Back to Multiple platform build/check report for BioC 3.19:   simplified   long
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This page was generated on 2024-07-12 17:38 -0400 (Fri, 12 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4741
palomino7Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4483
merida1macOS 12.7.4 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4512
kjohnson1macOS 13.6.6 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4461
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 715/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FELLA 1.24.0  (landing page)
Sergio Picart-Armada
Snapshot Date: 2024-07-10 14:00 -0400 (Wed, 10 Jul 2024)
git_url: https://git.bioconductor.org/packages/FELLA
git_branch: RELEASE_3_19
git_last_commit: ec13672
git_last_commit_date: 2024-04-30 11:04:43 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    TIMEOUT  skippedskipped
merida1macOS 12.7.4 Monterey / x86_64  OK    TIMEOUT  skippedskipped
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for FELLA on nebbiolo1

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: 1.24.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:FELLA.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings FELLA_1.24.0.tar.gz
StartedAt: 2024-07-10 23:01:03 -0400 (Wed, 10 Jul 2024)
EndedAt: 2024-07-10 23:36:45 -0400 (Wed, 10 Jul 2024)
EllapsedTime: 2142.0 seconds
RetCode: 0
Status:   OK  
CheckDir: FELLA.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:FELLA.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings FELLA_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/FELLA.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* 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 ‘1.24.0’
* 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 code 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 ... NOTE
Documented arguments not in \usage in Rd file 'dot-params.Rd':
  ‘databaseDir’ ‘internalDir’ ‘object’ ‘data’ ‘type’ ‘level’ ‘method’
  ‘methods’ ‘approx’ ‘loadMatrix’ ‘threshold’
  ‘thresholdConnectedComponent’ ‘plimit’ ‘nlimit’ ‘niter’ ‘layout’
  ‘graph’ ‘GOterm’ ‘GONamesAsLabels’ ‘LabelLengthAtPlot’
  ‘godata.options’ ‘mart.options’ ‘p.adjust’ ‘dampingFactor’ ‘t.df’
  ‘compounds’ ‘compoundsBackground’ ‘NamesAsLabels’ ‘capPscores’

Documented arguments not in \usage in Rd file 'infere.con2ec.Rd':
  ‘gene2enyzme’

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 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 6.337  0.178   6.515
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/FELLA.Rcheck/00check.log’
for details.


Installation output

FELLA.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL FELLA
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-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 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 12 | SKIP 0 | PASS 168 ]

[ FAIL 0 | WARN 12 | SKIP 0 | PASS 168 ]
> 
> proc.time()
   user  system elapsed 
 34.562   4.209  67.477 

Example timings

FELLA.Rcheck/FELLA-Ex.timings

nameusersystemelapsed
FELLA0.2500.0190.270
FELLA.sample0.0120.0000.013
checkArguments0.0020.0000.002
data-funs6.3370.1786.515
enrich-funs2.8980.0132.910
export-funs0.1980.0000.198
getBackground0.3400.0160.356
getCom0.0110.0000.012
getExcluded0.0130.0000.013
getGraph0.0100.0000.011
getInfo0.0110.0000.011
getInput0.0130.0000.013
getMatrix0.0170.0030.021
getName0.0110.0000.011
getPscores0.0440.0000.044
getPvaluesSize0.0220.0000.023
getStatus0.0110.0000.011
getSums0.4910.0080.499
getValid0.0290.0000.029
infere.con2ec0.0030.0000.004
input.sample0.0010.0000.001
is.FELLA.DATA0.0140.0000.014
is.FELLA.USER0.0290.0030.032
largestcc0.1390.0000.138
launchApp0.0010.0000.000
listApprox0.0010.0000.000
listCategories000
listInternalDatabases0.0000.0010.001
listMethods0.0000.0000.001
mytriangle0.0720.0010.072
plotBipartite0.0620.0080.070
plotLegend0.0320.0000.033
sanitise0.0010.0000.001