Package: PathwaySplice

Version: 1.6.1

Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:PathwaySplice.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings PathwaySplice_1.6.1.tar.gz

StartedAt: 2019-04-16 01:59:23 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 02:11:05 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 702.2 seconds

RetCode: 0

Status:  OK

CheckDir: PathwaySplice.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:PathwaySplice.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings PathwaySplice_1.6.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/PathwaySplice.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (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 ‘1.6.1’
* 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    58.436  0.740  59.493
runPathwaySplice 53.516  0.184  53.994
compareResults   44.096  0.788  45.724
lrTestBias       17.540  0.004  17.571
makeGeneTable    16.080  0.000  16.098
gmtGene2Cat      13.020  0.112  13.374
* 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
  ‘/home/biocbuild/bbs-3.8-bioc/meat/PathwaySplice.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL PathwaySplice
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/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 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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.

> 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 
216.548   2.232 220.548 

name	user	system	elapsed
compareResults	44.096	0.788	45.724
enrichmentMap	58.436	0.740	59.493
gmtGene2Cat	13.020	0.112	13.374
lrTestBias	17.540	0.004	17.571
makeGeneTable	16.080	0.000	16.098
outKegg2Gmt	0	0	0
runPathwaySplice	53.516	0.184	53.994