| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:08:18 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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 piano package: - Please 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 How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1425/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| piano 2.11.0 (landing page) Leif Varemo Wigge
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | ERROR | skipped | skipped | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | ERROR | skipped | skipped | |||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | ERROR | skipped | skipped | |||||||||
| Package: piano |
| Version: 2.11.0 |
| Command: chmod a+r piano -R && D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data piano |
| StartedAt: 2022-03-17 17:37:30 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 17:38:10 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 39.4 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### chmod a+r piano -R && D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data piano
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* 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
Running gene set analysis:
Final gene/gene-set association: 1136 genes and 50 gene sets
Details:
Calculating gene set statistics from 1136 out of 2000 gene-level statistics
Using all 2000 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
--- finished 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...
Error: processing vignette 'piano-vignette.Rnw' failed with diagnostics:
chunk 10
Error in `[.data.frame`(topTab, , c("ID", "tmp", "logFC", "AveExpr", "t", :
undefined columns selected
--- failed re-building 'piano-vignette.Rnw'
SUMMARY: processing the following file failed:
'piano-vignette.Rnw'
Error: Vignette re-building failed.
Execution halted