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This page was generated on 2024-11-20 12:08 -0500 (Wed, 20 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4481
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4479
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4359
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4539
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (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 1654/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RAIDS 1.4.0  (landing page)
Pascal Belleau
Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 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)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  
palomino8Windows Server 2022 Datacenter / x64  ERROR    ERROR  skippedskipped
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  


CHECK results for RAIDS on kunpeng2

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: RAIDS
Version: 1.4.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:RAIDS.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings RAIDS_1.4.0.tar.gz
StartedAt: 2024-11-20 11:24:50 -0000 (Wed, 20 Nov 2024)
EndedAt: 2024-11-20 11:33:34 -0000 (Wed, 20 Nov 2024)
EllapsedTime: 524.2 seconds
RetCode: 0
Status:   OK  
CheckDir: RAIDS.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:RAIDS.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings RAIDS_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/RAIDS.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* 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 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 10.576  0.209  10.722
readSNVVCF                        8.216  0.071   8.307
selParaPCAUpQuartile              7.155  0.021   7.194
* 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:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL RAIDS
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.4.1/site-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 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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
Loading required package: GENESIS
> 
> ## Run all unit tests
> test_check("RAIDS")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 442 ]
> 
> proc.time()
   user  system elapsed 
 43.999   1.300  45.038 

Example timings

RAIDS.Rcheck/RAIDS-Ex.timings

nameusersystemelapsed
add1KG2SampleGDS0.0750.0040.088
addBlockFromDetFile0.0030.0000.005
addBlockInGDSAnnot0.0020.0040.009
addGDS1KGLDBlock0.0000.0020.002
addGDSRef0.0030.0010.005
addGDSStudyPruning0.0010.0000.001
addGeneBlockGDSRefAnnot1.0410.0561.099
addGeneBlockRefAnnot0.0020.0000.002
addRef2GDS1KG0.0060.0000.005
addStudy1Kg0.0130.0000.013
addStudyGDSSample0.0070.0030.011
addUpdateLap0.0020.0000.003
addUpdateSegment0.0010.0010.002
appendGDSRefSample0.0050.0030.008
appendGDSSampleOnly0.0010.0000.002
appendGDSgenotype0.0180.0040.033
appendGDSgenotypeMat0.0010.0000.002
calcAFMLRNA0.0050.0000.006
computeAlleleFraction0.0030.0000.004
computeAllelicFractionDNA0.1980.0070.210
computeAllelicFractionRNA0.4840.0110.500
computeAllelicImbDNAChr0.0080.0010.008
computeAncestryFromSynthetic0.0120.0060.021
computeAncestryFromSyntheticFile10.576 0.20910.722
computeKNNRefSample0.0220.0000.023
computeKNNRefSynthetic2.1220.0202.148
computeLOHBlocksDNAChr0.0110.0000.011
computePCAMultiSynthetic0.0050.0040.009
computePCARefRMMulti1.7020.0081.709
computePCARefSample2.1420.0042.064
computePoolSyntheticAncestryGr2.3620.0162.217
computeSyntheticConfMat0.0140.0040.018
computeSyntheticROC0.0550.0000.055
createAUROCGraph0.9900.0321.026
createAccuracyGraph1.0150.0041.022
createStudy2GDS1KG0.0800.0000.083
demoKnownSuperPop1KG2.2430.0082.256
demoPCA1KG0.0020.0080.011
demoPCASyntheticProfiles2.1710.0122.188
demoPedigreeEx10.0190.0040.023
estimateAllelicFraction0.1480.0000.148
generateGDS1KG0.0170.0000.018
generateGDS1KGgenotypeFromSNPPileup0.0580.0040.063
generateGDSRefSample0.0060.0000.006
generateGDSSNPinfo0.0050.0000.006
generateGDSgenotype0.0170.0000.017
generateGeneBlock0.0010.0000.001
generateMapSnvSel0.0030.0000.005
generatePhase1KG2GDS0.0140.0040.018
generatePhaseRef0.0130.0040.017
getBlockIDs0.0030.0000.003
getRef1KGPop0.0040.0000.005
getRefSuperPop0.0030.0000.003
getTableSNV0.0160.0000.015
groupChr1KGSNV0.0560.0160.074
identifyRelative0.0110.0000.010
identifyRelativeRef0.0070.0000.007
inferAncestry0.0180.0000.018
inferAncestryGeneAware0.0190.0000.019
matKNNSynthetic0.0550.0000.054
pedSynthetic0.0550.0000.055
prepPed1KG0.0050.0000.007
prepPedSynthetic1KG0.0070.0000.008
prepSynthetic0.0140.0000.015
processBlockChr0.0000.0030.003
profileAncestry0.0200.0040.024
pruning1KGbyChr0.0050.0000.005
pruningSample0.0620.0000.068
readSNVFileGeneric0.0020.0040.006
readSNVPileupFile0.0430.0000.045
readSNVVCF8.2160.0718.307
runExomeAncestry0.0190.0050.023
runIBDKING0.0610.0000.061
runLDPruning0.0300.0030.035
runProfileAncestry0.0210.0030.024
runRNAAncestry0.0220.0000.022
runWrapperAncestry0.0190.0030.022
selParaPCAUpQuartile7.1550.0217.194
select1KGPop0.0020.0040.006
select1KGPopForSynthetic0.0060.0000.006
snpPositionDemo0.0000.0040.004
snvListVCF0.0040.0000.005
splitSelectByPop0.0010.0000.002
syntheticGeno0.040.000.04
tableBlockAF0.0290.0000.029
testAlleleFractionChange0.0020.0000.002
testEmptyBox0.0020.0000.002
validateAdd1KG2SampleGDS0.0020.0000.002
validateAddStudy1Kg0.0010.0000.002
validateCharacterString000
validateComputeAncestryFromSyntheticFile0.0010.0000.002
validateComputeKNNRefSample0.0030.0020.005
validateComputeKNNRefSynthetic0.0040.0010.006
validateComputePCAMultiSynthetic0.0040.0000.004
validateComputePCARefSample0.0020.0000.002
validateComputePoolSyntheticAncestryGr0.0020.0000.002
validateComputeSyntheticRoc0.0140.0000.014
validateCreateAccuracyGraph0.0010.0000.001
validateCreateStudy2GDS1KG0.0020.0000.002
validateDataRefSynParameter0.0000.0000.001
validateEstimateAllelicFraction0.0010.0020.004
validateGDSClass0.0010.0000.002
validateGenerateGDS1KG0.0010.0000.002
validateLogical000
validatePEDStudyParameter0.0000.0000.001
validatePepSynthetic0.0020.0000.002
validatePositiveIntegerVector000
validatePrepPed1KG0.0010.0000.001
validateProfileGDSExist0.0010.0000.001
validatePruningSample0.0010.0000.001
validateRunExomeOrRNAAncestry0.0050.0000.005
validateSingleRatio000
validateStudyDataFrameParameter0.0010.0000.001
validateSyntheticGeno0.0020.0000.002
wrapperAncestry0.0230.0000.022