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This page was generated on 2025-09-25 12:07 -0400 (Thu, 25 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4831
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4618
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4562
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4560
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 2200/2334HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
tLOH 1.17.0  (landing page)
Michelle Webb
Snapshot Date: 2025-09-24 13:45 -0400 (Wed, 24 Sep 2025)
git_url: https://git.bioconductor.org/packages/tLOH
git_branch: devel
git_last_commit: 79f1f5c
git_last_commit_date: 2025-04-15 12:28:29 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  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
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for tLOH on kjohnson3

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.

raw results


Summary

Package: tLOH
Version: 1.17.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:tLOH.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings tLOH_1.17.0.tar.gz
StartedAt: 2025-09-24 22:09:41 -0400 (Wed, 24 Sep 2025)
EndedAt: 2025-09-24 22:13:39 -0400 (Wed, 24 Sep 2025)
EllapsedTime: 237.9 seconds
RetCode: 0
Status:   OK  
CheckDir: tLOH.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:tLOH.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings tLOH_1.17.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/tLOH.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘tLOH/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘tLOH’ version ‘1.17.0’
* 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 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 21.243  1.111  22.398
regionAnalysis       15.490  0.678  16.218
runHMM_3             15.504  0.566  17.945
runHMM_2             15.222  0.576  19.450
prepareHMMdataframes  9.449  0.359   9.814
runHMM_1              9.280  0.286   9.572
splitByChromosome     9.060  0.318   9.392
tLOHCalcUpdate        9.043  0.298   9.345
* 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
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/tLOH.Rcheck/00check.log’
for details.


Installation output

tLOH.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘tLOH’ ...
** this is package ‘tLOH’ version ‘1.17.0’
** 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
aggregateCHRPlot2.1710.0992.277
alleleFrequencyPlot2.5770.1082.696
documentErrorRegions0.0010.0000.001
hiddenMarkovAnalysis21.243 1.11122.398
humanGBMsampleAC0.0180.0010.019
initialStartProbabilities0.0010.0010.001
marginalLikelihoodM10.0000.0000.001
marginalLikelihoodM20.0000.0000.001
marginalM1Calc000
marginalM2CalcBHET0.0010.0000.001
marginalM2CalcBLOH000
modePeakCalc0.0000.0000.001
prepareHMMdataframes9.4490.3599.814
regionAnalysis15.490 0.67816.218
regionFinalize000
removeOutlierFromCalc0.0000.0000.001
runHMM_19.2800.2869.572
runHMM_215.222 0.57619.450
runHMM_315.504 0.56617.945
splitByChromosome9.0600.3189.392
summarizeRegions1000
summarizeRegions2000
tLOHCalc1.6190.0871.708
tLOHCalcUpdate9.0430.2989.345
tLOHDataImport000