Multiple platform build/check report for BioC 3.21 - BUILD results for customCMPdb on lconway

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"	4831
palomino7	Windows Server 2022 Datacenter	x64	4.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six"	4573
lconway	macOS 12.7.1 Monterey	x86_64	4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"	4599
kjohnson3	macOS 13.7.1 Ventura	arm64	4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"	4553
kunpeng2	Linux (openEuler 24.03 LTS)	aarch64	R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"	4570
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*

BUILD results for customCMPdb on lconway

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.

raw results

Summary

Package: customCMPdb

Version: 1.18.0

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data customCMPdb

StartedAt: 2025-04-21 16:27:43 -0400 (Mon, 21 Apr 2025)

EndedAt: 2025-04-21 16:28:14 -0400 (Mon, 21 Apr 2025)

EllapsedTime: 31.0 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/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:                1.18.0
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_21
git_last_commit:        170349f
git_last_commit_date:   2025-04-15
Repository:             Bioconductor 3.21
Date/Publication:       2025-04-21
Author:                 Yuzhu Duan [aut, cre], Thomas Girke [aut]
Maintainer:             Yuzhu Duan <yduan004@ucr.edu>
Built:                  R 4.5.0; ; 2025-04-21 20:27:44 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 customCMPdb.Rmd:97-104 [sql]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! no such table: drugAgeAnnot
---
Backtrace:
     ▆
  1. ├─DBI::dbReadTable(conn, "drugAgeAnnot")
  2. └─RSQLite::dbReadTable(conn, "drugAgeAnnot")
  3.   └─RSQLite (local) .local(conn, name, ...)
  4.     ├─DBI::dbGetQuery(...)
  5.     └─DBI::dbGetQuery(...)
  6.       └─DBI (local) .local(conn, statement, ...)
  7.         ├─DBI::dbSendQuery(conn, statement, ...)
  8.         └─RSQLite::dbSendQuery(conn, statement, ...)
  9.           └─RSQLite (local) .local(conn, statement, ...)
 10.             ├─methods::new(...)
 11.             │ ├─methods::initialize(value, ...)
 12.             │ └─methods::initialize(value, ...)
 13.             └─RSQLite:::result_create(conn@ptr, statement)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'customCMPdb.Rmd' failed with diagnostics:
no such table: drugAgeAnnot
--- failed re-building ‘customCMPdb.Rmd’

SUMMARY: processing the following file failed:
  ‘customCMPdb.Rmd’

Error: Vignette re-building failed.
Execution halted