Multiple platform build/check report for BioC 3.18 - CHECK results for RAIDS on merida1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.3.3 (2024-02-29) -- "Angel Food Cake"	4676
palomino4	Windows Server 2022 Datacenter	x64	4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake"	4414
merida1	macOS 12.7.1 Monterey	x86_64	4.3.3 (2024-02-29) -- "Angel Food Cake"	4437
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*

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### Running command:
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###   /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
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/RAIDS.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    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 14.721  0.510  16.636
readSNVVCF                       14.301  0.088  14.530
selParaPCAUpQuartile             12.500  0.068  12.822
* 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

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL RAIDS
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* 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


R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 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 
 61.592   3.618  69.492

Example timings

name	user	system	elapsed
add1KG2SampleGDS	0.125	0.023	0.171
addBlockInGDSAnnot	0.009	0.006	0.018
addGDSRef	0.005	0.005	0.010
addGDSStudyPruning	0.002	0.004	0.006
addGeneBlockGDSRefAnnot	1.674	0.207	1.986
addRef2GDS1KG	0.008	0.008	0.017
addStudy1Kg	0.022	0.014	0.038
addStudyGDSSample	0.015	0.008	0.024
addUpdateLap	0.002	0.004	0.005
addUpdateSegment	0.002	0.003	0.005
appendGDSRefSample	0.013	0.008	0.022
appendGDSSampleOnly	0.002	0.003	0.006
appendGDSgenotype	0.030	0.018	0.053
appendGDSgenotypeMat	0.002	0.003	0.006
calcAFMLRNA	0.008	0.004	0.013
computeAlleleFraction	0.006	0.001	0.008
computeAllelicFractionDNA	0.314	0.019	0.360
computeAllelicFractionRNA	0.609	0.026	0.670
computeAllelicImbDNAChr	0.015	0.004	0.021
computeAncestryFromSyntheticFile	14.721	0.510	16.636
computeKNNRefSample	0.037	0.013	0.056
computeKNNRefSynthetic	3.626	0.166	4.001
computeLOHBlocksDNAChr	0.021	0.004	0.025
computePCAMultiSynthetic	0.015	0.008	0.023
computePCARefRMMulti	0.316	0.014	0.352
computePCARefSample	0.375	0.010	0.400
computePoolSyntheticAncestryGr	1.017	0.033	1.062
computeSyntheticConfMat	0.031	0.007	0.040
computeSyntheticROC	0.092	0.010	0.107
createStudy2GDS1KG	0.116	0.024	0.143
demoKnownSuperPop1KG	3.521	0.075	3.669
demoPCA1KG	0.012	0.007	0.019
demoPCASyntheticProfiles	3.517	0.046	3.608
demoPedigreeEx1	0.039	0.006	0.046
estimateAllelicFraction	0.214	0.008	0.226
generateGDS1KG	0.027	0.014	0.043
generateGDS1KGgenotypeFromSNPPileup	0.103	0.016	0.123
generateGDSRefSample	0.010	0.005	0.015
generateGDSSNPinfo	0.007	0.006	0.015
generateGDSgenotype	0.027	0.015	0.045
generateGeneBlock	0.003	0.001	0.004
generateMapSnvSel	0.006	0.004	0.010
generatePhase1KG2GDS	0.029	0.018	0.050
getBlockIDs	0.004	0.003	0.008
getRef1KGPop	0.006	0.002	0.008
getTableSNV	0.025	0.006	0.033
groupChr1KGSNV	0.107	0.113	0.226
identifyRelative	0.024	0.008	0.032
matKNNSynthetic	0.095	0.009	0.104
pedSynthetic	0.091	0.009	0.101
prepPed1KG	0.009	0.003	0.013
prepPedSynthetic1KG	0.011	0.003	0.015
prepSynthetic	0.027	0.009	0.037
pruning1KGbyChr	0.007	0.003	0.011
pruningSample	0.080	0.017	0.099
readSNVFileGeneric	0.008	0.003	0.011
readSNVPileupFile	0.081	0.004	0.086
readSNVVCF	14.301	0.088	14.530
runExomeAncestry	0.039	0.006	0.045
runIBDKING	0.066	0.007	0.074
runLDPruning	0.039	0.013	0.053
runProfileAncestry	0.045	0.007	0.051
runRNAAncestry	0.035	0.006	0.042
runWrapperAncestry	0.040	0.006	0.046
selParaPCAUpQuartile	12.500	0.068	12.822
select1KGPop	0.010	0.003	0.013
snpPositionDemo	0.005	0.004	0.009
snvListVCF	0.007	0.004	0.012
splitSelectByPop	0.002	0.001	0.003
syntheticGeno	0.066	0.011	0.079
tableBlockAF	0.053	0.005	0.058
testAlleleFractionChange	0.003	0.002	0.005
testEmptyBox	0.003	0.001	0.004
validateAdd1KG2SampleGDS	0.002	0.001	0.004
validateAddStudy1Kg	0.003	0.002	0.005
validateCharacterString	0.000	0.000	0.001
validateComputeAncestryFromSyntheticFile	0.003	0.003	0.006
validateComputeKNNRefSample	0.006	0.006	0.012
validateComputeKNNRefSynthetic	0.009	0.007	0.016
validateComputePCAMultiSynthetic	0.006	0.005	0.012
validateComputePCARefSample	0.002	0.002	0.005
validateComputePoolSyntheticAncestryGr	0.003	0.002	0.005
validateComputeSyntheticRoc	0.024	0.006	0.031
validateCreateStudy2GDS1KG	0.005	0.003	0.007
validateDataRefSynParameter	0.002	0.001	0.004
validateEstimateAllelicFraction	0.007	0.003	0.012
validateGDSClass	0.002	0.002	0.005
validateGenerateGDS1KG	0.003	0.002	0.004
validateLogical	0.000	0.001	0.001
validatePEDStudyParameter	0.002	0.001	0.003
validatePepSynthetic	0.003	0.002	0.005
validatePositiveIntegerVector	0.000	0.000	0.001
validatePrepPed1KG	0.002	0.002	0.004
validateProfileGDSExist	0.002	0.001	0.003
validatePruningSample	0.003	0.003	0.006
validateRunExomeOrRNAAncestry	0.010	0.003	0.013
validateSingleRatio	0.000	0.001	0.001
validateStudyDataFrameParameter	0.001	0.001	0.002
validateSyntheticGeno	0.003	0.004	0.007

CHECK results for RAIDS on merida1

Summary

Command output

Installation output

Tests output

Example timings