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BioC 3.4: CHECK report for IdeoViz on malbec1

This page was generated on 2017-04-15 16:12:28 -0400 (Sat, 15 Apr 2017).

Package 618/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
IdeoViz 1.8.0
Shraddha Pai
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/IdeoViz
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: IdeoViz
Version: 1.8.0
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings IdeoViz_1.8.0.tar.gz
StartedAt: 2017-04-14 23:16:22 -0400 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 23:20:13 -0400 (Fri, 14 Apr 2017)
EllapsedTime: 231.1 seconds
RetCode: 0
Status:  OK 
CheckDir: IdeoViz.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings IdeoViz_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/IdeoViz.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.8.0’
* 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 ... 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
.plotChromosome: no visible global function definition for ‘modifyList’
.plot_values: no visible global function definition for ‘modifyList’
.plot_values: no visible global function definition for ‘loess’
.plot_values: no visible binding for global variable ‘span’
.plot_values: no visible global function definition for ‘predict’
avgByBin: no visible global function definition for ‘ave’
plotChromValuePair: no visible global function definition for
  ‘modifyList’
Undefined global functions or variables:
  ave loess modifyList predict span
Consider adding
  importFrom("stats", "ave", "loess", "predict")
  importFrom("utils", "modifyList")
to your NAMESPACE file.
* 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 ... OK
Examples with CPU or elapsed time > 5s
          user system elapsed
avgByBin 1.848  0.048  25.881
getBins  0.760  0.016  24.434
getIdeo  0.580  0.012  22.306
* 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-3.4-bioc/meat/IdeoViz.Rcheck/00check.log’
for details.


IdeoViz.Rcheck/00install.out:

* 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)

IdeoViz.Rcheck/IdeoViz-Ex.timings:

nameusersystemelapsed
GSM733664_broadPeaks0.0960.0000.097
avgByBin 1.848 0.04825.881
binned_fullGenome0.0280.0000.025
binned_multiSeries0.0120.0000.014
binned_singleSeries0.0120.0000.012
getBins 0.760 0.01624.434
getIdeo 0.580 0.01222.306
hg18_ideo0.0120.0000.012
plotChromValuePair0.1160.0040.119
plotOnIdeo0.2920.0000.294
wins0.0160.0000.015
wins_discrete0.0120.0000.013
wins_entiregenome0.0120.0000.012