BioC 2.13: CHECK report for epivizr on perceval

Package: epivizr

Version: 1.0.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch epivizr_1.0.0.tar.gz

StartedAt: 2014-04-05 01:05:48 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 01:09:01 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 192.9 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: epivizr.Rcheck

Warnings: 1

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/epivizr.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘epivizr/DESCRIPTION’ ... OK
* this is package ‘epivizr’ 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 ‘epivizr’ can be installed ... [18s/19s] 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 ... NOTE
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘EpivizServer’
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... WARNING
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                              old_size new_size compress
  tcga_colon_example.rda         290Kb    234Kb       xz
  tcga_colon_expression.RData    1.0Mb    651Kb       xz
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [10s/10s] OK
* 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

WARNING: There was 1 warning.
NOTE: There was 1 note.
See
  ‘/Users/biocbuild/bbs-2.13-bioc/meat/epivizr.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
EpivizDeviceMgr-class	0.304	0.006	0.313
EpivizServer-class	0.012	0.003	0.015
IndexedArray-class	0.017	0.003	0.020
Queue-class	0.014	0.002	0.016
startEpiviz	0.007	0.001	0.007
tcga_colon_example	0.671	0.023	0.695
tcga_colon_expression	0.435	0.009	0.448