Back to Multiple platform build/check report for BioC 3.18:   simplified   long
ABCDE[F]GHIJKLMNOPQRSTUVWXYZ

This page was generated on 2024-03-02 11:35:43 -0500 (Sat, 02 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" 4692
palomino4Windows Server 2022 Datacenterx644.3.2 (2023-10-31 ucrt) -- "Eye Holes" 4445
lconwaymacOS 12.7.1 Montereyx86_644.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" 4466
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 704/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FELLA 1.22.0  (landing page)
Sergio Picart-Armada
Snapshot Date: 2024-03-01 14:05:09 -0500 (Fri, 01 Mar 2024)
git_url: https://git.bioconductor.org/packages/FELLA
git_branch: RELEASE_3_18
git_last_commit: 3444f45
git_last_commit_date: 2023-10-24 11:03:30 -0500 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    TIMEOUT  
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for FELLA on nebbiolo2


To the developers/maintainers of the FELLA package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: FELLA
Version: 1.22.0
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:FELLA.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings FELLA_1.22.0.tar.gz
StartedAt: 2024-03-01 22:11:18 -0500 (Fri, 01 Mar 2024)
EndedAt: 2024-03-01 22:51:19 -0500 (Fri, 01 Mar 2024)
EllapsedTime: 2400.4 seconds
RetCode: None
Status:   TIMEOUT  
CheckDir: FELLA.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:FELLA.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings FELLA_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/FELLA.Rcheck’
* using R version 4.3.2 Patched (2023-11-13 r85521)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘FELLA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘FELLA’ version ‘1.22.0’
* 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 loading without being on the library search path ... 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
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
data-funs   7.182  0.592   8.391
enrich-funs 7.274  0.233   9.517
* 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 ...
  ‘musmusculus.Rmd’ using ‘UTF-8’... OK
  ‘quickstart.Rmd’ using ‘UTF-8’... OK
  ‘zebrafish.Rmd’ using ‘UTF-8’... OK
  ‘FELLA.Rnw’ using ‘UTF-8’... OK
 OK
* checking re-building of vignette outputs ...

Installation output

FELLA.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL FELLA
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-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 4.3.2 Patched (2023-11-13 r85521) -- "Eye Holes"
Copyright (C) 2023 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")

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |==============                                                        |  20%
  |                                                                            
  |============================                                          |  40%
  |                                                                            
  |==========================================                            |  60%
  |                                                                            
  |========================================================              |  80%
  |                                                                            
  |======================================================================| 100%

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |=======                                                               |  10%
  |                                                                            
  |==============                                                        |  20%
  |                                                                            
  |=====================                                                 |  30%
  |                                                                            
  |============================                                          |  40%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |==========================================                            |  60%
  |                                                                            
  |=================================================                     |  70%
  |                                                                            
  |========================================================              |  80%
  |                                                                            
  |===============================================================       |  90%
  |                                                                            
  |======================================================================| 100%

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |=======                                                               |  10%
  |                                                                            
  |==============                                                        |  20%
  |                                                                            
  |=====================                                                 |  30%
  |                                                                            
  |============================                                          |  40%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |==========================================                            |  60%
  |                                                                            
  |=================================================                     |  70%
  |                                                                            
  |========================================================              |  80%
  |                                                                            
  |===============================================================       |  90%
  |                                                                            
  |======================================================================| 100%

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |=======                                                               |  10%
  |                                                                            
  |==============                                                        |  20%
  |                                                                            
  |=====================                                                 |  30%
  |                                                                            
  |============================                                          |  40%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |==========================================                            |  60%
  |                                                                            
  |=================================================                     |  70%
  |                                                                            
  |========================================================              |  80%
  |                                                                            
  |===============================================================       |  90%
  |                                                                            
  |======================================================================| 100%
[ FAIL 0 | WARN 12 | SKIP 0 | PASS 168 ]

[ FAIL 0 | WARN 12 | SKIP 0 | PASS 168 ]
> 
> proc.time()
   user  system elapsed 
 35.729   4.227  70.103 

Example timings

FELLA.Rcheck/FELLA-Ex.timings

nameusersystemelapsed
FELLA0.2140.0060.221
FELLA.sample0.0110.0000.011
checkArguments0.0020.0000.001
data-funs7.1820.5928.391
enrich-funs7.2740.2339.517
export-funs0.4160.0360.451
getBackground0.5730.0080.581
getCom0.0170.0040.020
getExcluded0.0210.0020.024
getGraph0.0190.0010.019
getInfo0.0190.0000.019
getInput0.0220.0000.022
getMatrix0.0390.0000.039
getName0.0190.0000.019
getPscores0.0510.0040.055
getPvaluesSize0.0760.0000.076
getStatus0.0190.0000.019
getSums0.9320.0681.000
getValid0.0430.0000.044
infere.con2ec0.0040.0000.004
input.sample0.0020.0000.002
is.FELLA.DATA0.0180.0000.019
is.FELLA.USER0.0440.0000.044
largestcc0.1950.0280.222
launchApp0.0010.0000.000
listApprox000
listCategories000
listInternalDatabases0.0010.0000.001
listMethods000
mytriangle0.0880.0040.092
plotBipartite0.1180.0040.121
plotLegend0.0680.0000.068
sanitise0.0010.0000.001