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This page was generated on 2025-01-28 11:45 -0500 (Tue, 28 Jan 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" 4659
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" 4454
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences" 4465
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" 4419
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4409
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 2152/2286HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
tLOH 1.15.0  (landing page)
Michelle Webb
Snapshot Date: 2025-01-27 13:40 -0500 (Mon, 27 Jan 2025)
git_url: https://git.bioconductor.org/packages/tLOH
git_branch: devel
git_last_commit: fba6f99
git_last_commit_date: 2024-10-29 10:59:07 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows 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  NO, package depends on 'VariantAnnotation' which is only available as a source package that needs compilation
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  NO, package depends on 'VariantAnnotation' which is only available as a source package that needs compilation
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    NA  


CHECK results for tLOH on lconway

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: 1.15.0
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_1.15.0.tar.gz
StartedAt: 2025-01-27 23:25:50 -0500 (Mon, 27 Jan 2025)
EndedAt: 2025-01-27 23:36:31 -0500 (Mon, 27 Jan 2025)
EllapsedTime: 641.1 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_1.15.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/tLOH.Rcheck’
* using R Under development (unstable) (2025-01-22 r87618)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘tLOH/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘tLOH’ version ‘1.15.0’
* 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 67.276  2.050  75.536
regionAnalysis       50.546  0.878  57.341
runHMM_3             43.243  0.954  44.354
runHMM_2             42.494  0.874  43.499
prepareHMMdataframes 27.188  0.416  33.234
runHMM_1             26.929  0.424  27.416
splitByChromosome    24.220  0.495  24.837
tLOHCalcUpdate       23.013  0.390  23.458
aggregateCHRPlot      7.097  0.197   7.314
alleleFrequencyPlot   6.800  0.170   6.985
* 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-3.21-bioc/meat/tLOH.Rcheck/00check.log’
for details.


Installation output

tLOH.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘tLOH’ ...
** this is package ‘tLOH’ version ‘1.15.0’
** 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
aggregateCHRPlot7.0970.1977.314
alleleFrequencyPlot6.8000.1706.985
documentErrorRegions0.0020.0010.003
hiddenMarkovAnalysis67.276 2.05075.536
humanGBMsampleAC0.0460.0030.074
initialStartProbabilities0.0010.0020.003
marginalLikelihoodM10.0030.0010.003
marginalLikelihoodM20.0020.0010.002
marginalM1Calc0.0000.0010.001
marginalM2CalcBHET0.0020.0010.002
marginalM2CalcBLOH0.0020.0000.003
modePeakCalc0.0010.0000.002
prepareHMMdataframes27.188 0.41633.234
regionAnalysis50.546 0.87857.341
regionFinalize0.0000.0010.000
removeOutlierFromCalc0.0010.0000.001
runHMM_126.929 0.42427.416
runHMM_242.494 0.87443.499
runHMM_343.243 0.95444.354
splitByChromosome24.220 0.49524.837
summarizeRegions10.0000.0000.001
summarizeRegions20.0000.0010.000
tLOHCalc4.2240.1024.342
tLOHCalcUpdate23.013 0.39023.458
tLOHDataImport0.0000.0010.000