Pascal Belleau
| Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024) |
| git_url: https://git.bioconductor.org/packages/RAIDS |
| git_branch: RELEASE_3_20 |
| git_last_commit: 6b32a2c |
| git_last_commit_date: 2024-10-29 11:24:12 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-11-20 12:08 -0500 (Wed, 20 Nov 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
| 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 1654/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| RAIDS 1.4.0 (landing page) Pascal Belleau
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | ERROR | ERROR | skipped | skipped | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
|
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: RAIDS |
| Version: 1.4.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:RAIDS.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings RAIDS_1.4.0.tar.gz |
| StartedAt: 2024-11-20 11:24:50 -0000 (Wed, 20 Nov 2024) |
| EndedAt: 2024-11-20 11:33:34 -0000 (Wed, 20 Nov 2024) |
| EllapsedTime: 524.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: RAIDS.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:RAIDS.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings RAIDS_1.4.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/RAIDS.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* 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 loading without being on the library search path ... 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 10.576 0.209 10.722
readSNVVCF 8.216 0.071 8.307
selParaPCAUpQuartile 7.155 0.021 7.194
* 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
RAIDS.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL RAIDS ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.1/site-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 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
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
Loading required package: GENESIS
>
> ## Run all unit tests
> test_check("RAIDS")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 442 ]
>
> proc.time()
user system elapsed
43.999 1.300 45.038
RAIDS.Rcheck/RAIDS-Ex.timings
| name | user | system | elapsed | |
| add1KG2SampleGDS | 0.075 | 0.004 | 0.088 | |
| addBlockFromDetFile | 0.003 | 0.000 | 0.005 | |
| addBlockInGDSAnnot | 0.002 | 0.004 | 0.009 | |
| addGDS1KGLDBlock | 0.000 | 0.002 | 0.002 | |
| addGDSRef | 0.003 | 0.001 | 0.005 | |
| addGDSStudyPruning | 0.001 | 0.000 | 0.001 | |
| addGeneBlockGDSRefAnnot | 1.041 | 0.056 | 1.099 | |
| addGeneBlockRefAnnot | 0.002 | 0.000 | 0.002 | |
| addRef2GDS1KG | 0.006 | 0.000 | 0.005 | |
| addStudy1Kg | 0.013 | 0.000 | 0.013 | |
| addStudyGDSSample | 0.007 | 0.003 | 0.011 | |
| addUpdateLap | 0.002 | 0.000 | 0.003 | |
| addUpdateSegment | 0.001 | 0.001 | 0.002 | |
| appendGDSRefSample | 0.005 | 0.003 | 0.008 | |
| appendGDSSampleOnly | 0.001 | 0.000 | 0.002 | |
| appendGDSgenotype | 0.018 | 0.004 | 0.033 | |
| appendGDSgenotypeMat | 0.001 | 0.000 | 0.002 | |
| calcAFMLRNA | 0.005 | 0.000 | 0.006 | |
| computeAlleleFraction | 0.003 | 0.000 | 0.004 | |
| computeAllelicFractionDNA | 0.198 | 0.007 | 0.210 | |
| computeAllelicFractionRNA | 0.484 | 0.011 | 0.500 | |
| computeAllelicImbDNAChr | 0.008 | 0.001 | 0.008 | |
| computeAncestryFromSynthetic | 0.012 | 0.006 | 0.021 | |
| computeAncestryFromSyntheticFile | 10.576 | 0.209 | 10.722 | |
| computeKNNRefSample | 0.022 | 0.000 | 0.023 | |
| computeKNNRefSynthetic | 2.122 | 0.020 | 2.148 | |
| computeLOHBlocksDNAChr | 0.011 | 0.000 | 0.011 | |
| computePCAMultiSynthetic | 0.005 | 0.004 | 0.009 | |
| computePCARefRMMulti | 1.702 | 0.008 | 1.709 | |
| computePCARefSample | 2.142 | 0.004 | 2.064 | |
| computePoolSyntheticAncestryGr | 2.362 | 0.016 | 2.217 | |
| computeSyntheticConfMat | 0.014 | 0.004 | 0.018 | |
| computeSyntheticROC | 0.055 | 0.000 | 0.055 | |
| createAUROCGraph | 0.990 | 0.032 | 1.026 | |
| createAccuracyGraph | 1.015 | 0.004 | 1.022 | |
| createStudy2GDS1KG | 0.080 | 0.000 | 0.083 | |
| demoKnownSuperPop1KG | 2.243 | 0.008 | 2.256 | |
| demoPCA1KG | 0.002 | 0.008 | 0.011 | |
| demoPCASyntheticProfiles | 2.171 | 0.012 | 2.188 | |
| demoPedigreeEx1 | 0.019 | 0.004 | 0.023 | |
| estimateAllelicFraction | 0.148 | 0.000 | 0.148 | |
| generateGDS1KG | 0.017 | 0.000 | 0.018 | |
| generateGDS1KGgenotypeFromSNPPileup | 0.058 | 0.004 | 0.063 | |
| generateGDSRefSample | 0.006 | 0.000 | 0.006 | |
| generateGDSSNPinfo | 0.005 | 0.000 | 0.006 | |
| generateGDSgenotype | 0.017 | 0.000 | 0.017 | |
| generateGeneBlock | 0.001 | 0.000 | 0.001 | |
| generateMapSnvSel | 0.003 | 0.000 | 0.005 | |
| generatePhase1KG2GDS | 0.014 | 0.004 | 0.018 | |
| generatePhaseRef | 0.013 | 0.004 | 0.017 | |
| getBlockIDs | 0.003 | 0.000 | 0.003 | |
| getRef1KGPop | 0.004 | 0.000 | 0.005 | |
| getRefSuperPop | 0.003 | 0.000 | 0.003 | |
| getTableSNV | 0.016 | 0.000 | 0.015 | |
| groupChr1KGSNV | 0.056 | 0.016 | 0.074 | |
| identifyRelative | 0.011 | 0.000 | 0.010 | |
| identifyRelativeRef | 0.007 | 0.000 | 0.007 | |
| inferAncestry | 0.018 | 0.000 | 0.018 | |
| inferAncestryGeneAware | 0.019 | 0.000 | 0.019 | |
| matKNNSynthetic | 0.055 | 0.000 | 0.054 | |
| pedSynthetic | 0.055 | 0.000 | 0.055 | |
| prepPed1KG | 0.005 | 0.000 | 0.007 | |
| prepPedSynthetic1KG | 0.007 | 0.000 | 0.008 | |
| prepSynthetic | 0.014 | 0.000 | 0.015 | |
| processBlockChr | 0.000 | 0.003 | 0.003 | |
| profileAncestry | 0.020 | 0.004 | 0.024 | |
| pruning1KGbyChr | 0.005 | 0.000 | 0.005 | |
| pruningSample | 0.062 | 0.000 | 0.068 | |
| readSNVFileGeneric | 0.002 | 0.004 | 0.006 | |
| readSNVPileupFile | 0.043 | 0.000 | 0.045 | |
| readSNVVCF | 8.216 | 0.071 | 8.307 | |
| runExomeAncestry | 0.019 | 0.005 | 0.023 | |
| runIBDKING | 0.061 | 0.000 | 0.061 | |
| runLDPruning | 0.030 | 0.003 | 0.035 | |
| runProfileAncestry | 0.021 | 0.003 | 0.024 | |
| runRNAAncestry | 0.022 | 0.000 | 0.022 | |
| runWrapperAncestry | 0.019 | 0.003 | 0.022 | |
| selParaPCAUpQuartile | 7.155 | 0.021 | 7.194 | |
| select1KGPop | 0.002 | 0.004 | 0.006 | |
| select1KGPopForSynthetic | 0.006 | 0.000 | 0.006 | |
| snpPositionDemo | 0.000 | 0.004 | 0.004 | |
| snvListVCF | 0.004 | 0.000 | 0.005 | |
| splitSelectByPop | 0.001 | 0.000 | 0.002 | |
| syntheticGeno | 0.04 | 0.00 | 0.04 | |
| tableBlockAF | 0.029 | 0.000 | 0.029 | |
| testAlleleFractionChange | 0.002 | 0.000 | 0.002 | |
| testEmptyBox | 0.002 | 0.000 | 0.002 | |
| validateAdd1KG2SampleGDS | 0.002 | 0.000 | 0.002 | |
| validateAddStudy1Kg | 0.001 | 0.000 | 0.002 | |
| validateCharacterString | 0 | 0 | 0 | |
| validateComputeAncestryFromSyntheticFile | 0.001 | 0.000 | 0.002 | |
| validateComputeKNNRefSample | 0.003 | 0.002 | 0.005 | |
| validateComputeKNNRefSynthetic | 0.004 | 0.001 | 0.006 | |
| validateComputePCAMultiSynthetic | 0.004 | 0.000 | 0.004 | |
| validateComputePCARefSample | 0.002 | 0.000 | 0.002 | |
| validateComputePoolSyntheticAncestryGr | 0.002 | 0.000 | 0.002 | |
| validateComputeSyntheticRoc | 0.014 | 0.000 | 0.014 | |
| validateCreateAccuracyGraph | 0.001 | 0.000 | 0.001 | |
| validateCreateStudy2GDS1KG | 0.002 | 0.000 | 0.002 | |
| validateDataRefSynParameter | 0.000 | 0.000 | 0.001 | |
| validateEstimateAllelicFraction | 0.001 | 0.002 | 0.004 | |
| validateGDSClass | 0.001 | 0.000 | 0.002 | |
| validateGenerateGDS1KG | 0.001 | 0.000 | 0.002 | |
| validateLogical | 0 | 0 | 0 | |
| validatePEDStudyParameter | 0.000 | 0.000 | 0.001 | |
| validatePepSynthetic | 0.002 | 0.000 | 0.002 | |
| validatePositiveIntegerVector | 0 | 0 | 0 | |
| validatePrepPed1KG | 0.001 | 0.000 | 0.001 | |
| validateProfileGDSExist | 0.001 | 0.000 | 0.001 | |
| validatePruningSample | 0.001 | 0.000 | 0.001 | |
| validateRunExomeOrRNAAncestry | 0.005 | 0.000 | 0.005 | |
| validateSingleRatio | 0 | 0 | 0 | |
| validateStudyDataFrameParameter | 0.001 | 0.000 | 0.001 | |
| validateSyntheticGeno | 0.002 | 0.000 | 0.002 | |
| wrapperAncestry | 0.023 | 0.000 | 0.022 | |