BioC 3.1: CHECK report for EMDomics on moscato2

Package: EMDomics

Version: 1.0.0

Command: rm -rf EMDomics.buildbin-libdir EMDomics.Rcheck && mkdir EMDomics.buildbin-libdir EMDomics.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=EMDomics.buildbin-libdir EMDomics_1.0.0.tar.gz >EMDomics.Rcheck\00install.out 2>&1 && cp EMDomics.Rcheck\00install.out EMDomics-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=EMDomics.buildbin-libdir --install="check:EMDomics-install.out" --force-multiarch --no-vignettes --timings EMDomics_1.0.0.tar.gz

StartedAt: 2015-10-09 01:27:59 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 01:44:56 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 1017.2 seconds

RetCode: 0

Status:  OK

CheckDir: EMDomics.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf EMDomics.buildbin-libdir EMDomics.Rcheck && mkdir EMDomics.buildbin-libdir EMDomics.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=EMDomics.buildbin-libdir EMDomics_1.0.0.tar.gz >EMDomics.Rcheck\00install.out 2>&1 && cp EMDomics.Rcheck\00install.out EMDomics-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=EMDomics.buildbin-libdir --install="check:EMDomics-install.out" --force-multiarch --no-vignettes --timings EMDomics_1.0.0.tar.gz
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* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/EMDomics.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'EMDomics/DESCRIPTION' ... OK
* this is package 'EMDomics' version '1.0.0'
* 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 whether package 'EMDomics' 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... [481s] OK
Examples with CPU or elapsed time > 5s
             user system elapsed
plot_emdnull 1.48   0.64  157.29
plot_density 1.27   0.59  161.54
plot_perms   1.31   0.51  158.20
** running examples for arch 'x64' ... [493s] OK
Examples with CPU or elapsed time > 5s
             user system elapsed
plot_density 1.57   0.48  159.30
plot_emdnull 1.45   0.44  165.22
plot_perms   1.34   0.39  164.86
* 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
  'E:/biocbld/bbs-3.1-bioc/meat/EMDomics.Rcheck/00check.log'
for details.

install for i386

* 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

install for x64

* installing *source* package 'EMDomics' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'EMDomics' as EMDomics_1.0.0.zip
* DONE (EMDomics)

name	user	system	elapsed
calculate_emd	2.16	0.02	2.18
calculate_emd_gene	0.01	0.00	0.02
plot_density	1.27	0.59	161.54
plot_emdnull	1.48	0.64	157.29
plot_perms	1.31	0.51	158.20

name	user	system	elapsed
calculate_emd	1.78	0.02	1.80
calculate_emd_gene	0.02	0.00	0.01
plot_density	1.57	0.48	159.30
plot_emdnull	1.45	0.44	165.22
plot_perms	1.34	0.39	164.86