Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-10-15 15:05:40 -0400 (Fri, 15 Oct 2021).

CHECK results for FELLA on nebbiolo1

To the developers/maintainers of the FELLA package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/FELLA.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 628/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FELLA 1.12.0  (landing page)
Sergio Picart-Armada
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/FELLA
git_branch: RELEASE_3_13
git_last_commit: a4fcd75
git_last_commit_date: 2021-05-19 12:34:03 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: FELLA
Version: 1.12.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:FELLA.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings FELLA_1.12.0.tar.gz
StartedAt: 2021-10-14 09:50:04 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 09:52:57 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 172.4 seconds
RetCode: 0
Status:   OK  
CheckDir: FELLA.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:FELLA.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings FELLA_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/FELLA.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘FELLA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘FELLA’ version ‘1.12.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘FELLA’ 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
* 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
buildGraphFromKEGGREST: no visible global function definition for
  ‘capture.output’
Undefined global functions or variables:
  capture.output
Consider adding
  importFrom("utils", "capture.output")
to your NAMESPACE file.
* 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 ... OK
* 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 ... OK
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.13-bioc/meat/FELLA.Rcheck/00check.log’
for details.



Installation output

FELLA.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL FELLA
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘FELLA’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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
* DONE (FELLA)

Tests output

FELLA.Rcheck/tests/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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(FELLA)
> 
> test_check("FELLA")

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[ FAIL 0 | WARN 0 | SKIP 0 | PASS 168 ]
> 
> proc.time()
   user  system elapsed 
 16.314   4.020  71.323 

Example timings

FELLA.Rcheck/FELLA-Ex.timings

nameusersystemelapsed
FELLA0.2120.0190.232
FELLA.sample0.0100.0060.016
checkArguments0.0000.0020.002
data-funs2.2390.1052.344
enrich-funs2.3590.0162.375
export-funs0.1830.0120.196
getBackground1.1620.0041.165
getCom0.0120.0000.013
getExcluded0.0130.0000.013
getGraph0.0110.0000.011
getInfo0.0110.0000.011
getInput0.0130.0000.013
getMatrix0.0160.0040.020
getName0.0120.0000.011
getPscores0.0300.0000.031
getPvaluesSize0.0200.0030.023
getStatus0.0120.0000.012
getSums0.4090.0040.414
getValid0.0240.0010.024
infere.con2ec0.0000.0030.002
input.sample0.0010.0000.002
is.FELLA.DATA0.010.000.01
is.FELLA.USER0.0250.0000.026
largestcc0.0160.0000.017
launchApp0.0010.0000.000
listApprox000
listCategories0.0000.0000.001
listInternalDatabases0.0010.0000.001
listMethods000
mytriangle0.0170.0000.017
plotBipartite0.0580.0000.058
plotLegend0.0260.0000.025
sanitise0.0000.0010.000