BioC 3.2: CHECK report for epivizr on zin1

Package: epivizr

Version: 1.7.8

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings epivizr_1.7.8.tar.gz

StartedAt: 2015-08-23 23:37:45 -0700 (Sun, 23 Aug 2015)

EndedAt: 2015-08-23 23:40:24 -0700 (Sun, 23 Aug 2015)

EllapsedTime: 159.0 seconds

RetCode: 0

Status:  OK

CheckDir: epivizr.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings epivizr_1.7.8.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/epivizr.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘epivizr/DESCRIPTION’ ... OK
* this is package ‘epivizr’ version ‘1.7.8’
* 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 ... [17s/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
register,ExpressionSet : .local: no visible global function definition
  for ‘IRanges’
* 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 line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... NOTE
The following directory looks like a leftover from 'knitr':
  ‘figure’
Please remove from your package.
* checking examples ... [7s/7s] 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
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.2-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	0.001	0.000	0.001
EpivizServer-class	0.000	0.000	0.001
IndexedArray-class	0.006	0.000	0.006
Queue-class	0.003	0.000	0.003
makeGeneTrackAnnotation	0.001	0.000	0.000
startEpiviz	0.000	0.000	0.001
startStandalone	0	0	0
tcga_colon_example	0.173	0.004	0.178
tcga_colon_expression	0.112	0.000	0.112