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CHECK report for fcoex on merida1

This page was generated on 2021-05-06 12:34:57 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the fcoex package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 596/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
fcoex 1.4.0  (landing page)
Tiago Lubiana
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/fcoex
Branch: RELEASE_3_12
Last Commit: 4e80420
Last Changed Date: 2020-10-27 11:51:24 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    ERROR  
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    ERROR    OK  
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    ERROR    OK  

Summary

Package: fcoex
Version: 1.4.0
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_1.4.0.tar.gz
StartedAt: 2021-05-06 01:42:54 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 01:49:27 -0400 (Thu, 06 May 2021)
EllapsedTime: 392.8 seconds
RetCode: 1
Status:   ERROR  
CheckDir: fcoex.Rcheck
Warnings: NA

Command output

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###
### Running 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_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/fcoex.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘fcoex/DESCRIPTION’ ... OK
* this is package ‘fcoex’ version ‘1.4.0’
* 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 ... ERROR
Running examples in ‘fcoex-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: save_plots
> ### Title: Save fcoex object plots
> ### Aliases: save_plots save_plots,fcoex-method
> 
> ### ** Examples
> 
> data(fc)
> save_plots(fc, name = "Example")
Saving available plots.
$TYROBP
Error in `$<-.data.frame`(`*tmp*`, "point.size", value = numeric(0)) : 
  replacement has 0 rows, data has 10
Calls: save_plots ... makeContent.labelrepeltree -> $<- -> $<-.data.frame
Execution halted
* 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 ERROR, 1 WARNING
See
  ‘/Users/biocbuild/bbs-3.12-bioc/meat/fcoex.Rcheck/00check.log’
for details.


Installation output

fcoex.Rcheck/00install.out

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##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL fcoex
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘fcoex’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB

** 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)

Tests output

fcoex.Rcheck/tests/testthat.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 =  101"
Round 1 
[1] "first_prime  round ( |s_prime| = 101 )"
   0.05022302   0.02800735   Removed feature  71 
   0.04193089   0.02538638   Removed feature  41 
   0.07231093   0.02538638   Removed feature  92 
   0.06919078   0.02459877   Removed feature  122 
   0.0744544   0.02273447   Removed feature  63 
   0.05193766   0.02094474   Removed feature  82 
   0.03096357   0.01964875   Removed feature  36 
   0.03906883   0.01790847   Removed feature  50 
   0.06122103   0.01453744   Removed feature  153 
   0.0440913   0.01224877   Removed feature  68 
   0.03613477   0.0112316   Removed feature  84 
   0.03096357   0.009981355   Removed feature  172 
   0.02772334   0.00940938   Removed feature  102 
   0.01142727   0.00940938   Removed feature  162 
   0.01688854   0.008543364   Removed feature  47 
   0.0199702   0.007676308   Removed feature  30 
   0.01949123   0.007429651   Removed feature  7 
   0.04749644   0.007429651   Removed feature  26 
   0.02866871   0.006587856   Removed feature  40 
   0.006860312   0.006362556   Removed feature  156 
   0.006860312   0.006362556   Removed feature  165 
   0.006860312   0.006362556   Removed feature  173 
   0.01231224   0.006187113   Removed feature  185 
   0.008587836   0.005855937   Removed feature  5 
   0.03311042   0.00564683   Removed feature  94 
   0.005672964   0.005581295   Removed feature  17 
   0.006868633   0.005575571   Removed feature  120 
   0.0139714   0.004975612   Removed feature  3 
   0.008420069   0.004132786   Removed feature  108 
   0.008420069   0.004132786   Removed feature  158 
Round 2 
[1] "first_prime  round ( |s_prime| = 71 )"
   0.05445084   0.03099085   Removed feature  12 
   0.02822074   0.0249483   Removed feature  116 
   0.05198037   0.02414231   Removed feature  128 
   0.03116066   0.02332464   Removed feature  78 
   0.03470023   0.02273447   Removed feature  135 
   0.02501797   0.02094474   Removed feature  83 
   0.04700393   0.01224877   Removed feature  178 
   0.009397187   0.009373247   Removed feature  195 
   0.03933544   0.008943111   Removed feature  14 
   0.03933544   0.008943111   Removed feature  74 
   0.03933544   0.008943111   Removed feature  152 
   0.02501797   0.007429651   Removed feature  119 
   0.02009678   0.007075971   Removed feature  20 
   0.02391217   0.006587856   Removed feature  52 
   0.006794482   0.006187113   Removed feature  107 
   0.0183332   0.006187113   Removed feature  112 
   0.007825161   0.005575571   Removed feature  93 
   0.01103889   0.004975612   Removed feature  171 
   0.01281803   0.004132786   Removed feature  46 
   0.01281803   0.004132786   Removed feature  85 
Round 3 
[1] "first_prime  round ( |s_prime| = 51 )"
   0.08245128   0.0420584   Removed feature  72 
   0.04385959   0.03348817   Removed feature  196 
   0.06932237   0.03113641   Removed feature  97 
   0.05520553   0.03075492   Removed feature  42 
   0.03706233   0.02752658   Removed feature  95 
   0.03356928   0.02332464   Removed feature  103 
   0.03712066   0.01786321   Removed feature  28 
   0.03720522   0.0173703   Removed feature  9 
   0.02683458   0.01599553   Removed feature  160 
   0.02587161   0.01390786   Removed feature  87 
   0.02493902   0.01321344   Removed feature  106 
   0.02270736   0.01258914   Removed feature  35 
   0.01118375   0.01067603   Removed feature  164 
   0.02628614   0.01067603   Removed feature  177 
   0.01481801   0.008424484   Removed feature  166 
   0.01302918   0.007075971   Removed feature  79 
   0.008948431   0.007075971   Removed feature  134 
   0.01142804   0.005855937   Removed feature  123 
Round 4 
[1] "first_prime  round ( |s_prime| = 33 )"
   0.04596162   0.03267455   Removed feature  150 
   0.03571198   0.02660303   Removed feature  18 
   0.06624465   0.02414231   Removed feature  76 
   0.008521535   0.007429651   Removed feature  43 
   0.06363032   0.007429651   Removed feature  49 
Round 5 
[1] "first_prime  round ( |s_prime| = 28 )"
   0.05963869   0.02800735   Removed feature  10 
   0.05630028   0.02094474   Removed feature  69 
   0.04601279   0.01790847   Removed feature  48 
Round 6 
[1] "first_prime  round ( |s_prime| = 25 )"
   0.02458249   0.01908965   Removed feature  179 
   0.009705588   0.007075971   Removed feature  181 
Round 7 
[1] "first_prime  round ( |s_prime| = 23 )"
   0.02772072   0.0249483   Removed feature  126 
   0.02146851   0.02103363   Removed feature  189 
   0.02908251   0.01790847   Removed feature  45 
   0.007160824   0.004391526   Removed feature  39 
Round 8 
[1] "first_prime  round ( |s_prime| = 19 )"
   0.04296097   0.03561466   Removed feature  124 
   0.02969945   0.02862863   Removed feature  90 
Round 9 
[1] "first_prime  round ( |s_prime| = 17 )"
Round 10 
[1] "first_prime  round ( |s_prime| = 17 )"
   0.04610779   0.02917261   Removed feature  60 
Round 11 
[1] "first_prime  round ( |s_prime| = 16 )"
   0.03361105   0.02075894   Removed feature  54 
   0.05594574   0.006587856   Removed feature  193 
Round 12 
[1] "first_prime  round ( |s_prime| = 14 )"
   0.01642568   0.01453744   Removed feature  21 
Round 13 
[1] "first_prime  round ( |s_prime| = 13 )"
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 3 ]
> 
> 
> proc.time()
   user  system elapsed 
 20.197   0.703  21.093 

Example timings

fcoex.Rcheck/fcoex-Ex.timings

nameusersystemelapsed
discretize2.8690.1142.991
fc1.1940.0461.241
find_cbf_modules28.176 0.58228.791
get_nets28.795 0.44429.453
idents0.6440.0050.648
mini_pbmc3k0.3570.0100.368
mod_colors0.6190.0070.626
mod_gene_num1.2620.0351.298
mod_names0.6010.0210.622
mod_ora3.2400.0553.299
module_genes0.6640.0140.747
new_fcoex0.8770.3161.468
nmodules0.5070.0150.533
ora_data0.5120.0080.521
plot_ora3.4150.0673.491
recluster1.7080.0281.739