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CHECK report for EBSeqHMM on malbec2

This page was generated on 2019-04-09 11:40:23 -0400 (Tue, 09 Apr 2019).

Package 474/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
EBSeqHMM 1.17.1
Ning Leng
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/EBSeqHMM
Branch: master
Last Commit: 8600f85
Last Changed Date: 2019-01-04 13:30:28 -0400 (Fri, 04 Jan 2019)
malbec2 Linux (Ubuntu 18.04.2 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
celaya2 OS X 10.11.6 El Capitan / x86_64  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 

Summary

Package: EBSeqHMM
Version: 1.17.1
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:EBSeqHMM.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings EBSeqHMM_1.17.1.tar.gz
StartedAt: 2019-04-09 00:16:19 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 00:17:10 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 51.1 seconds
RetCode: 0
Status:  OK 
CheckDir: EBSeqHMM.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:EBSeqHMM.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings EBSeqHMM_1.17.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/EBSeqHMM.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-pc-linux-gnu (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 ‘1.17.1’
* 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 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
  ‘/home/biocbuild/bbs-3.9-bioc/meat/EBSeqHMM.Rcheck/00check.log’
for details.



Installation output

EBSeqHMM.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL EBSeqHMM
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘EBSeqHMM’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (EBSeqHMM)

Tests output


Example timings

EBSeqHMM.Rcheck/EBSeqHMM-Ex.timings

nameusersystemelapsed
EBHMMNBMultiEM_2chain0.4880.0040.492
EBHMMNBfun0.0440.0000.044
EBHMMNBfunForMulti0.1930.0080.201
EBSeqHMM-package0.4960.0000.497
EBSeqHMMTest0.480.000.48
EBTest_ext0.0910.0000.090
GeneExampleData0.0060.0000.006
GetAllPaths0.5190.0000.519
GetConfidentCalls0.4980.0000.498
GetDECalls0.4890.0040.493
IsoExampleList0.0060.0000.006
LikefunNBHMM0.0050.0000.005
PlotExp0.0040.0000.005
beta.mom0.0000.0000.001
f00.0000.0010.001