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This page was generated on 2021-12-01 17:18:37 -0500 (Wed, 01 Dec 2021).

CHECK results for TSRchitect on machv2

To the developers/maintainers of the TSRchitect package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/TSRchitect.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here 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 2013/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TSRchitect 1.20.0  (landing page)
R. Taylor Raborn
Snapshot Date: 2021-11-30 04:15:05 -0500 (Tue, 30 Nov 2021)
git_url: https://git.bioconductor.org/packages/TSRchitect
git_branch: RELEASE_3_14
git_last_commit: 3f5e213
git_last_commit_date: 2021-10-26 12:35:22 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: TSRchitect
Version: 1.20.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:TSRchitect.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings TSRchitect_1.20.0.tar.gz
StartedAt: 2021-11-30 22:38:30 -0500 (Tue, 30 Nov 2021)
EndedAt: 2021-11-30 22:43:44 -0500 (Tue, 30 Nov 2021)
EllapsedTime: 313.4 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: TSRchitect.Rcheck
Warnings: 3

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:TSRchitect.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings TSRchitect_1.20.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/TSRchitect.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TSRchitect/DESCRIPTION’ ... OK
* this is package ‘TSRchitect’ version ‘1.20.0’
* 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 (user + system) or elapsed time > 5s
                    user system elapsed
loadTSSobj-methods 4.487  1.305   4.157
* 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-3.14-bioc/meat/TSRchitect.Rcheck/00check.log’
for details.



Installation output

TSRchitect.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL TSRchitect
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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)

Tests output


Example timings

TSRchitect.Rcheck/TSRchitect-Ex.timings

nameusersystemelapsed
TSRchitectUsersGuide0.0010.0010.001
addAnnotationToTSR-methods0.4260.0150.441
addTagCountsToTSR-methods0.0700.0030.072
createSummarizedExperiment-methods0.2070.0170.226
determineTSR-methods0.0890.0040.093
getBamDataFirstRead-methods0.1250.0090.135
getFileNames-methods0.0620.0010.063
getTSRdata-methods0.0580.0020.060
getTSScountData-methods0.0700.0060.076
getTSStagData-methods0.1220.0080.130
getTitle-methods0.0570.0020.058
gsq2bed-methods0.1520.0180.178
importAnnotationExternal-methods0.4480.0270.476
inputToTSS-methods0.9390.0100.951
loadTSSobj-methods4.4871.3054.157
makeGRangesFromTSR-methods0.0840.0230.108
mergeSampleData-methods0.1380.0110.150
processTSS-methods0.3510.0290.379
tssObject0.0000.0010.001
writeTSR-methods0.0670.0030.069
writeTSS-methods0.0660.0020.068