BioC 2.13: CHECK report for sRAP on zin1

Package: sRAP

Version: 1.4.0

Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings sRAP_1.4.0.tar.gz

StartedAt: 2014-04-05 04:11:25 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 04:13:00 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 94.7 seconds

RetCode: 0

Status:  OK

CheckDir: sRAP.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/sRAP.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘sRAP/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sRAP’ 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 ‘sRAP’ can be installed ... [1s/1s] 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 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
RNA.bdfunc.fc: no visible binding for global variable
  ‘bdfunc.enrichment.human’
RNA.bdfunc.fc: no visible binding for global variable
  ‘bdfunc.enrichment.mouse’
RNA.bdfunc.signal: no visible binding for global variable
  ‘bdfunc.enrichment.human’
RNA.bdfunc.signal: no visible binding for global variable
  ‘bdfunc.enrichment.mouse’
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [76s/77s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
RNA.bdfunc.signal 36.902  1.216  38.449
RNA.deg           15.281  0.536  15.928
RNA.bdfunc.fc     15.324  0.384  15.822
* 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

NOTE: There was 1 note.
See
  ‘/home/biocbuild/bbs-2.13-bioc/meat/sRAP.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
RNA.bdfunc.fc	15.324	0.384	15.822
RNA.bdfunc.signal	36.902	1.216	38.449
RNA.deg	15.281	0.536	15.928
RNA.norm	2.828	0.144	2.990
RNA.prepare.input	0.020	0.000	0.025
RNA.qc	2.868	0.188	3.092