Package: mirIntegrator

Version: 1.8.0

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings mirIntegrator_1.8.0.tar.gz

StartedAt: 2018-04-12 01:10:06 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 01:12:08 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 121.3 seconds

RetCode: 0

Status:  OK

CheckDir: mirIntegrator.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings mirIntegrator_1.8.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/mirIntegrator.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (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 ‘1.8.0’
* 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 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 5.568  0.052   5.623
* 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
  ‘/home/biocbuild/bbs-3.6-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)

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("mirIntegrator")

Loading required package: graph
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min



RUNIT TEST PROTOCOL -- Thu Apr 12 01:12:06 2018 
*********************************************** 
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
mirIntegrator RUnit Tests - 2 test functions, 0 errors, 0 failures
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  7.008   0.148   7.152 

name	user	system	elapsed
GSE43592_mRNA	0.136	0.000	0.135
GSE43592_miRNA	0.008	0.000	0.009
augmented_pathways	0.468	0.012	0.482
integrate_mir	2.856	0.028	2.886
kegg_pathways	0.188	0.000	0.186
mirTarBase	0.072	0.000	0.072
names_pathways	0.004	0.000	0.002
pathways2pdf	5.568	0.052	5.623
plot_augmented_pathway	1.812	0.016	1.830
plot_change	1.628	0.004	1.632
smallest_pathway	0.412	0.004	0.415