Build/check report for BioC 3.24 - BIOCCHECK results for immunotation on nebbiolo2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.4 LTS)	x86_64	4.6.0 RC (2026-04-17 r89917) -- "Because it was There"	4890
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

BIOCCHECK results for immunotation on nebbiolo2

To the developers/maintainers of the immunotation package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/immunotation.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: immunotation

Version: 1.21.0

Command: /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('immunotation_1.21.0.tar.gz','quit-with-status'=TRUE)"

StartedAt: 2026-05-09 07:00:27 -0400 (Sat, 09 May 2026)

EndedAt: 2026-05-09 07:00:53 -0400 (Sat, 09 May 2026)

EllapsedTime: 26.0 seconds

RetCode: 1

Status: ERRORS

CheckDir: None

Warnings: NA

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('immunotation_1.21.0.tar.gz','quit-with-status'=TRUE)"
###
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── Installing immunotation ─────────────────────────────────────────────────────
✖ ERROR: /tmp/Rtmp4pgot2/filebb59d75c12ff4/immunotation must be installable and
loadable.
✔ Package installed successfully
── immunotation session metadata ───────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp4pgot2/filebb59d75c12ff4/immunotation
→ BiocVersion: 3.24
→ Package: immunotation
→ PackageVersion: 1.21.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/immunotation.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmp4pgot2/filebb59d75c12ff4/immunotation
→ installDir: /tmp/Rtmp4pgot2/filebb59d31ac4fe9
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on immunotation ───────────────────────────────────────────
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking version number validity...
* Checking R version dependency...
ℹ NOTE: Update R version dependency from 4.1 to 4.6.0
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
→ 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 if 'Package:' field matches directory / tarball...
* Checking for Version: field...
ℹ NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R' with
'comment=c(ORCID="...")'
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
ℹ NOTE: Provide 'URL' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
! WARNING: No Bioconductor dependencies detected. Note that some infrastructure
packages may not have Bioconductor dependencies. For more information, reach
out to the Bioconductor community and/or consider a CRAN submission.
* 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:
    • immunotation_vignette.Rmd
* Checking package installation calls in R code...
* Checking for library/require of immunotation...
* Checking coding practice...
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/external_resources_input.R (line 65, column 31)
    • R/external_resources_input.R (line 124, column 33)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 4 times)
  • suppressWarnings() in R/external_resources_input.R (line 88, column 28)
  • ...
  • suppressMessages() in R/external_resources_input.R (line 116, column 24)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There is 1
function greater than 50 lines.
  The longest 5 functions are:
    • assemble_chain_lookup_table() (R/MRO_interface.R): 51 lines
* Checking man page documentation...
Error in loadNamespace(pkgname, lib.loc = lib.loc) : 
  there is no package called ‘immunotation’
Calls: <Anonymous> ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted