Tiago Lubiana
| Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020) |
| URL: https://git.bioconductor.org/packages/fcoex |
| Branch: master |
| Last Commit: 6d957d7 |
| Last Changed Date: 2019-10-29 13:43:47 -0500 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-01-16 13:55:59 -0500 (Thu, 16 Jan 2020).
| Package 564/1818 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| fcoex 1.1.0 Tiago Lubiana
| malbec2 | Linux (Ubuntu 18.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: fcoex |
| Version: 1.1.0 |
| 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_1.1.0.tar.gz |
| StartedAt: 2020-01-16 04:24:22 -0500 (Thu, 16 Jan 2020) |
| EndedAt: 2020-01-16 04:34:06 -0500 (Thu, 16 Jan 2020) |
| EllapsedTime: 584.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: fcoex.Rcheck |
| Warnings: 0 |
##############################################################################
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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_1.1.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/fcoex.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘1.1.0’
* 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 ... OK
* 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 (user + system) or elapsed time > 5s
user system elapsed
find_cbf_modules 41.230 2.082 43.477
get_nets 40.984 1.560 42.560
plot_interactions 40.437 1.445 41.920
* 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: OK
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 Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
Copyright (C) 2019 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 = 102"
Round 1
[1] "first_prime round ( |s_prime| = 102 )"
0.04032318 0.02485001 Removed feature 19
0.02827152 0.02414231 Removed feature 68
0.02252227 0.01964875 Removed feature 87
0.02969945 0.01599553 Removed feature 163
0.02353605 0.01488066 Removed feature 169
0.02866871 0.01453744 Removed feature 160
0.02866871 0.01453744 Removed feature 185
0.06806373 0.01396718 Removed feature 40
0.02916192 0.01396718 Removed feature 140
0.01755657 0.01258098 Removed feature 138
0.02271678 0.01152678 Removed feature 79
0.02271678 0.01152678 Removed feature 148
0.0240649 0.008943111 Removed feature 51
0.01601679 0.008424484 Removed feature 65
0.01601679 0.008424484 Removed feature 147
0.008228572 0.00773253 Removed feature 37
0.01003218 0.007429651 Removed feature 27
0.03336207 0.007429651 Removed feature 76
0.02977398 0.007429651 Removed feature 98
0.03336207 0.007429651 Removed feature 111
0.007579221 0.007075971 Removed feature 195
0.03571198 0.006362556 Removed feature 57
0.0157402 0.006187113 Removed feature 124
0.02916192 0.006187113 Removed feature 149
0.006369047 0.006187113 Removed feature 153
0.03525863 0.005855937 Removed feature 184
0.006535429 0.00564683 Removed feature 127
0.008490896 0.005575571 Removed feature 38
0.007716162 0.005575571 Removed feature 178
0.03189157 0.004975612 Removed feature 39
0.02808487 0.004788064 Removed feature 186
0.01488066 0.004621561 Removed feature 52
0.02604067 0.004132786 Removed feature 188
0.005336671 0.003830409 Removed feature 135
0.01639507 0.003830409 Removed feature 156
0.005336671 0.003830409 Removed feature 176
0.01639507 0.003830409 Removed feature 194
0.007130495 0.003587986 Removed feature 77
0.003873031 0.003587986 Removed feature 174
0.003873031 0.003587986 Removed feature 179
Round 2
[1] "first_prime round ( |s_prime| = 62 )"
0.02252227 0.01964875 Removed feature 64
0.03294965 0.01790847 Removed feature 130
0.03984022 0.01505173 Removed feature 101
0.02353605 0.01488066 Removed feature 29
0.02866871 0.01453744 Removed feature 116
0.01523756 0.0112316 Removed feature 23
0.01464326 0.00940938 Removed feature 159
0.01025779 0.009373247 Removed feature 95
0.01700548 0.009373247 Removed feature 128
0.01704682 0.008935977 Removed feature 187
0.009358053 0.008424484 Removed feature 120
0.0447076 0.007676308 Removed feature 164
0.007579221 0.007075971 Removed feature 161
0.01705345 0.005010845 Removed feature 21
0.01162765 0.004391526 Removed feature 97
0.01957512 0.004391526 Removed feature 144
0.014602 0.003830409 Removed feature 99
0.007130495 0.003587986 Removed feature 114
Round 3
[1] "first_prime round ( |s_prime| = 44 )"
0.06036912 0.01851095 Removed feature 136
0.02115528 0.01561266 Removed feature 58
0.02019743 0.01488066 Removed feature 62
0.05560979 0.01453744 Removed feature 122
0.03848265 0.01152678 Removed feature 199
0.01846413 0.01060396 Removed feature 93
0.0362569 0.00940938 Removed feature 115
0.01087465 0.005581295 Removed feature 1
0.02516448 0.005581295 Removed feature 66
0.04828629 0.004391526 Removed feature 190
Round 4
[1] "first_prime round ( |s_prime| = 34 )"
0.02422342 0.01599553 Removed feature 18
0.02422342 0.01599553 Removed feature 173
0.06363131 0.01390786 Removed feature 59
0.03613477 0.0112316 Removed feature 35
0.02642214 0.01067603 Removed feature 63
0.01034012 0.00940938 Removed feature 15
0.04749644 0.007429651 Removed feature 167
0.02422342 0.007075971 Removed feature 67
0.01231224 0.006187113 Removed feature 43
0.02464403 0.005855937 Removed feature 83
0.01297339 0.00488621 Removed feature 125
0.03906883 0.004391526 Removed feature 74
Round 5
[1] "first_prime round ( |s_prime| = 22 )"
0.05691771 0.02538638 Removed feature 81
0.02785622 0.01488066 Removed feature 73
0.01269962 0.01224877 Removed feature 175
0.01246525 0.007848506 Removed feature 89
Round 6
[1] "first_prime round ( |s_prime| = 18 )"
0.01360264 0.007075971 Removed feature 90
0.01737201 0.005855937 Removed feature 14
Round 7
[1] "first_prime round ( |s_prime| = 16 )"
0.04655338 0.0420584 Removed feature 132
0.01005192 0.006187113 Removed feature 32
Round 8
[1] "first_prime round ( |s_prime| = 14 )"
0.04066398 0.01060396 Removed feature 137
Round 9
[1] "first_prime round ( |s_prime| = 13 )"
0.02567026 0.01321344 Removed feature 117
0.02120648 0.01321344 Removed feature 157
Round 10
[1] "first_prime round ( |s_prime| = 11 )"
Round 11
[1] "first_prime round ( |s_prime| = 11 )"
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 3 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
>
> proc.time()
user system elapsed
34.850 1.994 36.951
fcoex.Rcheck/fcoex-Ex.timings
| name | user | system | elapsed | |
| discretize | 4.129 | 0.255 | 4.384 | |
| fc | 1.367 | 0.125 | 1.493 | |
| find_cbf_modules | 41.230 | 2.082 | 43.477 | |
| get_nets | 40.984 | 1.560 | 42.560 | |
| idents | 0.701 | 0.107 | 0.808 | |
| mini_pbmc3k | 0.174 | 0.044 | 0.218 | |
| mod_colors | 1.388 | 0.077 | 1.465 | |
| mod_gene_num | 0.544 | 0.029 | 0.573 | |
| mod_names | 1.238 | 0.050 | 1.288 | |
| mod_ora | 3.829 | 0.337 | 4.167 | |
| module_genes | 0.842 | 0.115 | 0.957 | |
| new_fcoex | 1.419 | 0.098 | 1.516 | |
| nmodules | 0.637 | 0.029 | 0.664 | |
| ora_data | 0.649 | 0.016 | 0.665 | |
| plot_interactions | 40.437 | 1.445 | 41.920 | |
| plot_ora | 3.831 | 0.358 | 4.191 | |
| recluster | 1.936 | 0.167 | 2.104 | |
| save_plots | 4.432 | 0.175 | 4.610 | |
| show-fcoex-method | 0.603 | 0.022 | 0.638 | |
| show_net | 4.576 | 0.060 | 4.670 | |
| show_ora | 0.609 | 0.015 | 0.623 | |