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This page was generated on 2024-06-14 14:38 -0400 (Fri, 14 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4757
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4491
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: 2024-06-12 14:00 -0400 (Wed, 12 Jun 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


CHECK results for tLOH on palomino3

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: 1.12.0
Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:tLOH.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings tLOH_1.12.0.tar.gz
StartedAt: 2024-06-13 13:09:43 -0400 (Thu, 13 Jun 2024)
EndedAt: 2024-06-13 13:28:54 -0400 (Thu, 13 Jun 2024)
EllapsedTime: 1150.5 seconds
RetCode: 0
Status:   OK  
CheckDir: tLOH.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:tLOH.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings tLOH_1.12.0.tar.gz
###
##############################################################################
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* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/tLOH.Rcheck'
* using R version 4.4.0 (2024-04-24 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* 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 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 78.12   4.97   83.14
regionAnalysis       57.53   1.54   59.06
runHMM_3             55.70   1.69   57.38
runHMM_2             52.39   1.61   53.98
runHMM_1             32.74   0.69   33.42
tLOHCalcUpdate       30.51   0.69   31.20
prepareHMMdataframes 30.40   0.60   31.00
splitByChromosome    29.63   0.48   30.11
aggregateCHRPlot      8.78   0.43    9.23
alleleFrequencyPlot   8.41   0.20    8.61
tLOHCalc              5.92   0.14    6.06
* 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
  'F:/biocbuild/bbs-3.19-bioc/meat/tLOH.Rcheck/00check.log'
for details.


Installation output

tLOH.Rcheck/00install.out

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###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL tLOH
###
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* installing to library 'F:/biocbuild/bbs-3.19-bioc/R/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
aggregateCHRPlot8.780.439.23
alleleFrequencyPlot8.410.208.61
documentErrorRegions000
hiddenMarkovAnalysis78.12 4.9783.14
humanGBMsampleAC0.040.010.04
initialStartProbabilities000
marginalLikelihoodM1000
marginalLikelihoodM2000
marginalM1Calc000
marginalM2CalcBHET000
marginalM2CalcBLOH000
modePeakCalc000
prepareHMMdataframes30.4 0.631.0
regionAnalysis57.53 1.5459.06
regionFinalize000
removeOutlierFromCalc000
runHMM_132.74 0.6933.42
runHMM_252.39 1.6153.98
runHMM_355.70 1.6957.38
splitByChromosome29.63 0.4830.11
summarizeRegions1000
summarizeRegions2000
tLOHCalc5.920.146.06
tLOHCalcUpdate30.51 0.6931.20
tLOHDataImport000