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CHECK report for ABSSeq on celaya2

This page was generated on 2019-10-16 12:52:58 -0400 (Wed, 16 Oct 2019).

Package 10/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ABSSeq 1.38.0
Wentao Yang
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/ABSSeq
Branch: RELEASE_3_9
Last Commit: b686d92
Last Changed Date: 2019-05-02 11:53:47 -0400 (Thu, 02 May 2019)
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

Summary

Package: ABSSeq
Version: 1.38.0
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_1.38.0.tar.gz
StartedAt: 2019-10-16 00:23:04 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 00:26:36 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 212.3 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_1.38.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/ABSSeq.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.38.0’
* 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 : : 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
callParameter        16.167  1.818  18.213
ABSSeq               15.836  2.058  17.899
results              16.055  1.821  17.890
callDEs              15.536  1.801  17.426
plotDifftoBase       15.433  1.805  17.253
excounts             12.768  1.585  14.607
ReplaceOutliersByMAD 12.447  1.760  14.207
ABSSeqlm              9.454  1.627  11.319
aFoldcomplexDesign    5.957  0.920   6.877
genAFold              5.708  0.786   6.516
* 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’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ABSSeq)

Tests output


Example timings

ABSSeq.Rcheck/ABSSeq-Ex.timings

nameusersystemelapsed
ABSDataSet0.0490.0000.050
ABSSeq15.836 2.05817.899
ABSSeqlm 9.454 1.62711.319
LevelstoNormFC0.0360.0080.043
ReplaceOutliersByMAD12.447 1.76014.207
aFoldcomplexDesign5.9570.9206.877
callDEs15.536 1.80117.426
callParameter16.167 1.81818.213
callParameterwithoutReplicates2.6370.1642.831
counts0.0540.0160.072
estimateSizeFactorsForMatrix0.0840.0270.110
excounts12.768 1.58514.607
genAFold5.7080.7866.516
groups0.0460.0110.056
maxRates0.0550.0140.069
minRates0.0510.0140.066
minimalDispersion0.0530.0130.066
normMethod0.0550.0150.070
normalFactors3.4510.8664.321
paired0.0370.0060.043
plotDifftoBase15.433 1.80517.253
qtotalNormalized3.6150.8584.475
results16.055 1.82117.890
sFactors3.7740.7464.554
simuN50.0470.0070.058