Multiple platform build/check report for BioC 3.9 - CHECK report for TSRchitect on malbec2

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:TSRchitect.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings TSRchitect_1.10.12.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/TSRchitect.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.10.12’
* 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 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 5.223   1.07   5.992
* 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-3.9-bioc/meat/TSRchitect.Rcheck/00check.log’
for details.

Installation output

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL TSRchitect
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* installing to library ‘/home/biocbuild/bbs-3.9-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

name	user	system	elapsed
TSRchitectUsersGuide	0.001	0.000	0.001
addAnnotationToTSR-methods	0.216	0.000	0.239
addTagCountsToTSR-methods	0.044	0.000	0.044
createSummarizedExperiment-methods	0.058	0.016	0.074
determineTSR-methods	0.048	0.000	0.049
getBamDataFirstRead-methods	0.061	0.000	0.062
getFileNames-methods	0.034	0.000	0.034
getTSRdata-methods	0.057	0.000	0.057
getTSScountData-methods	0.044	0.000	0.044
getTSStagData-methods	0.069	0.000	0.069
getTitle-methods	0.034	0.000	0.034
gsq2bed-methods	0.171	0.034	0.281
importAnnotationExternal-methods	0.361	0.031	0.412
inputToTSS-methods	0.628	0.047	0.676
loadTSSobj-methods	5.223	1.070	5.992
makeGRangesFromTSR-methods	0.332	0.239	0.090
mergeSampleData-methods	0.067	0.004	0.072
processTSS-methods	0.190	0.012	0.204
tssObject	0	0	0
writeTSR-methods	0.066	0.000	0.066
writeTSS-methods	0.064	0.000	0.064

CHECK report for TSRchitect on malbec2

Summary

Command output

Installation output

Tests output

Example timings