Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-10-16 13:00:14 -0400 (Wed, 16 Oct 2019).
Package 1685/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
TSRchitect 1.10.12 R. Taylor Raborn
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||
celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK |
Package: TSRchitect |
Version: 1.10.12 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:TSRchitect.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings TSRchitect_1.10.12.tar.gz |
StartedAt: 2019-10-16 07:35:00 -0400 (Wed, 16 Oct 2019) |
EndedAt: 2019-10-16 07:40:28 -0400 (Wed, 16 Oct 2019) |
EllapsedTime: 328.1 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: TSRchitect.Rcheck |
Warnings: 3 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:TSRchitect.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings TSRchitect_1.10.12.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/TSRchitect.Rcheck’ * using R version 3.6.1 (2019-07-05) * using platform: x86_64-apple-darwin15.6.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘TSRchitect/DESCRIPTION’ ... OK * this is package ‘TSRchitect’ version ‘1.10.12’ * 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 ‘TSRchitect’ 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 ... NOTE File LICENSE is not mentioned in the DESCRIPTION file. * checking for left-over files ... OK * checking index information ... WARNING Empty or missing file ‘demo/00Index’. See sections ‘The INDEX file’ and ‘Package subdirectories’ in the ‘Writing R Extensions’ manual. * checking package subdirectories ... WARNING Subdirectory ‘demo’ contains no demos. * 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 ... NOTE mergeSampleData,tssObject-numeric-numeric : mergeTSSdf: no visible binding for global variable ‘TSS’ mergeSampleData,tssObject-numeric-numeric : mergeTSSdf: no visible binding for global variable ‘nTAGs’ Undefined global functions or variables: TSS nTAGs * 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 ... WARNING Undocumented arguments in documentation object 'determineTSR' ‘...’ Undocumented arguments in documentation object 'loadTSSobj' ‘...’ Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking sizes of PDF files under ‘inst/doc’ ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU or elapsed time > 5s user system elapsed loadTSSobj-methods 6.001 1.533 6.741 * 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: 3 WARNINGs, 2 NOTEs See ‘/Users/biocbuild/bbs-3.9-bioc/meat/TSRchitect.Rcheck/00check.log’ for details.
TSRchitect.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL TSRchitect ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘TSRchitect’ ... ** using staged installation ** R ** demo ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ‘TSRchitect.Rmd’ using ‘UTF-8’ ‘TSRchitectUsersGuide.Rmd’ using ‘UTF-8’ ** 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 (TSRchitect)
TSRchitect.Rcheck/TSRchitect-Ex.timings
name | user | system | elapsed | |
TSRchitectUsersGuide | 0.001 | 0.001 | 0.002 | |
addAnnotationToTSR-methods | 0.381 | 0.010 | 0.392 | |
addTagCountsToTSR-methods | 0.072 | 0.007 | 0.079 | |
createSummarizedExperiment-methods | 0.160 | 0.018 | 0.177 | |
determineTSR-methods | 0.092 | 0.009 | 0.101 | |
getBamDataFirstRead-methods | 0.117 | 0.006 | 0.123 | |
getFileNames-methods | 0.061 | 0.002 | 0.064 | |
getTSRdata-methods | 0.066 | 0.003 | 0.070 | |
getTSScountData-methods | 0.062 | 0.007 | 0.068 | |
getTSStagData-methods | 0.130 | 0.002 | 0.132 | |
getTitle-methods | 0.053 | 0.001 | 0.053 | |
gsq2bed-methods | 0.240 | 0.041 | 0.297 | |
importAnnotationExternal-methods | 0.341 | 0.009 | 0.357 | |
inputToTSS-methods | 0.854 | 0.076 | 0.931 | |
loadTSSobj-methods | 6.001 | 1.533 | 6.741 | |
makeGRangesFromTSR-methods | 0.781 | 0.712 | 0.134 | |
mergeSampleData-methods | 0.094 | 0.012 | 0.106 | |
processTSS-methods | 0.368 | 0.062 | 0.430 | |
tssObject | 0.001 | 0.001 | 0.001 | |
writeTSR-methods | 0.075 | 0.004 | 0.079 | |
writeTSS-methods | 0.070 | 0.004 | 0.074 | |