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 12:16:31 -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: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:fcoex.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings fcoex_1.0.0.tar.gz |
| StartedAt: 2020-04-15 07:04:32 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 07:10:09 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 337.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: fcoex.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:fcoex.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings fcoex_1.0.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/fcoex.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.0.0’
* 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
get_nets 21.652 0.032 21.712
find_cbf_modules 20.732 0.068 20.833
plot_interactions 18.436 0.032 18.488
* 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
‘/home/biocbuild/bbs-3.10-bioc/meat/fcoex.Rcheck/00check.log’
for details.
fcoex.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL fcoex ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/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-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 )"
0.06295043 0.03561466 Removed feature 94
0.0424457 0.03230742 Removed feature 173
0.02689811 0.02267899 Removed feature 72
0.04601279 0.01790847 Removed feature 177
0.05531096 0.01321344 Removed feature 44
0.02439911 0.01224877 Removed feature 131
0.03427804 0.01152678 Removed feature 160
0.02921285 0.0112316 Removed feature 76
0.01246593 0.01101197 Removed feature 33
0.02099891 0.01078958 Removed feature 179
0.01455243 0.01067603 Removed feature 166
0.01978665 0.01067603 Removed feature 187
0.06624465 0.01060396 Removed feature 106
0.01409271 0.009981355 Removed feature 49
0.0521341 0.00940938 Removed feature 112
0.08880117 0.008943111 Removed feature 70
0.01282365 0.007676308 Removed feature 147
0.06363032 0.007429651 Removed feature 171
0.008942882 0.007429651 Removed feature 199
0.01258878 0.007075971 Removed feature 91
0.01194434 0.005581295 Removed feature 56
0.01830382 0.005575571 Removed feature 100
0.005078301 0.005010845 Removed feature 105
0.03318079 0.004713998 Removed feature 95
0.01030498 0.004132786 Removed feature 69
0.004594351 0.003583068 Removed feature 40
0.01409271 0.003583068 Removed feature 86
0.05855207 0.003210166 Removed feature 156
Round 2
[1] "first_prime round ( |s_prime| = 71 )"
0.04140495 0.02538638 Removed feature 154
0.03330758 0.01453744 Removed feature 87
0.02453649 0.01321344 Removed feature 16
0.03582558 0.01224877 Removed feature 29
0.01705592 0.01224877 Removed feature 190
0.02230396 0.01067603 Removed feature 39
0.02955637 0.009981355 Removed feature 116
0.04584853 0.00940938 Removed feature 30
0.0157402 0.006587856 Removed feature 132
0.02775753 0.006362556 Removed feature 164
0.009410819 0.006187113 Removed feature 9
0.009410819 0.006187113 Removed feature 42
0.01119645 0.005575571 Removed feature 71
0.005444046 0.004975612 Removed feature 103
0.01012551 0.004506593 Removed feature 123
0.02323906 0.004391526 Removed feature 125
0.01231224 0.003587986 Removed feature 47
0.004342569 0.003583068 Removed feature 10
0.02914778 0.003379136 Removed feature 82
0.006958987 0.003379136 Removed feature 175
Round 3
[1] "first_prime round ( |s_prime| = 51 )"
0.1272046 0.02332464 Removed feature 182
0.06100985 0.01964875 Removed feature 167
0.01595773 0.01224877 Removed feature 107
0.01552836 0.01224877 Removed feature 188
0.01367712 0.01207179 Removed feature 35
0.01624823 0.01152678 Removed feature 58
0.02087483 0.0112316 Removed feature 8
0.02115528 0.01060396 Removed feature 66
0.01880088 0.009981355 Removed feature 169
0.02502602 0.005855937 Removed feature 85
0.04247725 0.00564683 Removed feature 193
0.05055045 0.004391526 Removed feature 21
0.05802731 0.003587986 Removed feature 197
0.00658608 0.003583068 Removed feature 27
0.008872522 0.003210166 Removed feature 115
Round 4
[1] "first_prime round ( |s_prime| = 36 )"
0.05010521 0.03075492 Removed feature 23
0.03365093 0.02862863 Removed feature 25
0.02337331 0.02245981 Removed feature 41
0.03294965 0.01790847 Removed feature 83
0.01215 0.01060396 Removed feature 135
0.01464326 0.00940938 Removed feature 26
0.05015261 0.008943111 Removed feature 51
Round 5
[1] "first_prime round ( |s_prime| = 29 )"
0.04001455 0.03501836 Removed feature 24
0.04152877 0.03428977 Removed feature 37
0.0529248 0.03347788 Removed feature 46
0.03154167 0.01964875 Removed feature 73
0.02197305 0.01790847 Removed feature 102
0.03127645 0.0173703 Removed feature 143
0.0231787 0.01599553 Removed feature 68
0.0387668 0.01060396 Removed feature 157
0.03154167 0.009981355 Removed feature 20
0.02120648 0.005855937 Removed feature 7
0.005078301 0.005010845 Removed feature 162
Round 6
[1] "first_prime round ( |s_prime| = 18 )"
Round 7
[1] "first_prime round ( |s_prime| = 18 )"
0.01363157 0.01060396 Removed feature 67
Round 8
[1] "first_prime round ( |s_prime| = 17 )"
0.02600396 0.02103363 Removed feature 74
0.009705588 0.007075971 Removed feature 141
Round 9
[1] "first_prime round ( |s_prime| = 15 )"
0.02642937 0.02273447 Removed feature 183
0.01389237 0.01067603 Removed feature 65
Round 10
[1] "first_prime round ( |s_prime| = 13 )"
Round 11
[1] "first_prime round ( |s_prime| = 13 )"
Round 12
[1] "first_prime round ( |s_prime| = 13 )"
Round 13
[1] "first_prime round ( |s_prime| = 13 )"
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 3 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
>
> proc.time()
user system elapsed
14.488 0.404 14.921
fcoex.Rcheck/fcoex-Ex.timings
| name | user | system | elapsed | |
| discretize | 2.164 | 0.048 | 2.214 | |
| fc | 0.964 | 0.024 | 0.986 | |
| find_cbf_modules | 20.732 | 0.068 | 20.833 | |
| get_nets | 21.652 | 0.032 | 21.712 | |
| idents | 0.376 | 0.024 | 0.400 | |
| mini_pbmc3k | 0.096 | 0.000 | 0.097 | |
| mod_colors | 0.416 | 0.032 | 0.448 | |
| mod_gene_num | 0.932 | 0.056 | 0.992 | |
| mod_names | 0.340 | 0.044 | 0.387 | |
| mod_ora | 2.276 | 0.040 | 2.315 | |
| module_genes | 0.968 | 0.040 | 1.009 | |
| new_fcoex | 0.228 | 0.000 | 0.228 | |
| nmodules | 0.408 | 0.032 | 0.441 | |
| ora_data | 0.400 | 0.044 | 0.445 | |
| plot_interactions | 18.436 | 0.032 | 18.488 | |
| plot_ora | 2.336 | 0.032 | 2.371 | |
| recluster | 1.180 | 0.036 | 1.218 | |
| save_plots | 2.052 | 0.052 | 2.108 | |
| show-fcoex-method | 0.920 | 0.036 | 0.957 | |
| show_net | 2.076 | 0.052 | 2.132 | |
| show_ora | 0.392 | 0.040 | 0.430 | |