Multiple platform build/check report for BioC 3.9 - CHECK report for TSRchitect on celaya2

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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_1.9.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/TSRchitect.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.9.0’
* 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
  inst/LICENSE
will install at top-level and is not mentioned in the DESCRIPTION file.
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* 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
writeTSR-methods   75.902  7.446   0.167
loadTSSobj-methods 12.234  1.308  12.341
processTSS-methods  0.370  0.231  21.503
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/TSRchitect.Rcheck/00check.log’
for details.

Installation output

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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/3.6/Resources/library’
* installing *source* package ‘TSRchitect’ ...
** using staged installation
** R
** 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
** 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	0.002	0.000	0.002
addAnnotationToTSR-methods	0.360	0.003	0.365
addTagCountsToTSR-methods	0.118	0.002	0.121
cDNAtoBED-methods	0.214	0.121	0.351
createSummarizedExperiment-methods	0.144	0.006	0.150
determineTSR-methods	0.091	0.002	0.094
getBamData-methods	0.096	0.003	0.098
getFileNames-methods	0.045	0.001	0.046
getTSRdata-methods	0.054	0.002	0.056
getTSScountData-methods	0.057	0.010	0.066
getTSStagData-methods	0.113	0.010	0.123
getTitle-methods	0.067	0.003	0.070
importAnnotationExternal-methods	0.429	0.017	0.450
inputToTSS-methods	0.875	0.073	0.948
loadTSSobj-methods	12.234	1.308	12.341
makeGRangesFromTSR-methods	0.084	0.036	0.120
mergeSampleData-methods	0.538	0.089	0.627
processTSS-methods	0.370	0.231	21.503
tssObject	0.001	0.001	0.002
writeTSR-methods	75.902	7.446	0.167

CHECK report for TSRchitect on celaya2

Summary

Command output

Installation output

Tests output

Example timings