BioC 3.3: CHECK report for mirIntegrator on morelia

Package: mirIntegrator

Version: 1.1.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings mirIntegrator_1.1.0.tar.gz

StartedAt: 2016-04-21 05:05:27 -0700 (Thu, 21 Apr 2016)

EndedAt: 2016-04-21 05:07:40 -0700 (Thu, 21 Apr 2016)

EllapsedTime: 133.1 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_1.1.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/mirIntegrator.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* 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 ‘1.1.0’
* 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 ... [9s/10s] 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
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 ‘colors’
plotPathway2Colors: no visible global function definition for ‘legend’
Undefined global functions or variables:
  colors graphics.off legend par pdf x y
Consider adding
  importFrom("grDevices", "colors", "graphics.off", "pdf")
  importFrom("graphics", "legend", "par")
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 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 ... [20s/20s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
pathways2pdf 7.037  0.227    7.29
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [8s/8s]
 [8s/8s] 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-3.3-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	0.125	0.008	0.133
GSE43592_miRNA	0.010	0.004	0.014
augmented_pathways	0.927	0.024	0.953
integrate_mir	3.126	0.192	3.319
kegg_pathways	0.276	0.012	0.290
mirTarBase	0.082	0.011	0.094
names_pathways	0.004	0.001	0.004
pathways2pdf	7.037	0.227	7.290
plot_augmented_pathway	2.140	0.063	2.206
plot_change	1.057	0.027	1.085
smallest_pathway	0.459	0.009	0.468