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This page was generated on 2021-07-23 15:06:34 -0400 (Fri, 23 Jul 2021).

CHECK results for fcoex on machv2

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: 2021-07-22 04:50:13 -0400 (Thu, 22 Jul 2021)
URL: https://git.bioconductor.org/packages/fcoex
Branch: RELEASE_3_13
Last Commit: f4e35ed
Last Changed 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: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:fcoex.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings fcoex_1.6.0.tar.gz
StartedAt: 2021-07-22 18:39:05 -0400 (Thu, 22 Jul 2021)
EndedAt: 2021-07-22 18:45:43 -0400 (Thu, 22 Jul 2021)
EllapsedTime: 397.9 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: fcoex.Rcheck
Warnings: 2

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:fcoex.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings fcoex_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/fcoex.Rcheck’
* using R version 4.1.0 (2021-05-18)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... 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 ‘/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
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
find_cbf_modules 27.428  0.562  28.009
get_nets         27.430  0.388  27.848
* 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
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/fcoex.Rcheck/00check.log’
for details.



Installation output

fcoex.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL fcoex
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/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 version 4.1.0 (2021-05-18) -- "Camp Pontanezen"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 
 14.165   0.656  14.832 

Example timings

fcoex.Rcheck/fcoex-Ex.timings

nameusersystemelapsed
discretize3.4000.1583.559
fc0.6250.0600.686
find_cbf_modules27.428 0.56228.009
get_nets27.430 0.38827.848
idents0.6210.0110.636
mini_pbmc3k0.7960.0110.809
mod_colors0.6370.0100.647
mod_gene_num0.6090.0200.629
mod_names1.2450.0201.266
mod_ora3.7340.0893.826
module_genes0.7260.0120.737
new_fcoex0.4170.0150.433
nmodules0.5880.0070.596
ora_data1.1680.0281.197
plot_ora2.9700.0503.021
recluster0.9970.0421.040
save_plots0.0000.0000.001
show-fcoex-method0.6480.0080.658
show_net000
show_ora1.3040.0201.325