Package: PathwaySplice

Version: 1.10.0

Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:PathwaySplice.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings PathwaySplice_1.10.0.tar.gz

StartedAt: 2020-04-15 05:10:06 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 05:24:00 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 834.2 seconds

RetCode: 0

Status:  OK

CheckDir: PathwaySplice.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:PathwaySplice.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings PathwaySplice_1.10.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/PathwaySplice.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.10.0’
* 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    57.960  0.820  59.216
runPathwaySplice 49.920  0.308  50.423
compareResults   44.280  0.708  46.155
makeGeneTable    16.836  0.020  16.917
gmtGene2Cat      16.404  0.128  16.706
lrTestBias       14.612  0.004  14.649
* 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-3.10-bioc/meat/PathwaySplice.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL PathwaySplice
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘PathwaySplice’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (PathwaySplice)

R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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: 0 | SKIPPED: 1 | WARNINGS: 5 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
245.572   2.692 282.367 

name	user	system	elapsed
compareResults	44.280	0.708	46.155
enrichmentMap	57.960	0.820	59.216
gmtGene2Cat	16.404	0.128	16.706
lrTestBias	14.612	0.004	14.649
makeGeneTable	16.836	0.020	16.917
outKegg2Gmt	0.000	0.000	0.001
runPathwaySplice	49.920	0.308	50.423