| Back to Multiple platform build/check report for BioC 3.12 |
|
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 596/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| fcoex 1.4.0 (landing page) Tiago Lubiana
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | ERROR | OK | |||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | ERROR | OK | |||||||||
| 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 |
##############################################################################
##############################################################################
###
### 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.
fcoex.Rcheck/00install.out
############################################################################## ############################################################################## ### ### 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)
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
fcoex.Rcheck/fcoex-Ex.timings
| name | user | system | elapsed | |
| discretize | 2.869 | 0.114 | 2.991 | |
| fc | 1.194 | 0.046 | 1.241 | |
| find_cbf_modules | 28.176 | 0.582 | 28.791 | |
| get_nets | 28.795 | 0.444 | 29.453 | |
| idents | 0.644 | 0.005 | 0.648 | |
| mini_pbmc3k | 0.357 | 0.010 | 0.368 | |
| mod_colors | 0.619 | 0.007 | 0.626 | |
| mod_gene_num | 1.262 | 0.035 | 1.298 | |
| mod_names | 0.601 | 0.021 | 0.622 | |
| mod_ora | 3.240 | 0.055 | 3.299 | |
| module_genes | 0.664 | 0.014 | 0.747 | |
| new_fcoex | 0.877 | 0.316 | 1.468 | |
| nmodules | 0.507 | 0.015 | 0.533 | |
| ora_data | 0.512 | 0.008 | 0.521 | |
| plot_ora | 3.415 | 0.067 | 3.491 | |
| recluster | 1.708 | 0.028 | 1.739 | |