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BioC 3.4: CHECK report for ABSSeq on morelia

This page was generated on 2017-04-15 16:25:25 -0400 (Sat, 15 Apr 2017).

Package 9/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ABSSeq 1.20.4
Wentao Yang
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/ABSSeq
Last Changed Rev: 126789 / Revision: 128728
Last Changed Date: 2017-02-17 06:49:20 -0500 (Fri, 17 Feb 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: ABSSeq
Version: 1.20.4
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ABSSeq_1.20.4.tar.gz
StartedAt: 2017-04-14 22:21:06 -0700 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 22:22:22 -0700 (Fri, 14 Apr 2017)
EllapsedTime: 75.9 seconds
RetCode: 0
Status:  OK 
CheckDir: ABSSeq.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ABSSeq_1.20.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/ABSSeq.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.20.4’
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
ReplaceOutliersByMAD: no visible global function definition for
  ‘model.matrix’
ReplaceOutliersByMAD: no visible global function definition for
  ‘predict’
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 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 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’
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 ‘quantile’
genAFold: no visible global function definition for ‘var’
normalFactors : rowQuar: no visible global function definition for
  ‘quantile’
plotDifftoBase: no visible global function definition for ‘plot’
preAFold: no visible global function definition for ‘predict’
replaceByrow: no visible global function definition for ‘median’
replaceByrow: no visible global function definition for ‘mad’
Undefined global functions or variables:
  mad median model.matrix p.adjust p.adjust.methods plot pnbinom pnorm
  predict quantile sd var
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "mad", "median", "model.matrix", "p.adjust",
             "p.adjust.methods", "pnbinom", "pnorm", "predict",
             "quantile", "sd", "var")
to your NAMESPACE file.
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
callParameter  7.001  0.047   7.056
callDEs        6.787  0.042   6.836
ABSSeq         6.644  0.065   6.712
results        6.602  0.056   6.663
plotDifftoBase 6.491  0.052   6.549
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.4-bioc/meat/ABSSeq.Rcheck/00check.log’
for details.


ABSSeq.Rcheck/00install.out:

* installing *source* package ‘ABSSeq’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ABSSeq)

ABSSeq.Rcheck/ABSSeq-Ex.timings:

nameusersystemelapsed
ABSDataSet0.0170.0010.018
ABSSeq6.6440.0656.712
LevelstoNormFC0.0320.0040.036
ReplaceOutliersByMAD2.9110.0242.937
callDEs6.7870.0426.836
callParameter7.0010.0477.056
callParameterwithoutReplicates1.5100.0161.526
counts0.0320.0050.038
estimateSizeFactorsForMatrix0.0530.0050.059
excounts2.9980.0193.019
genAFold2.5270.0262.562
groups0.0390.0050.043
maxRates0.0380.0030.041
minRates0.0710.0050.076
minimalDispersion0.0410.0030.045
normMethod0.0320.0040.035
normalFactors0.0620.0070.069
paired0.0350.0100.044
plotDifftoBase6.4910.0526.549
results6.6020.0566.663
sFactors0.0710.0110.081
simuN50.0360.0050.041