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CHECK report for CGHbase on malbec1

This page was generated on 2019-04-16 11:48:35 -0400 (Tue, 16 Apr 2019).

Package 228/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CGHbase 1.42.0
Mark van de Wiel
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/CGHbase
Branch: RELEASE_3_8
Last Commit: 56c1525
Last Changed Date: 2018-10-30 11:41:44 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: CGHbase
Version: 1.42.0
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:CGHbase.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings CGHbase_1.42.0.tar.gz
StartedAt: 2019-04-15 22:45:25 -0400 (Mon, 15 Apr 2019)
EndedAt: 2019-04-15 22:46:02 -0400 (Mon, 15 Apr 2019)
EllapsedTime: 37.0 seconds
RetCode: 0
Status:  OK 
CheckDir: CGHbase.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:CGHbase.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings CGHbase_1.42.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/CGHbase.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CGHbase/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CGHbase’ version ‘1.42.0’
* 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 ‘CGHbase’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' call which should be '::': ‘Biobase:::assayDataElement’
  See the note in ?`:::` about the use of this operator.
Unexported object imported by a ':::' call: ‘Biobase:::assayDataDims’
  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
.makeEmptyFeatureData: no visible global function definition for ‘is’
.makeEmptyFeatureData: no visible global function definition for ‘new’
.makeEmptyFeatureDataForRegions: no visible global function definition
  for ‘is’
.makeEmptyFeatureDataForRegions: no visible global function definition
  for ‘new’
frequencyPlotCalls: no visible global function definition for ‘rect’
frequencyPlotCalls: no visible global function definition for ‘box’
frequencyPlotCalls: no visible global function definition for ‘abline’
frequencyPlotCalls: no visible global function definition for ‘axis’
frequencyPlotCalls: no visible global function definition for ‘mtext’
frequencyPlotCalls: no visible global function definition for ‘median’
make_cghRaw: no visible global function definition for ‘read.table’
make_cghRaw: no visible global function definition for ‘new’
summaryPlot: no visible global function definition for ‘rect’
summaryPlot: no visible global function definition for ‘box’
summaryPlot: no visible global function definition for ‘abline’
summaryPlot: no visible global function definition for ‘axis’
summaryPlot: no visible global function definition for ‘mtext’
summaryPlot: no visible global function definition for ‘median’
frequencyPlot,cghRegions-missing: no visible global function definition
  for ‘par’
frequencyPlot,cghRegions-missing: no visible global function definition
  for ‘barplot’
frequencyPlot,cghRegions-missing: no visible global function definition
  for ‘segments’
frequencyPlot,cghRegions-missing: no visible global function definition
  for ‘gray’
frequencyPlot,cghRegions-missing: no visible global function definition
  for ‘box’
frequencyPlot,cghRegions-missing: no visible global function definition
  for ‘axis’
initialize,cghCall: no visible global function definition for ‘new’
initialize,cghCall: no visible global function definition for
  ‘callNextMethod’
initialize,cghRaw: no visible global function definition for ‘new’
initialize,cghRaw: no visible global function definition for
  ‘callNextMethod’
initialize,cghRegions: no visible global function definition for ‘new’
initialize,cghRegions: no visible global function definition for
  ‘callNextMethod’
initialize,cghSeg: no visible global function definition for ‘new’
initialize,cghSeg: no visible global function definition for
  ‘callNextMethod’
plot.cghRegions,cghRegions-missing: no visible global function
  definition for ‘layout’
plot.cghRegions,cghRegions-missing: no visible global function
  definition for ‘par’
plot.cghRegions,cghRegions-missing: no visible global function
  definition for ‘segments’
plot.cghRegions,cghRegions-missing: no visible global function
  definition for ‘axis’
plot,cghCall-missing: no visible global function definition for ‘par’
plot,cghCall-missing: no visible global function definition for ‘rect’
plot,cghCall-missing: no visible global function definition for ‘axis’
plot,cghCall-missing: no visible global function definition for ‘box’
plot,cghCall-missing: no visible global function definition for
  ‘abline’
plot,cghCall-missing: no visible global function definition for ‘mtext’
plot,cghCall-missing: no visible global function definition for ‘title’
plot,cghCall-missing: no visible global function definition for
  ‘segments’
plot,cghCall-missing: no visible global function definition for
  ‘median’
plot,cghCall-missing : <anonymous>: no visible global function
  definition for ‘mad’
plot,cghRaw-missing: no visible global function definition for ‘mtext’
plot,cghRaw-missing: no visible global function definition for ‘abline’
plot,cghRaw-missing: no visible global function definition for ‘axis’
plot,cghRaw-missing: no visible global function definition for ‘median’
plot,cghRaw-missing : <anonymous>: no visible global function
  definition for ‘mad’
plot,cghSeg-missing: no visible global function definition for ‘mtext’
plot,cghSeg-missing: no visible global function definition for ‘abline’
plot,cghSeg-missing: no visible global function definition for ‘axis’
plot,cghSeg-missing: no visible global function definition for
  ‘segments’
plot,cghSeg-missing: no visible global function definition for ‘median’
plot,cghSeg-missing : <anonymous>: no visible global function
  definition for ‘mad’
Undefined global functions or variables:
  abline axis barplot box callNextMethod gray is layout mad median
  mtext new par read.table rect segments title
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "abline", "axis", "barplot", "box", "layout",
             "mtext", "par", "rect", "segments", "title")
  importFrom("methods", "callNextMethod", "is", "new")
  importFrom("stats", "mad", "median")
  importFrom("utils", "read.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 examples ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.8-bioc/meat/CGHbase.Rcheck/00check.log’
for details.



Installation output

CGHbase.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL CGHbase
###
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘CGHbase’ ...
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (CGHbase)

Tests output


Example timings

CGHbase.Rcheck/CGHbase-Ex.timings

nameusersystemelapsed
class.cghCall0.1120.0080.120
class.cghRaw0.3480.0120.359
class.cghRegions0.2600.0000.258
class.cghSeg0.0480.0040.052
copynumber0.0560.0000.055
frequencyPlot0.0000.0000.001
frequencyPlotCalls000
make_cghRaw0.0760.0080.088
summaryPlot0.0000.0000.001