Package: FCBF

Version: 1.2.5

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:FCBF.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings FCBF_1.2.5.tar.gz

StartedAt: 2019-10-16 01:36:28 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 01:41:25 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 296.8 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: FCBF.Rcheck

Warnings: 2

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:FCBF.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings FCBF_1.2.5.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/FCBF.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘FCBF/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘FCBF’ version ‘1.2.5’
* package encoding: UTF-8
* 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 ‘FCBF’ 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 dependencies in R code ... WARNING
'::' or ':::' imports not declared from:
  ‘igraph’ ‘intergraph’ ‘network’ ‘sna’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plot_one_module: no visible global function definition for
  ‘graph.adjacency’
plot_one_module: no visible global function definition for
  ‘geom_label_repel’
Undefined global functions or variables:
  geom_label_repel graph.adjacency
* 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 ... WARNING
Undocumented arguments in documentation object 'IG'
  ‘base’

Undocumented arguments in documentation object 'SU'
  ‘base’

Documented arguments not in \usage in documentation object 'plot_one_module':
  ‘genes’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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
fcbf     38.671  0.068  38.757
scDengue 21.685  0.060  21.749
get_su   16.074  0.048  16.122
get_ig   15.814  0.024  15.846
su_plot  15.458  0.040  15.508
IG        5.427  0.155   5.614
* 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 WARNINGs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/FCBF.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL FCBF
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘FCBF’ ...
** using staged installation
** R
** data
** 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 (FCBF)

R version 3.6.1 (2019-07-05) -- "Action of the Toes"
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)
> library(FCBF)
> 
> test_check("FCBF")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 2 | SKIPPED: 0 | WARNINGS: 2 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  7.630   0.299   7.948 

name	user	system	elapsed
IG	5.427	0.155	5.614
SU	3.177	0.084	3.269
discretize_exprs	3.177	0.084	3.263
discretize_exprs_supervised	2.815	0.024	2.856
discretize_gene_supervised	0.509	0.000	0.511
fcbf	38.671	0.068	38.757
get_ig	15.814	0.024	15.846
get_su	16.074	0.048	16.122
scDengue	21.685	0.060	21.749
su_plot	15.458	0.040	15.508