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

Package: IdeoViz

Version: 1.5.0

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings IdeoViz_1.5.0.tar.gz

StartedAt: 2015-10-27 04:56:19 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 04:59:13 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 174.3 seconds

RetCode: 0

Status:  OK

CheckDir: IdeoViz.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings IdeoViz_1.5.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/IdeoViz.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 ‘IdeoViz/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘IdeoViz’ version ‘1.5.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘Biobase’ ‘IRanges’ ‘GenomicRanges’ ‘RColorBrewer’ ‘rtracklayer’
  ‘GenomeInfoDb’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘IdeoViz’ can be installed ... [10s/10s] 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
.plot_values: no visible binding for global variable ‘span’
Undefined global functions or variables:
  span
* checking Rd files ... NOTE
prepare_Rd: GSM733664_broadPeaks.Rd:11-12: Dropping empty section \format
prepare_Rd: GSM733664_broadPeaks.Rd:16-18: Dropping empty section \source
prepare_Rd: binned_fullGenome.Rd:12-13: Dropping empty section \format
prepare_Rd: binned_fullGenome.Rd:14-16: Dropping empty section \details
prepare_Rd: binned_fullGenome.Rd:20-22: Dropping empty section \references
prepare_Rd: binned_multiSeries.Rd:12-13: Dropping empty section \format
prepare_Rd: binned_multiSeries.Rd:14-15: Dropping empty section \details
prepare_Rd: binned_multiSeries.Rd:19-20: Dropping empty section \references
prepare_Rd: binned_singleSeries.Rd:11-12: Dropping empty section \format
prepare_Rd: binned_singleSeries.Rd:13-15: Dropping empty section \details
prepare_Rd: binned_singleSeries.Rd:19-21: Dropping empty section \references
prepare_Rd: hg18_ideo.Rd:11-12: Dropping empty section \format
prepare_Rd: hg18_ideo.Rd:13-14: Dropping empty section \details
prepare_Rd: hg18_ideo.Rd:18-19: Dropping empty section \references
prepare_Rd: wins.Rd:12-13: Dropping empty section \format
prepare_Rd: wins.Rd:14-15: Dropping empty section \details
prepare_Rd: wins.Rd:19-20: Dropping empty section \references
prepare_Rd: wins_discrete.Rd:11-12: Dropping empty section \format
prepare_Rd: wins_discrete.Rd:13-15: Dropping empty section \details
prepare_Rd: wins_discrete.Rd:19-21: Dropping empty section \references
prepare_Rd: wins_entiregenome.Rd:11-12: Dropping empty section \format
prepare_Rd: wins_entiregenome.Rd:13-15: Dropping empty section \details
prepare_Rd: wins_entiregenome.Rd:19-21: Dropping empty section \references
* 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 files in ‘vignettes’ ... OK
* checking examples ... [10s/65s] OK
Examples with CPU or elapsed time > 5s
          user system elapsed
avgByBin 1.801  0.040  23.244
getBins  0.815  0.009  17.613
getIdeo  0.471  0.012  17.306
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.3-bioc/meat/IdeoViz.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
GSM733664_broadPeaks	0.088	0.000	0.088
avgByBin	1.801	0.040	23.244
binned_fullGenome	0.017	0.000	0.017
binned_multiSeries	0.012	0.000	0.012
binned_singleSeries	0.011	0.000	0.011
getBins	0.815	0.009	17.613
getIdeo	0.471	0.012	17.306
hg18_ideo	0.011	0.000	0.011
plotChromValuePair	0.407	0.000	0.407
plotOnIdeo	0.269	0.000	0.269
wins	0.011	0.004	0.015
wins_discrete	0.018	0.000	0.018
wins_entiregenome	0.014	0.000	0.014