BioC 3.5: CHECK report for mirIntegrator on oaxaca

Package: mirIntegrator

Version: 1.5.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings mirIntegrator_1.5.0.tar.gz

StartedAt: 2017-03-04 05:55:21 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 05:57:49 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 147.6 seconds

RetCode: 0

Status:  OK

CheckDir: mirIntegrator.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 mirIntegrator_1.5.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/mirIntegrator.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘mirIntegrator/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mirIntegrator’ version ‘1.5.0’
* 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 ‘mirIntegrator’ 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
* 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
integrate_mir : isGraphNEL: no visible global function definition for
  ‘is’
pathways2pdf: no visible global function definition for ‘pdf’
pathways2pdf: no visible global function definition for ‘par’
pathways2pdf: no visible global function definition for ‘graphics.off’
plotLines: no visible binding for global variable ‘x’
plotLines: no visible binding for global variable ‘y’
plotLines: no visible binding for global variable ‘pathways_set’
plotPathway2Colors: no visible global function definition for ‘legend’
plot_change: no visible global function definition for ‘complete.cases’
Undefined global functions or variables:
  complete.cases graphics.off is legend par pathways_set pdf x y
Consider adding
  importFrom("grDevices", "graphics.off", "pdf")
  importFrom("graphics", "legend", "par")
  importFrom("methods", "is")
  importFrom("stats", "complete.cases")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... 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
pathways2pdf 7.509  0.219   7.774
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* 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
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/mirIntegrator.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
GSE43592_mRNA	0.154	0.009	0.164
GSE43592_miRNA	0.011	0.004	0.015
augmented_pathways	0.636	0.028	0.663
integrate_mir	3.591	0.245	3.838
kegg_pathways	0.304	0.009	0.314
mirTarBase	0.095	0.007	0.101
names_pathways	0.005	0.001	0.006
pathways2pdf	7.509	0.219	7.774
plot_augmented_pathway	2.406	0.059	2.468
plot_change	2.219	0.061	2.281
smallest_pathway	0.384	0.010	0.396