| Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:27 -0400 (Fri, 15 Oct 2021).
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To the developers/maintainers of the wppi package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/wppi.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 2023/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| wppi 1.0.0 (landing page) Ana Galhoz
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | ERROR | skipped | skipped | |||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | ERROR | skipped | skipped | |||||||||
| Package: wppi |
| Version: 1.0.0 |
| Command: chmod a+r wppi -R && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data wppi |
| StartedAt: 2021-10-14 19:09:13 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 19:10:26 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 72.3 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### chmod a+r wppi -R && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data wppi ### ############################################################################## ############################################################################## * checking for file 'wppi/DESCRIPTION' ... OK * preparing 'wppi': * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building 'wppi_workflow.Rmd' using rmarkdown [2021-10-14 19:09:31] [INFO] [wppi] Executing WPPI workflow. [2021-10-14 19:09:31] [INFO] [wppi] Collecting database knowledge. [2021-10-14 19:09:33] [SUCCESS] [OmnipathR] Human Phenotype Ontology (ci.monarchinitiative.org): loaded 234119 records from cache [2021-10-14 19:09:39] [SUCCESS] [OmnipathR] Gene Ontology (geneontology.org): loaded 619347 records from cache [2021-10-14 19:09:41] [SUCCESS] [OmnipathR] Loaded 75957 interactions from cache. [2021-10-14 19:09:41] [INFO] [wppi] Finished collecting database knowledge. [2021-10-14 19:09:41] [INFO] [wppi] Using all HPO annotations available. [2021-10-14 19:09:41] [INFO] [wppi] Calculating weighted adjacency matrix. [2021-10-14 19:09:41] [INFO] [wppi] Preprocessing annotations (Gene Ontology). [2021-10-14 19:09:41] [INFO] [wppi] Preprocessing annotations (Human Phenotype Ontology). [2021-10-14 19:09:41] [INFO] [wppi] Graph size: 300 nodes and 3526 edges; GO: 4024 terms, 298 genes, 13044 annotations; HPO: 2770 terms, 139 genes, 8883 annotations. [2021-10-14 19:09:54] [INFO] [wppi] Finished calculating weighted adjacency matrix. [2021-10-14 19:09:54] [INFO] [wppi] Performing random walk with restart (restart probablilty: 0.4, threshold: 1e-05, number of genes: 300). [2021-10-14 19:10:00] [INFO] [wppi] Calculating WPPI gene scores (genes of interest: 8, genes in network: 300). [2021-10-14 19:10:00] [SUCCESS] [wppi] WPPI workflow completed. [2021-10-14 19:10:01] [SUCCESS] [OmnipathR] Loaded 42541 interactions from cache. Quitting from lines 124-132 (wppi_workflow.Rmd) Error: processing vignette 'wppi_workflow.Rmd' failed with diagnostics: attempt to use zero-length variable name --- failed re-building 'wppi_workflow.Rmd' SUMMARY: processing the following file failed: 'wppi_workflow.Rmd' Error: Vignette re-building failed. Execution halted