| Back to Multiple platform build/check report for BioC 3.12 |
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This page was generated on 2021-05-06 12:27:33 -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: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:fcoex.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings fcoex_1.4.0.tar.gz |
| StartedAt: 2021-05-06 01:31:05 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 01:37:06 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 361.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: fcoex.Rcheck |
| Warnings: NA |
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###
### Running command:
###
### /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:fcoex.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings fcoex_1.4.0.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/fcoex.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (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
‘/home/biocbuild/bbs-3.12-bioc/meat/fcoex.Rcheck/00check.log’
for details.
fcoex.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL fcoex ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/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-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(fcoex)
>
> test_check("fcoex")
[1] "Number of prospective features = 99"
Round 1
[1] "first_prime round ( |s_prime| = 99 )"
0.04163362 0.02862863 Removed feature 182
0.05923759 0.02786455 Removed feature 42
0.04021 0.02660303 Removed feature 89
0.04278525 0.0249483 Removed feature 53
0.03647797 0.02273447 Removed feature 24
0.02067235 0.01790847 Removed feature 84
0.03770705 0.01599553 Removed feature 43
0.03770705 0.01599553 Removed feature 111
0.01648113 0.01505173 Removed feature 21
0.03521787 0.01488066 Removed feature 92
0.04021 0.01488066 Removed feature 142
0.02323304 0.01453744 Removed feature 33
0.04811627 0.01453744 Removed feature 198
0.04544764 0.01321344 Removed feature 163
0.04821213 0.01258914 Removed feature 116
0.02569197 0.01224877 Removed feature 151
0.03631067 0.01224877 Removed feature 185
0.01933393 0.0112316 Removed feature 146
0.03895043 0.01067603 Removed feature 87
0.0839551 0.01060396 Removed feature 19
0.02196897 0.008943111 Removed feature 70
0.02196897 0.008943111 Removed feature 165
0.01613164 0.00821823 Removed feature 186
0.0352612 0.007676308 Removed feature 80
0.02447199 0.007429651 Removed feature 48
0.02447199 0.007429651 Removed feature 188
0.04163362 0.007075971 Removed feature 3
0.03770705 0.007075971 Removed feature 83
0.04163362 0.007075971 Removed feature 86
0.04021 0.006587856 Removed feature 13
0.04021 0.006587856 Removed feature 46
0.04021 0.006587856 Removed feature 121
0.02689811 0.006362556 Removed feature 85
0.02689811 0.006362556 Removed feature 135
0.02513497 0.005855937 Removed feature 161
0.06387064 0.004975612 Removed feature 72
0.0110025 0.00488621 Removed feature 6
0.01744642 0.004662265 Removed feature 51
Round 2
[1] "first_prime round ( |s_prime| = 61 )"
0.06213344 0.05164468 Removed feature 12
0.05046299 0.0420584 Removed feature 187
0.03589418 0.03267455 Removed feature 189
0.04448369 0.02538638 Removed feature 104
0.02606289 0.02273447 Removed feature 78
0.02622913 0.01964875 Removed feature 57
0.02622913 0.01964875 Removed feature 67
0.04749644 0.01453744 Removed feature 118
0.0384776 0.01396718 Removed feature 173
0.04636336 0.01207179 Removed feature 29
0.01970584 0.01152678 Removed feature 109
0.01085236 0.01060396 Removed feature 45
0.01085236 0.01060396 Removed feature 66
0.01507476 0.008935977 Removed feature 50
0.07071099 0.008424484 Removed feature 155
0.03218501 0.007950507 Removed feature 139
0.07653382 0.007676308 Removed feature 108
0.05046299 0.007429651 Removed feature 183
0.01172033 0.006587856 Removed feature 65
0.01003218 0.006587856 Removed feature 136
0.008942882 0.006362556 Removed feature 9
0.008942882 0.006362556 Removed feature 180
0.01335475 0.006187113 Removed feature 127
Round 3
[1] "first_prime round ( |s_prime| = 38 )"
0.0541637 0.04469203 Removed feature 75
0.04986238 0.04152422 Removed feature 145
0.0369118 0.02800735 Removed feature 56
0.03116066 0.02538638 Removed feature 73
0.02498594 0.02332464 Removed feature 168
0.02270691 0.02152782 Removed feature 193
0.04800737 0.01908965 Removed feature 181
0.02746402 0.01790847 Removed feature 147
0.02916532 0.01790847 Removed feature 191
0.03862882 0.01786321 Removed feature 166
0.03356928 0.01599553 Removed feature 62
0.06134609 0.009981355 Removed feature 200
0.01375183 0.006187113 Removed feature 22
Round 4
[1] "first_prime round ( |s_prime| = 25 )"
0.02983705 0.02800735 Removed feature 31
0.02983705 0.02800735 Removed feature 103
0.01705592 0.006187113 Removed feature 170
0.00592127 0.005855937 Removed feature 94
Round 5
[1] "first_prime round ( |s_prime| = 21 )"
Round 6
[1] "first_prime round ( |s_prime| = 21 )"
0.04140495 0.02538638 Removed feature 88
0.01335475 0.007429651 Removed feature 68
0.009410819 0.006187113 Removed feature 63
0.01719455 0.00488621 Removed feature 15
Round 7
[1] "first_prime round ( |s_prime| = 17 )"
0.04950029 0.02538638 Removed feature 11
0.04950029 0.008943111 Removed feature 14
Round 8
[1] "first_prime round ( |s_prime| = 15 )"
0.04486812 0.02752658 Removed feature 199
0.02623789 0.02589617 Removed feature 64
Round 9
[1] "first_prime round ( |s_prime| = 13 )"
Round 10
[1] "first_prime round ( |s_prime| = 13 )"
0.07192151 0.01599553 Removed feature 153
Round 11
[1] "first_prime round ( |s_prime| = 12 )"
Round 12
[1] "first_prime round ( |s_prime| = 12 )"
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 3 ]
>
>
> proc.time()
user system elapsed
19.492 0.316 20.050
fcoex.Rcheck/fcoex-Ex.timings
| name | user | system | elapsed | |
| discretize | 3.144 | 0.088 | 3.244 | |
| fc | 1.048 | 0.048 | 1.094 | |
| find_cbf_modules | 23.560 | 0.136 | 23.739 | |
| get_nets | 23.132 | 0.024 | 23.184 | |
| idents | 0.584 | 0.044 | 0.632 | |
| mini_pbmc3k | 0.400 | 0.012 | 0.410 | |
| mod_colors | 0.976 | 0.048 | 1.027 | |
| mod_gene_num | 0.368 | 0.040 | 0.408 | |
| mod_names | 1.100 | 0.044 | 1.148 | |
| mod_ora | 2.940 | 0.092 | 3.648 | |
| module_genes | 0.612 | 0.032 | 0.645 | |
| new_fcoex | 1.000 | 0.032 | 1.035 | |
| nmodules | 0.472 | 0.028 | 0.501 | |
| ora_data | 0.384 | 0.024 | 0.407 | |
| plot_ora | 3.304 | 0.120 | 3.434 | |
| recluster | 1.032 | 0.020 | 1.062 | |