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This page was generated on 2021-10-15 15:06:04 -0400 (Fri, 15 Oct 2021).

CHECK results for fcoex on tokay2

To the developers/maintainers of the fcoex package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/fcoex.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 623/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
fcoex 1.6.0  (landing page)
Tiago Lubiana
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/fcoex
git_branch: RELEASE_3_13
git_last_commit: f4e35ed
git_last_commit_date: 2021-05-19 12:47:53 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: fcoex
Version: 1.6.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:fcoex.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings fcoex_1.6.0.tar.gz
StartedAt: 2021-10-14 23:05:04 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 23:12:11 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 427.1 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: fcoex.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:fcoex.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings fcoex_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/fcoex.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '1.6.0'
* 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 ... WARNING
Found the following significant warnings:
  Warning: replacing previous import 'Matrix::head' by 'utils::head' when loading 'fcoex'
See 'C:/Users/biocbuild/bbs-3.13-bioc/meat/fcoex.Rcheck/00install.out' for details.
* 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 LazyData ... 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 (user + system) or elapsed time > 5s
                  user system elapsed
find_cbf_modules 19.32   0.54   19.86
get_nets         18.72   0.19   18.91
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
find_cbf_modules 18.88   0.21   19.08
get_nets         18.36   0.09   18.45
* 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 WARNINGs
See
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/fcoex.Rcheck/00check.log'
for details.

Installation output

fcoex.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/fcoex_1.6.0.tar.gz && rm -rf fcoex.buildbin-libdir && mkdir fcoex.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=fcoex.buildbin-libdir fcoex_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL fcoex_1.6.0.zip && rm fcoex_1.6.0.tar.gz fcoex_1.6.0.zip
###
##############################################################################
##############################################################################


  % 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  943k  100  943k    0     0  1622k      0 --:--:-- --:--:-- --:--:-- 1626k

install for i386

* installing *source* package 'fcoex' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB

Warning: replacing previous import 'Matrix::head' by 'utils::head' when loading 'fcoex'
in method for 'mod_ora' with signature '"fcoex"': no definition for class "fcoex"
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'Matrix::head' by 'utils::head' when loading 'fcoex'
in method for 'mod_ora' with signature '"fcoex"': no definition for class "fcoex"
** 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
Warning: replacing previous import 'Matrix::head' by 'utils::head' when loading 'fcoex'
** testing if installed package can be loaded from final location
Warning: replacing previous import 'Matrix::head' by 'utils::head' when loading 'fcoex'
** 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
Warning: replacing previous import 'Matrix::head' by 'utils::head' when loading 'fcoex'
* MD5 sums
packaged installation of 'fcoex' as fcoex_1.6.0.zip
* DONE (fcoex)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'fcoex' successfully unpacked and MD5 sums checked

Tests output

fcoex.Rcheck/tests_i386/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
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)

Warning message:
replacing previous import 'Matrix::head' by 'utils::head' when loading 'fcoex' 
> 
> test_check("fcoex")
[1] 0.1
[1] "Number of features features =  40"
[1] "Number of prospective features =  14"
Round 1 
[1] "first_prime  round ( |s_prime| = 14 )"
   0.1867632   0.1586357   Removed feature  13 
   0.1256985   0.1198729   Removed feature  38 
   0.1168656   0.1068907   Removed feature  18 
   0.2045022   0.09770198   Removed feature  34 
   0.1736622   0.08930267   Removed feature  32 
Round 2 
[1] "first_prime  round ( |s_prime| = 9 )"
   0.2161864   0.1610819   Removed feature  39 
Round 3 
[1] "first_prime  round ( |s_prime| = 8 )"
   0.128325   0.1124689   Removed feature  30 
Round 4 
[1] "first_prime  round ( |s_prime| = 7 )"
Round 5 
[1] "first_prime  round ( |s_prime| = 7 )"
Round 6 
[1] "first_prime  round ( |s_prime| = 7 )"
Round 7 
[1] "first_prime  round ( |s_prime| = 7 )"
[1] "Number of final features =  7"
[1] "Gene-1"
[1] "Gene-40"
[1] "Gene-28"
[1] "Gene-39"
[1] "Gene-13"
[1] "Gene-26"
[1] "Gene-12"
[1] "Gene-25"
[1] "Gene-38"
[1] "Gene-35"
[1] "Gene-30"
[1] "Gene-18"
[1] "Gene-34"
[1] "Gene-32"
[1] "Gene-1"
[1] "Gene-40"
[1] "Gene-28"
[1] "Gene-26"
[1] "Gene-12"
[1] "Gene-25"
[1] "Gene-35"
[ FAIL 0 | WARN 14 | SKIP 0 | PASS 4 ]
> 
> proc.time()
   user  system elapsed 
  10.21    0.89   11.07

fcoex.Rcheck/tests_x64/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
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)

Warning message:
replacing previous import 'Matrix::head' by 'utils::head' when loading 'fcoex' 
> 
> test_check("fcoex")
[1] 0.1
[1] "Number of features features =  40"
[1] "Number of prospective features =  14"
Round 1 
[1] "first_prime  round ( |s_prime| = 14 )"
   0.1867632   0.1586357   Removed feature  13 
   0.1256985   0.1198729   Removed feature  38 
   0.1168656   0.1068907   Removed feature  18 
   0.2045022   0.09770198   Removed feature  34 
   0.1736622   0.08930267   Removed feature  32 
Round 2 
[1] "first_prime  round ( |s_prime| = 9 )"
   0.2161864   0.1610819   Removed feature  39 
Round 3 
[1] "first_prime  round ( |s_prime| = 8 )"
   0.128325   0.1124689   Removed feature  30 
Round 4 
[1] "first_prime  round ( |s_prime| = 7 )"
Round 5 
[1] "first_prime  round ( |s_prime| = 7 )"
Round 6 
[1] "first_prime  round ( |s_prime| = 7 )"
Round 7 
[1] "first_prime  round ( |s_prime| = 7 )"
[1] "Number of final features =  7"
[1] "Gene-1"
[1] "Gene-40"
[1] "Gene-28"
[1] "Gene-39"
[1] "Gene-13"
[1] "Gene-26"
[1] "Gene-12"
[1] "Gene-25"
[1] "Gene-38"
[1] "Gene-35"
[1] "Gene-30"
[1] "Gene-18"
[1] "Gene-34"
[1] "Gene-32"
[1] "Gene-1"
[1] "Gene-40"
[1] "Gene-28"
[1] "Gene-26"
[1] "Gene-12"
[1] "Gene-25"
[1] "Gene-35"
[ FAIL 0 | WARN 14 | SKIP 0 | PASS 4 ]
> 
> proc.time()
   user  system elapsed 
   9.85    0.40   10.25

Example timings

fcoex.Rcheck/examples_i386/fcoex-Ex.timings

nameusersystemelapsed
discretize2.690.252.94
fc0.790.050.85
find_cbf_modules19.32 0.5419.86
get_nets18.72 0.1918.91
idents0.270.020.28
mini_pbmc3k0.780.030.81
mod_colors0.330.020.34
mod_gene_num0.370.010.39
mod_names0.860.100.96
mod_ora2.190.032.22
module_genes0.330.040.36
new_fcoex0.260.030.30
nmodules0.270.070.34
ora_data0.840.050.89
plot_ora2.280.022.30
recluster0.610.060.67
save_plots000
show-fcoex-method0.330.020.34
show_net000
show_ora0.310.010.33

fcoex.Rcheck/examples_x64/fcoex-Ex.timings

nameusersystemelapsed
discretize2.840.042.87
fc0.780.040.83
find_cbf_modules18.88 0.2119.08
get_nets18.36 0.0918.45
idents0.190.030.22
mini_pbmc3k0.550.030.57
mod_colors0.230.020.25
mod_gene_num0.220.040.27
mod_names0.250.020.26
mod_ora2.950.063.02
module_genes0.270.030.29
new_fcoex0.260.020.29
nmodules0.270.050.31
ora_data0.230.010.25
plot_ora2.450.102.54
recluster1.500.061.57
save_plots000
show-fcoex-method0.250.030.28
show_net000
show_ora0.270.030.30