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This page was generated on 2023-01-02 09:00:29 -0500 (Mon, 02 Jan 2023).

HostnameOSArch (*)R versionInstalled pkgs
palomino5Windows Server 2022 Datacenterx64R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" 4165
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CHECK results for fcoex on palomino5


To the developers/maintainers of the fcoex package:
Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 656/2158HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
fcoex 1.13.0  (landing page)
Tiago Lubiana
Snapshot Date: 2022-12-28 11:00:06 -0500 (Wed, 28 Dec 2022)
git_url: https://git.bioconductor.org/packages/fcoex
git_branch: master
git_last_commit: 78bae2d
git_last_commit_date: 2022-11-01 11:20:57 -0500 (Tue, 01 Nov 2022)
palomino5Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  

Summary

Package: fcoex
Version: 1.13.0
Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:fcoex.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings fcoex_1.13.0.tar.gz
StartedAt: 2022-12-28 23:45:48 -0500 (Wed, 28 Dec 2022)
EndedAt: 2022-12-28 23:49:58 -0500 (Wed, 28 Dec 2022)
EllapsedTime: 250.1 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: fcoex.Rcheck
Warnings: 2

Command output

##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:fcoex.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings fcoex_1.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/fcoex.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 10.4.0
    GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'fcoex/DESCRIPTION' ... OK
* this is package 'fcoex' version '1.13.0'
* 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 'F:/biocbuild/bbs-3.17-bioc-rtools43/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
* 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 ... NOTE
discretize,fcoex: no visible global function definition for 'as'
initialize,fcoex: no visible global function definition for 'as'
mod_ora,fcoex: no visible global function definition for 'is'
Undefined global functions or variables:
  as is
Consider adding
  importFrom("methods", "as", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
find_cbf_modules 16.48   0.52   17.00
get_nets         15.38   0.19   15.58
* 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: 2 WARNINGs, 1 NOTE
See
  'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/fcoex.Rcheck/00check.log'
for details.



Installation output

fcoex.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL fcoex
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library'
* 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
** 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
* DONE (fcoex)

Tests output

fcoex.Rcheck/tests/testthat.Rout


R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2022 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] "Number of features features =  40"
[1] "Number of prospective features =  14"
[1] "Number of final features =  7"
[ FAIL 0 | WARN 14 | SKIP 0 | PASS 4 ]

[ FAIL 0 | WARN 14 | SKIP 0 | PASS 4 ]
> 
> proc.time()
   user  system elapsed 
   8.82    0.71    9.51 

Example timings

fcoex.Rcheck/fcoex-Ex.timings

nameusersystemelapsed
discretize2.640.082.72
fc0.160.030.18
find_cbf_modules16.48 0.5217.00
get_nets15.38 0.1915.58
idents0.200.010.22
mini_pbmc3k0.30.00.3
mod_colors0.200.020.22
mod_gene_num0.710.030.73
mod_names0.180.030.22
mod_ora1.570.091.66
module_genes0.180.050.23
new_fcoex0.740.030.77
nmodules0.190.020.20
ora_data0.170.030.20
plot_ora1.560.081.64
recluster0.440.010.46
save_plots000
show-fcoex-method0.250.020.26
show_net000
show_ora0.230.000.24