Package: TSRchitect

Version: 1.4.0

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings TSRchitect_1.4.0.tar.gz

StartedAt: 2018-04-12 03:28:14 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 03:31:42 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 208.5 seconds

RetCode: 0

Status:  OK

CheckDir: TSRchitect.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings TSRchitect_1.4.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/TSRchitect.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.4.0’
* 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 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 9.064  0.264   9.511
processTSS-methods 0.276  0.176  13.133
* 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
  ‘/home/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	0	0
addAnnotationToTSR-methods	0.712	0.024	0.738
addTagCountsToTSR-methods	0.060	0.004	0.064
cDNAtoBED-methods	0.112	0.012	0.152
createSummarizedExperiment-methods	0.372	0.028	0.400
determineTSR-methods	0.088	0.000	0.087
getBamData-methods	0.140	0.000	0.141
getFileNames-methods	0.044	0.000	0.041
getTSRdata-methods	0.040	0.000	0.042
getTSScountData-methods	0.040	0.004	0.046
getTSStagData-methods	0.104	0.000	0.102
getTitle-methods	0.040	0.000	0.042
importAnnotationExternal-methods	0.264	0.000	0.266
inputToTSS-methods	0.708	0.004	0.713
loadTSSobj-methods	9.064	0.264	9.511
makeGRangesFromTSR-methods	0.080	0.012	0.096
mergeSampleData-methods	0.244	0.024	0.269
processTSS-methods	0.276	0.176	13.133
tssObject	0.000	0.000	0.001
writeTSR-methods	0.056	0.000	0.058