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This page was generated on 2024-03-28 11:37:12 -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 nebbiolo1


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: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:tLOH.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings tLOH_1.11.0.tar.gz
StartedAt: 2024-03-28 03:26:31 -0400 (Thu, 28 Mar 2024)
EndedAt: 2024-03-28 03:37:34 -0400 (Thu, 28 Mar 2024)
EllapsedTime: 663.4 seconds
RetCode: 0
Status:   OK  
CheckDir: tLOH.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:tLOH.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings tLOH_1.11.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/tLOH.Rcheck’
* using R Under development (unstable) (2024-03-18 r86148)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* 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 loading without being on the library search path ... 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 75.677  0.824  82.123
regionAnalysis       46.736  0.320  47.058
runHMM_2             42.621  0.232  42.853
runHMM_3             41.691  0.176  41.867
runHMM_1             24.768  0.087  24.855
splitByChromosome    23.895  0.152  24.047
prepareHMMdataframes 23.227  0.028  23.256
tLOHCalcUpdate       22.904  0.040  22.945
alleleFrequencyPlot  12.033  0.280  16.965
aggregateCHRPlot      6.467  0.216   6.675
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/tLOH.Rcheck/00check.log’
for details.


Installation output

tLOH.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL tLOH
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-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
aggregateCHRPlot6.4670.2166.675
alleleFrequencyPlot12.033 0.28016.965
documentErrorRegions0.0030.0000.004
hiddenMarkovAnalysis75.677 0.82482.123
humanGBMsampleAC0.0380.0040.041
initialStartProbabilities0.0010.0000.001
marginalLikelihoodM10.0030.0000.002
marginalLikelihoodM20.0020.0000.002
marginalM1Calc000
marginalM2CalcBHET0.0010.0000.002
marginalM2CalcBLOH0.0020.0000.001
modePeakCalc0.0010.0000.001
prepareHMMdataframes23.227 0.02823.256
regionAnalysis46.736 0.32047.058
regionFinalize000
removeOutlierFromCalc0.0000.0000.001
runHMM_124.768 0.08724.855
runHMM_242.621 0.23242.853
runHMM_341.691 0.17641.867
splitByChromosome23.895 0.15224.047
summarizeRegions1000
summarizeRegions2000
tLOHCalc3.9220.0513.974
tLOHCalcUpdate22.904 0.04022.945
tLOHDataImport000