| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:31:07 -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: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:fcoex.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings fcoex_1.4.0.tar.gz |
| StartedAt: 2021-05-06 02:45:16 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 02:53:57 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 521.5 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: fcoex.Rcheck |
| Warnings: NA |
##############################################################################
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:fcoex.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings fcoex_1.4.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/fcoex.Rcheck'
* using R version 4.0.5 (2021-03-31)
* 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 '1.4.0'
* 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 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' ... 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
** running examples for arch 'x64' ... 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 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: 2 ERRORs, 1 WARNING
See
'C:/Users/biocbuild/bbs-3.12-bioc/meat/fcoex.Rcheck/00check.log'
for details.
fcoex.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/fcoex_1.4.0.tar.gz && rm -rf fcoex.buildbin-libdir && mkdir fcoex.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=fcoex.buildbin-libdir fcoex_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL fcoex_1.4.0.zip && rm fcoex_1.4.0.tar.gz fcoex_1.4.0.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 1573k 100 1573k 0 0 3942k 0 --:--:-- --:--:-- --:--:-- 3953k
install for i386
* 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
converting help for package 'fcoex'
finding HTML links ... done
discretize html
dot-get_correlates 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_one_interaction 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_1.4.0.zip
* DONE (fcoex)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'fcoex' successfully unpacked and MD5 sums checked
|
fcoex.Rcheck/tests_i386/testthat.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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 = 101"
Round 1
[1] "first_prime round ( |s_prime| = 101 )"
0.04633928 0.04368795 Removed feature 40
0.03889596 0.03113641 Removed feature 150
0.02505543 0.02485001 Removed feature 52
0.08446205 0.02273447 Removed feature 83
0.03631938 0.02094474 Removed feature 3
0.03631938 0.02094474 Removed feature 143
0.02568782 0.01561809 Removed feature 178
0.08098656 0.01067603 Removed feature 88
0.01330006 0.01060396 Removed feature 6
0.01330006 0.01060396 Removed feature 94
0.02028984 0.008943111 Removed feature 50
0.04700393 0.008943111 Removed feature 81
0.02259109 0.008424484 Removed feature 154
0.01143034 0.007429651 Removed feature 2
0.01143034 0.007429651 Removed feature 61
0.03274996 0.007075971 Removed feature 107
0.02255514 0.006587856 Removed feature 172
0.02839767 0.005855937 Removed feature 110
0.02896364 0.004975612 Removed feature 109
0.02074814 0.004506593 Removed feature 21
0.04422823 0.004506593 Removed feature 37
0.008097137 0.004132786 Removed feature 33
0.03541429 0.003830409 Removed feature 112
0.009653969 0.003830409 Removed feature 176
0.005301989 0.003587986 Removed feature 168
0.005301989 0.003587986 Removed feature 184
Round 2
[1] "first_prime round ( |s_prime| = 75 )"
0.03414152 0.03099085 Removed feature 91
0.04700393 0.02800735 Removed feature 18
0.02931435 0.02128054 Removed feature 145
0.06213344 0.02094474 Removed feature 14
0.02098327 0.01964875 Removed feature 97
0.0145043 0.01258098 Removed feature 64
0.01304903 0.01060396 Removed feature 187
0.0261192 0.009981355 Removed feature 55
0.03761253 0.008943111 Removed feature 124
0.02140148 0.008424484 Removed feature 73
0.0240649 0.006587856 Removed feature 129
0.04950029 0.006362556 Removed feature 78
0.04140495 0.006187113 Removed feature 76
0.03256909 0.005855937 Removed feature 25
0.0631113 0.005855937 Removed feature 195
0.06968416 0.00564683 Removed feature 101
0.03668537 0.004391526 Removed feature 74
0.02205742 0.003830409 Removed feature 12
0.008715915 0.003830409 Removed feature 90
Round 3
[1] "first_prime round ( |s_prime| = 56 )"
0.0223029 0.02128054 Removed feature 30
0.02186843 0.01599553 Removed feature 166
0.05010521 0.01488066 Removed feature 142
0.03913381 0.01258914 Removed feature 117
0.02781677 0.01258098 Removed feature 104
0.03455323 0.009981355 Removed feature 158
0.00943645 0.008424484 Removed feature 16
0.0143547 0.007325623 Removed feature 35
0.02432298 0.006362556 Removed feature 34
0.007200867 0.006362556 Removed feature 116
0.02328091 0.006362556 Removed feature 134
0.01034012 0.003587986 Removed feature 119
0.007205587 0.003583068 Removed feature 140
0.007205587 0.003583068 Removed feature 164
Round 4
[1] "first_prime round ( |s_prime| = 42 )"
0.04029774 0.03428977 Removed feature 139
0.04483034 0.01679217 Removed feature 66
0.02770806 0.01390786 Removed feature 127
0.01320667 0.01224877 Removed feature 57
0.03812936 0.01224877 Removed feature 121
0.01884354 0.00821823 Removed feature 132
0.01957512 0.004391526 Removed feature 51
0.009760746 0.003583068 Removed feature 111
Round 5
[1] "first_prime round ( |s_prime| = 34 )"
0.05055045 0.03099085 Removed feature 80
0.04372365 0.02800735 Removed feature 147
0.0687901 0.02752658 Removed feature 181
0.03294965 0.02660303 Removed feature 174
0.04828629 0.02414231 Removed feature 153
0.03906883 0.01453744 Removed feature 29
0.05472121 0.01396718 Removed feature 171
0.04605524 0.008943111 Removed feature 144
0.02365906 0.007848506 Removed feature 11
0.01162765 0.006587856 Removed feature 170
Round 6
[1] "first_prime round ( |s_prime| = 24 )"
0.03588761 0.03348817 Removed feature 58
0.0269171 0.02094474 Removed feature 54
0.02074814 0.01224877 Removed feature 175
Round 7
[1] "first_prime round ( |s_prime| = 21 )"
0.04659369 0.02800735 Removed feature 7
0.02088483 0.01396718 Removed feature 146
0.02804137 0.01078958 Removed feature 125
0.02011654 0.009981355 Removed feature 163
Round 8
[1] "first_prime round ( |s_prime| = 17 )"
0.01529466 0.01488066 Removed feature 10
0.04478564 0.00773253 Removed feature 93
0.0291168 0.007676308 Removed feature 128
Round 9
[1] "first_prime round ( |s_prime| = 14 )"
0.01737201 0.01321344 Removed feature 149
0.01256637 0.01164451 Removed feature 72
0.01529366 0.01129448 Removed feature 36
Round 10
[1] "first_prime round ( |s_prime| = 11 )"
0.03423411 0.009981355 Removed feature 89
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 3 ]
>
>
> proc.time()
user system elapsed
14.50 1.07 15.67
|
fcoex.Rcheck/tests_x64/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-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 = 103"
Round 1
[1] "first_prime round ( |s_prime| = 103 )"
0.03835272 0.02485001 Removed feature 165
0.06291203 0.02332464 Removed feature 185
0.0223029 0.01851095 Removed feature 87
0.05460751 0.01786321 Removed feature 44
0.04323106 0.01757082 Removed feature 131
0.0270514 0.01561266 Removed feature 83
0.03898516 0.01561266 Removed feature 134
0.01700548 0.01488066 Removed feature 136
0.0225012 0.01453744 Removed feature 32
0.01428237 0.01396718 Removed feature 10
0.06448613 0.01258098 Removed feature 43
0.02823505 0.01152678 Removed feature 174
0.06354703 0.01067603 Removed feature 95
0.01409774 0.009981355 Removed feature 6
0.01220858 0.009981355 Removed feature 8
0.0223029 0.00940938 Removed feature 196
0.009397187 0.008943111 Removed feature 169
0.01210953 0.007423912 Removed feature 114
0.02233104 0.007075971 Removed feature 172
0.02752663 0.006362556 Removed feature 1
0.02752663 0.006362556 Removed feature 91
0.02082965 0.006362556 Removed feature 130
0.00922351 0.006362556 Removed feature 137
0.08841006 0.004975612 Removed feature 59
0.01064068 0.004975612 Removed feature 184
0.01476712 0.004506593 Removed feature 93
0.01205803 0.004391526 Removed feature 140
0.01225326 0.004132786 Removed feature 18
0.0225012 0.003587986 Removed feature 55
0.00500954 0.003587986 Removed feature 70
0.00500954 0.003587986 Removed feature 124
0.01208551 0.003587986 Removed feature 198
Round 2
[1] "first_prime round ( |s_prime| = 71 )"
0.04140495 0.03922634 Removed feature 25
0.04700393 0.02800735 Removed feature 139
0.02822074 0.0249483 Removed feature 28
0.04448369 0.02094474 Removed feature 126
0.03668537 0.01790847 Removed feature 98
0.03668537 0.01790847 Removed feature 155
0.03071134 0.01453744 Removed feature 143
0.02822074 0.01396718 Removed feature 168
0.08791547 0.01321344 Removed feature 4
0.03470023 0.01152678 Removed feature 115
0.03470023 0.01152678 Removed feature 192
0.03396632 0.0112316 Removed feature 170
0.02715013 0.01067603 Removed feature 79
0.01496429 0.01050465 Removed feature 163
0.01593592 0.00940938 Removed feature 122
0.02931435 0.009373247 Removed feature 105
0.01073201 0.008935977 Removed feature 132
0.04945164 0.008424484 Removed feature 12
0.01631872 0.007676308 Removed feature 100
0.02501797 0.007429651 Removed feature 80
0.04448369 0.007429651 Removed feature 183
0.02009678 0.007075971 Removed feature 159
0.02009678 0.007075971 Removed feature 182
0.007048816 0.006587856 Removed feature 21
0.01634608 0.006362556 Removed feature 104
0.01376893 0.005855937 Removed feature 197
0.03712016 0.005581295 Removed feature 90
0.01029202 0.005575571 Removed feature 13
0.008546848 0.00488621 Removed feature 22
0.005622364 0.003587986 Removed feature 85
Round 3
[1] "first_prime round ( |s_prime| = 41 )"
0.05551031 0.02332464 Removed feature 161
0.02628614 0.02103363 Removed feature 51
0.02528849 0.0196221 Removed feature 157
0.03783668 0.0173703 Removed feature 27
0.0589976 0.01425559 Removed feature 190
0.02526528 0.01258098 Removed feature 58
0.03365093 0.006587856 Removed feature 11
0.007579221 0.006587856 Removed feature 49
0.006797007 0.005353485 Removed feature 129
0.01987894 0.004132786 Removed feature 71
Round 4
[1] "first_prime round ( |s_prime| = 31 )"
0.04372365 0.02800735 Removed feature 35
0.02916532 0.02332464 Removed feature 148
0.03424999 0.01790847 Removed feature 20
0.03424999 0.01790847 Removed feature 147
0.04372365 0.01224877 Removed feature 144
0.02077781 0.0112316 Removed feature 53
0.009719231 0.008424484 Removed feature 99
0.04141173 0.007429651 Removed feature 9
0.01957512 0.006587856 Removed feature 151
0.01484423 0.005575571 Removed feature 101
0.02018285 0.00488621 Removed feature 158
0.005978405 0.004506593 Removed feature 102
0.06422182 0.004132786 Removed feature 179
Round 5
[1] "first_prime round ( |s_prime| = 18 )"
0.02030074 0.01067603 Removed feature 64
0.02476948 0.008543364 Removed feature 7
0.02752663 0.006362556 Removed feature 176
0.0176005 0.005575571 Removed feature 107
0.005993871 0.004788064 Removed feature 66
Round 6
[1] "first_prime round ( |s_prime| = 13 )"
0.03982315 0.005575571 Removed feature 34
Round 7
[1] "first_prime round ( |s_prime| = 12 )"
0.02827077 0.02103363 Removed feature 33
Round 8
[1] "first_prime round ( |s_prime| = 11 )"
0.03848265 0.02273447 Removed feature 94
0.02763913 0.00940938 Removed feature 63
Round 9
[1] "first_prime round ( |s_prime| = 9 )"
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 3 ]
>
>
> proc.time()
user system elapsed
22.37 0.57 23.10
|
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fcoex.Rcheck/examples_i386/fcoex-Ex.timings
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fcoex.Rcheck/examples_x64/fcoex-Ex.timings
|