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CHECK report for ABSSeq on malbec1

This page was generated on 2020-04-15 12:08:33 -0400 (Wed, 15 Apr 2020).

Package 10/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ABSSeq 1.40.0
Wentao Yang
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/ABSSeq
Branch: RELEASE_3_10
Last Commit: 13635c2
Last Changed Date: 2019-10-29 13:08:54 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  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: ABSSeq
Version: 1.40.0
Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:ABSSeq.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings ABSSeq_1.40.0.tar.gz
StartedAt: 2020-04-15 02:08:00 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 02:10:16 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 135.2 seconds
RetCode: 0
Status:  OK 
CheckDir: ABSSeq.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:ABSSeq.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings ABSSeq_1.40.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/ABSSeq.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (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 ‘1.40.0’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
ABSSeq               13.212  0.032  13.271
callDEs              12.152  0.008  12.180
callParameter        12.156  0.000  12.177
results              10.792  0.004  10.820
plotDifftoBase       10.516  0.004  10.550
ReplaceOutliersByMAD 10.440  0.000  10.465
excounts              8.908  0.004   8.920
ABSSeqlm              7.940  0.008   7.978
aFoldcomplexDesign    5.208  0.004   5.224
* 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
  ‘/home/biocbuild/bbs-3.10-bioc/meat/ABSSeq.Rcheck/00check.log’
for details.



Installation output

ABSSeq.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL ABSSeq
###
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/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
ABSDataSet0.0680.0000.067
ABSSeq13.212 0.03213.271
ABSSeqlm7.9400.0087.978
LevelstoNormFC0.0360.0000.035
ReplaceOutliersByMAD10.440 0.00010.465
aFoldcomplexDesign5.2080.0045.224
callDEs12.152 0.00812.180
callParameter12.156 0.00012.177
callParameterwithoutReplicates1.3640.0001.368
counts0.0280.0000.032
estimateSizeFactorsForMatrix0.0440.0000.047
excounts8.9080.0048.920
genAFold4.8600.0004.873
groups0.0560.0000.053
maxRates0.0480.0040.051
minRates0.040.000.04
minimalDispersion0.0320.0000.033
normMethod0.0360.0000.034
normalFactors3.1720.0003.178
paired0.0480.0040.055
plotDifftoBase10.516 0.00410.550
qtotalNormalized2.5320.0002.530
results10.792 0.00410.820
sFactors3.0880.0003.092
simuN50.0480.0000.047