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CHECK report for ABSSeq on merida2

This page was generated on 2018-10-17 08:52:45 -0400 (Wed, 17 Oct 2018).

Package 9/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ABSSeq 1.34.1
Wentao Yang
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/ABSSeq
Branch: RELEASE_3_7
Last Commit: 0c3a251
Last Changed Date: 2018-06-28 13:58:45 -0400 (Thu, 28 Jun 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: ABSSeq
Version: 1.34.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ABSSeq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ABSSeq_1.34.1.tar.gz
StartedAt: 2018-10-16 19:46:55 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 19:50:03 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 187.5 seconds
RetCode: 0
Status:  OK 
CheckDir: ABSSeq.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ABSSeq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ABSSeq_1.34.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/ABSSeq.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ABSSeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ABSSeq’ version ‘1.34.1’
* 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 ‘ABSSeq’ 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 dependencies in R code ... NOTE
'library' or 'require' call to ‘edgeR’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
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.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
ABSDataSet: no visible global function definition for ‘new’
ABSSeqlm: no visible global function definition for ‘pnorm’
ABSSeqlm: no visible global function definition for ‘p.adjust’
ReplaceOutliersByMAD: no visible global function definition for ‘is’
ReplaceOutliersByMAD: no visible global function definition for
  ‘model.matrix’
ReplaceOutliersByMAD: no visible global function definition for
  ‘predict’
aFoldcomplexDesign: no visible binding for global variable ‘sd’
aFoldcomplexDesign: no visible binding for global variable ‘var’
aFoldcomplexDesign: no visible global function definition for ‘sd’
callDEs: no visible global function definition for ‘is’
callDEs: no visible binding for global variable ‘p.adjust.methods’
callDEs: no visible global function definition for ‘pnorm’
callDEs: no visible global function definition for ‘pnbinom’
callDEs: no visible global function definition for ‘p.adjust’
callParameter: no visible global function definition for ‘is’
callParameter: no visible binding for global variable ‘var’
callParameter: no visible global function definition for ‘quantile’
callParameter: no visible global function definition for ‘predict’
callParameter: no visible global function definition for ‘model.matrix’
callParameterwithoutReplicates: no visible global function definition
  for ‘is’
callParameterwithoutReplicates: no visible binding for global variable
  ‘sd’
callParameterwithoutReplicates: no visible global function definition
  for ‘predict’
callParameterwithoutReplicates: no visible binding for global variable
  ‘var’
callParameterwithoutReplicates: no visible global function definition
  for ‘quantile’
callParameterwithoutReplicates: no visible global function definition
  for ‘model.matrix’
callPergroup: no visible binding for global variable ‘var’
estimateSizeFactorsForMatrix: no visible binding for global variable
  ‘median’
genAFold: no visible binding for global variable ‘var’
genAFold: no visible binding for global variable ‘sd’
genAFold: no visible global function definition for ‘sd’
normalFactors: no visible global function definition for ‘is’
normalFactors: no visible global function definition for ‘validObject’
normalFactors : rowQuar: no visible global function definition for
  ‘quantile’
normalFactors: no visible global function definition for
  ‘calcNormFactors’
plotDifftoBase: no visible global function definition for ‘is’
plotDifftoBase: no visible global function definition for ‘plot’
preAFold: no visible global function definition for ‘quantile’
preAFold: no visible global function definition for ‘var’
preAFold: no visible global function definition for ‘predict’
preAFoldComplex: no visible global function definition for ‘quantile’
preAFoldComplex: no visible global function definition for ‘var’
preAFoldComplex: no visible global function definition for ‘predict’
qtotalNormalized : rowQuar: no visible global function definition for
  ‘quantile’
qtotalNormalized : rowQuar: no visible global function definition for
  ‘sd’
qtotalNormalized : rowQuar: no visible global function definition for
  ‘median’
qtotalNormalized : rowQuar : <anonymous>: no visible global function
  definition for ‘median’
replaceByrow: no visible global function definition for ‘median’
replaceByrow: no visible global function definition for ‘mad’
LevelstoNormFC<-,ABSDataSet-numeric: no visible global function
  definition for ‘validObject’
[[<-,SumInfo-character-missing: no visible global function definition
  for ‘as’
counts<-,ABSDataSet-matrix: no visible global function definition for
  ‘validObject’
excounts<-,ABSDataSet-matrix: no visible global function definition for
  ‘validObject’
groups<-,ABSDataSet-factor: no visible global function definition for
  ‘validObject’
maxRates<-,ABSDataSet-numeric: no visible global function definition
  for ‘validObject’
minRates<-,ABSDataSet-numeric: no visible global function definition
  for ‘validObject’
minimalDispersion<-,ABSDataSet-numeric: no visible global function
  definition for ‘validObject’
normMethod<-,ABSDataSet-character: no visible global function
  definition for ‘validObject’
paired<-,ABSDataSet-logical: no visible global function definition for
  ‘validObject’
sFactors<-,ABSDataSet-numeric: no visible global function definition
  for ‘validObject’
Undefined global functions or variables:
  as calcNormFactors is mad median model.matrix new p.adjust
  p.adjust.methods plot pnbinom pnorm predict quantile sd validObject
  var
Consider adding
  importFrom("graphics", "plot")
  importFrom("methods", "as", "is", "new", "validObject")
  importFrom("stats", "mad", "median", "model.matrix", "p.adjust",
             "p.adjust.methods", "pnbinom", "pnorm", "predict",
             "quantile", "sd", "var")
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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
results              19.337  0.864  21.628
plotDifftoBase       17.013  0.762  17.884
ABSSeq               16.695  0.810  17.612
callDEs              15.822  0.762  16.679
callParameter        14.923  0.816  15.812
ABSSeqlm             10.291  0.632  11.021
ReplaceOutliersByMAD  9.486  0.706  10.276
excounts              9.448  0.718  10.256
genAFold              7.851  0.377   8.297
aFoldcomplexDesign    6.963  0.331   7.344
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.7-bioc/meat/ABSSeq.Rcheck/00check.log’
for details.



Installation output

ABSSeq.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ABSSeq
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘ABSSeq’ ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ABSSeq)

Tests output


Example timings

ABSSeq.Rcheck/ABSSeq-Ex.timings

nameusersystemelapsed
ABSDataSet0.0750.0010.078
ABSSeq16.695 0.81017.612
ABSSeqlm10.291 0.63211.021
LevelstoNormFC0.0530.0060.060
ReplaceOutliersByMAD 9.486 0.70610.276
aFoldcomplexDesign6.9630.3317.344
callDEs15.822 0.76216.679
callParameter14.923 0.81615.812
callParameterwithoutReplicates3.5490.0903.681
counts0.0430.0050.049
estimateSizeFactorsForMatrix0.0610.0040.066
excounts 9.448 0.71810.256
genAFold7.8510.3778.297
groups0.0470.0040.051
maxRates0.0480.0040.051
minRates0.0430.0040.048
minimalDispersion0.0470.0040.051
normMethod0.0530.0040.057
normalFactors2.6630.3633.039
paired0.0500.0050.055
plotDifftoBase17.013 0.76217.884
qtotalNormalized3.2890.3933.707
results19.337 0.86421.628
sFactors3.1350.3533.539
simuN50.0430.0040.046