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This page was generated on 2021-10-15 15:05:55 -0400 (Fri, 15 Oct 2021).

CHECK results for TSRchitect on nebbiolo1

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 1972/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TSRchitect 1.18.0  (landing page)
R. Taylor Raborn
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/TSRchitect
git_branch: RELEASE_3_13
git_last_commit: daeccc8
git_last_commit_date: 2021-05-19 12:27:50 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 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: 1.18.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:TSRchitect.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings TSRchitect_1.18.0.tar.gz
StartedAt: 2021-10-14 11:57:17 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 12:01:15 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 237.8 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: TSRchitect.Rcheck
Warnings: 3

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:TSRchitect.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings TSRchitect_1.18.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/TSRchitect.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TSRchitect/DESCRIPTION’ ... OK
* this is package ‘TSRchitect’ version ‘1.18.0’
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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
  ‘/home/biocbuild/bbs-3.13-bioc/meat/TSRchitect.Rcheck/00check.log’
for details.



Installation output

TSRchitect.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL TSRchitect
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/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
TSRchitectUsersGuide0.0010.0000.001
addAnnotationToTSR-methods0.2740.0010.276
addTagCountsToTSR-methods0.0380.0040.042
createSummarizedExperiment-methods0.1030.0160.119
determineTSR-methods0.0420.0080.050
getBamDataFirstRead-methods0.0740.0000.073
getFileNames-methods0.0360.0000.036
getTSRdata-methods0.0340.0040.037
getTSScountData-methods0.0300.0080.039
getTSStagData-methods0.0690.0080.077
getTitle-methods0.0290.0040.033
gsq2bed-methods0.1010.0110.114
importAnnotationExternal-methods0.2630.0120.277
inputToTSS-methods0.5120.0200.532
loadTSSobj-methods4.0850.6864.079
makeGRangesFromTSR-methods0.2370.1250.072
mergeSampleData-methods0.0930.0030.098
processTSS-methods0.1970.0200.217
tssObject0.0010.0000.000
writeTSR-methods0.0360.0000.035
writeTSS-methods0.0340.0000.035