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BioC 3.5: CHECK report for EBSeqHMM on oaxaca

This page was generated on 2017-03-04 16:48:43 -0500 (Sat, 04 Mar 2017).

Package 369/1339HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
EBSeqHMM 1.9.0
Ning Leng
Snapshot Date: 2017-03-03 17:15:47 -0500 (Fri, 03 Mar 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/EBSeqHMM
Last Changed Rev: 122712 / Revision: 127142
Last Changed Date: 2016-10-17 15:10:43 -0400 (Mon, 17 Oct 2016)
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: EBSeqHMM
Version: 1.9.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings EBSeqHMM_1.9.0.tar.gz
StartedAt: 2017-03-04 02:09:15 -0800 (Sat, 04 Mar 2017)
EndedAt: 2017-03-04 02:09:54 -0800 (Sat, 04 Mar 2017)
EllapsedTime: 39.2 seconds
RetCode: 0
Status:  OK 
CheckDir: EBSeqHMM.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings EBSeqHMM_1.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/EBSeqHMM.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 ‘EBSeqHMM/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘EBSeqHMM’ version ‘1.9.0’
* 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 ‘EBSeqHMM’ 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
EBHMMNBfun: no visible binding for global variable ‘median’
EBHMMNBfun : <anonymous>: no visible global function definition for
  ‘quantile’
EBHMMNBfun: no visible global function definition for ‘optim’
EBHMMNBfunForMulti: no visible binding for global variable ‘median’
EBHMMNBfunForMulti : <anonymous>: no visible global function definition
  for ‘quantile’
EBHMMNBfunForMulti: no visible global function definition for ‘optim’
EBSeqHMMTest : <anonymous>: no visible global function definition for
  ‘quantile’
EBTest_ext: no visible global function definition for ‘quantile’
EBTest_ext: no visible binding for global variable ‘var’
PlotExp: no visible global function definition for ‘plot’
PlotExp: no visible global function definition for ‘axis’
PlotExp : <anonymous>: no visible global function definition for
  ‘median’
PlotExp: no visible global function definition for ‘lines’
beta.mom: no visible global function definition for ‘var’
Undefined global functions or variables:
  axis lines median optim plot quantile var
Consider adding
  importFrom("graphics", "axis", "lines", "plot")
  importFrom("stats", "median", "optim", "quantile", "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
* 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/EBSeqHMM.Rcheck/00check.log’
for details.


EBSeqHMM.Rcheck/00install.out:

* installing *source* package ‘EBSeqHMM’ ...
** 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 (EBSeqHMM)

EBSeqHMM.Rcheck/EBSeqHMM-Ex.timings:

nameusersystemelapsed
EBHMMNBMultiEM_2chain3.3710.0293.403
EBHMMNBfun0.1150.0010.116
EBHMMNBfunForMulti0.3670.0060.373
EBSeqHMM-package1.0750.0071.082
EBSeqHMMTest0.9690.0070.976
EBTest_ext0.2010.0010.202
GeneExampleData0.0090.0010.010
GetAllPaths0.8700.0070.876
GetConfidentCalls0.8060.0110.818
GetDECalls0.7840.0100.794
IsoExampleList0.0100.0010.011
LikefunNBHMM0.0100.0010.012
PlotExp0.0080.0020.009
beta.mom0.0010.0000.001
f00.0010.0010.002