Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:05 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (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 1654/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
RAIDS 1.4.0 (landing page) Pascal Belleau
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
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. |
Package: RAIDS |
Version: 1.4.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:RAIDS.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings RAIDS_1.4.0.tar.gz |
StartedAt: 2024-12-20 05:00:09 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 05:08:41 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 512.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: RAIDS.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:RAIDS.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings RAIDS_1.4.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/RAIDS.Rcheck' * using R version 4.4.2 (2024-10-31 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.3.0 GNU Fortran (GCC) 13.3.0 * running under: Windows Server 2022 x64 (build 20348) * 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 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 7.70 0.17 7.88 readSNVVCF 6.50 0.19 6.69 selParaPCAUpQuartile 5.75 0.06 5.81 * 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
RAIDS.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL RAIDS ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/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)
RAIDS.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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 34.07 2.57 37.68
RAIDS.Rcheck/RAIDS-Ex.timings
name | user | system | elapsed | |
add1KG2SampleGDS | 0.09 | 0.02 | 0.14 | |
addBlockFromDetFile | 0.00 | 0.00 | 0.05 | |
addBlockInGDSAnnot | 0.01 | 0.00 | 0.01 | |
addGDS1KGLDBlock | 0 | 0 | 0 | |
addGDSRef | 0.00 | 0.00 | 0.01 | |
addGDSStudyPruning | 0 | 0 | 0 | |
addGeneBlockGDSRefAnnot | 0.94 | 0.26 | 1.74 | |
addGeneBlockRefAnnot | 0 | 0 | 0 | |
addRef2GDS1KG | 0.01 | 0.02 | 0.06 | |
addStudy1Kg | 0.02 | 0.01 | 0.05 | |
addStudyGDSSample | 0.01 | 0.00 | 0.01 | |
addUpdateLap | 0 | 0 | 0 | |
addUpdateSegment | 0 | 0 | 0 | |
appendGDSRefSample | 0.02 | 0.00 | 0.02 | |
appendGDSSampleOnly | 0 | 0 | 0 | |
appendGDSgenotype | 0.0 | 0.0 | 0.2 | |
appendGDSgenotypeMat | 0 | 0 | 0 | |
calcAFMLRNA | 0.00 | 0.02 | 0.01 | |
computeAlleleFraction | 0 | 0 | 0 | |
computeAllelicFractionDNA | 0.20 | 0.01 | 0.35 | |
computeAllelicFractionRNA | 0.36 | 0.00 | 0.38 | |
computeAllelicImbDNAChr | 0.00 | 0.02 | 0.01 | |
computeAncestryFromSynthetic | 0.03 | 0.00 | 0.08 | |
computeAncestryFromSyntheticFile | 7.70 | 0.17 | 7.88 | |
computeKNNRefSample | 0.03 | 0.01 | 0.04 | |
computeKNNRefSynthetic | 4.45 | 0.08 | 4.55 | |
computeLOHBlocksDNAChr | 0.02 | 0.00 | 0.02 | |
computePCAMultiSynthetic | 0.00 | 0.02 | 0.01 | |
computePCARefRMMulti | 0.39 | 0.03 | 0.42 | |
computePCARefSample | 0.47 | 0.00 | 0.47 | |
computePoolSyntheticAncestryGr | 0.81 | 0.09 | 0.91 | |
computeSyntheticConfMat | 0.02 | 0.00 | 0.01 | |
computeSyntheticROC | 0.04 | 0.02 | 0.07 | |
createAUROCGraph | 0.68 | 0.08 | 0.75 | |
createAccuracyGraph | 0.78 | 0.04 | 0.82 | |
createStudy2GDS1KG | 0.06 | 0.02 | 0.10 | |
demoKnownSuperPop1KG | 1.59 | 0.06 | 1.65 | |
demoPCA1KG | 0.00 | 0.02 | 0.02 | |
demoPCASyntheticProfiles | 1.74 | 0.04 | 1.78 | |
demoPedigreeEx1 | 0.03 | 0.00 | 0.03 | |
estimateAllelicFraction | 0.06 | 0.02 | 0.10 | |
generateGDS1KG | 0.02 | 0.00 | 0.01 | |
generateGDS1KGgenotypeFromSNPPileup | 0.08 | 0.00 | 0.11 | |
generateGDSRefSample | 0.01 | 0.00 | 0.02 | |
generateGDSSNPinfo | 0.00 | 0.00 | 0.01 | |
generateGDSgenotype | 0.00 | 0.02 | 0.02 | |
generateGeneBlock | 0.02 | 0.00 | 0.01 | |
generateMapSnvSel | 0.00 | 0.00 | 0.03 | |
generatePhase1KG2GDS | 0.00 | 0.01 | 0.04 | |
generatePhaseRef | 0.01 | 0.02 | 0.03 | |
getBlockIDs | 0.02 | 0.00 | 0.01 | |
getRef1KGPop | 0.00 | 0.00 | 0.02 | |
getRefSuperPop | 0 | 0 | 0 | |
getTableSNV | 0.01 | 0.01 | 0.03 | |
groupChr1KGSNV | 0.11 | 0.06 | 1.31 | |
identifyRelative | 0.02 | 0.00 | 0.03 | |
identifyRelativeRef | 0.01 | 0.00 | 0.02 | |
inferAncestry | 0.02 | 0.02 | 0.03 | |
inferAncestryGeneAware | 0.02 | 0.00 | 0.02 | |
matKNNSynthetic | 0.03 | 0.03 | 0.06 | |
pedSynthetic | 0.03 | 0.02 | 0.05 | |
prepPed1KG | 0.00 | 0.00 | 0.02 | |
prepPedSynthetic1KG | 0.02 | 0.01 | 0.03 | |
prepSynthetic | 0.02 | 0.00 | 0.04 | |
processBlockChr | 0.01 | 0.00 | 0.02 | |
profileAncestry | 0.02 | 0.02 | 0.03 | |
pruning1KGbyChr | 0.01 | 0.00 | 0.01 | |
pruningSample | 0.03 | 0.01 | 0.10 | |
readSNVFileGeneric | 0 | 0 | 0 | |
readSNVPileupFile | 0.05 | 0.00 | 0.05 | |
readSNVVCF | 6.50 | 0.19 | 6.69 | |
runExomeAncestry | 0.05 | 0.00 | 0.04 | |
runIBDKING | 0.03 | 0.00 | 0.08 | |
runLDPruning | 0.01 | 0.01 | 0.03 | |
runProfileAncestry | 0.02 | 0.02 | 0.03 | |
runRNAAncestry | 0.03 | 0.01 | 0.05 | |
runWrapperAncestry | 0.00 | 0.02 | 0.02 | |
selParaPCAUpQuartile | 5.75 | 0.06 | 5.81 | |
select1KGPop | 0.02 | 0.00 | 0.01 | |
select1KGPopForSynthetic | 0.01 | 0.00 | 0.02 | |
snpPositionDemo | 0 | 0 | 0 | |
snvListVCF | 0 | 0 | 0 | |
splitSelectByPop | 0 | 0 | 0 | |
syntheticGeno | 0.03 | 0.00 | 0.08 | |
tableBlockAF | 0.03 | 0.00 | 0.04 | |
testAlleleFractionChange | 0 | 0 | 0 | |
testEmptyBox | 0 | 0 | 0 | |
validateAdd1KG2SampleGDS | 0 | 0 | 0 | |
validateAddStudy1Kg | 0 | 0 | 0 | |
validateCharacterString | 0 | 0 | 0 | |
validateComputeAncestryFromSyntheticFile | 0 | 0 | 0 | |
validateComputeKNNRefSample | 0.01 | 0.00 | 0.02 | |
validateComputeKNNRefSynthetic | 0.03 | 0.00 | 0.03 | |
validateComputePCAMultiSynthetic | 0 | 0 | 0 | |
validateComputePCARefSample | 0.02 | 0.00 | 0.01 | |
validateComputePoolSyntheticAncestryGr | 0.01 | 0.00 | 0.02 | |
validateComputeSyntheticRoc | 0 | 0 | 0 | |
validateCreateAccuracyGraph | 0 | 0 | 0 | |
validateCreateStudy2GDS1KG | 0.02 | 0.00 | 0.01 | |
validateDataRefSynParameter | 0 | 0 | 0 | |
validateEstimateAllelicFraction | 0 | 0 | 0 | |
validateGDSClass | 0.02 | 0.00 | 0.02 | |
validateGenerateGDS1KG | 0 | 0 | 0 | |
validateLogical | 0 | 0 | 0 | |
validatePEDStudyParameter | 0 | 0 | 0 | |
validatePepSynthetic | 0 | 0 | 0 | |
validatePositiveIntegerVector | 0 | 0 | 0 | |
validatePrepPed1KG | 0 | 0 | 0 | |
validateProfileGDSExist | 0.01 | 0.00 | 0.02 | |
validatePruningSample | 0 | 0 | 0 | |
validateRunExomeOrRNAAncestry | 0 | 0 | 0 | |
validateSingleRatio | 0 | 0 | 0 | |
validateStudyDataFrameParameter | 0 | 0 | 0 | |
validateSyntheticGeno | 0.02 | 0.00 | 0.04 | |
wrapperAncestry | 0.04 | 0.00 | 0.05 | |