Package: EMDomics

Version: 2.17.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:EMDomics.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings EMDomics_2.17.0.tar.gz

StartedAt: 2020-01-16 04:05:28 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 04:07:54 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 145.7 seconds

RetCode: 0

Status:  OK

CheckDir: EMDomics.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:EMDomics.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings EMDomics_2.17.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/EMDomics.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘2.17.0’
* 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 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
calculate_cvm    13.489  0.373  13.866
plot_cvmperms    13.371  0.308  13.679
plot_cvm_density 13.279  0.302  13.581
plot_emd_density  7.741  0.226   7.970
plot_emdperms     7.599  0.217   7.816
calculate_emd     7.282  0.261   7.544
plot_cvmnull      5.070  0.111   5.182
* 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-3.11-bioc/meat/EMDomics.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL EMDomics
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘EMDomics’ ...
** using staged installation
** R
** 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 (EMDomics)

name	user	system	elapsed
calculate_cvm	13.489	0.373	13.866
calculate_cvm_gene	0.014	0.001	0.015
calculate_emd	7.282	0.261	7.544
calculate_emd_gene	0.009	0.001	0.010
calculate_ks	2.033	0.101	2.136
calculate_ks_gene	0.018	0.004	0.021
plot_cvm_density	13.279	0.302	13.581
plot_cvmnull	5.070	0.111	5.182
plot_cvmperms	13.371	0.308	13.679
plot_emd_density	7.741	0.226	7.970
plot_emdnull	2.963	0.095	3.058
plot_emdperms	7.599	0.217	7.816
plot_ks_density	2.471	0.101	2.571
plot_ksnull	1.063	0.044	1.107
plot_ksperms	2.411	0.086	2.497