Package: TSRchitect

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings TSRchitect_1.4.0.tar.gz

StartedAt: 2018-04-12 10:34:04 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 10:37:46 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 222.6 seconds

RetCode: 0

Status:  OK

CheckDir: TSRchitect.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings TSRchitect_1.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/TSRchitect.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.4.0’
* 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 loading without being on the library search path ... 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   41.396  2.263   0.084
loadTSSobj-methods  9.024  0.267   9.624
processTSS-methods  0.368  0.100  18.278
* 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-3.6-bioc/meat/TSRchitect.Rcheck/00check.log’
for details.

* installing *source* package ‘TSRchitect’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (TSRchitect)

name	user	system	elapsed
TSRchitectUsersGuide	0.001	0.000	0.001
addAnnotationToTSR-methods	0.805	0.029	0.843
addTagCountsToTSR-methods	0.072	0.001	0.072
cDNAtoBED-methods	0.152	0.017	0.181
createSummarizedExperiment-methods	0.365	0.003	0.383
determineTSR-methods	0.080	0.001	0.085
getBamData-methods	0.135	0.002	0.138
getFileNames-methods	0.048	0.001	0.049
getTSRdata-methods	0.045	0.000	0.047
getTSScountData-methods	0.049	0.003	0.052
getTSStagData-methods	0.117	0.002	0.119
getTitle-methods	0.045	0.001	0.046
importAnnotationExternal-methods	0.305	0.005	0.311
inputToTSS-methods	0.841	0.003	0.854
loadTSSobj-methods	9.024	0.267	9.624
makeGRangesFromTSR-methods	0.105	0.025	0.131
mergeSampleData-methods	0.381	0.048	0.433
processTSS-methods	0.368	0.100	18.278
tssObject	0.001	0.000	0.001
writeTSR-methods	41.396	2.263	0.084