Multiple platform build/check report for BioC 3.21 - BUILD results for FELLA on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences"	4754
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences"	4472
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"	4426
kjohnson3	macOS 13.7.1 Ventura	arm64	R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"	4381
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"	4373
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*

BUILD results for FELLA on kjohnson3

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: 1.27.0

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data FELLA

StartedAt: 2024-12-23 16:21:42 -0500 (Mon, 23 Dec 2024)

EndedAt: 2024-12-23 16:31:12 -0500 (Mon, 23 Dec 2024)

EllapsedTime: 569.3 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data FELLA
###
##############################################################################
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* checking for file ‘FELLA/DESCRIPTION’ ... OK
* preparing ‘FELLA’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘musmusculus.Rmd’ using rmarkdown
! Undefined control sequence.
l.179 diffusion process (\citeproc
                                  {ref-picart2017null}{Picart-Armada et al. ...

Error: processing vignette 'musmusculus.Rmd' failed with diagnostics:
LaTeX failed to compile /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpvAT8rQ/Rbuild171364583e1bd/FELLA/vignettes/musmusculus.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See musmusculus.log for more info.
--- failed re-building ‘musmusculus.Rmd’

--- re-building ‘quickstart.Rmd’ using rmarkdown
2024-12-23 16:24:50.657 R[95237:166428212] XType: Using static font registry.
--- finished re-building ‘quickstart.Rmd’

--- re-building ‘zebrafish.Rmd’ using rmarkdown
! Undefined control sequence.
l.178 ...d bream (\emph{Sparus aurata}) (\citeproc
                                                  {ref-ziarrusta2018bream}{Z...

Error: processing vignette 'zebrafish.Rmd' failed with diagnostics:
LaTeX failed to compile /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpvAT8rQ/Rbuild171364583e1bd/FELLA/vignettes/zebrafish.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See zebrafish.log for more info.
--- failed 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 /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp65zGNH/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:/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp65zGNH/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:/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp65zGNH/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.
287 nodes below the threshold have been limited to 150 nodes.
287 nodes below the threshold have been limited to 150 nodes.

Warning in (function (OrgDb = NULL, annoDb = NULL, keytype = "ENTREZID",  :
  use 'annoDb' instead of 'OrgDb'

preparing gene to GO mapping data...
preparing IC data...
Writing diffusion results...
Done.
Writing diffusion enzymes...
Null GOterm provided to addGOToGraph. Only the GO labels will be added. To include similarity values as well, please specify a GOterm
Done.
Exporting to a csv file...
Writing diffusion results...
Done.
Done
287 nodes below the threshold have been limited to 250 nodes.
Exporting to the format pajek using igraph...
Done
No background compounds specified. Default background will be used.
Warning in defineCompounds(compounds = compounds, compoundsBackground = compoundsBackground,  :
  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.
176 nodes below the threshold have been limited to 150 nodes.
No background compounds specified. Default background will be used.
Warning in defineCompounds(compounds = compounds, compoundsBackground = compoundsBackground,  :
  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.
176 nodes below the threshold have been limited to 50 nodes.
--- finished re-building ‘FELLA.Rnw’

SUMMARY: processing the following files failed:
  ‘musmusculus.Rmd’ ‘zebrafish.Rmd’

Error: Vignette re-building failed.
Execution halted