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BioC 3.5: CHECK report for ABSSeq on oaxaca

This page was generated on 2017-03-04 16:47:12 -0500 (Sat, 04 Mar 2017).

Package 9/1339HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ABSSeq 1.20.3
Wentao Yang
Snapshot Date: 2017-03-03 17:15:47 -0500 (Fri, 03 Mar 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ABSSeq
Last Changed Rev: 126788 / Revision: 127142
Last Changed Date: 2017-02-17 06:47:12 -0500 (Fri, 17 Feb 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK 

Summary

Package: ABSSeq
Version: 1.20.3
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ABSSeq_1.20.3.tar.gz
StartedAt: 2017-03-03 22:47:39 -0800 (Fri, 03 Mar 2017)
EndedAt: 2017-03-03 22:49:04 -0800 (Fri, 03 Mar 2017)
EllapsedTime: 84.7 seconds
RetCode: 0
Status:  OK 
CheckDir: ABSSeq.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ABSSeq_1.20.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/ABSSeq.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* 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 ‘1.20.3’
* 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
ABSSeq         8.589  0.086   8.689
callDEs        8.247  0.046   8.295
plotDifftoBase 7.611  0.061   7.675
callParameter  7.376  0.045   7.422
results        7.148  0.057   7.207
* 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-3.5-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
ABSDataSet0.1560.0030.159
ABSSeq8.5890.0868.689
LevelstoNormFC0.0350.0020.037
ReplaceOutliersByMAD3.7590.0213.781
callDEs8.2470.0468.295
callParameter7.3760.0457.422
callParameterwithoutReplicates1.7230.0151.738
counts0.0320.0070.039
estimateSizeFactorsForMatrix0.0600.0060.066
excounts3.4200.0293.449
genAFold2.7720.0252.802
groups0.0450.0030.048
maxRates0.0450.0030.047
minRates0.0420.0020.044
minimalDispersion0.0450.0020.047
normMethod0.0510.0030.054
normalFactors0.0730.0070.080
paired0.0510.0030.055
plotDifftoBase7.6110.0617.675
results7.1480.0577.207
sFactors0.1240.0090.133
simuN50.0330.0030.036