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CHECK report for EBSeqHMM on merida2

This page was generated on 2018-10-17 08:53:57 -0400 (Wed, 17 Oct 2018).

Package 429/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
EBSeqHMM 1.14.0
Ning Leng
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/EBSeqHMM
Branch: RELEASE_3_7
Last Commit: 6b2a0ec
Last Changed Date: 2018-04-30 10:35:35 -0400 (Mon, 30 Apr 2018)
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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: EBSeqHMM
Version: 1.14.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:EBSeqHMM.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings EBSeqHMM_1.14.0.tar.gz
StartedAt: 2018-10-16 21:08:12 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 21:09:17 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 64.9 seconds
RetCode: 0
Status:  OK 
CheckDir: EBSeqHMM.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:EBSeqHMM.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings EBSeqHMM_1.14.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/EBSeqHMM.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.14.0’
* 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 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 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-3.7-bioc/meat/EBSeqHMM.Rcheck/00check.log’
for details.



Installation output

EBSeqHMM.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL EBSeqHMM
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘EBSeqHMM’ ...
** R
** data
** demo
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (EBSeqHMM)

Tests output


Example timings

EBSeqHMM.Rcheck/EBSeqHMM-Ex.timings

nameusersystemelapsed
EBHMMNBMultiEM_2chain0.9830.0271.020
EBHMMNBfun0.0810.0020.086
EBHMMNBfunForMulti0.2700.0120.283
EBSeqHMM-package0.9700.0140.994
EBSeqHMMTest1.0520.0101.081
EBTest_ext0.1570.0010.158
GeneExampleData0.0070.0010.008
GetAllPaths0.8770.0070.896
GetConfidentCalls0.9890.0071.013
GetDECalls0.9740.0080.993
IsoExampleList0.0120.0020.014
LikefunNBHMM0.0080.0010.009
PlotExp0.0070.0020.010
beta.mom0.0010.0000.002
f00.0020.0010.002