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CHECK report for ABSSeq on celaya2

This page was generated on 2020-01-16 13:38:43 -0500 (Thu, 16 Jan 2020).

Package 10/1818HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ABSSeq 1.41.0
Wentao Yang
Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020)
URL: https://git.bioconductor.org/packages/ABSSeq
Branch: master
Last Commit: c32f4db
Last Changed Date: 2019-10-29 13:37:20 -0500 (Tue, 29 Oct 2019)
malbec2 Linux (Ubuntu 18.04.3 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: 1.41.0
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_1.41.0.tar.gz
StartedAt: 2020-01-16 01:31:58 -0500 (Thu, 16 Jan 2020)
EndedAt: 2020-01-16 01:35:39 -0500 (Thu, 16 Jan 2020)
EllapsedTime: 221.0 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_1.41.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/ABSSeq.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘1.41.0’
* 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 (user + system) or elapsed time > 5s
                       user system elapsed
callParameter        17.285  1.648  19.216
callDEs              16.876  1.649  18.711
ABSSeq               16.585  1.796  18.400
plotDifftoBase       16.597  1.698  18.307
results              16.590  1.652  18.250
excounts             12.880  1.442  14.566
ReplaceOutliersByMAD 12.611  1.578  14.189
ABSSeqlm              9.952  1.520  11.659
aFoldcomplexDesign    5.832  0.799   6.633
genAFold              5.694  0.731   6.443
* 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-3.11-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/4.0/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
ABSDataSet0.1000.0000.101
ABSSeq16.585 1.79618.400
ABSSeqlm 9.952 1.52011.659
LevelstoNormFC0.0570.0110.068
ReplaceOutliersByMAD12.611 1.57814.189
aFoldcomplexDesign5.8320.7996.633
callDEs16.876 1.64918.711
callParameter17.285 1.64819.216
callParameterwithoutReplicates2.4490.1682.637
counts0.0530.0090.061
estimateSizeFactorsForMatrix0.0630.0110.076
excounts12.880 1.44214.566
genAFold5.6940.7316.443
groups0.0520.0110.062
maxRates0.0570.0170.073
minRates0.0360.0100.046
minimalDispersion0.0460.0110.057
normMethod0.0460.0130.060
normalFactors3.6310.8074.439
paired0.0550.0090.064
plotDifftoBase16.597 1.69818.307
qtotalNormalized3.5980.7794.387
results16.590 1.65218.250
sFactors3.7190.7834.502
simuN50.0470.0080.055