===============================
R CMD BUILD
===============================
* checking for file ‘shinyDSP/DESCRIPTION’ ... OK
* preparing ‘shinyDSP’:
* checking DESCRIPTION meta-information ... OK
* installing the package 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
* building ‘shinyDSP_0.99.5.tar.gz’
===============================
BiocCheckGitClone('shinyDSP')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3629/5b8a6d60084461fbc9d324ecb0adad7fa912983b/shinyDSP
→ BiocVersion: 3.21
→ Package: shinyDSP
→ PackageVersion: 0.99.5
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3629/5b8a6d60084461fbc9d324ecb0adad7fa912983b/shinyDSP.BiocCheck
→ BiocCheckVersion: 1.43.12
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3629/5b8a6d60084461fbc9d324ecb0adad7fa912983b/shinyDSP
→ installDir: NULL
→ isTarBall: FALSE
→ platform: unix
* Checking valid files...
* Checking individual file sizes...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
i NOTE: (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()'.
── BiocCheck v1.43.12 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 1 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3629/5b8a6d60084461fbc9d324ecb0adad7fa912983b/shinyDSP.Rcheck’
* using R Under development (unstable) (2025-03-13 r87965)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘shinyDSP/DESCRIPTION’ ... OK
* this is package ‘shinyDSP’ version ‘0.99.5’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... ERROR
Namespace dependency missing from DESCRIPTION Imports/Depends entries: ‘withr’
Imports includes 34 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable. Move as many as possible to Suggests and
use conditionally.
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
* DONE
Status: 1 ERROR
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3629/5b8a6d60084461fbc9d324ecb0adad7fa912983b/shinyDSP.Rcheck/00check.log’
for details.
===============================
BiocCheck('shinyDSP_0.99.5.tar.gz')
===============================
── Installing shinyDSP ─────────────────────────────────────────────────────────
✔ Package installed successfully
── shinyDSP session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpQ2SvBg/file129dae6b7546bc/shinyDSP
→ BiocVersion: 3.21
→ Package: shinyDSP
→ PackageVersion: 0.99.5
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3629/5b8a6d60084461fbc9d324ecb0adad7fa912983b/shinyDSP.BiocCheck
→ BiocCheckVersion: 1.43.12
→ sourceDir: /tmp/RtmpQ2SvBg/file129dae6b7546bc/shinyDSP
→ installDir: /tmp/RtmpQ2SvBg/file129dae4c2fbecf
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on shinyDSP ───────────────────────────────────────────────
* 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 to 4.6.0.
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
→ Software
* 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 for proper Description: field...
* Checking if DESCRIPTION is well formatted...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version: field...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
i Bioconductor dependencies found in Imports & Depends (29%).
* Checking for pinned package versions in DESCRIPTION...
* Checking for 'fnd' role in Authors@R...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
i NOTE: 'sessionInfo' not found in vignette(s)
Missing from file(s):
• vignettes/shinyDSP_secondary.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of shinyDSP...
* Checking coding practice...
* 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 22
functions greater than 50 lines.
The longest 5 functions are:
• .outputQcNavPanel2() (R/output_qc.R): 227 lines
• ...
• .interfacePcaNavPanel() (R/interface_pca_nav_panel.R): 130 lines
* Checking man page documentation...
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
i NOTE: Consider shorter lines; 52 lines (1%) are > 80 characters long.
First few lines:
• R/interface_qc_nav_panel.R#L18 shiny::actionButton( ...
• ...
• vignettes/shinyDSP.Rmd#L238 For details on underlying functions, ple ...
i NOTE: Consider multiples of 4 spaces for line indents; 14 lines (0%) are not.
First few lines:
• R/output_sidebar.R#L29 treatment." ...
• ...
• vignettes/shinyDSP_secondary.Rmd#L149 ROIshapes, ROIc ...
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.
✖ ERROR: Add package to Watched Tags in your Support Site profile; visit
https://support.bioconductor.org/accounts/edit/profile
── BiocCheck v1.43.12 results ──────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 0 WARNINGS | i 5 NOTES
i See the shinyDSP.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.