Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-11-20 12:06 -0500 (Wed, 20 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
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
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | ERROR | ERROR | skipped | skipped | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | 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: /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: 2024-11-20 01:35:03 -0500 (Wed, 20 Nov 2024) |
EndedAt: 2024-11-20 01:45:16 -0500 (Wed, 20 Nov 2024) |
EllapsedTime: 613.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: RAIDS.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### 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 4.4.1 (2024-06-14) * using platform: x86_64-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 Monterey 12.7.6 * 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 ...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 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 * 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: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL RAIDS ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/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)
RAIDS.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-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 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 21.842 1.700 52.657
RAIDS.Rcheck/RAIDS-Ex.timings
name | user | system | elapsed | |
add1KG2SampleGDS | 0.044 | 0.013 | 1.871 | |
addBlockFromDetFile | 0.002 | 0.003 | 0.076 | |
addBlockInGDSAnnot | 0.004 | 0.004 | 0.611 | |
addGDS1KGLDBlock | 0.001 | 0.002 | 0.031 | |
addGDSRef | 0.002 | 0.002 | 0.217 | |
addGDSStudyPruning | 0.001 | 0.002 | 0.130 | |
addGeneBlockGDSRefAnnot | 0.647 | 0.062 | 2.344 | |
addGeneBlockRefAnnot | 0.001 | 0.002 | 0.031 | |
addRef2GDS1KG | 0.004 | 0.004 | 0.580 | |
addStudy1Kg | 0.011 | 0.009 | 1.219 | |
addStudyGDSSample | 0.007 | 0.006 | 0.693 | |
addUpdateLap | 0.001 | 0.001 | 0.151 | |
addUpdateSegment | 0.001 | 0.001 | 0.128 | |
appendGDSRefSample | 0.007 | 0.005 | 0.622 | |
appendGDSSampleOnly | 0.001 | 0.002 | 0.151 | |
appendGDSgenotype | 0.015 | 0.013 | 1.370 | |
appendGDSgenotypeMat | 0.001 | 0.002 | 0.194 | |
calcAFMLRNA | 0.003 | 0.002 | 0.004 | |
computeAlleleFraction | 0.002 | 0.000 | 0.002 | |
computeAllelicFractionDNA | 0.102 | 0.006 | 0.215 | |
computeAllelicFractionRNA | 0.168 | 0.008 | 0.283 | |
computeAllelicImbDNAChr | 0.005 | 0.002 | 0.007 | |
computeAncestryFromSynthetic | 0.011 | 0.004 | 0.155 | |
computeAncestryFromSyntheticFile | 4.715 | 0.094 | 4.810 | |
computeKNNRefSample | 0.011 | 0.002 | 0.014 | |
computeKNNRefSynthetic | 1.033 | 0.073 | 1.212 | |
computeLOHBlocksDNAChr | 0.007 | 0.001 | 0.008 | |
computePCAMultiSynthetic | 0.006 | 0.002 | 0.008 | |
computePCARefRMMulti | 0.152 | 0.004 | 0.156 | |
computePCARefSample | 0.160 | 0.002 | 0.161 | |
computePoolSyntheticAncestryGr | 0.343 | 0.011 | 0.354 | |
computeSyntheticConfMat | 0.009 | 0.002 | 0.011 | |
computeSyntheticROC | 0.028 | 0.003 | 0.031 | |
createAUROCGraph | 0.454 | 0.025 | 0.523 | |
createAccuracyGraph | 0.457 | 0.010 | 0.468 | |
createStudy2GDS1KG | 0.048 | 0.015 | 1.370 | |
demoKnownSuperPop1KG | 1.096 | 0.072 | 1.170 | |
demoPCA1KG | 0.005 | 0.003 | 0.007 | |
demoPCASyntheticProfiles | 1.078 | 0.074 | 1.152 | |
demoPedigreeEx1 | 0.011 | 0.002 | 0.013 | |
estimateAllelicFraction | 0.054 | 0.003 | 0.185 | |
generateGDS1KG | 0.012 | 0.009 | 1.201 | |
generateGDS1KGgenotypeFromSNPPileup | 0.044 | 0.013 | 1.274 | |
generateGDSRefSample | 0.004 | 0.004 | 0.388 | |
generateGDSSNPinfo | 0.005 | 0.004 | 0.444 | |
generateGDSgenotype | 0.012 | 0.010 | 0.599 | |
generateGeneBlock | 0.001 | 0.001 | 0.002 | |
generateMapSnvSel | 0.003 | 0.003 | 0.059 | |
generatePhase1KG2GDS | 0.013 | 0.012 | 1.118 | |
generatePhaseRef | 0.011 | 0.009 | 1.025 | |
getBlockIDs | 0.001 | 0.000 | 0.003 | |
getRef1KGPop | 0.002 | 0.001 | 0.011 | |
getRefSuperPop | 0.002 | 0.001 | 0.002 | |
getTableSNV | 0.008 | 0.002 | 0.026 | |
groupChr1KGSNV | 0.043 | 0.073 | 0.177 | |
identifyRelative | 0.021 | 0.010 | 0.052 | |
identifyRelativeRef | 0.005 | 0.001 | 0.037 | |
inferAncestry | 0.010 | 0.001 | 0.011 | |
inferAncestryGeneAware | 0.009 | 0.002 | 0.011 | |
matKNNSynthetic | 0.030 | 0.003 | 0.032 | |
pedSynthetic | 0.029 | 0.003 | 0.031 | |
prepPed1KG | 0.003 | 0.001 | 0.025 | |
prepPedSynthetic1KG | 0.004 | 0.001 | 0.026 | |
prepSynthetic | 0.008 | 0.004 | 0.095 | |
processBlockChr | 0.002 | 0.001 | 0.003 | |
profileAncestry | 0.013 | 0.003 | 0.015 | |
pruning1KGbyChr | 0.002 | 0.002 | 0.027 | |
pruningSample | 0.026 | 0.006 | 0.183 | |
readSNVFileGeneric | 0.002 | 0.000 | 0.021 | |
readSNVPileupFile | 0.032 | 0.001 | 0.112 | |
readSNVVCF | 3.660 | 0.027 | 3.789 | |
runExomeAncestry | 0.011 | 0.002 | 0.013 | |
runIBDKING | 0.028 | 0.004 | 0.306 | |
runLDPruning | 0.015 | 0.008 | 0.067 | |
runProfileAncestry | 0.012 | 0.003 | 0.015 | |
runRNAAncestry | 0.010 | 0.003 | 0.013 | |
runWrapperAncestry | 0.011 | 0.002 | 0.013 | |
selParaPCAUpQuartile | 3.619 | 0.019 | 3.640 | |
select1KGPop | 0.003 | 0.001 | 0.005 | |
select1KGPopForSynthetic | 0.003 | 0.001 | 0.004 | |
snpPositionDemo | 0.001 | 0.001 | 0.003 | |
snvListVCF | 0.003 | 0.002 | 0.130 | |
splitSelectByPop | 0.001 | 0.000 | 0.001 | |
syntheticGeno | 0.020 | 0.006 | 0.458 | |
tableBlockAF | 0.013 | 0.002 | 0.015 | |
testAlleleFractionChange | 0.001 | 0.001 | 0.001 | |
testEmptyBox | 0.001 | 0.001 | 0.001 | |
validateAdd1KG2SampleGDS | 0.002 | 0.001 | 0.002 | |
validateAddStudy1Kg | 0.001 | 0.001 | 0.002 | |
validateCharacterString | 0.000 | 0.001 | 0.000 | |
validateComputeAncestryFromSyntheticFile | 0.002 | 0.001 | 0.002 | |
validateComputeKNNRefSample | 0.003 | 0.002 | 0.005 | |
validateComputeKNNRefSynthetic | 0.004 | 0.002 | 0.006 | |
validateComputePCAMultiSynthetic | 0.002 | 0.002 | 0.004 | |
validateComputePCARefSample | 0.001 | 0.001 | 0.002 | |
validateComputePoolSyntheticAncestryGr | 0.001 | 0.001 | 0.002 | |
validateComputeSyntheticRoc | 0.008 | 0.002 | 0.010 | |
validateCreateAccuracyGraph | 0.001 | 0.001 | 0.002 | |
validateCreateStudy2GDS1KG | 0.002 | 0.001 | 0.003 | |
validateDataRefSynParameter | 0.000 | 0.000 | 0.001 | |
validateEstimateAllelicFraction | 0.003 | 0.002 | 0.005 | |
validateGDSClass | 0.002 | 0.002 | 0.003 | |
validateGenerateGDS1KG | 0.002 | 0.002 | 0.004 | |
validateLogical | 0 | 0 | 0 | |
validatePEDStudyParameter | 0.001 | 0.000 | 0.001 | |
validatePepSynthetic | 0.002 | 0.001 | 0.002 | |
validatePositiveIntegerVector | 0 | 0 | 0 | |
validatePrepPed1KG | 0.000 | 0.000 | 0.001 | |
validateProfileGDSExist | 0.001 | 0.001 | 0.001 | |
validatePruningSample | 0.001 | 0.001 | 0.002 | |
validateRunExomeOrRNAAncestry | 0.003 | 0.001 | 0.005 | |
validateSingleRatio | 0 | 0 | 0 | |
validateStudyDataFrameParameter | 0.001 | 0.000 | 0.001 | |
validateSyntheticGeno | 0.002 | 0.001 | 0.025 | |
wrapperAncestry | 0.011 | 0.002 | 0.013 | |