Package: TSRchitect

Version: 1.8.9

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_1.8.9.tar.gz

StartedAt: 2018-10-17 00:32:09 -0400 (Wed, 17 Oct 2018)

EndedAt: 2018-10-17 00:36:03 -0400 (Wed, 17 Oct 2018)

EllapsedTime: 234.4 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: TSRchitect.Rcheck

Warnings: 2

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### Running command:
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###   /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_1.8.9.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/TSRchitect.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.8.9’
* 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
  inst/LICENSE
will install at top-level and 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 ... 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 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 8.481  0.435   8.778
* 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: 2 WARNINGs, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.7-bioc/meat/TSRchitect.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL TSRchitect
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘TSRchitect’ ...
** 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’ 
Warning in res[i] <- withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),  :
  number of items to replace is not a multiple of replacement length
Warning in res[i] <- withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),  :
  number of items to replace is not a multiple of replacement length
Warning in res[i] <- withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),  :
  number of items to replace is not a multiple of replacement length
Warning in res[i] <- withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),  :
  number of items to replace is not a multiple of replacement length
Warning in res[i] <- withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),  :
  number of items to replace is not a multiple of replacement length
** testing if installed package can be loaded
* DONE (TSRchitect)

name	user	system	elapsed
TSRchitectUsersGuide	0.001	0.000	0.002
addAnnotationToTSR-methods	0.901	0.006	0.914
addTagCountsToTSR-methods	0.116	0.001	0.118
cDNAtoBED-methods	0.214	0.021	0.246
createSummarizedExperiment-methods	0.124	0.002	0.128
determineTSR-methods	0.097	0.002	0.100
getBamData-methods	0.091	0.003	0.094
getFileNames-methods	0.062	0.001	0.063
getTSRdata-methods	0.072	0.001	0.073
getTSScountData-methods	0.058	0.003	0.062
getTSStagData-methods	0.114	0.007	0.124
getTitle-methods	0.073	0.002	0.074
importAnnotationExternal-methods	0.362	0.036	0.404
inputToTSS-methods	0.825	0.031	0.864
loadTSSobj-methods	8.481	0.435	8.778
makeGRangesFromTSR-methods	0.109	0.038	0.147
mergeSampleData-methods	0.351	0.036	0.389
processTSS-methods	0.285	0.028	0.316
tssObject	0.001	0.001	0.002
writeTSR-methods	0.068	0.003	0.072