Sergio Picart-Armada
| Snapshot Date: 2025-03-06 13:00 -0500 (Thu, 06 Mar 2025) |
| git_url: https://git.bioconductor.org/packages/FELLA |
| git_branch: RELEASE_3_20 |
| git_last_commit: f61c33f |
| git_last_commit_date: 2024-10-29 10:26:25 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2025-03-10 12:12 -0400 (Mon, 10 Mar 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4670 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.3 (2025-02-28 ucrt) -- "Trophy Case" | 4355 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4446 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4439 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4306 |
| 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 708/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| FELLA 1.26.0 (landing page) Sergio Picart-Armada
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | TIMEOUT | skipped | skipped | |||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | ERROR | skipped | ||||||||||
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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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: FELLA |
| Version: 1.26.0 |
| Command: /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data FELLA |
| StartedAt: 2025-03-07 01:14:07 -0000 (Fri, 07 Mar 2025) |
| EndedAt: 2025-03-07 01:40:10 -0000 (Fri, 07 Mar 2025) |
| EllapsedTime: 1562.5 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data FELLA ### ############################################################################## ############################################################################## * 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 Quitting from lines 42-67 [unnamed-chunk-1] (musmusculus.Rmd) Error: processing vignette 'musmusculus.Rmd' failed with diagnostics: there is no package called 'org.Mm.eg.db' --- failed re-building ‘musmusculus.Rmd’ --- re-building ‘quickstart.Rmd’ using rmarkdown --- finished re-building ‘quickstart.Rmd’ --- re-building ‘zebrafish.Rmd’ using rmarkdown Warning: LaTeX Warning: You have requested package `/home/biocbuild/R/R-4.4.3/site-libra Warning: ry/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 /home/biocbuild/tmp/RtmpyweLSu/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:/home/biocbuild/tmp/RtmpyweLSu/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:/home/biocbuild/tmp/RtmpyweLSu/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. 280 nodes below the threshold have been limited to 150 nodes. 280 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 280 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. 178 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. 178 nodes below the threshold have been limited to 50 nodes. --- finished re-building ‘FELLA.Rnw’ SUMMARY: processing the following file failed: ‘musmusculus.Rmd’ Error: Vignette re-building failed. Execution halted