===============================
R CMD BUILD
===============================
* checking for file ‘ProteinBatcher/DESCRIPTION’ ... OK
* preparing ‘ProteinBatcher’:
* 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
* building ‘ProteinBatcher_0.99.3.tar.gz’
===============================
BiocCheckGitClone('ProteinBatcher')
===============================
── Running Git clone checks on ProteinBatcher ──────────────────────────────────
* Checking valid files...
* Checking for inst/doc folders...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* 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()'.
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/4235/03dcdf186c59aa9532243dcba936cbbe435a4295/ProteinBatcher.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* 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: 2026-06-19 09:42:15 UTC
* using option ‘--no-vignettes’
* checking for file ‘ProteinBatcher/DESCRIPTION’ ... OK
* this is package ‘ProteinBatcher’ version ‘0.99.3’
* 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 serialization versions ... OK
* checking whether package ‘ProteinBatcher’ can be installed ... OK
* checking installed package size ... INFO
installed size is 11.7Mb
sub-directories of 1Mb or more:
extdata 11.4Mb
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 ... [8s/8s] OK
* checking whether the package can be loaded with stated dependencies ... [8s/8s] OK
* checking whether the package can be unloaded cleanly ... [8s/8s] OK
* checking whether the namespace can be loaded with stated dependencies ... [7s/7s] OK
* checking whether the namespace can be unloaded cleanly ... [9s/9s] OK
* checking loading without being on the library search path ... [8s/8s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘readxl’
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [29s/29s] OK
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [18s/18s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [46s/46s]
[46s/46s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... [4s/4s] OK
* DONE
Status: 1 NOTE
See
‘/home/pkgbuild/packagebuilder/workers/jobs/4235/03dcdf186c59aa9532243dcba936cbbe435a4295/ProteinBatcher.Rcheck/00check.log’
for details.
===============================
BiocCheck('ProteinBatcher_0.99.3.tar.gz')
===============================
── Installing ProteinBatcher ───────────────────────────────────────────────────
✔ Package installed successfully
── ProteinBatcher session metadata ─────────────────────────────────────────────
→ sourceDir: /tmp/RtmpkPX3Zm/file28dd095ed2362a/ProteinBatcher
→ BiocVersion: 3.23
→ Package: ProteinBatcher
→ PackageVersion: 0.99.3
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4235/03dcdf186c59aa9532243dcba936cbbe435a4295/ProteinBatcher.BiocCheck
→ BiocCheckVersion: 1.49.19
→ sourceDir: /tmp/RtmpkPX3Zm/file28dd095ed2362a/ProteinBatcher
→ installDir: /tmp/RtmpkPX3Zm/file28dd094749f3d8
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on ProteinBatcher ─────────────────────────────────────────
* 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 for whitespace in DESCRIPTION field names...
* Checking if 'Package:' field matches directory / tarball...
* 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 (25%).
* Checking for pinned package versions in DESCRIPTION...
* Checking for 'fnd' role in Authors@R...
* 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:
• Vignette.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of ProteinBatcher...
* Checking coding practice...
i NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
• print() in R/Step4_Volcano.R (line 201, column 9)
• ...
• print() in R/Wrapper_Imputation_helpers.R (line 386, column 9)
* 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 6
functions greater than 50 lines.
The longest 5 functions are:
• run_proteomics_pipeline() (R/Step6_Wrapper_Workflow.R): 83 lines
• ...
• make_se_from_files() (R/Wrapper_Imputation_helpers.R): 64 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; 19 lines (1%) are > 80 characters long.
First few lines:
• R/Step4_Volcano.R#L199 ...
• ...
• vignettes/Vignette.Rmd#L363 effects, rather than listing all statist ...
i NOTE: Consider 4 spaces instead of tabs; 1 lines (0%) contain tabs.
First few lines:
• R/Wrapper_Imputation_helpers.R#L144 # file sample sample_name condition
...
i NOTE: Consider multiples of 4 spaces for line indents; 146 lines (6%) are
not.
First few lines:
• R/Deregulogram_helpers.R#L4 paste0("p.adj_", main), ...
• ...
• vignettes/Vignette.Rmd#L417 plots = FALSE ...
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 'proteinbatcher' is already in your 'Watched Tags' on the Support Site.
── BiocCheck v1.49.19 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 6 NOTES
i See the ProteinBatcher.BiocCheck folder and run
`browseVignettes(package = 'BiocCheck')`
for details.