Multiple platform build/check report for BioC 3.20 - BUILD results for FELLA on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4643
palomino6	Windows Server 2022 Datacenter	x64	4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"	4414
lconway	macOS 12.7.1 Monterey	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4442
kjohnson3	macOS 13.6.5 Ventura	arm64	4.4.1 (2024-06-14) -- "Race for Your Life"	4391
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	4.4.1 (2024-06-14) -- "Race for Your Life"	3833
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: 1.25.0

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

StartedAt: 2024-07-05 17:46:49 -0400 (Fri, 05 Jul 2024)

EndedAt: 2024-07-05 18:01:05 -0400 (Fri, 05 Jul 2024)

EllapsedTime: 855.4 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/Rtmp6WV34R/Rbuild84b153fd9230/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
2024-07-05 17:51:24.150 R[34322:77093355] 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/Rtmp6WV34R/Rbuild84b153fd9230/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//RtmpMG8uGk/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//RtmpMG8uGk/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//RtmpMG8uGk/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.
284 nodes below the threshold have been limited to 150 nodes.
284 nodes below the threshold have been limited to 150 nodes.

Error: processing vignette 'FELLA.Rnw' failed with diagnostics:
 chunk 15 (label = 04_go) 
Error in checkDataset(dataset = dataset, mart = mart) : 
  The given dataset:  hsapiens_gene_ensembl , is not valid.  Correct dataset names can be obtained with the listDatasets() function.

--- failed re-building ‘FELLA.Rnw’

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

Error: Vignette re-building failed.
Execution halted