BioC 2.13: CHECK report for maskBAD on zin1

Package: maskBAD

Version: 1.6.0

Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings maskBAD_1.6.0.tar.gz

StartedAt: 2014-04-05 02:15:31 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 02:17:23 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 111.3 seconds

RetCode: 0

Status:  OK

CheckDir: maskBAD.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/maskBAD.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 ‘maskBAD/DESCRIPTION’ ... OK
* this is package ‘maskBAD’ version ‘1.6.0’
* 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 ‘maskBAD’ can be installed ... [9s/9s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Non-standard license specification:
  GPL version 2 or newer
Standardizable: TRUE
Standardized license specification:
  GPL (>= 2)
* 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
prepareMaskedAffybatch : .cdf.env.fromTable: warning in assign(nn[i],
  l[[i]], pos = env, inherit = FALSE): partial argument match of
  'inherit' to 'inherits'
prepareMaskedAffybatch : .cdf.env.fromTable: warning in assign(nn[i],
  pmm[i, , drop = FALSE], pos = env, inherit = FALSE): partial argument
  match of 'inherit' to 'inherits'
* 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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘maskBAD.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [23s/23s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
mask                8.676  0.084   8.927
overlapExprExtMasks 8.269  0.016   8.345
* 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 were 3 notes.
See
  ‘/home/biocbuild/bbs-2.13-bioc/meat/maskBAD.Rcheck/00check.log’
for details.

* installing *source* package ‘maskBAD’ ...
** 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 (maskBAD)

name	user	system	elapsed
mask	8.676	0.084	8.927
overlapExprExtMasks	8.269	0.016	8.345
plotProbe	0.804	0.056	0.871
prepareMaskedAffybatch	0.756	0.080	0.841