===============================
R CMD BUILD
===============================
* checking for file ‘Aerith/DESCRIPTION’ ... OK
* preparing ‘Aerith’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... OK
* cleaning src
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘Aerith_0.99.11.tar.gz’
===============================
BiocCheckGitClone('Aerith')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3828/Aerith_20251114080552/Aerith
→ BiocVersion: 3.22
→ Package: Aerith
→ PackageVersion: 0.99.11
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3828/Aerith_20251114080552/Aerith.BiocCheck
→ BiocCheckVersion: 1.47.1
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3828/Aerith_20251114080552/Aerith
→ 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 NAMESPACE...
* Checking for valid maintainer...
* Checking CITATION...
* Checking that provided CITATION file is correctly formatted...
── BiocCheck v1.47.1 results ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 0 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3828/Aerith_20251114080552/Aerith.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 ‘Aerith/DESCRIPTION’ ... OK
* this is package ‘Aerith’ version ‘0.99.11’
* 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 ‘Aerith’ can be installed ... ERROR
Installation failed.
See ‘/home/pkgbuild/packagebuilder/workers/jobs/3828/Aerith_20251114080552/Aerith.Rcheck/00install.out’ for details.
* DONE
Status: 1 ERROR
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3828/Aerith_20251114080552/Aerith.Rcheck/00check.log’
for details.
===============================
BiocCheck('Aerith_0.99.11.tar.gz')
===============================
── Installing Aerith ───────────────────────────────────────────────────────────
✔ Package installed successfully
── Aerith session metadata ─────────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmph2RDqv/file2031b23730f584/Aerith
→ BiocVersion: 3.22
→ Package: Aerith
→ PackageVersion: 0.99.11
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3828/Aerith_20251114080552/Aerith.BiocCheck
→ BiocCheckVersion: 1.47.1
→ sourceDir: /tmp/Rtmph2RDqv/file2031b23730f584/Aerith
→ installDir: /tmp/Rtmph2RDqv/file2031b25342ad1b
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on Aerith ─────────────────────────────────────────────────
* 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 4.4.0 to 4.5.0
* 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 (17%).
* 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...
i NOTE: Vignette(s) found with missing chunk labels
Found in files:
• Aerith.Rmd
• ...
• Visualization-of-SIP-proteomic-result.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of Aerith...
* 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 3
functions greater than 50 lines.
The longest 5 functions are:
• plotPSMannotation() (R/plotAAspectra.R): 73 lines
• plotPSMsipPCT() (R/plotProteinSipPct.R): 59 lines
• plotMolecularIsotopes() (R/SIPmontecarlo.R): 51 lines
* Checking man page documentation...
i NOTE: Consider adding runnable examples to man pages that document exported
objects.
• plotFilteredPCTIntensitySummary.Rd
• plotSIPfilteredPCTIntensityBySample.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; 537 lines (12%) are > 80 characters long.
First few lines:
• R/Aerith-package.R#L4 #' @description Visualisation of peptide ...
• ...
• vignettes/Visualization-of-SIP-proteomic-result.Rmd#L62 Aerith integrates
contemporary best prac ...
i NOTE: Consider multiples of 4 spaces for line indents; 24 lines (1%) are not.
First few lines:
• R/plotAAspectra.R#L95 Atom = "C13", ...
• ...
• R/readMzml.R#L76 peaks) { ...
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 v1.47.1 results ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 7 NOTES
i See the Aerith.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.