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This page was generated on 2023-05-10 10:04:29 -0000 (Wed, 10 May 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences" | 6211 |
| 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 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. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 464/2194 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| customCMPdb 1.11.0 (landing page) Yuzhu Duan
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | ERROR | skipped | |||||||||
| Package: customCMPdb |
| Version: 1.11.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data customCMPdb |
| StartedAt: 2023-05-09 00:50:42 -0000 (Tue, 09 May 2023) |
| EndedAt: 2023-05-09 00:51:22 -0000 (Tue, 09 May 2023) |
| EllapsedTime: 40.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data customCMPdb
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* 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: 1.11.0
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: devel
git_last_commit: ff4d6d3
git_last_commit_date: 2023-04-25
Date/Publication: 2023-05-08
Author: Yuzhu Duan [aut, cre], Thomas Girke [aut]
Maintainer: Yuzhu Duan <yduan004@ucr.edu>
Built: R 4.3.0; ; 2023-05-09 00:50:42 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 98-104 (customCMPdb.Rmd)
Error: processing vignette 'customCMPdb.Rmd' failed with diagnostics:
database disk image is malformed
--- failed re-building ‘customCMPdb.Rmd’
SUMMARY: processing the following file failed:
‘customCMPdb.Rmd’
Error: Vignette re-building failed.
Execution halted