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"	4669
palomino4	Windows Server 2022 Datacenter	x64	4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake"	4404
merida1	macOS 12.7.1 Monterey	x86_64	4.3.3 (2024-02-29) -- "Angel Food Cake"	4427
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*

##############################################################################
##############################################################################
###
### Running command:
###
###   /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
###
##############################################################################
##############################################################################


* 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 14.927  0.667  18.299
readSNVVCF                       14.588  0.115  15.461
selParaPCAUpQuartile             12.676  0.083  13.035
* 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

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


* 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 
 59.871   3.575  66.394

Example timings

name	user	system	elapsed
add1KG2SampleGDS	0.128	0.031	0.379
addBlockInGDSAnnot	0.009	0.008	0.022
addGDSRef	0.005	0.005	0.011
addGDSStudyPruning	0.002	0.004	0.011
addGeneBlockGDSRefAnnot	1.734	0.246	2.598
addRef2GDS1KG	0.009	0.013	0.074
addStudy1Kg	0.022	0.019	0.068
addStudyGDSSample	0.018	0.010	0.082
addUpdateLap	0.003	0.005	0.016
addUpdateSegment	0.002	0.005	0.006
appendGDSRefSample	0.013	0.011	0.026
appendGDSSampleOnly	0.002	0.005	0.008
appendGDSgenotype	0.029	0.024	0.104
appendGDSgenotypeMat	0.002	0.006	0.009
calcAFMLRNA	0.008	0.004	0.014
computeAlleleFraction	0.006	0.002	0.036
computeAllelicFractionDNA	0.321	0.025	0.418
computeAllelicFractionRNA	0.632	0.038	0.785
computeAllelicImbDNAChr	0.016	0.005	0.021
computeAncestryFromSyntheticFile	14.927	0.667	18.299
computeKNNRefSample	0.039	0.015	0.064
computeKNNRefSynthetic	3.705	0.207	4.642
computeLOHBlocksDNAChr	0.022	0.005	0.034
computePCAMultiSynthetic	0.014	0.009	0.031
computePCARefRMMulti	0.334	0.019	0.383
computePCARefSample	0.384	0.016	0.422
computePoolSyntheticAncestryGr	1.025	0.032	1.138
computeSyntheticConfMat	0.031	0.009	0.048
computeSyntheticROC	0.098	0.013	0.142
createStudy2GDS1KG	0.118	0.029	0.233
demoKnownSuperPop1KG	3.574	0.065	3.901
demoPCA1KG	0.013	0.008	0.056
demoPCASyntheticProfiles	3.589	0.061	3.952
demoPedigreeEx1	0.038	0.007	0.047
estimateAllelicFraction	0.216	0.009	0.240
generateGDS1KG	0.027	0.016	0.046
generateGDS1KGgenotypeFromSNPPileup	0.103	0.023	0.149
generateGDSRefSample	0.010	0.006	0.016
generateGDSSNPinfo	0.007	0.007	0.016
generateGDSgenotype	0.026	0.015	0.046
generateGeneBlock	0.003	0.001	0.005
generateMapSnvSel	0.006	0.004	0.012
generatePhase1KG2GDS	0.028	0.021	0.080
getBlockIDs	0.004	0.002	0.007
getRef1KGPop	0.006	0.003	0.008
getTableSNV	0.025	0.007	0.034
groupChr1KGSNV	0.112	0.123	0.249
identifyRelative	0.023	0.007	0.031
matKNNSynthetic	0.093	0.010	0.108
pedSynthetic	0.093	0.009	0.105
prepPed1KG	0.009	0.002	0.013
prepPedSynthetic1KG	0.011	0.004	0.017
prepSynthetic	0.024	0.009	0.033
pruning1KGbyChr	0.007	0.004	0.012
pruningSample	0.081	0.017	0.107
readSNVFileGeneric	0.007	0.002	0.010
readSNVPileupFile	0.080	0.004	0.090
readSNVVCF	14.588	0.115	15.461
runExomeAncestry	0.040	0.009	0.049
runIBDKING	0.067	0.008	0.079
runLDPruning	0.041	0.015	0.059
runProfileAncestry	0.047	0.008	0.056
runRNAAncestry	0.038	0.007	0.047
runWrapperAncestry	0.041	0.007	0.049
selParaPCAUpQuartile	12.676	0.083	13.035
select1KGPop	0.009	0.002	0.012
snpPositionDemo	0.005	0.004	0.010
snvListVCF	0.008	0.004	0.011
splitSelectByPop	0.002	0.000	0.003
syntheticGeno	0.064	0.011	0.079
tableBlockAF	0.051	0.005	0.056
testAlleleFractionChange	0.003	0.002	0.004
testEmptyBox	0.003	0.002	0.004
validateAdd1KG2SampleGDS	0.003	0.002	0.004
validateAddStudy1Kg	0.003	0.002	0.005
validateCharacterString	0.000	0.000	0.001
validateComputeAncestryFromSyntheticFile	0.004	0.003	0.007
validateComputeKNNRefSample	0.007	0.005	0.012
validateComputeKNNRefSynthetic	0.008	0.007	0.016
validateComputePCAMultiSynthetic	0.007	0.004	0.011
validateComputePCARefSample	0.003	0.002	0.005
validateComputePoolSyntheticAncestryGr	0.003	0.002	0.005
validateComputeSyntheticRoc	0.025	0.006	0.032
validateCreateStudy2GDS1KG	0.004	0.001	0.006
validateDataRefSynParameter	0.001	0.001	0.002
validateEstimateAllelicFraction	0.007	0.003	0.010
validateGDSClass	0.003	0.002	0.004
validateGenerateGDS1KG	0.002	0.001	0.003
validateLogical	0.000	0.000	0.001
validatePEDStudyParameter	0.002	0.001	0.002
validatePepSynthetic	0.003	0.001	0.005
validatePositiveIntegerVector	0.000	0.000	0.001
validatePrepPed1KG	0.002	0.001	0.003
validateProfileGDSExist	0.001	0.001	0.002
validatePruningSample	0.003	0.002	0.005
validateRunExomeOrRNAAncestry	0.010	0.002	0.013
validateSingleRatio	0.001	0.001	0.000
validateStudyDataFrameParameter	0.002	0.001	0.002
validateSyntheticGeno	0.003	0.003	0.006

CHECK results for RAIDS on merida1

Summary

Command output

Installation output

Tests output

Example timings