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This page was generated on 2024-05-04 11:41:13 -0400 (Sat, 04 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4753
palomino3Windows Server 2022 Datacenterx644.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" 4486
lconwaymacOS 12.7.1 Montereyx86_644.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" 4519
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4479
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 2171/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
tLOH 1.12.0  (landing page)
Michelle Webb
Snapshot Date: 2024-05-03 14:00:19 -0400 (Fri, 03 May 2024)
git_url: https://git.bioconductor.org/packages/tLOH
git_branch: RELEASE_3_19
git_last_commit: 677831a
git_last_commit_date: 2024-04-30 11:33:45 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for tLOH on kunpeng2


To the developers/maintainers of the tLOH package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/tLOH.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.

raw results


Summary

Package: tLOH
Version: 1.12.0
Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:tLOH.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings tLOH_1.12.0.tar.gz
StartedAt: 2024-05-04 12:49:05 -0000 (Sat, 04 May 2024)
EndedAt: 2024-05-04 13:03:12 -0000 (Sat, 04 May 2024)
EllapsedTime: 846.6 seconds
RetCode: 0
Status:   OK  
CheckDir: tLOH.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:tLOH.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings tLOH_1.12.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/tLOH.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* 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 ‘tLOH/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘tLOH’ version ‘1.12.0’
* 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 ‘tLOH’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... NOTE
Problems with news in ‘NEWS.md’:
No news entries found.
* 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
hiddenMarkovAnalysis 94.988  0.706 103.147
regionAnalysis       70.609  0.368  71.118
runHMM_2             65.464  0.244  65.829
runHMM_3             63.870  0.179  64.177
runHMM_1             37.817  0.096  37.983
splitByChromosome    35.639  0.164  35.870
prepareHMMdataframes 35.628  0.048  35.745
tLOHCalcUpdate       34.753  0.024  34.840
alleleFrequencyPlot  10.315  0.331  15.090
aggregateCHRPlot      9.128  0.453   9.616
tLOHCalc              6.554  0.044   6.610
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/tLOH.Rcheck/00check.log’
for details.


Installation output

tLOH.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL tLOH
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library’
* installing *source* package ‘tLOH’ ...
** 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 (tLOH)

Tests output


Example timings

tLOH.Rcheck/tLOH-Ex.timings

nameusersystemelapsed
aggregateCHRPlot9.1280.4539.616
alleleFrequencyPlot10.315 0.33115.090
documentErrorRegions0.0010.0010.003
hiddenMarkovAnalysis 94.988 0.706103.147
humanGBMsampleAC0.0410.0000.041
initialStartProbabilities0.0010.0000.001
marginalLikelihoodM10.0040.0000.003
marginalLikelihoodM20.0020.0000.002
marginalM1Calc000
marginalM2CalcBHET0.0000.0020.002
marginalM2CalcBLOH0.0010.0000.002
modePeakCalc0.0010.0000.001
prepareHMMdataframes35.628 0.04835.745
regionAnalysis70.609 0.36871.118
regionFinalize0.0010.0000.000
removeOutlierFromCalc0.0010.0000.001
runHMM_137.817 0.09637.983
runHMM_265.464 0.24465.829
runHMM_363.870 0.17964.177
splitByChromosome35.639 0.16435.870
summarizeRegions1000
summarizeRegions2000
tLOHCalc6.5540.0446.610
tLOHCalcUpdate34.753 0.02434.840
tLOHDataImport000