Back to the "Multiple platform build/check report" A  B  C  D [E] F  G  H  I  J  K  L  M  N  O  P  Q  R  S  T  U  V  W  X  Y  Z 

BioC 3.4: CHECK report for EBSeqHMM on malbec1

This page was generated on 2017-04-15 16:12:35 -0400 (Sat, 15 Apr 2017).

Package 362/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
EBSeqHMM 1.8.0
Ning Leng
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/EBSeqHMM
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: EBSeqHMM
Version: 1.8.0
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings EBSeqHMM_1.8.0.tar.gz
StartedAt: 2017-04-14 22:15:04 -0400 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 22:15:31 -0400 (Fri, 14 Apr 2017)
EllapsedTime: 27.1 seconds
RetCode: 0
Status:  OK 
CheckDir: EBSeqHMM.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings EBSeqHMM_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/EBSeqHMM.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.8.0’
* 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 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
  ‘/home/biocbuild/bbs-3.4-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_2chain0.6720.0080.683
EBHMMNBfun0.040.000.04
EBHMMNBfunForMulti0.3720.0000.373
EBSeqHMM-package0.6480.0000.648
EBSeqHMMTest0.6440.0000.642
EBTest_ext0.0960.0000.099
GeneExampleData0.0040.0000.005
GetAllPaths0.6480.0000.647
GetConfidentCalls0.6400.0040.643
GetDECalls0.6160.0000.616
IsoExampleList0.0040.0000.005
LikefunNBHMM0.0040.0000.006
PlotExp0.0040.0040.006
beta.mom000
f00.0040.0000.001