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This page was generated on 2024-02-22 11:37:09 -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 palomino4


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: F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:RAIDS.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings RAIDS_1.0.0.tar.gz
StartedAt: 2024-02-22 05:23:02 -0500 (Thu, 22 Feb 2024)
EndedAt: 2024-02-22 05:30:01 -0500 (Thu, 22 Feb 2024)
EllapsedTime: 418.4 seconds
RetCode: 0
Status:   OK  
CheckDir: RAIDS.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:RAIDS.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings RAIDS_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.18-bioc/meat/RAIDS.Rcheck'
* using R version 4.3.2 (2023-10-31 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.3.0
    GNU Fortran (GCC) 12.3.0
* running under: Windows Server 2022 x64 (build 20348)
* 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 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 6.53   0.26    6.81
readSNVVCF                       4.94   0.04    5.03
* 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:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL RAIDS
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.18-bioc/R/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 (2023-10-31 ucrt) -- "Eye Holes"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 
  28.98    2.45   32.12 

Example timings

RAIDS.Rcheck/RAIDS-Ex.timings

nameusersystemelapsed
add1KG2SampleGDS0.120.020.18
addBlockInGDSAnnot0.000.010.01
addGDSRef0.000.000.02
addGDSStudyPruning0.000.020.01
addGeneBlockGDSRefAnnot0.820.221.10
addRef2GDS1KG0.000.000.03
addStudy1Kg0.000.010.04
addStudyGDSSample0.010.000.02
addUpdateLap000
addUpdateSegment0.000.020.02
appendGDSRefSample0.020.000.01
appendGDSSampleOnly000
appendGDSgenotype0.030.000.14
appendGDSgenotypeMat0.020.000.01
calcAFMLRNA0.010.000.02
computeAlleleFraction000
computeAllelicFractionDNA0.160.010.26
computeAllelicFractionRNA0.240.020.29
computeAllelicImbDNAChr0.010.000.01
computeAncestryFromSyntheticFile6.530.266.81
computeKNNRefSample0.030.000.03
computeKNNRefSynthetic1.770.051.83
computeLOHBlocksDNAChr0.010.000.01
computePCAMultiSynthetic0.020.000.02
computePCARefRMMulti0.200.020.22
computePCARefSample0.280.000.29
computePoolSyntheticAncestryGr0.500.030.53
computeSyntheticConfMat0.030.000.03
computeSyntheticROC0.050.010.06
createStudy2GDS1KG0.060.020.11
demoKnownSuperPop1KG1.380.051.42
demoPCA1KG0.010.000.02
demoPCASyntheticProfiles1.390.011.41
demoPedigreeEx10.010.000.02
estimateAllelicFraction0.130.020.15
generateGDS1KG0.010.000.02
generateGDS1KGgenotypeFromSNPPileup0.050.000.08
generateGDSRefSample0.020.000.01
generateGDSSNPinfo0.010.000.02
generateGDSgenotype0.000.010.03
generateGeneBlock000
generateMapSnvSel0.000.000.01
generatePhase1KG2GDS0.000.020.05
getBlockIDs000
getRef1KGPop0.000.000.01
getTableSNV0.030.000.05
groupChr1KGSNV0.150.061.45
identifyRelative0.010.020.03
matKNNSynthetic0.050.000.05
pedSynthetic0.030.010.05
prepPed1KG0.000.000.01
prepPedSynthetic1KG0.000.000.02
prepSynthetic0.010.000.03
pruning1KGbyChr0.000.020.02
pruningSample0.020.030.06
readSNVFileGeneric0.000.000.02
readSNVPileupFile0.030.020.05
readSNVVCF4.940.045.03
runExomeAncestry0.020.020.03
runIBDKING0.040.010.08
runLDPruning0.020.000.02
runProfileAncestry0.030.000.03
runRNAAncestry0.020.000.01
runWrapperAncestry0.030.000.04
selParaPCAUpQuartile4.860.134.98
select1KGPop000
snpPositionDemo0.000.010.02
snvListVCF0.000.000.01
splitSelectByPop000
syntheticGeno0.060.000.08
tableBlockAF0.030.000.03
testAlleleFractionChange000
testEmptyBox000
validateAdd1KG2SampleGDS000
validateAddStudy1Kg0.000.000.02
validateCharacterString000
validateComputeAncestryFromSyntheticFile000
validateComputeKNNRefSample0.020.000.01
validateComputeKNNRefSynthetic0.000.020.02
validateComputePCAMultiSynthetic0.000.020.01
validateComputePCARefSample000
validateComputePoolSyntheticAncestryGr000
validateComputeSyntheticRoc0.010.000.02
validateCreateStudy2GDS1KG0.000.010.01
validateDataRefSynParameter000
validateEstimateAllelicFraction000
validateGDSClass0.000.020.02
validateGenerateGDS1KG000
validateLogical000
validatePEDStudyParameter000
validatePepSynthetic0.000.010.02
validatePositiveIntegerVector000
validatePrepPed1KG000
validateProfileGDSExist000
validatePruningSample000
validateRunExomeOrRNAAncestry0.020.000.01
validateSingleRatio000
validateStudyDataFrameParameter000
validateSyntheticGeno0.000.000.02