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This page was generated on 2024-02-20 11:38:12 -0500 (Tue, 20 Feb 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" 4690
palomino4Windows Server 2022 Datacenterx644.3.2 (2023-10-31 ucrt) -- "Eye Holes" 4443
lconwaymacOS 12.7.1 Montereyx86_644.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" 4464
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 1651/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RAIDS 1.0.0  (landing page)
Pascal Belleau
Snapshot Date: 2024-02-19 14:05:07 -0500 (Mon, 19 Feb 2024)
git_url: https://git.bioconductor.org/packages/RAIDS
git_branch: RELEASE_3_18
git_last_commit: 12ea1e7
git_last_commit_date: 2023-10-24 11:51:36 -0500 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for RAIDS on lconway


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: 1.0.0
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_1.0.0.tar.gz
StartedAt: 2024-02-19 22:30:41 -0500 (Mon, 19 Feb 2024)
EndedAt: 2024-02-19 22:38:29 -0500 (Mon, 19 Feb 2024)
EllapsedTime: 467.8 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_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/RAIDS.Rcheck’
* using R version 4.3.2 Patched (2023-11-01 r85457)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RAIDS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RAIDS’ version ‘1.0.0’
* 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 R 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 8.392  0.273   8.763
readSNVVCF                       6.006  0.079   6.130
selParaPCAUpQuartile             5.862  0.059   5.950
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... 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/4.3-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)

Tests output

RAIDS.Rcheck/tests/testthat.Rout


R version 4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (64-bit)

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 432 ]
> 
> proc.time()
   user  system elapsed 
 33.775   2.551  36.984 

Example timings

RAIDS.Rcheck/RAIDS-Ex.timings

nameusersystemelapsed
add1KG2SampleGDS0.0730.0250.125
addBlockInGDSAnnot0.0070.0060.019
addGDSRef0.0040.0040.008
addGDSStudyPruning0.0010.0030.005
addGeneBlockGDSRefAnnot1.2290.1151.373
addRef2GDS1KG0.0060.0070.020
addStudy1Kg0.0140.0140.032
addStudyGDSSample0.0100.0070.019
addUpdateLap0.0010.0030.005
addUpdateSegment0.0010.0030.009
appendGDSRefSample0.0080.0070.023
appendGDSSampleOnly0.0010.0030.005
appendGDSgenotype0.0200.0190.044
appendGDSgenotypeMat0.0020.0040.007
calcAFMLRNA0.0060.0030.014
computeAlleleFraction0.0040.0010.005
computeAllelicFractionDNA0.1770.0130.199
computeAllelicFractionRNA0.3010.0140.318
computeAllelicImbDNAChr0.0090.0030.011
computeAncestryFromSyntheticFile8.3920.2738.763
computeKNNRefSample0.0180.0040.021
computeKNNRefSynthetic1.6120.1031.735
computeLOHBlocksDNAChr0.0080.0010.009
computePCAMultiSynthetic0.0080.0040.012
computePCARefRMMulti0.3340.0070.344
computePCARefSample0.4090.0050.418
computePoolSyntheticAncestryGr0.6530.0200.680
computeSyntheticConfMat0.0150.0040.019
computeSyntheticROC0.0510.0050.057
createStudy2GDS1KG0.0860.0170.107
demoKnownSuperPop1KG1.6440.0481.711
demoPCA1KG0.0080.0040.012
demoPCASyntheticProfiles1.6830.0471.744
demoPedigreeEx10.0180.0040.022
estimateAllelicFraction0.0860.0050.093
generateGDS1KG0.0140.0100.027
generateGDS1KGgenotypeFromSNPPileup0.0570.0150.077
generateGDSRefSample0.0060.0030.011
generateGDSSNPinfo0.0040.0050.011
generateGDSgenotype0.0150.0140.031
generateGeneBlock0.0010.0010.003
generateMapSnvSel0.0030.0020.005
generatePhase1KG2GDS0.0160.0130.032
getBlockIDs0.0020.0020.003
getRef1KGPop0.0030.0020.005
getTableSNV0.0140.0030.017
groupChr1KGSNV0.0680.1020.208
identifyRelative0.0120.0060.019
matKNNSynthetic0.0520.0050.059
pedSynthetic0.0500.0050.056
prepPed1KG0.0050.0020.007
prepPedSynthetic1KG0.0060.0020.009
prepSynthetic0.0140.0060.024
pruning1KGbyChr0.0050.0030.012
pruningSample0.0440.0120.058
readSNVFileGeneric0.0040.0020.006
readSNVPileupFile0.0660.0050.073
readSNVVCF6.0060.0796.130
runExomeAncestry0.0200.0030.024
runIBDKING0.0430.0050.050
runLDPruning0.0210.0050.026
runProfileAncestry0.0160.0030.020
runRNAAncestry0.0130.0020.016
runWrapperAncestry0.0170.0030.019
selParaPCAUpQuartile5.8620.0595.950
select1KGPop0.0050.0020.007
snpPositionDemo0.0020.0020.003
snvListVCF0.0030.0020.007
splitSelectByPop0.0010.0000.002
syntheticGeno0.0380.0080.048
tableBlockAF0.0230.0030.026
testAlleleFractionChange0.0010.0000.002
testEmptyBox0.0010.0000.002
validateAdd1KG2SampleGDS0.0020.0010.002
validateAddStudy1Kg0.0020.0010.003
validateCharacterString0.0000.0000.001
validateComputeAncestryFromSyntheticFile0.0030.0010.004
validateComputeKNNRefSample0.0040.0030.007
validateComputeKNNRefSynthetic0.0060.0050.011
validateComputePCAMultiSynthetic0.0030.0030.006
validateComputePCARefSample0.0010.0010.002
validateComputePoolSyntheticAncestryGr0.0010.0010.003
validateComputeSyntheticRoc0.0150.0040.019
validateCreateStudy2GDS1KG0.0030.0020.005
validateDataRefSynParameter0.0010.0010.002
validateEstimateAllelicFraction0.0040.0010.006
validateGDSClass0.0010.0010.002
validateGenerateGDS1KG0.0000.0010.002
validateLogical000
validatePEDStudyParameter0.0000.0000.001
validatePepSynthetic0.0020.0010.003
validatePositiveIntegerVector0.0000.0010.001
validatePrepPed1KG0.0010.0010.002
validateProfileGDSExist0.0010.0010.001
validatePruningSample0.0010.0020.003
validateRunExomeOrRNAAncestry0.0050.0020.006
validateSingleRatio000
validateStudyDataFrameParameter0.0010.0000.002
validateSyntheticGeno0.0020.0020.004