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This page was generated on 2024-03-28 11:40:11 -0400 (Thu, 28 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4708
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" 4446
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4471
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" 4426
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 2143/2270HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
tLOH 1.11.0  (landing page)
Michelle Webb
Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024)
git_url: https://git.bioconductor.org/packages/tLOH
git_branch: devel
git_last_commit: 3e51bfc
git_last_commit_date: 2023-10-24 11:32:36 -0400 (Tue, 24 Oct 2023)
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  

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: 1.11.0
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_1.11.0.tar.gz
StartedAt: 2024-03-28 00:36:39 -0400 (Thu, 28 Mar 2024)
EndedAt: 2024-03-28 00:48:59 -0400 (Thu, 28 Mar 2024)
EllapsedTime: 739.8 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_1.11.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/tLOH.Rcheck’
* using R Under development (unstable) (2024-03-18 r86148)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘tLOH/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘tLOH’ version ‘1.11.0’
* 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 77.164  2.347  88.462
regionAnalysis       57.052  1.374  63.902
runHMM_3             51.279  1.280  53.131
runHMM_2             48.070  1.224  49.814
prepareHMMdataframes 30.365  0.668  38.810
runHMM_1             29.715  0.673  30.682
splitByChromosome    28.467  0.677  29.495
tLOHCalcUpdate       26.576  0.605  27.415
aggregateCHRPlot      8.120  0.212   8.391
alleleFrequencyPlot   7.982  0.246   8.307
tLOHCalc              5.272  0.106   5.434
* 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-3.19-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/4.4-x86_64/Resources/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
aggregateCHRPlot8.1200.2128.391
alleleFrequencyPlot7.9820.2468.307
documentErrorRegions0.0020.0010.002
hiddenMarkovAnalysis77.164 2.34788.462
humanGBMsampleAC0.0520.0020.100
initialStartProbabilities0.0010.0010.003
marginalLikelihoodM10.0030.0000.003
marginalLikelihoodM20.0020.0000.003
marginalM1Calc000
marginalM2CalcBHET0.0020.0000.002
marginalM2CalcBLOH0.0020.0000.007
modePeakCalc0.0010.0000.001
prepareHMMdataframes30.365 0.66838.810
regionAnalysis57.052 1.37463.902
regionFinalize000
removeOutlierFromCalc0.0010.0000.001
runHMM_129.715 0.67330.682
runHMM_248.070 1.22449.814
runHMM_351.279 1.28053.131
splitByChromosome28.467 0.67729.495
summarizeRegions10.0000.0000.001
summarizeRegions20.0000.0000.001
tLOHCalc5.2720.1065.434
tLOHCalcUpdate26.576 0.60527.415
tLOHDataImport0.0000.0000.001