Back to Multiple platform build/check report for BioC 3.18: simplified long |
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This page was generated on 2024-03-29 11:36:46 -0400 (Fri, 29 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4669 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4404 |
merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4427 |
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 704/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
FELLA 1.22.0 (landing page) Sergio Picart-Armada
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | TIMEOUT | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | ERROR | skipped | skipped | |||||||||
merida1 | macOS 12.7.1 Monterey / x86_64 | OK | TIMEOUT | skipped | skipped | |||||||||
kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
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: 1.22.0 |
Command: chmod a+r FELLA -R && F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data FELLA |
StartedAt: 2024-03-27 18:32:28 -0400 (Wed, 27 Mar 2024) |
EndedAt: 2024-03-27 19:05:17 -0400 (Wed, 27 Mar 2024) |
EllapsedTime: 1969.6 seconds |
RetCode: 1 |
Status: ERROR |
PackageFile: None |
PackageFileSize: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### chmod a+r FELLA -R && F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe 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 !!! Error: Cannot call Ghostscript: `mgs' (No such file or directory/The system cannot find the file specified)! pdfcrop: major issue: User/administrator updates are out-of-sync. Warning: LaTeX Warning: You have requested package `F:/biocbuild/bbs-3.18-bioc/R/library Warning: /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 !!! Error: Cannot call Ghostscript: `mgs' (No such file or directory/The system cannot find the file specified)! pdfcrop: major issue: User/administrator updates are out-of-sync. !!! Error: Cannot call Ghostscript: `mgs' (No such file or directory/The system cannot find the file specified)! pdfcrop: major issue: User/administrator updates are out-of-sync. Warning: LaTeX Warning: You have requested package `F:/biocbuild/bbs-3.18-bioc/R/library Warning: /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 F:\biocbuild\bbs-3.18-bioc\tmpdir\RtmpEfk7Yb/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:F:\biocbuild\bbs-3.18-bioc\tmpdir\RtmpEfk7Yb/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:F:\biocbuild\bbs-3.18-bioc\tmpdir\RtmpEfk7Yb/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. 282 nodes below the threshold have been limited to 150 nodes. 282 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 300009 milliseconds with 360068 bytes received --- failed re-building 'FELLA.Rnw' SUMMARY: processing the following file failed: 'FELLA.Rnw' Error: Vignette re-building failed. Execution halted