Package: fcoex

Version: 1.0.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:fcoex.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings fcoex_1.0.0.tar.gz

StartedAt: 2020-04-15 02:16:39 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 02:23:23 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 403.9 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: fcoex.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:fcoex.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings fcoex_1.0.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/fcoex.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘fcoex/DESCRIPTION’ ... OK
* this is package ‘fcoex’ version ‘1.0.0’
* 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 ‘fcoex’ 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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
Documented arguments not in \usage in documentation object '.plot_one_interaction':
  ‘...’

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
find_cbf_modules  31.813  0.770  32.979
get_nets          31.082  0.621  32.275
plot_interactions 29.857  0.634  30.666
* 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: 1 WARNING
See
  ‘/Users/biocbuild/bbs-3.10-bioc/meat/fcoex.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 fcoex
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘fcoex’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB

Registered S3 method overwritten by 'enrichplot':
  method               from
  fortify.enrichResult DOSE
** 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 (fcoex)

R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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)
> library(fcoex)

> 
> test_check("fcoex")
[1] "Number of prospective features =  99"
Round 1 
[1] "first_prime  round ( |s_prime| = 99 )"
   0.03895043   0.03501836   Removed feature  142 
   0.04928179   0.03113641   Removed feature  55 
   0.04163362   0.02862863   Removed feature  134 
   0.02513497   0.02358608   Removed feature  92 
   0.02689811   0.01786321   Removed feature  174 
   0.04163362   0.01599553   Removed feature  103 
   0.02928575   0.01561266   Removed feature  17 
   0.02323304   0.01453744   Removed feature  128 
   0.02323304   0.01453744   Removed feature  162 
   0.03405469   0.01258098   Removed feature  49 
   0.02569197   0.01224877   Removed feature  50 
   0.0176834   0.01207179   Removed feature  109 
   0.03647797   0.01152678   Removed feature  131 
   0.01933393   0.0112316   Removed feature  6 
   0.1800054   0.0112316   Removed feature  144 
   0.02809477   0.01060396   Removed feature  153 
   0.04148765   0.009981355   Removed feature  95 
   0.02736878   0.00940938   Removed feature  107 
   0.04410462   0.00940938   Removed feature  197 
   0.02101139   0.009373247   Removed feature  154 
   0.02196897   0.008943111   Removed feature  141 
   0.04681617   0.008935977   Removed feature  35 
   0.02306303   0.008935977   Removed feature  96 
   0.04681617   0.008935977   Removed feature  148 
   0.02447199   0.007429651   Removed feature  70 
   0.02447199   0.007429651   Removed feature  81 
   0.02447199   0.007429651   Removed feature  152 
   0.03770705   0.007075971   Removed feature  175 
   0.03770705   0.007075971   Removed feature  180 
   0.02689811   0.006362556   Removed feature  79 
   0.03164286   0.006362556   Removed feature  149 
   0.07829946   0.006187113   Removed feature  26 
   0.01794196   0.00564683   Removed feature  181 
   0.05109415   0.005353485   Removed feature  91 
   0.01830915   0.004975612   Removed feature  13 
   0.01830915   0.004975612   Removed feature  19 
   0.0138217   0.004506593   Removed feature  129 
   0.009047746   0.004391526   Removed feature  39 
   0.02067235   0.004391526   Removed feature  184 
   0.007530494   0.003830409   Removed feature  9 
   0.02323304   0.003587986   Removed feature  48 
   0.02323304   0.003587986   Removed feature  77 
   0.02323304   0.003587986   Removed feature  80 
   0.02323304   0.003587986   Removed feature  161 
   0.004868469   0.003587986   Removed feature  170 
   0.00534895   0.003583068   Removed feature  41 
Round 2 
[1] "first_prime  round ( |s_prime| = 53 )"
   0.04601279   0.03561466   Removed feature  185 
   0.03668537   0.02538638   Removed feature  106 
   0.02952633   0.01964875   Removed feature  160 
   0.04958907   0.01060396   Removed feature  182 
   0.03668537   0.008943111   Removed feature  3 
   0.01161533   0.008943111   Removed feature  178 
   0.04141173   0.007429651   Removed feature  20 
   0.01162765   0.006587856   Removed feature  33 
   0.04624081   0.005855937   Removed feature  83 
   0.006060038   0.005855937   Removed feature  132 
   0.05507264   0.004975612   Removed feature  112 
   0.01442437   0.004132786   Removed feature  11 
   0.01442437   0.004132786   Removed feature  34 
Round 3 
[1] "first_prime  round ( |s_prime| = 40 )"
   0.09158288   0.0420584   Removed feature  44 
   0.05947578   0.01790847   Removed feature  127 
   0.02068402   0.01321344   Removed feature  56 
   0.04089645   0.01224877   Removed feature  199 
   0.01218866   0.009981355   Removed feature  165 
   0.05501233   0.00940938   Removed feature  102 
   0.007552768   0.003830409   Removed feature  28 
Round 4 
[1] "first_prime  round ( |s_prime| = 33 )"
   0.0668301   0.01679217   Removed feature  8 
   0.03307435   0.01390786   Removed feature  30 
   0.01372177   0.01067603   Removed feature  156 
   0.01607733   0.007075971   Removed feature  200 
   0.02323906   0.006187113   Removed feature  189 
   0.02708731   0.005855937   Removed feature  90 
Round 5 
[1] "first_prime  round ( |s_prime| = 27 )"
   0.05979264   0.03099085   Removed feature  125 
   0.03374051   0.02128054   Removed feature  150 
   0.02301587   0.02094474   Removed feature  157 
   0.0230884   0.02012965   Removed feature  87 
   0.02088483   0.01851095   Removed feature  58 
   0.05472121   0.01790847   Removed feature  136 
   0.03692405   0.01599553   Removed feature  23 
   0.01775457   0.01396718   Removed feature  2 
   0.02822074   0.008943111   Removed feature  114 
Round 6 
[1] "first_prime  round ( |s_prime| = 18 )"
   0.03025296   0.02128054   Removed feature  14 
   0.07608982   0.02094474   Removed feature  78 
   0.0223029   0.01851095   Removed feature  47 
   0.0221273   0.01060396   Removed feature  72 
   0.01409774   0.009981355   Removed feature  130 
   0.04170955   0.007429651   Removed feature  101 
   0.01027843   0.004975612   Removed feature  62 
Round 7 
[1] "first_prime  round ( |s_prime| = 11 )"
   0.09073436   0.02538638   Removed feature  85 
Round 8 
[1] "first_prime  round ( |s_prime| = 10 )"
   0.0168037   0.01396718   Removed feature  24 
   0.03820232   0.007075971   Removed feature  139 
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 3 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> 
> proc.time()
   user  system elapsed 
 22.783   0.924  23.772 

name	user	system	elapsed
discretize	2.774	0.113	2.916
fc	1.009	0.053	1.077
find_cbf_modules	31.813	0.770	32.979
get_nets	31.082	0.621	32.275
idents	1.049	0.084	1.138
mini_pbmc3k	0.099	0.006	0.106
mod_colors	0.511	0.041	0.564
mod_gene_num	1.019	0.032	1.056
mod_names	0.471	0.018	0.492
mod_ora	3.098	0.188	3.301
module_genes	0.711	0.057	0.778
new_fcoex	0.388	0.047	0.494
nmodules	1.118	0.030	1.161
ora_data	0.560	0.028	0.595
plot_interactions	29.857	0.634	30.666
plot_ora	2.921	0.181	3.113
recluster	1.453	0.083	1.538
save_plots	2.726	0.034	2.768
show-fcoex-method	0.425	0.008	0.435
show_net	3.318	0.083	3.416
show_ora	0.509	0.007	0.517