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This page was generated on 2024-02-22 11:36:14 -0500 (Thu, 22 Feb 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" 4691
palomino4Windows Server 2022 Datacenterx644.3.2 (2023-10-31 ucrt) -- "Eye Holes" 4444
lconwaymacOS 12.7.1 Montereyx86_644.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" 4465
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: 2024-02-21 14:05:05 -0500 (Wed, 21 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 nebbiolo2


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: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:RAIDS.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings RAIDS_1.0.0.tar.gz
StartedAt: 2024-02-22 01:34:39 -0500 (Thu, 22 Feb 2024)
EndedAt: 2024-02-22 01:42:13 -0500 (Thu, 22 Feb 2024)
EllapsedTime: 453.9 seconds
RetCode: 0
Status:   OK  
CheckDir: RAIDS.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:RAIDS.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings RAIDS_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/RAIDS.Rcheck’
* using R version 4.3.2 Patched (2023-11-13 r85521)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* 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 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 6.065  0.284   6.350
readSNVVCF                       5.142  0.136   5.278
selParaPCAUpQuartile             5.067  0.024   5.091
* 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 ...
  ‘Create_Reference_GDS_File.Rmd’ using ‘UTF-8’... OK
  ‘RAIDS.Rmd’ using ‘UTF-8’... OK
 NONE
* 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-3.18-bioc/R/bin/R CMD INSTALL RAIDS
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.18-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 4.3.2 Patched (2023-11-13 r85521) -- "Eye Holes"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 
 27.990   1.194  29.174 

Example timings

RAIDS.Rcheck/RAIDS-Ex.timings

nameusersystemelapsed
add1KG2SampleGDS0.0500.0000.059
addBlockInGDSAnnot0.0040.0000.006
addGDSRef0.0030.0000.003
addGDSStudyPruning0.0010.0000.001
addGeneBlockGDSRefAnnot0.7490.0520.802
addRef2GDS1KG0.0050.0000.004
addStudy1Kg0.0050.0040.008
addStudyGDSSample0.0060.0000.006
addUpdateLap0.0010.0000.001
addUpdateSegment0.0010.0000.001
appendGDSRefSample0.0050.0000.005
appendGDSSampleOnly0.0000.0010.000
appendGDSgenotype0.0120.0030.015
appendGDSgenotypeMat0.0010.0000.001
calcAFMLRNA0.0040.0000.004
computeAlleleFraction0.0020.0000.002
computeAllelicFractionDNA0.1290.0040.134
computeAllelicFractionRNA0.3400.0120.353
computeAllelicImbDNAChr0.0010.0040.005
computeAncestryFromSyntheticFile6.0650.2846.350
computeKNNRefSample0.0170.0000.018
computeKNNRefSynthetic1.4990.0401.539
computeLOHBlocksDNAChr0.0090.0000.008
computePCAMultiSynthetic0.0080.0000.007
computePCARefRMMulti0.1560.0080.165
computePCARefSample0.1570.0000.157
computePoolSyntheticAncestryGr0.4490.0000.449
computeSyntheticConfMat0.0140.0000.014
computeSyntheticROC0.0400.0000.041
createStudy2GDS1KG0.050.000.05
demoKnownSuperPop1KG1.5100.0081.518
demoPCA1KG0.0070.0000.008
demoPCASyntheticProfiles1.5070.0241.531
demoPedigreeEx10.0150.0000.015
estimateAllelicFraction0.0740.0040.078
generateGDS1KG0.0120.0000.012
generateGDS1KGgenotypeFromSNPPileup0.0410.0000.042
generateGDSRefSample0.0040.0000.004
generateGDSSNPinfo0.0040.0000.004
generateGDSgenotype0.0120.0000.011
generateGeneBlock0.0010.0000.001
generateMapSnvSel0.0000.0020.003
generatePhase1KG2GDS0.0070.0060.012
getBlockIDs0.0020.0000.002
getRef1KGPop0.0020.0000.003
getTableSNV0.0100.0000.011
groupChr1KGSNV0.0550.0000.056
identifyRelative0.0120.0000.012
matKNNSynthetic0.0390.0000.039
pedSynthetic0.040.000.04
prepPed1KG0.0040.0000.004
prepPedSynthetic1KG0.0050.0000.005
prepSynthetic0.0110.0000.010
pruning1KGbyChr0.0040.0000.004
pruningSample0.0410.0000.041
readSNVFileGeneric0.0000.0030.003
readSNVPileupFile0.0310.0000.031
readSNVVCF5.1420.1365.278
runExomeAncestry0.0160.0000.016
runIBDKING0.0450.0080.054
runLDPruning0.0210.0000.022
runProfileAncestry0.0170.0000.017
runRNAAncestry0.0150.0000.015
runWrapperAncestry0.0110.0040.016
selParaPCAUpQuartile5.0670.0245.091
select1KGPop0.0040.0000.005
snpPositionDemo0.0020.0000.003
snvListVCF0.0030.0000.004
splitSelectByPop0.0010.0000.001
syntheticGeno0.0290.0000.028
tableBlockAF0.0190.0000.020
testAlleleFractionChange0.0010.0000.002
testEmptyBox0.0010.0000.001
validateAdd1KG2SampleGDS0.0010.0000.001
validateAddStudy1Kg0.0010.0000.002
validateCharacterString000
validateComputeAncestryFromSyntheticFile0.0020.0000.001
validateComputeKNNRefSample0.0030.0010.003
validateComputeKNNRefSynthetic0.0020.0030.004
validateComputePCAMultiSynthetic0.0040.0000.003
validateComputePCARefSample0.0010.0000.002
validateComputePoolSyntheticAncestryGr0.0010.0000.001
validateComputeSyntheticRoc0.0110.0000.011
validateCreateStudy2GDS1KG0.0000.0020.002
validateDataRefSynParameter0.0000.0010.001
validateEstimateAllelicFraction0.0030.0010.003
validateGDSClass0.0010.0000.001
validateGenerateGDS1KG0.0010.0000.001
validateLogical000
validatePEDStudyParameter0.0000.0000.001
validatePepSynthetic0.0010.0000.001
validatePositiveIntegerVector000
validatePrepPed1KG0.0000.0000.001
validateProfileGDSExist0.0010.0000.001
validatePruningSample0.0010.0000.002
validateRunExomeOrRNAAncestry0.0040.0000.004
validateSingleRatio000
validateStudyDataFrameParameter0.0010.0000.000
validateSyntheticGeno0.0020.0000.001