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CHECK report for charm on malbec1

This page was generated on 2018-04-12 13:08:58 -0400 (Thu, 12 Apr 2018).

Package 209/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
charm 2.24.0
Peter Murakami
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/charm
Branch: RELEASE_3_6
Last Commit: 5700d84
Last Changed Date: 2017-10-30 12:39:28 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: charm
Version: 2.24.0
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings charm_2.24.0.tar.gz
StartedAt: 2018-04-11 22:07:20 -0400 (Wed, 11 Apr 2018)
EndedAt: 2018-04-11 22:17:40 -0400 (Wed, 11 Apr 2018)
EllapsedTime: 619.8 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: charm.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings charm_2.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/charm.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘charm/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘charm’ version ‘2.24.0’
* 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 ‘charm’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘Biobase’
A package should be listed in only one of these fields.
* 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 dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘SQN’ ‘fields’ ‘genefilter’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' call which should be '::': ‘oligo:::pm’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
Rug: no visible global function definition for ‘Axis’
SQNff: no visible global function definition for ‘Mclust’
arrayImage: no visible global function definition for
  ‘discretize.image’
arrayPlot: no visible global function definition for ‘image.plot’
bgAdjustParameters: no visible global function definition for ‘approx’
cmdsplot: no visible global function definition for ‘pData’
cmdsplot: no visible global function definition for ‘ffapply’
cmdsplot: no visible global function definition for ‘rowSds’
cmdsplot: no visible global function definition for ‘dist’
cmdsplot: no visible global function definition for ‘cmdscale’
controlQC: no visible global function definition for ‘pData’
controlQC: no visible global function definition for ‘axis’
controlQC: no visible global function definition for ‘segments’
controlQC: no visible global function definition for ‘boxplot’
dmrFind: no visible global function definition for ‘ffapply’
dmrFind: no visible global function definition for ‘pt’
dmrPlot_paired: no visible global function definition for ‘matplot’
dmrPlot_paired: no visible global function definition for ‘matpoints’
dmrPlot_paired: no visible global function definition for ‘matlines’
dmrPlot_paired: no visible global function definition for ‘mtext’
dmrPlot_unpaired: no visible global function definition for ‘matplot’
dmrPlot_unpaired: no visible global function definition for ‘matlines’
dmrPlot_unpaired: no visible global function definition for ‘mtext’
dosmooth: no visible global function definition for ‘runmed’
edge.qvalue: no visible global function definition for ‘smooth.spline’
get.tt.paired: no visible global function definition for ‘rowVars’
plotDMRs: no visible global function definition for ‘matplot’
plotDMRs: no visible global function definition for ‘runmed’
plotRegions: no visible global function definition for ‘matplot’
plotRegions: no visible global function definition for ‘runmed’
plot_CpG: no visible global function definition for ‘start’
plot_CpG: no visible global function definition for ‘matchPattern’
regionMatch: no visible global function definition for ‘IRanges’
regionPlot_paired: no visible global function definition for ‘matplot’
regionPlot_paired: no visible global function definition for
  ‘matpoints’
regionPlot_paired: no visible global function definition for ‘matlines’
regionPlot_paired: no visible global function definition for ‘mtext’
regionPlot_unpaired: no visible global function definition for
  ‘matplot’
regionPlot_unpaired: no visible global function definition for
  ‘matlines’
regionPlot_unpaired: no visible global function definition for ‘mtext’
rowCor: no visible global function definition for ‘rowSds’
spatialAdjust: no visible global function definition for
  ‘discretize.image’
spatialAdjustVec: no visible global function definition for
  ‘image.smooth’
Undefined global functions or variables:
  Axis IRanges Mclust approx axis boxplot cmdscale discretize.image
  dist ffapply image.plot image.smooth matchPattern matlines matplot
  matpoints mtext pData pt rowSds rowVars runmed segments smooth.spline
  start
Consider adding
  importFrom("graphics", "Axis", "axis", "boxplot", "matlines",
             "matplot", "matpoints", "mtext", "segments")
  importFrom("stats", "approx", "cmdscale", "dist", "pt", "runmed",
             "smooth.spline", "start")
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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... WARNING
Found the following significant warnings:

  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
* 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, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.6-bioc/meat/charm.Rcheck/00check.log’
for details.

Installation output

charm.Rcheck/00install.out

* installing *source* package ‘charm’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (charm)

Tests output

Example timings

charm.Rcheck/charm-Ex.timings

nameusersystemelapsed
bgAdjust000
clusterMaker000
cmdsplot000
controlQC000