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This page was generated on 2024-11-20 12:02 -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 teran2

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: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:RAIDS.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings RAIDS_1.4.0.tar.gz
StartedAt: 2024-11-20 08:00:26 -0500 (Wed, 20 Nov 2024)
EndedAt: 2024-11-20 08:08:49 -0500 (Wed, 20 Nov 2024)
EllapsedTime: 502.9 seconds
RetCode: 0
Status:   OK  
CheckDir: RAIDS.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:RAIDS.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings RAIDS_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/RAIDS.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* 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 5.168  0.176   5.909
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

RAIDS.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL RAIDS
###
##############################################################################
##############################################################################


* installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/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 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-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
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 
 23.469   1.314  29.534 

Example timings

RAIDS.Rcheck/RAIDS-Ex.timings

nameusersystemelapsed
add1KG2SampleGDS0.0430.0020.113
addBlockFromDetFile0.0010.0010.005
addBlockInGDSAnnot0.0040.0000.014
addGDS1KGLDBlock0.0010.0000.001
addGDSRef0.0010.0010.008
addGDSStudyPruning0.0010.0000.001
addGeneBlockGDSRefAnnot0.8210.0891.182
addGeneBlockRefAnnot0.0010.0000.002
addRef2GDS1KG0.0030.0020.008
addStudy1Kg0.0030.0050.010
addStudyGDSSample0.0050.0000.007
addUpdateLap0.0010.0000.001
addUpdateSegment0.0000.0010.001
appendGDSRefSample0.0010.0030.005
appendGDSSampleOnly0.0010.0000.003
appendGDSgenotype0.0110.0020.033
appendGDSgenotypeMat0.0000.0010.002
calcAFMLRNA0.0030.0010.007
computeAlleleFraction0.0020.0000.005
computeAllelicFractionDNA0.1050.0070.153
computeAllelicFractionRNA0.2760.0040.294
computeAllelicImbDNAChr0.0050.0000.005
computeAncestryFromSynthetic0.0080.0020.014
computeAncestryFromSyntheticFile5.1680.1765.909
computeKNNRefSample0.0090.0020.012
computeKNNRefSynthetic1.4480.1141.651
computeLOHBlocksDNAChr0.0060.0010.008
computePCAMultiSynthetic0.0040.0020.007
computePCARefRMMulti0.0950.0300.136
computePCARefSample0.1090.0150.135
computePoolSyntheticAncestryGr0.3140.0060.430
computeSyntheticConfMat0.0100.0010.021
computeSyntheticROC0.0260.0030.063
createAUROCGraph0.5060.0020.876
createAccuracyGraph0.5000.0000.621
createStudy2GDS1KG0.0350.0010.039
demoKnownSuperPop1KG1.0220.0031.037
demoPCA1KG0.0040.0020.009
demoPCASyntheticProfiles0.9990.0011.032
demoPedigreeEx10.0130.0000.013
estimateAllelicFraction0.0780.0000.083
generateGDS1KG0.0090.0010.010
generateGDS1KGgenotypeFromSNPPileup0.0260.0040.031
generateGDSRefSample0.0030.0000.004
generateGDSSNPinfo0.0030.0000.003
generateGDSgenotype0.0070.0030.009
generateGeneBlock0.0000.0010.000
generateMapSnvSel0.0010.0010.003
generatePhase1KG2GDS0.0080.0010.010
generatePhaseRef0.0080.0010.009
getBlockIDs0.0020.0000.002
getRef1KGPop0.0010.0010.004
getRefSuperPop0.0020.0000.002
getTableSNV0.0080.0010.010
groupChr1KGSNV0.0330.0140.084
identifyRelative0.0060.0020.007
identifyRelativeRef0.0030.0020.005
inferAncestry0.0090.0010.010
inferAncestryGeneAware0.010.000.01
matKNNSynthetic0.0270.0020.029
pedSynthetic0.0260.0010.028
prepPed1KG0.0030.0000.004
prepPedSynthetic1KG0.0030.0010.004
prepSynthetic0.0060.0020.007
processBlockChr0.0020.0000.002
profileAncestry0.0130.0000.013
pruning1KGbyChr0.0030.0000.003
pruningSample0.0280.0040.033
readSNVFileGeneric0.0020.0010.004
readSNVPileupFile0.0200.0000.021
readSNVVCF4.6820.0084.841
runExomeAncestry0.0120.0000.013
runIBDKING0.0390.0000.075
runLDPruning0.0150.0080.049
runProfileAncestry0.0140.0000.014
runRNAAncestry0.0080.0030.012
runWrapperAncestry0.0120.0000.011
selParaPCAUpQuartile4.5420.0004.914
select1KGPop0.0040.0000.003
select1KGPopForSynthetic0.0020.0010.003
snpPositionDemo0.0010.0010.002
snvListVCF0.0030.0010.003
splitSelectByPop0.0010.0000.001
syntheticGeno0.0200.0020.034
tableBlockAF0.0140.0020.024
testAlleleFractionChange0.0010.0000.001
testEmptyBox0.0010.0000.001
validateAdd1KG2SampleGDS0.0010.0000.001
validateAddStudy1Kg0.0000.0010.001
validateCharacterString000
validateComputeAncestryFromSyntheticFile0.0010.0000.001
validateComputeKNNRefSample0.0030.0000.004
validateComputeKNNRefSynthetic0.0020.0020.004
validateComputePCAMultiSynthetic0.0020.0010.003
validateComputePCARefSample0.0010.0000.001
validateComputePoolSyntheticAncestryGr0.0010.0000.001
validateComputeSyntheticRoc0.0060.0020.008
validateCreateAccuracyGraph0.0010.0000.000
validateCreateStudy2GDS1KG0.0020.0000.001
validateDataRefSynParameter0.0000.0000.001
validateEstimateAllelicFraction0.0010.0010.003
validateGDSClass0.0010.0000.001
validateGenerateGDS1KG0.0010.0000.001
validateLogical000
validatePEDStudyParameter0.0000.0010.000
validatePepSynthetic0.0010.0000.001
validatePositiveIntegerVector0.0010.0000.000
validatePrepPed1KG0.0000.0000.001
validateProfileGDSExist0.0000.0000.001
validatePruningSample0.0010.0000.001
validateRunExomeOrRNAAncestry0.0030.0000.002
validateSingleRatio000
validateStudyDataFrameParameter000
validateSyntheticGeno0.0010.0010.002
wrapperAncestry0.0090.0020.013