Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-06-18 17:57 -0400 (Tue, 18 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4758 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4492 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4464 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4464 |
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 484/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
customCMPdb 1.14.0 (landing page) Yuzhu Duan
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | ERROR | skipped | skipped | |||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the customCMPdb package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/customCMPdb.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: customCMPdb |
Version: 1.14.0 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data customCMPdb |
StartedAt: 2024-06-16 16:56:57 -0400 (Sun, 16 Jun 2024) |
EndedAt: 2024-06-16 16:58:19 -0400 (Sun, 16 Jun 2024) |
EllapsedTime: 82.1 seconds |
RetCode: 1 |
Status: ERROR |
PackageFile: None |
PackageFileSize: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data customCMPdb ### ############################################################################## ############################################################################## * checking for file ‘customCMPdb/DESCRIPTION’ ... OK * preparing ‘customCMPdb’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘customCMPdb.Rmd’ using rmarkdown Information on package 'customCMPdb' Description: Package: customCMPdb Title: Customize and Query Compound Annotation Database Description: This package serves as a query interface for important community collections of small molecules, while also allowing users to include custom compound collections. Version: 1.14.0 Authors@R: c(person("Yuzhu", "Duan", role = c("aut", "cre"), email = "yduan004@ucr.edu"), person("Thomas", "Girke", role = "aut", email = "thomas.girke@ucr.edu")) Depends: R (>= 4.0) Imports: AnnotationHub, RSQLite, XML, utils, ChemmineR, methods, stats, rappdirs, BiocFileCache Suggests: knitr, rmarkdown, testthat, BiocStyle License: Artistic-2.0 biocViews: Software, Cheminformatics,AnnotationHubSoftware Encoding: UTF-8 VignetteBuilder: knitr URL: https://github.com/yduan004/customCMPdb/ BugReports: https://github.com/yduan004/customCMPdb/issues RoxygenNote: 7.1.2 NeedsCompilation: no git_url: https://git.bioconductor.org/packages/customCMPdb git_branch: RELEASE_3_19 git_last_commit: eccb3c8 git_last_commit_date: 2024-04-30 Repository: Bioconductor 3.19 Date/Publication: 2024-06-16 Author: Yuzhu Duan [aut, cre], Thomas Girke [aut] Maintainer: Yuzhu Duan <yduan004@ucr.edu> Built: R 4.4.0; ; 2024-06-16 20:56:58 UTC; unix Index: addCustomAnnot Add/Delete Custom Annotation buildCMAPdb Build CMAP Database buildDrugAgeDB Build DrugAge Annotation Database customCMPdb-package Customize and Query Compound Annotation Database dbxml2df Convert drugbank database (xml file) into dataframe. df2SQLite Store drugbank dataframe into an SQLite database loadAnnot Load Compound Annotation Database loadSDFwithName Load Compound Structures from Four Resources processDrugage Process Source DrugAge Dataset queryAnnotDB Annotation Queries with Compound IDs Quitting from lines 157-160 [download_db] (customCMPdb.Rmd) Error: processing vignette 'customCMPdb.Rmd' failed with diagnostics: failed to load resource name: AH79563 title: annot_0.1 reason: 1 resources failed to download --- failed re-building ‘customCMPdb.Rmd’ SUMMARY: processing the following file failed: ‘customCMPdb.Rmd’ Error: Vignette re-building failed. Execution halted