Pascal Belleau
| Snapshot Date: 2023-11-01 14:05:06 -0400 (Wed, 01 Nov 2023) |
| 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 Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2023-11-02 11:41:07 -0400 (Thu, 02 Nov 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4729 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4463 |
| lconway | macOS 12.6.5 Monterey | x86_64 | 4.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" | 4478 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4464 |
| 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
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.6.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
| 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: 1.0.0 |
| Command: /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:RAIDS.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings RAIDS_1.0.0.tar.gz |
| StartedAt: 2023-11-02 13:27:48 -0000 (Thu, 02 Nov 2023) |
| EndedAt: 2023-11-02 13:36:36 -0000 (Thu, 02 Nov 2023) |
| EllapsedTime: 527.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: RAIDS.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:RAIDS.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings RAIDS_1.0.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/RAIDS.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (GCC) 10.3.1
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 ‘1.0.0’
* 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 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 9.339 0.220 9.581
readSNVVCF 8.207 0.119 8.342
selParaPCAUpQuartile 7.447 0.008 7.470
* 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: ### ### /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL RAIDS ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.1/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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (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
46.165 1.197 47.460
RAIDS.Rcheck/RAIDS-Ex.timings
| name | user | system | elapsed | |
| add1KG2SampleGDS | 0.069 | 0.012 | 0.110 | |
| addBlockInGDSAnnot | 0.006 | 0.000 | 0.010 | |
| addGDSRef | 0.004 | 0.000 | 0.005 | |
| addGDSStudyPruning | 0.002 | 0.000 | 0.002 | |
| addGeneBlockGDSRefAnnot | 0.989 | 0.092 | 1.084 | |
| addRef2GDS1KG | 0.006 | 0.000 | 0.006 | |
| addStudy1Kg | 0.012 | 0.000 | 0.014 | |
| addStudyGDSSample | 0.007 | 0.003 | 0.011 | |
| addUpdateLap | 0.000 | 0.001 | 0.002 | |
| addUpdateSegment | 0.000 | 0.001 | 0.002 | |
| appendGDSRefSample | 0.008 | 0.000 | 0.009 | |
| appendGDSSampleOnly | 0.001 | 0.000 | 0.003 | |
| appendGDSgenotype | 0.018 | 0.003 | 0.030 | |
| appendGDSgenotypeMat | 0.002 | 0.000 | 0.002 | |
| calcAFMLRNA | 0.005 | 0.000 | 0.006 | |
| computeAlleleFraction | 0.003 | 0.000 | 0.004 | |
| computeAllelicFractionDNA | 0.207 | 0.012 | 0.449 | |
| computeAllelicFractionRNA | 0.380 | 0.004 | 0.387 | |
| computeAllelicImbDNAChr | 0.008 | 0.000 | 0.009 | |
| computeAncestryFromSyntheticFile | 9.339 | 0.220 | 9.581 | |
| computeKNNRefSample | 0.022 | 0.000 | 0.023 | |
| computeKNNRefSynthetic | 3.586 | 0.048 | 3.643 | |
| computeLOHBlocksDNAChr | 0.011 | 0.000 | 0.012 | |
| computePCAMultiSynthetic | 0.008 | 0.000 | 0.009 | |
| computePCARefRMMulti | 1.580 | 0.012 | 1.596 | |
| computePCARefSample | 1.831 | 0.000 | 1.836 | |
| computePoolSyntheticAncestryGr | 2.021 | 0.007 | 2.034 | |
| computeSyntheticConfMat | 0.014 | 0.004 | 0.018 | |
| computeSyntheticROC | 0.079 | 0.000 | 0.079 | |
| createStudy2GDS1KG | 0.075 | 0.000 | 0.076 | |
| demoKnownSuperPop1KG | 2.177 | 0.001 | 2.181 | |
| demoPCA1KG | 0.009 | 0.000 | 0.009 | |
| demoPCASyntheticProfiles | 2.249 | 0.007 | 2.261 | |
| demoPedigreeEx1 | 0.023 | 0.000 | 0.023 | |
| estimateAllelicFraction | 0.120 | 0.004 | 0.124 | |
| generateGDS1KG | 0.017 | 0.000 | 0.018 | |
| generateGDS1KGgenotypeFromSNPPileup | 0.059 | 0.000 | 0.060 | |
| generateGDSRefSample | 0.001 | 0.004 | 0.006 | |
| generateGDSSNPinfo | 0.001 | 0.004 | 0.006 | |
| generateGDSgenotype | 0.018 | 0.000 | 0.019 | |
| generateGeneBlock | 0.000 | 0.001 | 0.001 | |
| generateMapSnvSel | 0.000 | 0.004 | 0.004 | |
| generatePhase1KG2GDS | 0.013 | 0.005 | 0.019 | |
| getBlockIDs | 0.003 | 0.000 | 0.003 | |
| getRef1KGPop | 0.005 | 0.000 | 0.005 | |
| getTableSNV | 0.016 | 0.001 | 0.016 | |
| groupChr1KGSNV | 0.068 | 0.008 | 0.079 | |
| identifyRelative | 0.014 | 0.000 | 0.014 | |
| matKNNSynthetic | 0.054 | 0.000 | 0.054 | |
| pedSynthetic | 0.052 | 0.002 | 0.053 | |
| prepPed1KG | 0.004 | 0.001 | 0.006 | |
| prepPedSynthetic1KG | 0.006 | 0.001 | 0.007 | |
| prepSynthetic | 0.014 | 0.000 | 0.014 | |
| pruning1KGbyChr | 0.005 | 0.000 | 0.004 | |
| pruningSample | 0.047 | 0.011 | 0.059 | |
| readSNVFileGeneric | 0.005 | 0.000 | 0.005 | |
| readSNVPileupFile | 0.042 | 0.001 | 0.043 | |
| readSNVVCF | 8.207 | 0.119 | 8.342 | |
| runExomeAncestry | 0.023 | 0.000 | 0.024 | |
| runIBDKING | 0.063 | 0.000 | 0.068 | |
| runLDPruning | 0.031 | 0.000 | 0.032 | |
| runProfileAncestry | 0.025 | 0.000 | 0.025 | |
| runRNAAncestry | 0.024 | 0.000 | 0.024 | |
| runWrapperAncestry | 0.019 | 0.004 | 0.023 | |
| selParaPCAUpQuartile | 7.447 | 0.008 | 7.470 | |
| select1KGPop | 0.006 | 0.000 | 0.007 | |
| snpPositionDemo | 0.003 | 0.000 | 0.004 | |
| snvListVCF | 0.005 | 0.000 | 0.005 | |
| splitSelectByPop | 0.001 | 0.002 | 0.001 | |
| syntheticGeno | 0.042 | 0.002 | 0.045 | |
| tableBlockAF | 0.032 | 0.000 | 0.033 | |
| testAlleleFractionChange | 0.002 | 0.000 | 0.003 | |
| testEmptyBox | 0.002 | 0.000 | 0.002 | |
| validateAdd1KG2SampleGDS | 0.002 | 0.000 | 0.001 | |
| validateAddStudy1Kg | 0.002 | 0.000 | 0.002 | |
| validateCharacterString | 0 | 0 | 0 | |
| validateComputeAncestryFromSyntheticFile | 0.001 | 0.001 | 0.002 | |
| validateComputeKNNRefSample | 0.002 | 0.002 | 0.004 | |
| validateComputeKNNRefSynthetic | 0.006 | 0.000 | 0.005 | |
| validateComputePCAMultiSynthetic | 0.004 | 0.001 | 0.004 | |
| validateComputePCARefSample | 0.000 | 0.001 | 0.001 | |
| validateComputePoolSyntheticAncestryGr | 0.001 | 0.000 | 0.002 | |
| validateComputeSyntheticRoc | 0.014 | 0.000 | 0.015 | |
| validateCreateStudy2GDS1KG | 0.003 | 0.000 | 0.003 | |
| validateDataRefSynParameter | 0.001 | 0.000 | 0.001 | |
| validateEstimateAllelicFraction | 0.001 | 0.003 | 0.004 | |
| validateGDSClass | 0.001 | 0.000 | 0.002 | |
| validateGenerateGDS1KG | 0.001 | 0.000 | 0.001 | |
| validateLogical | 0 | 0 | 0 | |
| validatePEDStudyParameter | 0.001 | 0.000 | 0.001 | |
| validatePepSynthetic | 0.001 | 0.000 | 0.002 | |
| validatePositiveIntegerVector | 0 | 0 | 0 | |
| validatePrepPed1KG | 0.001 | 0.000 | 0.002 | |
| validateProfileGDSExist | 0.001 | 0.000 | 0.001 | |
| validatePruningSample | 0.001 | 0.000 | 0.002 | |
| validateRunExomeOrRNAAncestry | 0.006 | 0.000 | 0.005 | |
| validateSingleRatio | 0.001 | 0.000 | 0.000 | |
| validateStudyDataFrameParameter | 0.001 | 0.000 | 0.000 | |
| validateSyntheticGeno | 0.000 | 0.002 | 0.002 | |