Package: PathwaySplice

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:PathwaySplice.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings PathwaySplice_1.4.0.tar.gz

StartedAt: 2018-10-16 23:09:01 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 23:23:50 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 889.2 seconds

RetCode: 0

Status:  OK

CheckDir: PathwaySplice.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:PathwaySplice.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings PathwaySplice_1.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/PathwaySplice.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PathwaySplice/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PathwaySplice’ version ‘1.4.0’
* 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 ‘PathwaySplice’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 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
compareResults2: no visible global function definition for 'ggplot'
compareResults2: no visible global function definition for 'aes'
compareResults2: no visible binding for global variable
  'random_sampling_200k'
compareResults2: no visible binding for global variable 'PValue'
compareResults2: no visible binding for global variable 'PathwaySplice'
compareResults2: no visible global function definition for 'geom_point'
compareResults2: no visible global function definition for
  'geom_smooth'
compareResults2: no visible global function definition for 'labs'
compareResults2: no visible global function definition for
  'scale_colour_manual'
compareResults2: no visible global function definition for
  'scale_shape_manual'
netplot: no visible global function definition for 'get.col.scale'
Undefined global functions or variables:
  PValue PathwaySplice aes geom_point geom_smooth get.col.scale ggplot
  labs random_sampling_200k scale_colour_manual scale_shape_manual
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
enrichmentMap    68.527  5.437  74.516
runPathwaySplice 66.953  5.240  73.029
compareResults   54.656  1.585  57.044
makeGeneTable    23.360  0.073  23.530
lrTestBias       23.316  0.083  23.501
gmtGene2Cat      21.484  0.351  22.084
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.7-bioc/meat/PathwaySplice.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL PathwaySplice
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘PathwaySplice’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (PathwaySplice)

R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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.

> library(testthat)
> test_check("PathwaySplice")
Loading required package: PathwaySplice



[1] "P-value from logistic regression is 3.98e-205"
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 4 SKIPPED: 1 FAILED: 0
> 
> proc.time()
   user  system elapsed 
260.825  21.034 284.567 

name	user	system	elapsed
compareResults	54.656	1.585	57.044
enrichmentMap	68.527	5.437	74.516
gmtGene2Cat	21.484	0.351	22.084
lrTestBias	23.316	0.083	23.501
makeGeneTable	23.360	0.073	23.530
outKegg2Gmt	0.002	0.000	0.002
runPathwaySplice	66.953	5.240	73.029