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 12:33:36 -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: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:fcoex.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings fcoex_1.0.0.tar.gz |
| StartedAt: 2020-04-15 03:08:14 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 03:17:17 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 542.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: fcoex.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:fcoex.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings fcoex_1.0.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/fcoex.Rcheck'
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
find_cbf_modules 17.99 0.64 18.63
get_nets 17.81 0.13 17.94
plot_interactions 17.58 0.33 17.91
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
plot_interactions 31.11 0.20 31.59
find_cbf_modules 28.57 0.09 28.70
get_nets 27.51 0.07 27.75
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
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
'C:/Users/biocbuild/bbs-3.10-bioc/meat/fcoex.Rcheck/00check.log'
for details.
fcoex.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/fcoex_1.0.0.tar.gz && rm -rf fcoex.buildbin-libdir && mkdir fcoex.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=fcoex.buildbin-libdir fcoex_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL fcoex_1.0.0.zip && rm fcoex_1.0.0.tar.gz fcoex_1.0.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 1546k 100 1546k 0 0 12.0M 0 --:--:-- --:--:-- --:--:-- 12.3M
install for i386
* 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
converting help for package 'fcoex'
finding HTML links ... done
discretize html
dot-get_correlates html
dot-plot_one_interaction html
fc html
fcoex-class html
find_cbf_modules html
get_nets html
idents html
mini_pbmc3k html
mod_colors html
mod_gene_num html
mod_names html
mod_ora html
module_genes html
new_fcoex html
nmodules html
ora_data html
plot_interactions html
plot_ora html
plot_ora_single html
recluster html
save_plots html
show-fcoex-method html
show_net html
show_ora html
** 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
install for x64
* installing *source* package 'fcoex' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'fcoex' as fcoex_1.0.0.zip
* DONE (fcoex)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'fcoex' successfully unpacked and MD5 sums checked
|
fcoex.Rcheck/tests_i386/testthat.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 )"
0.04749644 0.01453744 Removed feature 1
0.0174638 0.01321344 Removed feature 41
0.0174638 0.01321344 Removed feature 67
0.02095391 0.01258914 Removed feature 121
0.05339441 0.01224877 Removed feature 117
0.04058675 0.0112316 Removed feature 165
0.01405974 0.01067603 Removed feature 53
0.0116518 0.009981355 Removed feature 31
0.01490299 0.009373247 Removed feature 38
0.01705661 0.009373247 Removed feature 110
0.04448369 0.008943111 Removed feature 28
0.01263963 0.007950507 Removed feature 32
0.0434495 0.007429651 Removed feature 173
0.01670953 0.007075971 Removed feature 36
0.01003218 0.006587856 Removed feature 180
0.008942882 0.006362556 Removed feature 79
0.008942882 0.006362556 Removed feature 137
0.01699993 0.005855937 Removed feature 88
0.01699993 0.005855937 Removed feature 122
0.01391162 0.00564683 Removed feature 139
0.01284249 0.005575571 Removed feature 19
0.04141173 0.004391526 Removed feature 48
0.006043951 0.004391526 Removed feature 191
0.01970584 0.004132786 Removed feature 190
0.04749644 0.003587986 Removed feature 54
0.003865938 0.003587986 Removed feature 104
0.009660529 0.003583068 Removed feature 96
0.009660529 0.003583068 Removed feature 103
0.009660529 0.003583068 Removed feature 167
0.0978907 0.003379136 Removed feature 127
0.02010306 0.003379136 Removed feature 171
0.007128042 0.003034393 Removed feature 6
0.007128042 0.003034393 Removed feature 46
0.05339441 0.003034393 Removed feature 97
0.007128042 0.003034393 Removed feature 174
0.007128042 0.003034393 Removed feature 192
0.1182495 0.002953687 Removed feature 70
0.07784661 0.002717629 Removed feature 100
Round 2
[1] "first_prime round ( |s_prime| = 61 )"
0.07763396 0.01488066 Removed feature 83
0.01118375 0.01067603 Removed feature 166
0.02844707 0.007429651 Removed feature 195
0.00865213 0.00564683 Removed feature 43
0.04082032 0.004391526 Removed feature 128
0.01118375 0.003830409 Removed feature 72
0.02422342 0.003587986 Removed feature 20
0.02422342 0.003587986 Removed feature 81
0.02286967 0.003587986 Removed feature 177
0.03274996 0.003034393 Removed feature 142
0.01081585 0.002779934 Removed feature 98
Round 3
[1] "first_prime round ( |s_prime| = 50 )"
0.0427447 0.03099085 Removed feature 151
0.02963252 0.0249483 Removed feature 194
0.02642209 0.01908965 Removed feature 29
0.02604067 0.01488066 Removed feature 65
0.03273185 0.01396718 Removed feature 85
0.01445375 0.01224877 Removed feature 57
0.01445375 0.01224877 Removed feature 112
0.01445375 0.01224877 Removed feature 168
0.0209785 0.01078958 Removed feature 94
0.03442195 0.009981355 Removed feature 44
0.02438042 0.008543364 Removed feature 120
0.01227447 0.008543364 Removed feature 133
0.008325633 0.007423912 Removed feature 107
0.02271678 0.006587856 Removed feature 42
0.03975832 0.006587856 Removed feature 162
0.01173844 0.004506593 Removed feature 130
0.004145226 0.003830409 Removed feature 17
0.01445375 0.003034393 Removed feature 82
Round 4
[1] "first_prime round ( |s_prime| = 32 )"
0.07671568 0.03833879 Removed feature 50
0.01982027 0.01224877 Removed feature 183
0.007882346 0.006187113 Removed feature 156
Round 5
[1] "first_prime round ( |s_prime| = 29 )"
0.04063231 0.02332464 Removed feature 26
0.0239084 0.02128054 Removed feature 27
0.0221273 0.02128054 Removed feature 193
0.03302013 0.008935977 Removed feature 155
0.02683179 0.005575571 Removed feature 189
0.008519982 0.003587986 Removed feature 134
Round 6
[1] "first_prime round ( |s_prime| = 23 )"
0.03906883 0.03347788 Removed feature 143
0.02513984 0.01851095 Removed feature 11
0.04082032 0.01599553 Removed feature 179
0.03112673 0.01258914 Removed feature 147
0.03668537 0.008943111 Removed feature 16
0.04141173 0.007429651 Removed feature 90
0.01484423 0.005575571 Removed feature 99
Round 7
[1] "first_prime round ( |s_prime| = 16 )"
0.03009736 0.0173703 Removed feature 140
0.02300102 0.01614804 Removed feature 106
Round 8
[1] "first_prime round ( |s_prime| = 14 )"
0.02299229 0.0173703 Removed feature 131
Round 9
[1] "first_prime round ( |s_prime| = 13 )"
0.02186843 0.01851095 Removed feature 150
0.02816067 0.01757082 Removed feature 149
0.04604039 0.01561266 Removed feature 91
0.02844707 0.007429651 Removed feature 58
== testthat results ===========================================================
[ OK: 3 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
>
> proc.time()
user system elapsed
18.21 1.37 19.57
|
fcoex.Rcheck/tests_x64/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-w64-mingw32/x64 (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 = 100"
Round 1
[1] "first_prime round ( |s_prime| = 100 )"
0.0424457 0.03561466 Removed feature 159
0.03386789 0.03075492 Removed feature 33
0.03396632 0.02538638 Removed feature 192
0.02473096 0.02414231 Removed feature 60
0.05897525 0.02273447 Removed feature 23
0.05897525 0.02273447 Removed feature 56
0.03826502 0.02094474 Removed feature 189
0.0527298 0.01908965 Removed feature 34
0.02465625 0.01505173 Removed feature 135
0.01807012 0.01488066 Removed feature 113
0.04784899 0.01453744 Removed feature 2
0.01466812 0.01390786 Removed feature 93
0.06256357 0.01321344 Removed feature 65
0.0403661 0.01224877 Removed feature 172
0.02946959 0.0112316 Removed feature 28
0.02946959 0.0112316 Removed feature 89
0.02946959 0.0112316 Removed feature 106
0.02946959 0.0112316 Removed feature 126
0.04919941 0.01067603 Removed feature 152
0.02473096 0.01060396 Removed feature 116
0.01679534 0.009981355 Removed feature 48
0.01179206 0.00940938 Removed feature 22
0.03396632 0.008943111 Removed feature 107
0.01608381 0.008943111 Removed feature 166
0.07673569 0.008935977 Removed feature 195
0.009350183 0.007429651 Removed feature 136
0.03826502 0.007429651 Removed feature 138
0.009350183 0.007429651 Removed feature 175
0.02347749 0.007075971 Removed feature 81
0.06109234 0.007075971 Removed feature 92
0.01225794 0.007075971 Removed feature 117
0.02347749 0.007075971 Removed feature 163
0.01523756 0.006587856 Removed feature 18
0.01523756 0.006587856 Removed feature 73
0.01839751 0.006187113 Removed feature 21
0.01009946 0.005855937 Removed feature 142
0.005700673 0.004975612 Removed feature 47
0.05067145 0.004975612 Removed feature 119
0.08548212 0.004975612 Removed feature 160
0.00472939 0.004713998 Removed feature 179
0.03174894 0.004391526 Removed feature 29
0.03174894 0.004391526 Removed feature 99
0.006550336 0.004132786 Removed feature 177
0.06323259 0.003830409 Removed feature 27
0.003999539 0.003830409 Removed feature 200
0.01234305 0.003587986 Removed feature 149
Round 2
[1] "first_prime round ( |s_prime| = 54 )"
0.03502467 0.02094474 Removed feature 45
0.04800737 0.01908965 Removed feature 157
0.0517291 0.0173703 Removed feature 13
0.02276724 0.01505173 Removed feature 87
0.04616065 0.01390786 Removed feature 100
0.0459724 0.01258098 Removed feature 41
0.0972149 0.01224877 Removed feature 170
0.03730323 0.01152678 Removed feature 108
0.02197703 0.008943111 Removed feature 68
0.02197703 0.008943111 Removed feature 143
0.02110472 0.008543364 Removed feature 153
0.01846634 0.008424484 Removed feature 173
0.009548246 0.007075971 Removed feature 36
0.009548246 0.007075971 Removed feature 51
0.00865213 0.007075971 Removed feature 53
0.00865213 0.007075971 Removed feature 122
0.00850776 0.006362556 Removed feature 35
0.0195474 0.005581295 Removed feature 150
0.007943374 0.003830409 Removed feature 42
0.01753455 0.003587986 Removed feature 59
Round 3
[1] "first_prime round ( |s_prime| = 34 )"
0.04090775 0.02103363 Removed feature 185
0.02353502 0.01964875 Removed feature 70
0.04919571 0.0185461 Removed feature 67
0.0447076 0.01488066 Removed feature 9
0.03546486 0.01060396 Removed feature 104
0.01427724 0.005575571 Removed feature 52
0.006314812 0.005575571 Removed feature 134
0.004551566 0.004391526 Removed feature 69
Round 4
[1] "first_prime round ( |s_prime| = 26 )"
0.05361072 0.01152678 Removed feature 98
0.05743083 0.01067603 Removed feature 38
0.01513646 0.00940938 Removed feature 196
0.006990818 0.005010845 Removed feature 37
Round 5
[1] "first_prime round ( |s_prime| = 22 )"
0.02458249 0.01224877 Removed feature 182
0.01769527 0.008424484 Removed feature 24
0.01591695 0.003587986 Removed feature 167
Round 6
[1] "first_prime round ( |s_prime| = 19 )"
0.0400682 0.01964875 Removed feature 105
Round 7
[1] "first_prime round ( |s_prime| = 18 )"
0.04575087 0.0249483 Removed feature 190
Round 8
[1] "first_prime round ( |s_prime| = 17 )"
Round 9
[1] "first_prime round ( |s_prime| = 17 )"
0.0257225 0.01224877 Removed feature 30
Round 10
[1] "first_prime round ( |s_prime| = 16 )"
0.03104106 0.01786321 Removed feature 169
Round 11
[1] "first_prime round ( |s_prime| = 15 )"
0.05479743 0.01258098 Removed feature 156
Round 12
[1] "first_prime round ( |s_prime| = 14 )"
Round 13
[1] "first_prime round ( |s_prime| = 14 )"
Round 14
[1] "first_prime round ( |s_prime| = 14 )"
== testthat results ===========================================================
[ OK: 3 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
>
> proc.time()
user system elapsed
16.10 0.46 16.56
|
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fcoex.Rcheck/examples_i386/fcoex-Ex.timings
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fcoex.Rcheck/examples_x64/fcoex-Ex.timings
|