BioC 3.2: CHECK report for EMDomics on perceval

Package: EMDomics

Version: 1.1.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings EMDomics_1.1.3.tar.gz

StartedAt: 2015-08-24 00:23:17 -0700 (Mon, 24 Aug 2015)

EndedAt: 2015-08-24 00:24:52 -0700 (Mon, 24 Aug 2015)

EllapsedTime: 95.1 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_1.1.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/EMDomics.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘EMDomics/DESCRIPTION’ ... OK
* this is package ‘EMDomics’ version ‘1.1.3’
* 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 ... [3s/3s] 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 ... [54s/55s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
plot_cvmperms    8.922  0.085   9.347
plot_cvm_density 8.793  0.099   9.086
calculate_cvm    8.131  0.080   8.277
calculate_emd    4.870  0.104   5.044
plot_emdperms    4.826  0.076   5.010
* 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	8.131	0.080	8.277
calculate_cvm_gene	0.010	0.000	0.011
calculate_emd	4.870	0.104	5.044
calculate_emd_gene	0.008	0.000	0.008
calculate_ks	1.704	0.069	1.826
calculate_ks_gene	0.022	0.001	0.023
plot_cvm_density	8.793	0.099	9.086
plot_cvmnull	3.131	0.036	3.171
plot_cvmperms	8.922	0.085	9.347
plot_emd_density	4.776	0.055	4.834
plot_emdnull	1.913	0.035	1.949
plot_emdperms	4.826	0.076	5.010
plot_ks_density	2.038	0.068	2.174
plot_ksnull	0.930	0.029	0.988
plot_ksperms	1.891	0.055	2.005