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This page was generated on 2023-01-02 09:00:54 -0500 (Mon, 02 Jan 2023).

HostnameOSArch (*)R versionInstalled pkgs
palomino5Windows Server 2022 Datacenterx64R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" 4165
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 palomino5


To the developers/maintainers of the tLOH package:
Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 2036/2158HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
tLOH 1.7.0  (landing page)
Michelle Webb
Snapshot Date: 2022-12-28 11:00:06 -0500 (Wed, 28 Dec 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)
palomino5Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  

Summary

Package: tLOH
Version: 1.7.0
Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:tLOH.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings tLOH_1.7.0.tar.gz
StartedAt: 2022-12-29 04:13:19 -0500 (Thu, 29 Dec 2022)
EndedAt: 2022-12-29 04:22:53 -0500 (Thu, 29 Dec 2022)
EllapsedTime: 573.8 seconds
RetCode: 0
Status:   OK  
CheckDir: tLOH.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:tLOH.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings tLOH_1.7.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/tLOH.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 10.4.0
    GNU Fortran (GCC) 10.4.0
* running under: Windows Server 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 '1.7.0'
* 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 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 61.69   2.41   64.13
regionAnalysis       51.85   0.46   54.47
runHMM_2             45.05   0.47   45.52
runHMM_3             42.43   0.22   42.67
runHMM_1             37.92   0.17   38.42
prepareHMMdataframes 29.26   0.17   29.43
tLOHCalcUpdate       28.30   0.09   28.39
splitByChromosome    28.22   0.07   28.31
alleleFrequencyPlot   6.50   0.06    6.58
aggregateCHRPlot      6.18   0.18    6.34
* 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
  'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/tLOH.Rcheck/00check.log'
for details.



Installation output

tLOH.Rcheck/00install.out

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###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL tLOH
###
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* installing to library 'F:/biocbuild/bbs-3.17-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
aggregateCHRPlot6.180.186.34
alleleFrequencyPlot6.500.066.58
documentErrorRegions000
hiddenMarkovAnalysis61.69 2.4164.13
humanGBMsampleAC0.030.000.03
initialStartProbabilities0.000.010.02
marginalLikelihoodM1000
marginalLikelihoodM2000
marginalM1Calc000
marginalM2CalcBHET000
marginalM2CalcBLOH000
modePeakCalc000
prepareHMMdataframes29.26 0.1729.43
regionAnalysis51.85 0.4654.47
regionFinalize000
removeOutlierFromCalc000
runHMM_137.92 0.1738.42
runHMM_245.05 0.4745.52
runHMM_342.43 0.2242.67
splitByChromosome28.22 0.0728.31
summarizeRegions1000
summarizeRegions20.000.020.02
tLOHCalc4.530.004.53
tLOHCalcUpdate28.30 0.0928.39
tLOHDataImport000