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: 2015-10-22 08:30:30 -0400 (Thu, 22 Oct 2015)

EndedAt: 2015-10-22 08:32:31 -0400 (Thu, 22 Oct 2015)

EllapsedTime: 120.9 seconds

RetCode: 0

Status:  OK

CheckDir: mirIntegrator.Rcheck

Warnings: 0

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


* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/mirIntegrator.Rcheck’
* using R Under development (unstable) (2015-10-08 r69496)
* 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 ... [8s/8s] 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
plotLines: no visible binding for global variable ‘x’
plotLines: no visible binding for global variable ‘y’
Undefined global functions or variables:
  x y
* 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 ... [18s/18s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
pathways2pdf 5.698   0.17   5.873
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [7s/7s]
 [7s/7s] 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	0.138	0.008	0.145
GSE43592_miRNA	0.008	0.004	0.012
augmented_pathways	0.618	0.020	0.638
integrate_mir	3.046	0.182	3.230
kegg_pathways	0.172	0.006	0.177
mirTarBase	0.060	0.005	0.065
names_pathways	0.002	0.001	0.003
pathways2pdf	5.698	0.170	5.873
plot_augmented_pathway	1.873	0.055	1.933
plot_change	1.057	0.020	1.078
smallest_pathway	0.625	0.011	0.637