BioC 3.2: CHECK report for EMDomics on oaxaca

Package: EMDomics

Version: 2.0.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings EMDomics_2.0.0.tar.gz

StartedAt: 2016-04-22 23:51:05 -0700 (Fri, 22 Apr 2016)

EndedAt: 2016-04-22 23:52:38 -0700 (Fri, 22 Apr 2016)

EllapsedTime: 92.3 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 --no-vignettes --timings EMDomics_2.0.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/EMDomics.Rcheck’
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘EMDomics/DESCRIPTION’ ... OK
* this is package ‘EMDomics’ version ‘2.0.0’
* 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 ... [2s/4s] 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 ... OK
* 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’ ... NOTE
The following directory looks like a leftover from 'knitr':
  ‘figure’
Please remove from your package.
* checking examples ... [46s/52s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
plot_cvmperms    9.042  0.032   9.244
plot_cvm_density 7.804  0.027   7.867
calculate_cvm    7.580  0.030   7.615
* 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-3.2-bioc/meat/EMDomics.Rcheck/00check.log’
for details.

* 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)

name	user	system	elapsed
calculate_cvm	7.580	0.030	7.615
calculate_cvm_gene	0.010	0.001	0.010
calculate_emd	4.027	0.035	4.083
calculate_emd_gene	0.007	0.000	0.008
calculate_ks	1.382	0.030	1.415
calculate_ks_gene	0.018	0.002	0.019
plot_cvm_density	7.804	0.027	7.867
plot_cvmnull	3.314	0.010	3.328
plot_cvmperms	9.042	0.032	9.244
plot_emd_density	3.855	0.037	4.339
plot_emdnull	1.221	0.016	1.516
plot_emdperms	3.642	0.033	4.640
plot_ks_density	1.348	0.029	3.451
plot_ksnull	0.648	0.013	2.057
plot_ksperms	1.303	0.026	1.408