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R CMD BUILD
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* checking for file ‘AnnotatedBCGEData/DESCRIPTION’ ... OK
* preparing ‘AnnotatedBCGEData’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
Omitted ‘LazyData’ from DESCRIPTION
* building ‘AnnotatedBCGEData_0.99.5.tar.gz’
===============================
BiocCheckGitClone('AnnotatedBCGEData')
===============================
── Running Git clone checks on AnnotatedBCGEData ───────────────────────────────
* Checking valid files...
* Checking for inst/doc folders...
* Checking DESCRIPTION readability...
* Checking for valid use of maintainer fields...
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/4209/AnnotatedBCGEData_20260818065430/AnnotatedBCGEData.Rcheck’
* using R version 4.6.1 (2026-06-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-08-18 10:57:18 UTC
* using option ‘--no-vignettes’
* checking for file ‘AnnotatedBCGEData/DESCRIPTION’ ... OK
* this is package ‘AnnotatedBCGEData’ version ‘0.99.5’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘AnnotatedBCGEData’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
‘dplyr’ ‘tibble’ ‘tidyr’
A package should be listed in only one of these fields.
WARNING
Dependence on R version ‘4.5.1’ not with patchlevel 0
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [0s/0s] ERROR
Loading this package had a fatal error status code 1
Loading log:
Error in library(AnnotatedBCGEData) :
there is no package called ‘AnnotatedBCGEData’
Execution halted
* DONE
Status: 1 ERROR, 1 WARNING, 1 NOTE
See
‘/home/pkgbuild/packagebuilder/workers/jobs/4209/AnnotatedBCGEData_20260818065430/AnnotatedBCGEData.Rcheck/00check.log’
for details.
===============================
BiocCheck('AnnotatedBCGEData_0.99.5.tar.gz')
===============================
── Installing AnnotatedBCGEData ────────────────────────────────────────────────
✔ Package installed successfully
── AnnotatedBCGEData session metadata ──────────────────────────────────────────
→ sourceDir: /tmp/RtmpWWM6Ze/file201b2b603931a5/AnnotatedBCGEData
→ BiocVersion: 3.23
→ Package: AnnotatedBCGEData
→ PackageVersion: 0.99.5
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4209/AnnotatedBCGEData_20260818065430/AnnotatedBCGEData.BiocCheck
→ BiocCheckVersion: 1.49.30
→ sourceDir: /tmp/RtmpWWM6Ze/file201b2b603931a5/AnnotatedBCGEData
→ installDir: /tmp/RtmpWWM6Ze/file201b2bb5e9941/lib
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on AnnotatedBCGEData ──────────────────────────────────────
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R version dependency...
i NOTE: Update R version dependency from 4.5.1 to 4.6.0
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
→ ExperimentData
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
* Checking build system compatibility...
* Checking if 'Package:' field matches directory / tarball...
* Checking for Version: field...
* Checking DESCRIPTION readability...
* Checking validity of DESCRIPTION fields...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for whitespace in DESCRIPTION field names...
* Checking for proper Description: field...
i NOTE: The Description field in the DESCRIPTION is made up of less than 3
sentences. Provide a more detailed description of the package.
* Checking for Bioconductor software dependencies...
i Bioconductor dependencies found in Imports & Depends (25%).
* Checking for pinned package versions in DESCRIPTION...
* Checking for 'fnd' role in Authors@R...
* Checking CITATION...
i (Optional) CITATION file not found. Only include a CITATION file if there is
a preprint or publication for this Bioconductor package. Note that Bioconductor
packages are not required to have a CITATION file but it is useful both for
users and for tracking Bioconductor project-wide metrics. When including a
CITATION file, add the publication using the 'doi' argument of 'bibentry()'.
* Checking NAMESPACE...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
i NOTE: Vignette(s) found with missing chunk labels
Found in files:
• AnnotatedBCGEData.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of AnnotatedBCGEData...
* Checking coding practice...
i NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
• R/helpers.R (line 167, column 25)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 2
functions greater than 50 lines.
The longest 5 functions are:
• downloadZenFile() (R/helpers.R): 85 lines
• checkVersions() (R/helpers.R): 51 lines
* Checking man page documentation...
* Checking package NEWS...
* Checking unit tests...
i NOTE: Consider adding unit tests. We strongly encourage them. See
https://contributions.bioconductor.org/tests.html
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
i NOTE: Consider shorter lines; 45 lines (4%) are > 80 characters long.
First few lines:
• R/getDataset.R#L15 #' @param cacheDirPath The optional dire ...
• ...
• vignettes/AnnotatedBCGEData.Rmd#L271 ggplot(combined_data, aes(x =
Gene_ID, y ...
i NOTE: Consider multiples of 4 spaces for line indents; 168 lines (14%) are
not.
First few lines:
• R/getDataset.R#L37 datasetID, 'v ...
• ...
• vignettes/AnnotatedBCGEData.Rmd#L276 coord_flip() ...
i See https://contributions.bioconductor.org/r-code.html
i See styler package: https://cran.r-project.org/package=styler as described in
the BiocCheck vignette.
* Checking if package already exists in CRAN...
* Checking if new package already exists in Bioconductor...
* Checking for bioc-devel mailing list subscription...
i Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
i Maintainer is registered at support site.
i 'annotatedbcgedata' is already in your 'Watched Tags' on the Support Site.
── BiocCheck v1.49.30 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 8 NOTES
i See the AnnotatedBCGEData.BiocCheck folder and run
`browseVignettes(package = 'BiocCheck')`
for details.