Multiple platform build/check report for BioC 3.20 - CHECK results for RAIDS on merida1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4744
palomino8	Windows Server 2022 Datacenter	x64	4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"	4487
merida1	macOS 12.7.5 Monterey	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4515
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4467
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*

CHECK results for RAIDS on merida1

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: 1.4.0

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_1.4.0.tar.gz

StartedAt: 2024-12-31 09:10:53 -0500 (Tue, 31 Dec 2024)

EndedAt: 2024-12-31 09:41:09 -0500 (Tue, 31 Dec 2024)

EllapsedTime: 1815.7 seconds

RetCode: 0

Status: OK

CheckDir: RAIDS.Rcheck

Warnings: 0

Command output

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### 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_1.4.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/RAIDS.Rcheck’
* using R version 4.4.2 (2024-10-31)
* 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 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RAIDS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RAIDS’ version ‘1.4.0’
* 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 code 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    10.920  0.326  11.350
readSNVVCF                           8.199  0.098  18.382
selParaPCAUpQuartile                 6.860  0.032   6.892
computeKNNRefSynthetic               3.429  0.161   7.239
addGeneBlockGDSRefAnnot              1.449  0.255 354.981
computeAllelicFractionDNA            0.372  0.066  81.234
add1KG2SampleGDS                     0.139  0.038  13.115
groupChr1KGSNV                       0.066  0.079  55.085
generateGDS1KGgenotypeFromSNPPileup  0.101  0.022  18.663
createStudy2GDS1KG                   0.085  0.022   9.645
runIBDKING                           0.061  0.010  41.533
syntheticGeno                        0.037  0.007  12.672
appendGDSgenotype                    0.025  0.016  33.892
generatePhase1KG2GDS                 0.019  0.017  17.817
generateGDSgenotype                  0.020  0.015  17.152
addStudy1Kg                          0.016  0.012  37.440
prepSynthetic                        0.014  0.006   9.369
addStudyGDSSample                    0.011  0.006  17.244
addRef2GDS1KG                        0.007  0.007  11.269
generateGDSRefSample                 0.007  0.005   9.512
appendGDSgenotypeMat                 0.002  0.003   5.170
* 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: OK

Installation output

RAIDS.Rcheck/00install.out

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


* 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

RAIDS.Rcheck/tests/testthat.Rout


R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
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 442 ]
> 
> proc.time()
   user  system elapsed 
 61.217   3.429  73.358

Example timings

RAIDS.Rcheck/RAIDS-Ex.timings

name	user	system	elapsed
add1KG2SampleGDS	0.139	0.038	13.115
addBlockFromDetFile	0.003	0.006	0.010
addBlockInGDSAnnot	0.008	0.006	0.016
addGDS1KGLDBlock	0.003	0.004	0.008
addGDSRef	0.005	0.004	0.011
addGDSStudyPruning	0.002	0.004	0.534
addGeneBlockGDSRefAnnot	1.449	0.255	354.981
addGeneBlockRefAnnot	0.002	0.003	0.612
addRef2GDS1KG	0.007	0.007	11.269
addStudy1Kg	0.016	0.012	37.440
addStudyGDSSample	0.011	0.006	17.244
addUpdateLap	0.002	0.002	3.479
addUpdateSegment	0.002	0.002	3.161
appendGDSRefSample	0.012	0.007	0.025
appendGDSSampleOnly	0.002	0.003	2.310
appendGDSgenotype	0.025	0.016	33.892
appendGDSgenotypeMat	0.002	0.003	5.170
calcAFMLRNA	0.006	0.002	0.045
computeAlleleFraction	0.006	0.001	0.008
computeAllelicFractionDNA	0.372	0.066	81.234
computeAllelicFractionRNA	0.646	0.018	0.830
computeAllelicImbDNAChr	0.015	0.003	0.027
computeAncestryFromSynthetic	0.031	0.009	0.058
computeAncestryFromSyntheticFile	10.920	0.326	11.350
computeKNNRefSample	0.032	0.007	2.382
computeKNNRefSynthetic	3.429	0.161	7.239
computeLOHBlocksDNAChr	0.020	0.004	0.024
computePCAMultiSynthetic	0.014	0.008	1.523
computePCARefRMMulti	0.292	0.012	0.307
computePCARefSample	0.329	0.011	0.343
computePoolSyntheticAncestryGr	0.909	0.023	0.941
computeSyntheticConfMat	0.030	0.007	0.035
computeSyntheticROC	0.089	0.009	0.098
createAUROCGraph	1.313	0.051	1.950
createAccuracyGraph	1.267	0.029	1.712
createStudy2GDS1KG	0.085	0.022	9.645
demoKnownSuperPop1KG	2.890	0.092	3.015
demoPCA1KG	0.013	0.007	0.020
demoPCASyntheticProfiles	3.028	0.072	3.125
demoPedigreeEx1	0.037	0.007	0.044
estimateAllelicFraction	0.195	0.010	1.828
generateGDS1KG	0.031	0.019	4.294
generateGDS1KGgenotypeFromSNPPileup	0.101	0.022	18.663
generateGDSRefSample	0.007	0.005	9.512
generateGDSSNPinfo	0.008	0.008	1.182
generateGDSgenotype	0.020	0.015	17.152
generateGeneBlock	0.001	0.001	0.002
generateMapSnvSel	0.004	0.003	2.425
generatePhase1KG2GDS	0.019	0.017	17.817
generatePhaseRef	0.026	0.017	0.050
getBlockIDs	0.004	0.003	0.006
getRef1KGPop	0.006	0.003	0.009
getRefSuperPop	0.005	0.003	0.007
getTableSNV	0.025	0.007	0.033
groupChr1KGSNV	0.066	0.079	55.085
identifyRelative	0.010	0.004	1.691
identifyRelativeRef	0.007	0.003	1.735
inferAncestry	0.020	0.002	0.021
inferAncestryGeneAware	0.019	0.002	0.022
matKNNSynthetic	0.050	0.006	0.055
pedSynthetic	0.050	0.005	0.055
prepPed1KG	0.006	0.002	0.809
prepPedSynthetic1KG	0.007	0.002	0.810
prepSynthetic	0.014	0.006	9.369
processBlockChr	0.003	0.001	0.810
profileAncestry	0.025	0.007	0.044
pruning1KGbyChr	0.004	0.003	0.804
pruningSample	0.048	0.010	4.999
readSNVFileGeneric	0.005	0.001	0.811
readSNVPileupFile	0.045	0.002	4.546
readSNVVCF	8.199	0.098	18.382
runExomeAncestry	0.022	0.003	0.027
runIBDKING	0.061	0.010	41.533
runLDPruning	0.039	0.016	0.058
runProfileAncestry	0.025	0.005	0.030
runRNAAncestry	0.023	0.004	0.027
runWrapperAncestry	0.023	0.003	0.027
selParaPCAUpQuartile	6.860	0.032	6.892
select1KGPop	0.005	0.001	0.007
select1KGPopForSynthetic	0.006	0.001	0.007
snpPositionDemo	0.003	0.001	0.004
snvListVCF	0.004	0.003	4.239
splitSelectByPop	0.002	0.000	0.002
syntheticGeno	0.037	0.007	12.672
tableBlockAF	0.029	0.003	0.032
testAlleleFractionChange	0.002	0.001	0.003
testEmptyBox	0.002	0.001	0.002
validateAdd1KG2SampleGDS	0.001	0.001	0.002
validateAddStudy1Kg	0.002	0.001	0.003
validateCharacterString	0.000	0.001	0.000
validateComputeAncestryFromSyntheticFile	0.002	0.002	0.004
validateComputeKNNRefSample	0.004	0.002	0.006
validateComputeKNNRefSynthetic	0.005	0.004	0.009
validateComputePCAMultiSynthetic	0.004	0.003	0.007
validateComputePCARefSample	0.002	0.001	0.002
validateComputePoolSyntheticAncestryGr	0.001	0.001	0.003
validateComputeSyntheticRoc	0.012	0.003	0.014
validateCreateAccuracyGraph	0.002	0.000	0.002
validateCreateStudy2GDS1KG	0.003	0.001	0.004
validateDataRefSynParameter	0.001	0.000	0.002
validateEstimateAllelicFraction	0.004	0.001	0.006
validateGDSClass	0.001	0.001	0.002
validateGenerateGDS1KG	0.001	0.001	0.002
validateLogical	0.000	0.000	0.001
validatePEDStudyParameter	0.001	0.001	0.002
validatePepSynthetic	0.002	0.001	0.003
validatePositiveIntegerVector	0	0	0
validatePrepPed1KG	0.001	0.001	0.002
validateProfileGDSExist	0.001	0.001	0.001
validatePruningSample	0.002	0.002	0.003
validateRunExomeOrRNAAncestry	0.006	0.002	0.007
validateSingleRatio	0	0	0
validateStudyDataFrameParameter	0.001	0.000	0.001
validateSyntheticGeno	0.002	0.001	1.008
wrapperAncestry	0.023	0.004	0.027