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BioC 3.5: CHECK report for EBSeq on toluca2

This page was generated on 2017-04-23 14:37:22 -0400 (Sun, 23 Apr 2017).

Package 382/1377HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
EBSeq 1.15.0
Ning Leng
Snapshot Date: 2017-04-22 17:18:01 -0400 (Sat, 22 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/EBSeq
Last Changed Rev: 122712 / Revision: 129046
Last Changed Date: 2016-10-17 15:10:43 -0400 (Mon, 17 Oct 2016)
malbec2 Linux (Ubuntu 16.04.1 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
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK 
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: EBSeq
Version: 1.15.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings EBSeq_1.15.0.tar.gz
StartedAt: 2017-04-23 03:17:43 -0400 (Sun, 23 Apr 2017)
EndedAt: 2017-04-23 03:18:45 -0400 (Sun, 23 Apr 2017)
EllapsedTime: 62.2 seconds
RetCode: 0
Status:  OK 
CheckDir: EBSeq.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings EBSeq_1.15.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/EBSeq.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘EBSeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘EBSeq’ version ‘1.15.0’
* 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 ‘EBSeq’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
DenNHist: no visible global function definition for ‘hist’
DenNHist: no visible global function definition for ‘lines’
DenNHist: no visible global function definition for ‘dbeta’
DenNHist: no visible global function definition for ‘legend’
EBMultiTest : <anonymous>: no visible global function definition for
  ‘quantile’
EBMultiTest: no visible global function definition for ‘quantile’
EBMultiTest : <anonymous>: no visible binding for global variable ‘var’
EBMultiTest: no visible binding for global variable ‘var’
EBTest : <anonymous>: no visible global function definition for
  ‘quantile’
EBTest: no visible global function definition for ‘quantile’
EBTest: no visible binding for global variable ‘var’
GetDEResults: no visible binding for global variable ‘median’
LogN: no visible global function definition for ‘optim’
LogNMulti: no visible global function definition for ‘optim’
MedianNorm : <anonymous>: no visible global function definition for
  ‘median’
MedianNorm : <anonymous> : <anonymous>: no visible global function
  definition for ‘median’
PlotPattern: no visible global function definition for ‘par’
PlotPattern: no visible global function definition for ‘rainbow’
PlotPattern: no visible global function definition for ‘heatmap’
PlotPostVsRawFC: no visible global function definition for ‘par’
PlotPostVsRawFC: no visible global function definition for ‘plot’
PlotPostVsRawFC: no visible global function definition for ‘abline’
PlotPostVsRawFC: no visible global function definition for ‘rect’
PolyFitPlot: no visible global function definition for ‘lm’
PolyFitPlot: no visible global function definition for ‘smoothScatter’
PolyFitPlot: no visible global function definition for ‘axis’
PolyFitPlot: no visible global function definition for ‘lines’
QQP: no visible global function definition for ‘rbeta’
QQP: no visible global function definition for ‘qqplot’
QQP: no visible global function definition for ‘lm’
QQP: no visible global function definition for ‘abline’
QuantileNorm : <anonymous>: no visible global function definition for
  ‘quantile’
beta.mom: no visible global function definition for ‘var’
Undefined global functions or variables:
  abline axis dbeta heatmap hist legend lines lm median optim par plot
  qqplot quantile rainbow rbeta rect smoothScatter var
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "abline", "axis", "hist", "legend", "lines",
             "par", "plot", "rect", "smoothScatter")
  importFrom("stats", "dbeta", "heatmap", "lm", "median", "optim",
             "qqplot", "quantile", "rbeta", "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
GetMultiFC  6.943  0.016   7.027
EBMultiTest 6.311  0.020   6.392
GetMultiPP  5.959  0.012   6.011
* 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-3.5-bioc/meat/EBSeq.Rcheck/00check.log’
for details.


EBSeq.Rcheck/00install.out:

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

EBSeq.Rcheck/EBSeq-Ex.timings:

nameusersystemelapsed
DenNHist2.3100.0482.392
EBMultiTest6.3110.0206.392
EBSeq_NingLeng-package1.4170.0131.444
EBTest0.4410.0090.454
GeneMat0.0030.0010.004
GetDEResults0.4310.0060.449
GetMultiFC6.9430.0167.027
GetMultiPP5.9590.0126.011
GetNg0.010.000.01
GetNormalizedMat0.0090.0000.010
GetPP0.4500.0060.461
GetPPMat0.5530.0080.567
GetPatterns0.0010.0000.002
IsoList0.0050.0010.005
IsoMultiList0.0020.0010.003
Likefun0.0010.0000.000
LikefunMulti000
LogN000
LogNMulti0.0000.0010.001
MedianNorm0.0040.0000.005
MultiGeneMat0.0020.0010.003
PlotPattern0.0090.0020.011
PlotPostVsRawFC0.8230.0080.834
PolyFitPlot0.0330.0010.034
PostFC0.5670.0070.576
QQP2.0320.0092.066
QuantileNorm0.0470.0010.049
RankNorm0.0140.0010.015
beta.mom0.0010.0000.000
crit_fun0.5650.0080.574
f00.0000.0000.001
f10.0010.0000.001