Tiago Lubiana
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/fcoex |
| Branch: RELEASE_3_10 |
| Last Commit: 8798edb |
| Last Changed Date: 2019-10-29 13:12:16 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:50:28 -0400 (Wed, 15 Apr 2020).
| Package 564/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| fcoex 1.0.0 Tiago Lubiana
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK | |
| 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 |
##############################################################################
##############################################################################
###
### 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_1.0.0.tar.gz
###
##############################################################################
##############################################################################
* 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.
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/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)
fcoex.Rcheck/tests/testthat.Rout
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
fcoex.Rcheck/fcoex-Ex.timings
| 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 | |