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BioC 3.4: CHECK report for mirIntegrator on morelia

This page was generated on 2016-09-21 03:54:35 -0700 (Wed, 21 Sep 2016).

Package 755/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mirIntegrator 1.3.2
Diana Diaz
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/mirIntegrator
Last Changed Rev: 119089 / Revision: 121152
Last Changed Date: 2016-07-02 08:25:58 -0700 (Sat, 02 Jul 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: mirIntegrator
Version: 1.3.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings mirIntegrator_1.3.2.tar.gz
StartedAt: 2016-09-20 09:23:57 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 09:25:56 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 119.2 seconds
RetCode: 0
Status:  OK 
CheckDir: mirIntegrator.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings mirIntegrator_1.3.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/mirIntegrator.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.3.2’
* 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 6.333  0.207   6.547
* 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-3.4-bioc/meat/mirIntegrator.Rcheck/00check.log’
for details.


mirIntegrator.Rcheck/00install.out:

* 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)

mirIntegrator.Rcheck/mirIntegrator-Ex.timings:

nameusersystemelapsed
GSE43592_mRNA0.1300.0090.138
GSE43592_miRNA0.0080.0030.011
augmented_pathways0.6700.0180.689
integrate_mir2.620.162.78
kegg_pathways0.2460.0140.260
mirTarBase0.0580.0090.067
names_pathways0.0020.0000.003
pathways2pdf6.3330.2076.547
plot_augmented_pathway1.9390.0551.996
plot_change1.0350.0411.077
smallest_pathway0.6010.0230.626