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This page was generated on 2023-06-06 11:00:31 -0000 (Tue, 06 Jun 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.0 (2023-04-21) -- "Already Tomorrow" | 4366 |
| 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 | ||||
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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. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 685/2199 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| FELLA 1.21.0 (landing page) Sergio Picart-Armada
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | ERROR | skipped | |||||||||
| Package: FELLA |
| Version: 1.21.0 |
| Command: /home/biocbuild/R/R-4.3.0/bin/R CMD build --keep-empty-dirs --no-resave-data FELLA |
| StartedAt: 2023-06-05 11:28:00 -0000 (Mon, 05 Jun 2023) |
| EndedAt: 2023-06-05 11:47:58 -0000 (Mon, 05 Jun 2023) |
| EllapsedTime: 1198.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.0/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 Warning: LaTeX Warning: You have requested package `/home/biocbuild/R/R-4.3.0/site-libra Warning: ry/BiocStyle/resources/tex/Bioconductor', Warning: but the package provides `Bioconductor'. --- finished 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-4.3.0/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 /tmp/Rtmp9RfnfA/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 1.0 GiB Done Computing diffusion.rowSums... Done. Loading KEGG graph data... Done. Loading hypergeom data... Loading matrix... 'hypergeom.matrix.RData' not present in:/tmp/Rtmp9RfnfA/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/Rtmp9RfnfA/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. 289 nodes below the threshold have been limited to 150 nodes. 289 nodes below the threshold have been limited to 150 nodes. preparing gene to GO mapping data... preparing IC data... Writing diffusion results... Done. Writing diffusion enzymes... Error: processing vignette 'FELLA.Rnw' failed with diagnostics: chunk 18 (label = 04_enzyme) Error in curl::curl_fetch_memory(url, handle = handle) : Timeout was reached: [www.ensembl.org:443] Operation timed out after 300000 milliseconds with 1104941 bytes received --- failed re-building ‘FELLA.Rnw’ SUMMARY: processing the following file failed: ‘FELLA.Rnw’ Error: Vignette re-building failed. Execution halted