BioC 3.3: CHECK report for epivizr on linux2.bioconductor.org

Package: epivizr

Version: 1.9.0

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings epivizr_1.9.0.tar.gz

StartedAt: 2015-10-27 03:40:13 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 03:42:52 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 158.6 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: epivizr.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings epivizr_1.9.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/epivizr.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* 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 ‘1.9.0’
* 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 ... [16s/16s] 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: no visible global function definition for
  ‘IRanges’
Undefined global functions or variables:
  IRanges
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'EpivizBlockData-class.Rd':
  ‘[GenomicRanges]{GIntervalTree}’

Missing link or links in documentation object 'EpivizBpData-class.Rd':
  ‘[GenomicRanges]{GIntervalTree}’

Missing link or links in documentation object 'EpivizDeviceMgr-class.Rd':
  ‘[GenomicRanges]{GIntervalTree}’

Missing link or links in documentation object 'EpivizFeatureData-class.Rd':
  ‘[GenomicRanges]{GIntervalTree}’

Missing link or links in documentation object 'EpivizGeneInfoData-class.Rd':
  ‘[GenomicRanges]{GIntervalTree}’

Missing link or links in documentation object 'EpivizTrackDevice-class.Rd':
  ‘[GenomicRanges]{GIntervalTree}’

Missing link or links in documentation object 'register-methods.Rd':
  ‘[GenomicRanges]{GIntervalTree}’

See section 'Cross-references' in the 'Writing R Extensions' manual.

* 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: 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.3-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	0.002
EpivizServer-class	0.000	0.000	0.001
IndexedArray-class	0.006	0.000	0.006
Queue-class	0.004	0.000	0.003
makeGeneTrackAnnotation	0.001	0.000	0.000
startEpiviz	0.001	0.000	0.000
startStandalone	0.001	0.000	0.000
tcga_colon_example	0.154	0.000	0.154
tcga_colon_expression	0.099	0.008	0.106