Bioconductor Single Package Builder - Build History

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 R CMD BUILD

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* checking for file ‘iModMix/DESCRIPTION’ ... OK
* preparing ‘iModMix’:
* 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 ‘iModMix_0.99.0.tar.gz’

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 BiocCheckGitClone('iModMix')

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→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3945/iModMix_20250915154755/iModMix
→ BiocVersion: 3.22
→ Package: iModMix
→ PackageVersion: 0.99.0
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3945/iModMix_20250915154755/iModMix.BiocCheck
→ BiocCheckVersion: 1.45.18
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3945/iModMix_20250915154755/iModMix
→ installDir: NULL
→ isTarBall: FALSE
→ platform: unix
* Checking valid files...
✖ ERROR: System files found that should not be Git tracked.
• iModmix.Rproj
* Checking individual file sizes...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking if DESCRIPTION is well formatted...
* Checking NAMESPACE...
* Checking for valid maintainer...
* Checking CITATION...
* Checking that provided CITATION file is correctly formatted...
── BiocCheck v1.45.18 results ──────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 0 WARNINGS | i 0 NOTES
i For more details, run
  browseVignettes(package = 'BiocCheck')




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 R CMD CHECK

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* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3945/iModMix_20250915154755/iModMix.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* 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 24.04.3 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘iModMix/DESCRIPTION’ ... OK
* this is package ‘iModMix’ version ‘0.99.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... ERROR
Package required and available but unsuitable version: ‘ExperimentHub’

Imports includes 22 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/3945/iModMix_20250915154755/iModMix.Rcheck/00check.log’
for details.





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 BiocCheck('iModMix_0.99.0.tar.gz')

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── Installing iModMix ──────────────────────────────────────────────────────────
✔ Package installed successfully
── iModMix session metadata ────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpoZZKGh/file3de0d8484c0241/iModMix
→ BiocVersion: 3.22
→ Package: iModMix
→ PackageVersion: 0.99.0
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3945/iModMix_20250915154755/iModMix.BiocCheck
→ BiocCheckVersion: 1.45.18
→ sourceDir: /tmp/RtmpoZZKGh/file3de0d8484c0241/iModMix
→ installDir: /tmp/RtmpoZZKGh/file3de0d83e6d0018
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on iModMix ────────────────────────────────────────────────
* 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...
* 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 (13%).
* Checking for pinned package versions in DESCRIPTION...
* Checking for 'fnd' role in Authors@R...
i NOTE: No 'fnd' role found in Authors@R. If the work is supported by a grant,
consider adding the 'fnd' role to the list of authors.
* Checking NAMESPACE...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of iModMix...
* 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 7
functions greater than 50 lines.
The longest 5 functions are:
• mod_module1_server() (R/mod_module1.R): 3009 lines
• ...
• FeaturesAnnot_correlation() (R/fct_FeaturesAnnot_correlation.R): 82 lines
* Checking man page documentation...
i NOTE: Consider adding runnable examples to man pages that document exported
objects.
• run_app.Rd
* 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; 877 lines (16%) are > 80 characters long.
First few lines:
• R/app_config.R#L5 #' For a safer name change mechanism, us ...
• ...
• vignettes/iModMixTutorial.Rmd#L321 | AKT3 | cluster_000019 | #B45B76 | A ...
i NOTE: Consider multiples of 4 spaces for line indents; 2234 lines (41%) are
not.
First few lines:
• R/app_config.R#L12 system.file(..., package = "iModMix") ...
• ...
• vignettes/iModMixTutorial.Rmd#L313 Enrichment Analysis Results[1:5,] ...
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 Package is in the Support Site Watched Tags.
── BiocCheck v1.45.18 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 5 NOTES
i See the iModMix.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.