BioC 3.0: CHECK report for pepStat on zin1

Package: pepStat

Version: 1.0.0

Command: /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings pepStat_1.0.0.tar.gz

StartedAt: 2015-04-10 02:55:02 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 02:58:34 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 212.1 seconds

RetCode: 0

Status:  OK

CheckDir: pepStat.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings pepStat_1.0.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/pepStat.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘pepStat/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘pepStat’ version ‘1.0.0’
* 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 ‘pepStat’ can be installed ... [15s/17s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* 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 ... NOTE
coerce,peptideSet-ExpressionSet: no visible global function definition
  for ‘annotation’
* 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 ... [50s/53s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
makeCalls         6.900  0.040   8.531
restab            6.605  0.020   7.671
summarizePeptides 6.525  0.008   6.559
plotArray         6.264  0.008   6.397
slidingMean       6.200  0.044   6.386
normalizeArray    6.164  0.036   6.222
* 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

NOTE: There was 1 note.
See
  ‘/home/biocbuild/bbs-3.0-bioc/meat/pepStat.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
create_db	0.244	0.000	0.242
makeCalls	6.900	0.040	8.531
makePeptideSet	3.745	0.024	3.782
normalizeArray	6.164	0.036	6.222
plotArray	6.264	0.008	6.397
restab	6.605	0.020	7.671
shinyPepStat	0	0	0
slidingMean	6.200	0.044	6.386
summarizePeptides	6.525	0.008	6.559