BioC 2.12: CHECK report for MiRaGE on petty

Package: MiRaGE

Version: 1.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch MiRaGE_1.2.0.tar.gz

StartedAt: 2013-10-07 23:04:00 -0700 (Mon, 07 Oct 2013)

EndedAt: 2013-10-07 23:07:24 -0700 (Mon, 07 Oct 2013)

EllapsedTime: 203.8 seconds

RetCode: 0

Status:  OK

CheckDir: MiRaGE.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/MiRaGE.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'MiRaGE/DESCRIPTION' ... OK
* this is package 'MiRaGE' version '1.2.0'
* 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 ... NOTE
Found the following hidden files and directories:
  inst/doc/.goutputstream-0CTGCW
  inst/doc/.goutputstream-E9SXCW
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'MiRaGE' can be installed ... [14s/15s] OK
* checking installed package size ... OK
* checking package 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 for unstated 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
getMiRaGEData: no visible global function definition for 'biocLite'
getMiRaGEData: no visible binding for global variable 'TBL2'
getMiRaGEData: no visible binding for global variable 'id_conv'
getMiRaGEData: no visible binding for global variable 'conv_id'
* 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [48s/48s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
MiRaGE        24.866  3.912  28.953
getMiRaGEData 10.946  0.808  11.787
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 2 notes.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/MiRaGE.Rcheck/00check.log'
for details.

* installing *source* package 'MiRaGE' ...
** 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 (MiRaGE)

name	user	system	elapsed
HS_conv_id	0.004	0.000	0.004
MM_conv_id	0.003	0.000	0.004
MiRaGE	24.866	3.912	28.953
TBL2_HS_gen	0.002	0.003	0.005
TBL2_MM_gen	0.001	0.003	0.005
getMiRaGEData	10.946	0.808	11.787
id_conv_gen	0.002	0.004	0.006