Pascal Belleau
| Snapshot Date: 2024-04-16 09:00:03 -0400 (Tue, 16 Apr 2024) |
| git_url: https://git.bioconductor.org/packages/RAIDS |
| git_branch: RELEASE_3_18 |
| git_last_commit: 12ea1e7 |
| git_last_commit_date: 2023-10-24 11:51:36 -0400 (Tue, 24 Oct 2023) |
| Back to Mac ARM64 build report for BioC 3.18 |
|
This page was generated on 2024-04-18 11:32:16 -0400 (Thu, 18 Apr 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson1 | macOS 13.6.1 Ventura | arm64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4388 |
| 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 | ||||
| Package 1651/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| RAIDS 1.0.0 (landing page) Pascal Belleau
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | OK | OK | OK | OK | | |||||||
|
To the developers/maintainers of the RAIDS package: - 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. |
| Package: RAIDS |
| Version: 1.0.0 |
| 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_1.0.0.tar.gz |
| StartedAt: 2024-04-18 00:20:15 -0400 (Thu, 18 Apr 2024) |
| EndedAt: 2024-04-18 00:28:12 -0400 (Thu, 18 Apr 2024) |
| EllapsedTime: 476.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: RAIDS.Rcheck |
| Warnings: 0 |
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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-mac-arm64/meat/RAIDS.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-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 Ventura 13.6.1
* 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 6.750 0.159 6.919
selParaPCAUpQuartile 5.193 0.051 5.259
* 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
RAIDS.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL RAIDS ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/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)
RAIDS.Rcheck/tests/testthat.Rout
R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-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
Loading required package: GENESIS
>
> ## Run all unit tests
> test_check("RAIDS")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 432 ]
>
> proc.time()
user system elapsed
33.071 1.780 35.020
RAIDS.Rcheck/RAIDS-Ex.timings
| name | user | system | elapsed | |
| add1KG2SampleGDS | 0.055 | 0.017 | 0.084 | |
| addBlockInGDSAnnot | 0.006 | 0.003 | 0.013 | |
| addGDSRef | 0.004 | 0.002 | 0.006 | |
| addGDSStudyPruning | 0.001 | 0.001 | 0.002 | |
| addGeneBlockGDSRefAnnot | 1.259 | 0.097 | 1.382 | |
| addRef2GDS1KG | 0.003 | 0.003 | 0.006 | |
| addStudy1Kg | 0.006 | 0.005 | 0.013 | |
| addStudyGDSSample | 0.003 | 0.002 | 0.007 | |
| addUpdateLap | 0.000 | 0.001 | 0.002 | |
| addUpdateSegment | 0.000 | 0.001 | 0.001 | |
| appendGDSRefSample | 0.003 | 0.002 | 0.005 | |
| appendGDSSampleOnly | 0.001 | 0.000 | 0.001 | |
| appendGDSgenotype | 0.009 | 0.007 | 0.021 | |
| appendGDSgenotypeMat | 0.000 | 0.001 | 0.002 | |
| calcAFMLRNA | 0.003 | 0.002 | 0.005 | |
| computeAlleleFraction | 0.001 | 0.000 | 0.001 | |
| computeAllelicFractionDNA | 0.099 | 0.007 | 0.107 | |
| computeAllelicFractionRNA | 0.208 | 0.010 | 0.219 | |
| computeAllelicImbDNAChr | 0.009 | 0.002 | 0.010 | |
| computeAncestryFromSyntheticFile | 6.750 | 0.159 | 6.919 | |
| computeKNNRefSample | 0.018 | 0.004 | 0.022 | |
| computeKNNRefSynthetic | 1.378 | 0.105 | 1.485 | |
| computeLOHBlocksDNAChr | 0.011 | 0.002 | 0.013 | |
| computePCAMultiSynthetic | 0.010 | 0.006 | 0.015 | |
| computePCARefRMMulti | 0.131 | 0.006 | 0.136 | |
| computePCARefSample | 0.147 | 0.004 | 0.152 | |
| computePoolSyntheticAncestryGr | 0.408 | 0.022 | 0.431 | |
| computeSyntheticConfMat | 0.019 | 0.004 | 0.024 | |
| computeSyntheticROC | 0.045 | 0.006 | 0.051 | |
| createStudy2GDS1KG | 0.071 | 0.013 | 0.088 | |
| demoKnownSuperPop1KG | 1.371 | 0.069 | 1.440 | |
| demoPCA1KG | 0.009 | 0.006 | 0.014 | |
| demoPCASyntheticProfiles | 1.255 | 0.047 | 1.306 | |
| demoPedigreeEx1 | 0.007 | 0.002 | 0.009 | |
| estimateAllelicFraction | 0.031 | 0.003 | 0.035 | |
| generateGDS1KG | 0.005 | 0.005 | 0.012 | |
| generateGDS1KGgenotypeFromSNPPileup | 0.024 | 0.010 | 0.037 | |
| generateGDSRefSample | 0.002 | 0.001 | 0.004 | |
| generateGDSSNPinfo | 0.002 | 0.002 | 0.004 | |
| generateGDSgenotype | 0.005 | 0.004 | 0.010 | |
| generateGeneBlock | 0.001 | 0.000 | 0.001 | |
| generateMapSnvSel | 0.002 | 0.002 | 0.004 | |
| generatePhase1KG2GDS | 0.007 | 0.004 | 0.013 | |
| getBlockIDs | 0.001 | 0.000 | 0.001 | |
| getRef1KGPop | 0.001 | 0.001 | 0.001 | |
| getTableSNV | 0.005 | 0.001 | 0.006 | |
| groupChr1KGSNV | 0.024 | 0.027 | 0.053 | |
| identifyRelative | 0.007 | 0.002 | 0.009 | |
| matKNNSynthetic | 0.018 | 0.003 | 0.022 | |
| pedSynthetic | 0.017 | 0.002 | 0.019 | |
| prepPed1KG | 0.002 | 0.001 | 0.003 | |
| prepPedSynthetic1KG | 0.002 | 0.001 | 0.003 | |
| prepSynthetic | 0.004 | 0.002 | 0.006 | |
| pruning1KGbyChr | 0.002 | 0.001 | 0.003 | |
| pruningSample | 0.017 | 0.006 | 0.023 | |
| readSNVFileGeneric | 0.002 | 0.001 | 0.002 | |
| readSNVPileupFile | 0.018 | 0.001 | 0.019 | |
| readSNVVCF | 4.243 | 0.045 | 4.320 | |
| runExomeAncestry | 0.015 | 0.004 | 0.019 | |
| runIBDKING | 0.063 | 0.005 | 0.072 | |
| runLDPruning | 0.029 | 0.009 | 0.040 | |
| runProfileAncestry | 0.020 | 0.005 | 0.025 | |
| runRNAAncestry | 0.015 | 0.004 | 0.020 | |
| runWrapperAncestry | 0.018 | 0.004 | 0.026 | |
| selParaPCAUpQuartile | 5.193 | 0.051 | 5.259 | |
| select1KGPop | 0.004 | 0.001 | 0.006 | |
| snpPositionDemo | 0.002 | 0.002 | 0.005 | |
| snvListVCF | 0.004 | 0.003 | 0.007 | |
| splitSelectByPop | 0.001 | 0.000 | 0.001 | |
| syntheticGeno | 0.034 | 0.006 | 0.042 | |
| tableBlockAF | 0.021 | 0.002 | 0.024 | |
| testAlleleFractionChange | 0.002 | 0.000 | 0.002 | |
| testEmptyBox | 0.001 | 0.000 | 0.002 | |
| validateAdd1KG2SampleGDS | 0.001 | 0.001 | 0.002 | |
| validateAddStudy1Kg | 0.001 | 0.001 | 0.003 | |
| validateCharacterString | 0 | 0 | 0 | |
| validateComputeAncestryFromSyntheticFile | 0.002 | 0.001 | 0.004 | |
| validateComputeKNNRefSample | 0.005 | 0.004 | 0.010 | |
| validateComputeKNNRefSynthetic | 0.006 | 0.004 | 0.010 | |
| validateComputePCAMultiSynthetic | 0.005 | 0.003 | 0.008 | |
| validateComputePCARefSample | 0.002 | 0.000 | 0.003 | |
| validateComputePoolSyntheticAncestryGr | 0.002 | 0.001 | 0.003 | |
| validateComputeSyntheticRoc | 0.016 | 0.003 | 0.019 | |
| validateCreateStudy2GDS1KG | 0.003 | 0.000 | 0.004 | |
| validateDataRefSynParameter | 0.001 | 0.000 | 0.001 | |
| validateEstimateAllelicFraction | 0.005 | 0.002 | 0.006 | |
| validateGDSClass | 0.002 | 0.001 | 0.002 | |
| validateGenerateGDS1KG | 0.002 | 0.000 | 0.002 | |
| validateLogical | 0 | 0 | 0 | |
| validatePEDStudyParameter | 0.000 | 0.000 | 0.001 | |
| validatePepSynthetic | 0.002 | 0.000 | 0.002 | |
| validatePositiveIntegerVector | 0.000 | 0.001 | 0.000 | |
| validatePrepPed1KG | 0.001 | 0.000 | 0.001 | |
| validateProfileGDSExist | 0.001 | 0.000 | 0.001 | |
| validatePruningSample | 0.002 | 0.001 | 0.003 | |
| validateRunExomeOrRNAAncestry | 0.006 | 0.001 | 0.007 | |
| validateSingleRatio | 0.001 | 0.000 | 0.000 | |
| validateStudyDataFrameParameter | 0.000 | 0.001 | 0.000 | |
| validateSyntheticGeno | 0.002 | 0.001 | 0.004 | |