Package: PathwaySplice

Version: 1.7.1

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_1.7.1.tar.gz

StartedAt: 2019-04-09 02:45:26 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 03:00:56 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 930.9 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_1.7.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/PathwaySplice.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* 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 ‘1.7.1’
* 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    69.038  5.797  75.571
runPathwaySplice 64.922  5.474  70.966
compareResults   64.665  2.779  73.394
makeGeneTable    22.862  0.072  23.021
gmtGene2Cat      22.083  0.353  22.714
lrTestBias       21.398  0.072  21.530
* 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-3.9-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/3.6/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 Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
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 
282.186  23.372 311.937 

name	user	system	elapsed
compareResults	64.665	2.779	73.394
enrichmentMap	69.038	5.797	75.571
gmtGene2Cat	22.083	0.353	22.714
lrTestBias	21.398	0.072	21.530
makeGeneTable	22.862	0.072	23.021
outKegg2Gmt	0.000	0.000	0.001
runPathwaySplice	64.922	5.474	70.966