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CHECK report for ABSSeq on merida2

This page was generated on 2019-04-09 13:29:29 -0400 (Tue, 09 Apr 2019).

Package 10/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ABSSeq 1.37.0
Wentao Yang
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/ABSSeq
Branch: master
Last Commit: 1781e4e
Last Changed Date: 2018-10-30 11:54:32 -0400 (Tue, 30 Oct 2018)
malbec2 Linux (Ubuntu 18.04.2 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
celaya2 OS X 10.11.6 El Capitan / x86_64  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 

Summary

Package: ABSSeq
Version: 1.37.0
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_1.37.0.tar.gz
StartedAt: 2019-04-08 23:07:28 -0400 (Mon, 08 Apr 2019)
EndedAt: 2019-04-08 23:10:59 -0400 (Mon, 08 Apr 2019)
EllapsedTime: 210.1 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_1.37.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/ABSSeq.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* 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 ‘1.37.0’
* 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 ‘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
plotDifftoBase       20.085  0.867  22.361
callDEs              19.719  0.754  20.790
ABSSeq               19.038  0.953  20.200
callParameter        18.088  0.606  18.897
results              17.674  0.871  18.689
ABSSeqlm             10.682  0.759  11.552
ReplaceOutliersByMAD 10.290  0.782  11.184
excounts             10.034  0.788  10.883
aFoldcomplexDesign    8.002  0.394   8.462
genAFold              7.982  0.378   8.472
* 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-3.9-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/3.6/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
ABSDataSet0.0540.0010.056
ABSSeq19.038 0.95320.200
ABSSeqlm10.682 0.75911.552
LevelstoNormFC0.0450.0030.049
ReplaceOutliersByMAD10.290 0.78211.184
aFoldcomplexDesign8.0020.3948.462
callDEs19.719 0.75420.790
callParameter18.088 0.60618.897
callParameterwithoutReplicates3.9480.1054.081
counts0.0530.0070.060
estimateSizeFactorsForMatrix0.0640.0060.070
excounts10.034 0.78810.883
genAFold7.9820.3788.472
groups0.0430.0040.047
maxRates0.0420.0040.046
minRates0.0360.0040.040
minimalDispersion0.0390.0040.043
normMethod0.0470.0050.053
normalFactors3.0640.4573.555
paired0.0440.0030.047
plotDifftoBase20.085 0.86722.361
qtotalNormalized3.1570.3463.532
results17.674 0.87118.689
sFactors2.9540.3373.315
simuN50.0370.0060.044