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This page was generated on 2022-12-01 11:11:09 -0500 (Thu, 01 Dec 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2022-10-25 r83175) -- "Unsuffered Consequences" 4462
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2022-10-11 r83083 ucrt) -- "Unsuffered Consequences" 4203
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-11-13 r83342) -- "Unsuffered Consequences" 4231
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

CHECK results for tLOH on merida1


To the developers/maintainers of the tLOH package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 2032/2154HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
tLOH 1.7.0  (landing page)
Michelle Webb
Snapshot Date: 2022-11-30 14:00:15 -0500 (Wed, 30 Nov 2022)
git_url: https://git.bioconductor.org/packages/tLOH
git_branch: master
git_last_commit: 73bffad
git_last_commit_date: 2022-11-01 11:24:47 -0500 (Tue, 01 Nov 2022)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'VariantAnnotation' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  NO, package depends on 'VariantAnnotation' which is not available

Summary

Package: tLOH
Version: 1.7.0
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_1.7.0.tar.gz
StartedAt: 2022-12-01 07:04:56 -0500 (Thu, 01 Dec 2022)
EndedAt: 2022-12-01 07:33:20 -0500 (Thu, 01 Dec 2022)
EllapsedTime: 1704.7 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_1.7.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/tLOH.Rcheck’
* using R Under development (unstable) (2022-11-13 r83342)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘tLOH/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘tLOH’ version ‘1.7.0’
* 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 ... OK
* 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 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 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 143.762  1.945 214.746
regionAnalysis       108.511  1.063 149.183
runHMM_2             103.313  1.078 146.225
runHMM_3             101.661  1.174 143.775
runHMM_1              62.019  0.633  88.565
prepareHMMdataframes  58.024  0.664  78.271
tLOHCalcUpdate        54.626  0.463  78.677
splitByChromosome     54.388  0.434  76.992
aggregateCHRPlot      16.726  0.357  34.574
alleleFrequencyPlot   14.860  0.253  23.478
tLOHCalc              11.957  0.098  16.978
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.17-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
###
##############################################################################
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3/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
aggregateCHRPlot16.726 0.35734.574
alleleFrequencyPlot14.860 0.25323.478
documentErrorRegions0.0030.0010.004
hiddenMarkovAnalysis143.762 1.945214.746
humanGBMsampleAC0.0680.0020.107
initialStartProbabilities0.0010.0010.003
marginalLikelihoodM10.0050.0000.004
marginalLikelihoodM20.0040.0000.004
marginalM1Calc0.0010.0000.000
marginalM2CalcBHET0.0020.0000.003
marginalM2CalcBLOH0.0020.0000.003
modePeakCalc0.0020.0000.002
prepareHMMdataframes58.024 0.66478.271
regionAnalysis108.511 1.063149.183
regionFinalize0.0000.0000.001
removeOutlierFromCalc0.0010.0010.001
runHMM_162.019 0.63388.565
runHMM_2103.313 1.078146.225
runHMM_3101.661 1.174143.775
splitByChromosome54.388 0.43476.992
summarizeRegions10.0010.0000.000
summarizeRegions20.0000.0000.007
tLOHCalc11.957 0.09816.978
tLOHCalcUpdate54.626 0.46378.677
tLOHDataImport000