Leif Varemo Wigge
| Snapshot Date: 2025-01-02 13:00 -0500 (Thu, 02 Jan 2025) |
| git_url: https://git.bioconductor.org/packages/piano |
| git_branch: RELEASE_3_20 |
| git_last_commit: 899745e |
| git_last_commit_date: 2024-10-29 09:45:43 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2025-01-09 12:11 -0500 (Thu, 09 Jan 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4358 |
| 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 1550/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| piano 2.22.0 (landing page) Leif Varemo Wigge
| 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 | OK | OK | OK | | ||||||||
| 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 piano package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/piano.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: piano |
| Version: 2.22.0 |
| Command: /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data piano |
| StartedAt: 2025-01-08 22:32:31 -0000 (Wed, 08 Jan 2025) |
| EndedAt: 2025-01-08 22:33:11 -0000 (Wed, 08 Jan 2025) |
| EllapsedTime: 40.0 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 piano ### ############################################################################## ############################################################################## * checking for file ‘piano/DESCRIPTION’ ... OK * preparing ‘piano’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘Running_gene-set_analysis_with_piano.Rmd’ using rmarkdown Error: processing vignette 'Running_gene-set_analysis_with_piano.Rmd' failed with diagnostics: Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed. --- failed re-building ‘Running_gene-set_analysis_with_piano.Rmd’ --- re-building ‘piano-vignette.Rnw’ using Sweave Loading data in text file... ...done Loading setup file... ...done Text file data: No normalization performed. Creating annotation... ...done Removing unmapped probes... ..done Warning in runQC(myArrayData) : can not run rnaDeg: argument arrayData does not contain dataRaw Warning in runQC(myArrayData) : can not run nuseRle: argument arrayData does not contain dataRaw Generating normalized data distribution plot... ...done Generating normalized data boxplot... dev.new(): using pdf(file="Rplots1.pdf") ...done Generating PCA... ...done dev.new(): using pdf(file="Rplots2.pdf") dev.new(): using pdf(file="Rplots3.pdf") dev.new(): using pdf(file="Rplots4.pdf") dev.new(): using pdf(file="Rplots5.pdf") Generating PCA... ...done dev.new(): using pdf(file="Rplots6.pdf") dev.new(): using pdf(file="Rplots7.pdf") dev.new(): using pdf(file="Rplots8.pdf") dev.new(): using pdf(file="Rplots9.pdf") Generating PCA... ...done dev.new(): using pdf(file="Rplots10.pdf") dev.new(): using pdf(file="Rplots11.pdf") dev.new(): using pdf(file="Rplots12.pdf") dev.new(): using pdf(file="Rplots13.pdf") Fitting linear models... ...done Generating Venn diagrams... dev.new(): using pdf(file="Rplots14.pdf") dev.new(): using pdf(file="Rplots15.pdf") ...done Calculating p-values for contrast aerobic_Clim - anaerobic_Clim... ...done Calculating p-values for contrast aerobic_Nlim - anaerobic_Nlim... ...done Generating heatmap... dev.new(): using pdf(file="Rplots16.pdf") dev.new(): using pdf(file="Rplots17.pdf") ...done Generating merged polar plot... dev.new(): using pdf(file="Rplots18.pdf") ...done Generating separate polar plots... dev.new(): using pdf(file="Rplots19.pdf") dev.new(): using pdf(file="Rplots20.pdf") ...done Generating polar plot legend... dev.new(): using pdf(file="Rplots21.pdf") ...done Generating volcano plot... dev.new(): using pdf(file="Rplots22.pdf") dev.new(): using pdf(file="Rplots23.pdf") ...done Running gene set analysis: Final gene/gene-set association: 4 genes and 4 gene sets Details: Calculating gene set statistics from 4 out of 4 gene-level statistics Using all 4 gene-level statistics for significance estimation Removed 0 genes from GSC due to lack of matching gene statistics Removed 0 gene sets containing no genes after gene removal Removed additionally 0 gene sets not matching the size limits Loaded additional information for 0 gene sets Running gene set analysis: Final gene/gene-set association: 643 genes and 163 gene sets Details: Calculating gene set statistics from 643 out of 5705 gene-level statistics Removed 0 genes from GSC due to lack of matching gene statistics Removed 0 gene sets containing no genes after gene removal Removed additionally 656 gene sets not matching the size limits Loaded additional information for 0 gene sets ------------------------------------------------------------------------------- A newer function 'networkPlot2()' with the same purpose is now available! ------------------------------------------------------------------------------- --- finished re-building ‘piano-vignette.Rnw’ SUMMARY: processing the following file failed: ‘Running_gene-set_analysis_with_piano.Rmd’ Error: Vignette re-building failed. Execution halted