Multiple platform build/check report for BioC 3.19 - CHECK results for RAIDS on merida1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 22.04.3 LTS)	x86_64	R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences"	4676
palomino3	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences"	4414
merida1	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences"	4441
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences"	4417
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_1.1.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/RAIDS.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* using platform: x86_64-apple-darwin20
* 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 ‘1.1.0’
* 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 ... NOTE
Documented arguments not in \usage in Rd file 'appendGDSSampleOnly.Rd':
  ‘listSample’

Documented arguments not in \usage in Rd file 'appendGDSgenotype.Rd':
  ‘listSamples’

Documented arguments not in \usage in Rd file 'validateProfileGDSExist.Rd':
  ‘currentProfile’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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
readSNVVCF                       15.015  0.184  17.817
computeAncestryFromSyntheticFile 14.025  0.538  16.244
selParaPCAUpQuartile             13.109  0.112  15.342
computeKNNRefSynthetic            4.918  0.101   5.916
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/RAIDS.Rcheck/00check.log’
for details.

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/4.4-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 Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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 
 61.219   3.691  74.373

Example timings

name	user	system	elapsed
add1KG2SampleGDS	0.128	0.026	0.185
addBlockInGDSAnnot	0.008	0.007	0.019
addGDSRef	0.005	0.005	0.013
addGDSStudyPruning	0.002	0.003	0.008
addGeneBlockGDSRefAnnot	1.646	0.238	2.107
addRef2GDS1KG	0.009	0.009	0.024
addStudy1Kg	0.024	0.016	0.049
addStudyGDSSample	0.018	0.008	0.031
addUpdateLap	0.002	0.003	0.009
addUpdateSegment	0.002	0.003	0.008
appendGDSRefSample	0.013	0.007	0.024
appendGDSSampleOnly	0.002	0.004	0.010
appendGDSgenotype	0.031	0.019	0.076
appendGDSgenotypeMat	0.002	0.004	0.006
calcAFMLRNA	0.008	0.004	0.013
computeAlleleFraction	0.007	0.002	0.011
computeAllelicFractionDNA	0.329	0.063	0.556
computeAllelicFractionRNA	0.641	0.031	0.711
computeAllelicImbDNAChr	0.015	0.004	0.019
computeAncestryFromSyntheticFile	14.025	0.538	16.244
computeKNNRefSample	0.065	0.012	0.092
computeKNNRefSynthetic	4.918	0.101	5.916
computeLOHBlocksDNAChr	0.021	0.004	0.031
computePCAMultiSynthetic	0.014	0.009	0.027
computePCARefRMMulti	0.338	0.016	0.415
computePCARefSample	0.390	0.011	0.474
computePoolSyntheticAncestryGr	1.053	0.019	1.261
computeSyntheticConfMat	0.032	0.008	0.047
computeSyntheticROC	0.097	0.010	0.127
createStudy2GDS1KG	0.146	0.026	0.281
demoKnownSuperPop1KG	3.692	0.053	4.555
demoPCA1KG	0.014	0.010	0.030
demoPCASyntheticProfiles	3.697	0.048	4.502
demoPedigreeEx1	0.038	0.007	0.058
estimateAllelicFraction	0.223	0.011	0.281
generateGDS1KG	0.027	0.016	0.055
generateGDS1KGgenotypeFromSNPPileup	0.105	0.022	0.170
generateGDSRefSample	0.010	0.007	0.028
generateGDSSNPinfo	0.009	0.008	0.024
generateGDSgenotype	0.028	0.017	0.064
generateGeneBlock	0.002	0.002	0.005
generateMapSnvSel	0.006	0.005	0.014
generatePhase1KG2GDS	0.029	0.020	0.063
getBlockIDs	0.005	0.003	0.008
getRef1KGPop	0.006	0.003	0.013
getTableSNV	0.026	0.009	0.121
groupChr1KGSNV	0.105	0.113	0.245
identifyRelative	0.023	0.010	0.036
matKNNSynthetic	0.101	0.012	0.135
pedSynthetic	0.101	0.012	0.134
prepPed1KG	0.010	0.004	0.017
prepPedSynthetic1KG	0.011	0.005	0.021
prepSynthetic	0.025	0.009	0.040
pruning1KGbyChr	0.007	0.005	0.014
pruningSample	0.085	0.019	0.125
readSNVFileGeneric	0.008	0.003	0.012
readSNVPileupFile	0.083	0.005	0.107
readSNVVCF	15.015	0.184	17.817
runExomeAncestry	0.039	0.008	0.057
runIBDKING	0.068	0.010	0.099
runLDPruning	0.035	0.006	0.047
runProfileAncestry	0.045	0.007	0.063
runRNAAncestry	0.039	0.007	0.051
runWrapperAncestry	0.040	0.007	0.053
selParaPCAUpQuartile	13.109	0.112	15.342
select1KGPop	0.010	0.002	0.015
snpPositionDemo	0.005	0.004	0.008
snvListVCF	0.007	0.004	0.014
splitSelectByPop	0.002	0.001	0.003
syntheticGeno	0.065	0.012	0.088
tableBlockAF	0.056	0.006	0.074
testAlleleFractionChange	0.003	0.002	0.006
testEmptyBox	0.003	0.001	0.005
validateAdd1KG2SampleGDS	0.003	0.002	0.005
validateAddStudy1Kg	0.003	0.003	0.007
validateCharacterString	0.000	0.001	0.001
validateComputeAncestryFromSyntheticFile	0.004	0.003	0.009
validateComputeKNNRefSample	0.006	0.006	0.013
validateComputeKNNRefSynthetic	0.009	0.007	0.021
validateComputePCAMultiSynthetic	0.006	0.005	0.018
validateComputePCARefSample	0.003	0.003	0.007
validateComputePoolSyntheticAncestryGr	0.003	0.002	0.006
validateComputeSyntheticRoc	0.024	0.006	0.035
validateCreateStudy2GDS1KG	0.005	0.002	0.008
validateDataRefSynParameter	0.001	0.001	0.002
validateEstimateAllelicFraction	0.006	0.004	0.010
validateGDSClass	0.002	0.003	0.004
validateGenerateGDS1KG	0.002	0.003	0.008
validateLogical	0.000	0.001	0.001
validatePEDStudyParameter	0.002	0.001	0.002
validatePepSynthetic	0.003	0.002	0.005
validatePositiveIntegerVector	0.001	0.000	0.001
validatePrepPed1KG	0.002	0.002	0.004
validateProfileGDSExist	0.001	0.001	0.005
validatePruningSample	0.003	0.002	0.006
validateRunExomeOrRNAAncestry	0.010	0.004	0.016
validateSingleRatio	0.001	0.001	0.001
validateStudyDataFrameParameter	0.001	0.001	0.002
validateSyntheticGeno	0.003	0.003	0.007

CHECK results for RAIDS on merida1

Summary

Command output

Installation output

Tests output

Example timings