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BioC 3.0: CHECK report for EBSeq on oaxaca

This page was generated on 2015-04-10 10:07:21 -0700 (Fri, 10 Apr 2015).

Package 266/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
EBSeq 1.6.0
Ning Leng
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/EBSeq
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK 

Summary

Package: EBSeq
Version: 1.6.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch EBSeq_1.6.0.tar.gz
StartedAt: 2015-04-09 23:08:38 -0700 (Thu, 09 Apr 2015)
EndedAt: 2015-04-09 23:09:40 -0700 (Thu, 09 Apr 2015)
EllapsedTime: 61.7 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 --no-multiarch EBSeq_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/EBSeq.Rcheck’
* using R version 3.1.3 (2015-03-09)
* 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 ‘1.6.0’
* 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 ... [2s/2s] 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 ‘gplots’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘blockmodeling’ ‘gplots’
  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
EBMultiTest : <anonymous>: no visible global function definition for
  ‘nkpartitions’
EBMultiTest: no visible global function definition for ‘nkpartitions’
GetPatterns : <anonymous>: no visible global function definition for
  ‘nkpartitions’
PlotPostVsRawFC: no visible global function definition for ‘redgreen’
* 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 ... [31s/31s] OK
Examples with CPU or elapsed time > 5s
             user system elapsed
GetMultiFC  6.479  0.012   6.554
EBMultiTest 6.467  0.016   6.567
GetMultiPP  6.253  0.013   6.284
* 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

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-3.0-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
DenNHist3.2120.0283.357
EBMultiTest6.4670.0166.567
EBSeq_NingLeng-package0.5310.0050.538
EBTest0.5580.0120.582
GeneMat0.0030.0000.004
GetMultiFC6.4790.0126.554
GetMultiPP6.2530.0136.284
GetNg0.0100.0020.011
GetNormalizedMat0.0080.0010.009
GetPP0.6040.0110.615
GetPPMat0.6160.0080.624
GetPatterns0.0020.0000.002
IsoList0.0040.0000.005
IsoMultiList0.0030.0000.003
Likefun0.0000.0000.001
LikefunMulti0.0010.0000.001
LogN0.0000.0000.001
LogNMulti0.0010.0000.001
MedianNorm0.0060.0010.006
MultiGeneMat0.0020.0010.003
PlotPattern0.0100.0010.011
PlotPostVsRawFC0.8980.0110.909
PolyFitPlot0.0170.0010.018
PostFC0.6170.0070.623
QQP3.1440.0143.160
QuantileNorm0.0050.0000.005
RankNorm0.0200.0010.020
beta.mom000
crit_fun0.7430.0080.752
f00.0000.0000.001
f1000