| Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-02-08 01:15:03 -0000 (Wed, 08 Feb 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4164 |
| 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: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 663/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| FELLA 1.19.0 (landing page) Sergio Picart-Armada
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | ERROR | skipped | |||||||||
| Package: FELLA |
| Version: 1.19.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data FELLA |
| StartedAt: 2023-02-06 08:13:23 -0000 (Mon, 06 Feb 2023) |
| EndedAt: 2023-02-06 08:37:06 -0000 (Mon, 06 Feb 2023) |
| EllapsedTime: 1423.8 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/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 ! LaTeX Error: Environment cslreferences undefined. Error: processing vignette 'musmusculus.Rmd' failed with diagnostics: LaTeX failed to compile /tmp/Rtmpcar7eb/Rbuild111aa645419646/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 The magick package is required to crop "/tmp/Rtmpcar7eb/Rbuild111aa645419646/FELLA/vignettes/quickstart_files/figure-html/unnamed-chunk-12-1.png" but not available. The magick package is required to crop "/tmp/Rtmpcar7eb/Rbuild111aa645419646/FELLA/vignettes/quickstart_files/figure-html/unnamed-chunk-13-1.png" but not available. The magick package is required to crop "/tmp/Rtmpcar7eb/Rbuild111aa645419646/FELLA/vignettes/quickstart_files/figure-html/unnamed-chunk-14-1.png" but not available. --- finished re-building ‘quickstart.Rmd’ --- re-building ‘zebrafish.Rmd’ using rmarkdown ! LaTeX Error: Environment cslreferences undefined. Error: processing vignette 'zebrafish.Rmd' failed with diagnostics: LaTeX failed to compile /tmp/Rtmpcar7eb/Rbuild111aa645419646/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 /tmp/RtmpteR6Pi/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/RtmpteR6Pi/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/RtmpteR6Pi/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. Killed