| Back to Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-02-25 11:32 -0500 (Wed, 25 Feb 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences" | 4874 |
| 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 734/2354 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| FELLA 1.31.0 (landing page) Sergio Picart-Armada
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| See other builds for FELLA in R Universe. | ||||||||||||||
|
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. |
| Package: FELLA |
| Version: 1.31.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:FELLA.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings FELLA_1.31.0.tar.gz |
| StartedAt: 2026-02-24 23:56:27 -0500 (Tue, 24 Feb 2026) |
| EndedAt: 2026-02-25 00:25:27 -0500 (Wed, 25 Feb 2026) |
| EllapsedTime: 1739.6 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: FELLA.Rcheck |
| Warnings: NA |
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### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:FELLA.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings FELLA_1.31.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/FELLA.Rcheck’
* using R Under development (unstable) (2026-01-15 r89304)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘FELLA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘FELLA’ version ‘1.31.0’
* 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 sizes of PDF files under ‘inst/doc’ ...* 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 ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘musmusculus.Rmd’ using rmarkdown
Warning: LaTeX Warning: You have requested package `/home/biocbuild/bbs-3.23-bioc/R/site
Warning: -library/BiocStyle/resources/tex/Bioconductor',
Warning: but the package provides `Bioconductor'.
--- finished re-building ‘musmusculus.Rmd’
--- re-building ‘quickstart.Rmd’ using rmarkdown
The magick package is required to crop "/home/biocbuild/bbs-3.23-bioc/meat/FELLA.Rcheck/vign_test/FELLA/vignettes/quickstart_files/figure-html/unnamed-chunk-12-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.23-bioc/meat/FELLA.Rcheck/vign_test/FELLA/vignettes/quickstart_files/figure-html/unnamed-chunk-13-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.23-bioc/meat/FELLA.Rcheck/vign_test/FELLA/vignettes/quickstart_files/figure-html/unnamed-chunk-14-1.png" but not available.
--- finished re-building ‘quickstart.Rmd’
--- re-building ‘zebrafish.Rmd’ using rmarkdown
Warning: LaTeX Warning: You have requested package `/home/biocbuild/bbs-3.23-bioc/R/site
Warning: -library/BiocStyle/resources/tex/Bioconductor',
Warning: but the package provides `Bioconductor'.
--- finished re-building ‘zebrafish.Rmd’
--- re-building ‘FELLA.Rnw’ using Sweave
Building through KEGGREST...
Available gene annotations: ncbi-geneid, ncbi-proteinid. Using ncbi-geneid
Done.
Building graph...
Filtering 5 pathways.
Done.
Pruning graph...
Current weight: 1 out of 4...
Current weight: 2 out of 4...
Current weight: 3 out of 4...
Current weight: 4 out of 4...
Done.
Computing probabilities for random subgraphs... (this may take a while)
Directory /tmp/RtmpZsFApE/my_database does not exist. Creating it...
Done.
Done.
Computing diffusion.matrix... (this may take a while and use some memory)
Warning in asMethod(object) :
sparse->dense coercion: allocating vector of size 1.1 GiB
Done
Computing diffusion.rowSums...
Done.
Loading KEGG graph data...
Done.
Loading hypergeom data...
Loading matrix...
'hypergeom.matrix.RData' not present in:/tmp/RtmpZsFApE/my_database/hypergeom.matrix.RData. Hypergeometric test won't execute.
Done.
Loading diffusion data...
Loading matrix...
Done.
Loading rowSums...
Done.
Loading pagerank data...
Loading matrix...
'pagerank.matrix.RData' not loaded. Simulated permutations may execute slower for pagerank.
Done.
Loading rowSums...
'pagerank.rowSums.RData' not present in:/tmp/RtmpZsFApE/my_database/pagerank.rowSums.RData. Z-scores won't be available for pagerank.
Done.
Data successfully loaded.
No background compounds specified. Default background will be used.
Warning in defineCompounds(compounds = compounds.epithelial, data = fella.data) :
Some compounds were introduced as affected but they do not belong to the background. These compounds will be excluded from the analysis. Use 'getExcluded' to see them.
Running diffusion...
Computing p-scores through the specified distribution.
Done.
288 nodes below the threshold have been limited to 150 nodes.
288 nodes below the threshold have been limited to 150 nodes.
Error: processing vignette 'FELLA.Rnw' failed with diagnostics:
chunk 15 (label = 04_go)
Error : Your query has been redirected to https://status.ensembl.org indicating this Ensembl service is currently unavailable.
Look at ?useEnsembl for details on how to try a mirror site.
--- failed re-building ‘FELLA.Rnw’
SUMMARY: processing the following file failed:
‘FELLA.Rnw’
Error: Vignette re-building failed.
Execution halted
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 2 NOTEs
See
‘/home/biocbuild/bbs-3.23-bioc/meat/FELLA.Rcheck/00check.log’
for details.
FELLA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL FELLA ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’ * installing *source* package ‘FELLA’ ... ** this is package ‘FELLA’ version ‘1.31.0’ ** 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)
FELLA.Rcheck/tests/testthat.Rout
R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences"
Copyright (C) 2026 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 14 | SKIP 0 | PASS 168 ]
[ FAIL 0 | WARN 14 | SKIP 0 | PASS 168 ]
>
> proc.time()
user system elapsed
21.523 4.526 58.978
FELLA.Rcheck/FELLA-Ex.timings
| name | user | system | elapsed | |
| FELLA | 0.275 | 0.018 | 0.295 | |
| FELLA.sample | 0.011 | 0.000 | 0.011 | |
| checkArguments | 0.001 | 0.001 | 0.002 | |
| data-funs | 2.664 | 0.139 | 2.802 | |
| enrich-funs | 2.559 | 0.040 | 2.599 | |
| export-funs | 0.263 | 0.013 | 0.276 | |
| getBackground | 0.314 | 0.025 | 0.339 | |
| getCom | 0.011 | 0.000 | 0.011 | |
| getExcluded | 0.010 | 0.002 | 0.013 | |
| getGraph | 0.009 | 0.001 | 0.011 | |
| getInfo | 0.010 | 0.000 | 0.011 | |
| getInput | 0.011 | 0.001 | 0.012 | |
| getMatrix | 0.016 | 0.003 | 0.018 | |
| getName | 0.010 | 0.001 | 0.011 | |
| getPscores | 0.042 | 0.001 | 0.043 | |
| getPvaluesSize | 0.020 | 0.001 | 0.021 | |
| getStatus | 0.009 | 0.002 | 0.011 | |
| getSums | 0.382 | 0.068 | 0.450 | |
| getValid | 0.039 | 0.001 | 0.040 | |
| infere.con2ec | 0.002 | 0.001 | 0.002 | |
| input.sample | 0.001 | 0.000 | 0.001 | |
| is.FELLA.DATA | 0.008 | 0.002 | 0.010 | |
| is.FELLA.USER | 0.036 | 0.001 | 0.037 | |
| largestcc | 0.059 | 0.001 | 0.060 | |
| launchApp | 0 | 0 | 0 | |
| listApprox | 0 | 0 | 0 | |
| listCategories | 0.000 | 0.000 | 0.001 | |
| listInternalDatabases | 0.002 | 0.000 | 0.001 | |
| listMethods | 0 | 0 | 0 | |
| mytriangle | 0.039 | 0.002 | 0.041 | |
| plotBipartite | 0.085 | 0.002 | 0.087 | |
| plotLegend | 0.040 | 0.000 | 0.039 | |
| sanitise | 0.000 | 0.000 | 0.001 | |