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BioC 3.5: CHECK report for EMDomics on veracruz2

This page was generated on 2017-10-18 14:33:19 -0400 (Wed, 18 Oct 2017).

Package 397/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
EMDomics 2.6.0
Sadhika Malladi and Daniel Schmolze
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/EMDomics
Branch: RELEASE_3_5
Last Commit: 692a791
Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017)
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
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: EMDomics
Version: 2.6.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings EMDomics_2.6.0.tar.gz
StartedAt: 2017-10-18 03:09:37 -0400 (Wed, 18 Oct 2017)
EndedAt: 2017-10-18 03:10:54 -0400 (Wed, 18 Oct 2017)
EllapsedTime: 77.1 seconds
RetCode: 0
Status:  OK 
CheckDir: EMDomics.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings EMDomics_2.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/EMDomics.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘EMDomics/DESCRIPTION’ ... OK
* this is package ‘EMDomics’ version ‘2.6.0’
* 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 ‘EMDomics’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Authors@R field gives more than one person with maintainer role:
  Sadhika Malladi <contact@sadhikamalladi.com> [aut, cre]
  Daniel Schmolze <emd@schmolze.com> [aut, cre]
* 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
.cvm_pairwise_q: no visible global function definition for ‘combn’
.cvm_pairwise_q : <anonymous>: no visible global function definition
  for ‘median’
.emd_gene_pairwise: no visible global function definition for ‘hist’
.emd_pairwise_q: no visible global function definition for ‘combn’
.emd_pairwise_q : <anonymous>: no visible global function definition
  for ‘median’
.ks_pairwise_table: no visible global function definition for ‘ks.test’
calculate_cvm: no visible global function definition for ‘combn’
calculate_cvm : <anonymous>: no visible global function definition for
  ‘median’
calculate_cvm_gene: no visible global function definition for ‘combn’
calculate_emd: no visible global function definition for ‘combn’
calculate_emd : <anonymous>: no visible global function definition for
  ‘median’
calculate_emd_gene: no visible global function definition for ‘combn’
calculate_ks: no visible global function definition for ‘combn’
calculate_ks : <anonymous>: no visible global function definition for
  ‘p.adjust’
calculate_ks : <anonymous>: no visible global function definition for
  ‘median’
calculate_ks_gene: no visible global function definition for ‘combn’
calculate_ks_gene: no visible global function definition for ‘ks.test’
Undefined global functions or variables:
  combn hist ks.test median p.adjust
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "ks.test", "median", "p.adjust")
  importFrom("utils", "combn")
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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
plot_cvm_density 8.400  0.065   8.683
plot_cvmperms    7.422  0.067   7.713
calculate_cvm    7.322  0.084   7.642
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/EMDomics.Rcheck/00check.log’
for details.


EMDomics.Rcheck/00install.out:

* installing *source* package ‘EMDomics’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (EMDomics)

EMDomics.Rcheck/EMDomics-Ex.timings:

nameusersystemelapsed
calculate_cvm7.3220.0847.642
calculate_cvm_gene0.0090.0000.009
calculate_emd4.1010.0514.244
calculate_emd_gene0.0060.0000.006
calculate_ks1.1720.0191.215
calculate_ks_gene0.0120.0010.014
plot_cvm_density8.4000.0658.683
plot_cvmnull3.1850.0253.276
plot_cvmperms7.4220.0677.713
plot_emd_density4.7030.0564.936
plot_emdnull1.6710.0221.747
plot_emdperms4.5510.0524.793
plot_ks_density1.5090.0261.582
plot_ksnull0.6950.0140.730
plot_ksperms1.3970.0241.497