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BioC 3.4: CHECK report for CoverageView on malbec1

This page was generated on 2017-04-15 16:12:02 -0400 (Sat, 15 Apr 2017).

Package 272/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CoverageView 1.10.0
Ernesto Lowy
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/CoverageView
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 ...NOT SUPPORTED...NOT SUPPORTED...NOT SUPPORTED...
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: CoverageView
Version: 1.10.0
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings CoverageView_1.10.0.tar.gz
StartedAt: 2017-04-14 21:50:33 -0400 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 21:53:03 -0400 (Fri, 14 Apr 2017)
EllapsedTime: 149.7 seconds
RetCode: 0
Status:  OK 
CheckDir: CoverageView.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings CoverageView_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/CoverageView.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 ‘CoverageView/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CoverageView’ version ‘1.10.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘CoverageView’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
imageScale: no visible global function definition for ‘heat.colors’
imageScale: no visible global function definition for ‘plot’
imageScale: no visible global function definition for ‘polygon’
draw.heatmap,list: no visible global function definition for ‘png’
draw.heatmap,list: no visible global function definition for ‘layout’
draw.heatmap,list : <anonymous>: no visible global function definition
  for ‘colorRampPalette’
draw.heatmap,list : <anonymous>: no visible global function definition
  for ‘par’
draw.heatmap,list : <anonymous>: no visible global function definition
  for ‘image’
draw.heatmap,list : <anonymous>: no visible global function definition
  for ‘box’
draw.heatmap,list : <anonymous>: no visible global function definition
  for ‘legend’
draw.heatmap,list: no visible global function definition for ‘dev.off’
draw.heatmap,matrix: no visible global function definition for
  ‘colorRampPalette’
draw.heatmap,matrix: no visible global function definition for ‘png’
draw.heatmap,matrix: no visible global function definition for ‘par’
draw.heatmap,matrix: no visible global function definition for ‘image’
draw.heatmap,matrix: no visible global function definition for
  ‘dev.off’
draw.profile,list: no visible global function definition for ‘png’
draw.profile,list : <anonymous>: no visible global function definition
  for ‘plot’
draw.profile,list : <anonymous>: no visible global function definition
  for ‘par’
draw.profile,list: no visible global function definition for ‘abline’
draw.profile,list: no visible global function definition for ‘grid’
draw.profile,list: no visible global function definition for ‘box’
draw.profile,list: no visible global function definition for ‘axis’
draw.profile,list: no visible global function definition for ‘legend’
draw.profile,list: no visible global function definition for ‘dev.off’
draw.profile,matrix: no visible global function definition for ‘png’
draw.profile,matrix: no visible global function definition for ‘abline’
draw.profile,matrix: no visible global function definition for ‘grid’
draw.profile,matrix: no visible global function definition for ‘box’
draw.profile,matrix: no visible global function definition for ‘par’
draw.profile,matrix: no visible global function definition for ‘axis’
draw.profile,matrix: no visible global function definition for
  ‘dev.off’
genome.covplot.cumdepth,CoverageBamFile: no visible global function
  definition for ‘png’
genome.covplot.cumdepth,CoverageBamFile: no visible global function
  definition for ‘plot’
genome.covplot.cumdepth,CoverageBamFile: no visible global function
  definition for ‘par’
genome.covplot.cumdepth,CoverageBamFile: no visible global function
  definition for ‘axis’
genome.covplot.cumdepth,CoverageBamFile: no visible global function
  definition for ‘dev.off’
genome.covplot.cumdepth,list: no visible global function definition for
  ‘png’
genome.covplot.cumdepth,list: no visible global function definition for
  ‘par’
genome.covplot.cumdepth,list : <anonymous>: no visible global function
  definition for ‘plot’
genome.covplot.cumdepth,list : <anonymous>: no visible global function
  definition for ‘par’
genome.covplot.cumdepth,list: no visible global function definition for
  ‘axis’
genome.covplot.cumdepth,list: no visible global function definition for
  ‘legend’
genome.covplot.cumdepth,list: no visible global function definition for
  ‘dev.off’
genome.covplot.depth,CoverageBamFile: no visible global function
  definition for ‘png’
genome.covplot.depth,CoverageBamFile: no visible global function
  definition for ‘par’
genome.covplot.depth,CoverageBamFile: no visible global function
  definition for ‘plot’
genome.covplot.depth,CoverageBamFile: no visible global function
  definition for ‘axis’
genome.covplot.depth,CoverageBamFile: no visible global function
  definition for ‘dev.off’
genome.covplot.depth,list: no visible global function definition for
  ‘png’
genome.covplot.depth,list: no visible global function definition for
  ‘par’
genome.covplot.depth,list : <anonymous>: no visible global function
  definition for ‘plot’
genome.covplot.depth,list : <anonymous>: no visible global function
  definition for ‘par’
genome.covplot.depth,list: no visible global function definition for
  ‘axis’
genome.covplot.depth,list: no visible global function definition for
  ‘legend’
genome.covplot.depth,list: no visible global function definition for
  ‘dev.off’
write.profile,matrix: no visible global function definition for
  ‘write.table’
Undefined global functions or variables:
  abline axis box colorRampPalette dev.off grid heat.colors image
  layout legend par plot png polygon write.table
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.off", "heat.colors",
             "png")
  importFrom("graphics", "abline", "axis", "box", "grid", "image",
             "layout", "legend", "par", "plot", "polygon")
  importFrom("utils", "write.table")
to your NAMESPACE file.
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
cov.matrix 4.216   1.12   3.099
* 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/CoverageView.Rcheck/00check.log’
for details.

CoverageView.Rcheck/00install.out:

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

CoverageView.Rcheck/CoverageView-Ex.timings:

nameusersystemelapsed
CoverageBamFile-class0.0160.0000.018
CoverageBigWigFile-class0.0040.0000.007
cov.interval0.9360.0000.939
cov.matrix4.2161.1203.099
draw.heatmap1.6160.0281.648
draw.profile0.5200.0520.572
export.wig0.1400.0000.141
genome.covplot.cumdepth0.4040.0000.404
genome.covplot.depth0.4080.0000.410
write.profile0.4360.1200.362