030.023
testAlleleFractionChange0.0020.0010.003
testEmptyBox0.0010.0010.002
validateAdd1KG2SampleGDS0.0010.0010.003
validateAddStudy1Kg0.0020.0010.002
validateCharacterString0.0000.0000.001
validateComputeAncestryFromSyntheticFile0.0020.0010.003
validateComputeKNNRefSample0.0050.0030.009
validateComputeKNNRefSynthetic0.0070.0040.011
validateComputePCAMultiSynthetic0.0050.0030.007
validateComputePCARefSample0.0010.0010.003
validateComputePoolSyntheticAncestryGr0.0010.0010.002
validateComputeSyntheticRoc0.0140.0040.018
validateCreateAccuracyGraph0.0010.0010.002
validateCreateStudy2GDS1KG0.0020.0000.003
validateDataRefSynParameter0.0010.0000.001
validateEstimateAllelicFraction0.0040.0020.006
validateGDSClass0.0010.0010.002
validateGenerateGDS1KG0.0010.0000.002
validateLogical000
validatePEDStudyParameter0.0010.0000.001
validatePepSynthetic0.0020.0000.002
validatePositiveIntegerVector0.0000.0010.000
validatePrepPed1KG0.0010.0000.001
validateProfileGDSExist0.0010.0000.001
validatePruningSample0.0020.0010.003
validateRunExomeOrRNAAncestry0.0050.0010.007
validateSingleRatio000
validateStudyDataFrameParameter0.0010.0000.000
validateSyntheticGeno0.0020.0010.003
wrapperAncestry0.0160.0030.019