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

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.3.2 Patched (2023-11-13 r85521) -- "Eye Holes"	4692
palomino4	Windows Server 2022 Datacenter	x64	4.3.2 (2023-10-31 ucrt) -- "Eye Holes"	4445
lconway	macOS 12.7.1 Monterey	x86_64	4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes"	4466
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 4.3.2 Patched (2023-11-01 r85457)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    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 8.653  0.267   8.986
readSNVVCF                       6.557  0.098   6.712
selParaPCAUpQuartile             6.148  0.075   6.275
* 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 4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes"
Copyright (C) 2023 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 
 34.442   2.552  37.434

Example timings

name	user	system	elapsed
add1KG2SampleGDS	0.061	0.018	0.092
addBlockInGDSAnnot	0.006	0.004	0.012
addGDSRef	0.003	0.003	0.008
addGDSStudyPruning	0.001	0.002	0.004
addGeneBlockGDSRefAnnot	1.140	0.095	1.245
addRef2GDS1KG	0.006	0.005	0.012
addStudy1Kg	0.013	0.013	0.029
addStudyGDSSample	0.008	0.005	0.015
addUpdateLap	0.001	0.003	0.004
addUpdateSegment	0.001	0.002	0.004
appendGDSRefSample	0.008	0.005	0.015
appendGDSSampleOnly	0.001	0.002	0.004
appendGDSgenotype	0.020	0.016	0.040
appendGDSgenotypeMat	0.002	0.002	0.004
calcAFMLRNA	0.005	0.002	0.007
computeAlleleFraction	0.003	0.001	0.003
computeAllelicFractionDNA	0.177	0.013	0.195
computeAllelicFractionRNA	0.291	0.015	0.310
computeAllelicImbDNAChr	0.010	0.002	0.012
computeAncestryFromSyntheticFile	8.653	0.267	8.986
computeKNNRefSample	0.020	0.005	0.025
computeKNNRefSynthetic	1.783	0.095	1.886
computeLOHBlocksDNAChr	0.011	0.002	0.012
computePCAMultiSynthetic	0.008	0.004	0.011
computePCARefRMMulti	0.271	0.006	0.278
computePCARefSample	0.330	0.005	0.336
computePoolSyntheticAncestryGr	0.644	0.024	0.674
computeSyntheticConfMat	0.018	0.004	0.022
computeSyntheticROC	0.054	0.006	0.059
createStudy2GDS1KG	0.085	0.021	0.109
demoKnownSuperPop1KG	1.693	0.044	1.746
demoPCA1KG	0.008	0.003	0.012
demoPCASyntheticProfiles	1.697	0.043	1.755
demoPedigreeEx1	0.020	0.003	0.023
estimateAllelicFraction	0.090	0.005	0.097
generateGDS1KG	0.016	0.013	0.032
generateGDS1KGgenotypeFromSNPPileup	0.066	0.016	0.086
generateGDSRefSample	0.005	0.004	0.010
generateGDSSNPinfo	0.005	0.006	0.012
generateGDSgenotype	0.016	0.013	0.030
generateGeneBlock	0.001	0.001	0.003
generateMapSnvSel	0.003	0.003	0.007
generatePhase1KG2GDS	0.017	0.012	0.032
getBlockIDs	0.002	0.001	0.004
getRef1KGPop	0.003	0.002	0.005
getTableSNV	0.013	0.004	0.017
groupChr1KGSNV	0.063	0.096	0.191
identifyRelative	0.014	0.005	0.021
matKNNSynthetic	0.047	0.004	0.051
pedSynthetic	0.053	0.004	0.057
prepPed1KG	0.005	0.002	0.007
prepPedSynthetic1KG	0.005	0.003	0.008
prepSynthetic	0.011	0.005	0.017
pruning1KGbyChr	0.004	0.003	0.008
pruningSample	0.043	0.011	0.054
readSNVFileGeneric	0.005	0.002	0.007
readSNVPileupFile	0.066	0.006	0.073
readSNVVCF	6.557	0.098	6.712
runExomeAncestry	0.018	0.003	0.022
runIBDKING	0.041	0.004	0.049
runLDPruning	0.025	0.012	0.038
runProfileAncestry	0.021	0.005	0.027
runRNAAncestry	0.020	0.004	0.025
runWrapperAncestry	0.018	0.004	0.023
selParaPCAUpQuartile	6.148	0.075	6.275
select1KGPop	0.006	0.001	0.007
snpPositionDemo	0.003	0.002	0.005
snvListVCF	0.003	0.002	0.006
splitSelectByPop	0.001	0.000	0.002
syntheticGeno	0.029	0.007	0.037
tableBlockAF	0.024	0.002	0.026
testAlleleFractionChange	0.001	0.001	0.001
testEmptyBox	0.002	0.001	0.002
validateAdd1KG2SampleGDS	0.002	0.001	0.003
validateAddStudy1Kg	0.001	0.001	0.003
validateCharacterString	0	0	0
validateComputeAncestryFromSyntheticFile	0.002	0.001	0.003
validateComputeKNNRefSample	0.003	0.003	0.006
validateComputeKNNRefSynthetic	0.004	0.003	0.007
validateComputePCAMultiSynthetic	0.004	0.002	0.006
validateComputePCARefSample	0.001	0.001	0.003
validateComputePoolSyntheticAncestryGr	0.002	0.001	0.003
validateComputeSyntheticRoc	0.013	0.003	0.016
validateCreateStudy2GDS1KG	0.002	0.001	0.003
validateDataRefSynParameter	0.001	0.000	0.000
validateEstimateAllelicFraction	0.004	0.001	0.005
validateGDSClass	0.001	0.001	0.002
validateGenerateGDS1KG	0.001	0.001	0.002
validateLogical	0.001	0.000	0.000
validatePEDStudyParameter	0.001	0.000	0.001
validatePepSynthetic	0.002	0.001	0.003
validatePositiveIntegerVector	0	0	0
validatePrepPed1KG	0.001	0.001	0.003
validateProfileGDSExist	0.001	0.001	0.002
validatePruningSample	0.002	0.002	0.003
validateRunExomeOrRNAAncestry	0.005	0.001	0.006
validateSingleRatio	0	0	0
validateStudyDataFrameParameter	0.000	0.000	0.001
validateSyntheticGeno	0.002	0.001	0.003

CHECK results for RAIDS on lconway

Summary

Command output

Installation output

Tests output

Example timings