===============================
R CMD BUILD
===============================
* checking for file ‘immGLIPH/DESCRIPTION’ ... OK
* preparing ‘immGLIPH’:
* 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
* looking to see if a ‘data/datalist’ file should be added
* building ‘immGLIPH_0.99.4.tar.gz’
===============================
BiocCheckGitClone('immGLIPH')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4143/5cd56e90ca8897e363fb3346dd263256e9df0efa/immGLIPH
→ BiocVersion: 3.23
→ Package: immGLIPH
→ PackageVersion: 0.99.4
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4143/5cd56e90ca8897e363fb3346dd263256e9df0efa/immGLIPH.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4143/5cd56e90ca8897e363fb3346dd263256e9df0efa/immGLIPH
→ 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 remote package usage...
* Checking NAMESPACE...
* Checking for valid maintainer...
* Checking CITATION...
* Checking that provided CITATION file is correctly formatted...
── BiocCheck v1.49.4 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/4143/5cd56e90ca8897e363fb3346dd263256e9df0efa/immGLIPH.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: 2026-05-03 11:13:37 UTC
* using option ‘--no-vignettes’
* checking for file ‘immGLIPH/DESCRIPTION’ ... OK
* this is package ‘immGLIPH’ version ‘0.99.4’
* 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 ‘immGLIPH’ can be installed ... OK
* checking installed package size ... OK
* 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 ... [1s/1s] OK
* checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the package can be unloaded cleanly ... [1s/1s] OK
* checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
* checking loading without being on the library search path ... [1s/1s] OK
* checking whether startup messages can be suppressed ... [1s/1s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [10s/10s] 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [6s/6s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [13s/13s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
clusterScoring 5.775 0.401 6.174
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [16s/16s]
[16s/16s] 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 ... [5s/5s] OK
* DONE
Status: OK
===============================
BiocCheck('immGLIPH_0.99.4.tar.gz')
===============================
── Installing immGLIPH ─────────────────────────────────────────────────────────
✔ Package installed successfully
── immGLIPH session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp1VtDDo/file2eed7f64b5d195/immGLIPH
→ BiocVersion: 3.23
→ Package: immGLIPH
→ PackageVersion: 0.99.4
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4143/5cd56e90ca8897e363fb3346dd263256e9df0efa/immGLIPH.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmp1VtDDo/file2eed7f64b5d195/immGLIPH
→ installDir: /tmp/Rtmp1VtDDo/file2eed7f270859d7
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on immGLIPH ───────────────────────────────────────────────
* Checking for deprecated package usage...
adding rname 'https://bioconductor.org/checkResults/3.24/bioc-LATEST/meat-index.dcf'
* 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 4.5.0 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...
i NOTE: Consider adding these automatically suggested biocViews: ATACSeq,
GeneSetEnrichment
i Search 'biocViews' at https://contributions.bioconductor.org
* 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...
* Checking for Bioconductor software dependencies...
i Bioconductor dependencies found in Imports & Depends (15%).
* 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:
• immGLIPH.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of immGLIPH...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
i NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 15 times)
• suppressWarnings() in R/clusterScoring.R (line 155, column 11)
• ...
• suppressWarnings() in R/utils-output.R (line 9, column 17)
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 17
functions greater than 50 lines.
The longest 5 functions are:
• runGLIPH() (R/runGLIPH.R): 682 lines
• ...
• .cluster_gliph2() (R/clustering.R): 397 lines
* Checking man page documentation...
i NOTE: Usage of dontrun / donttest tags found in man page examples. 3% of man
pages use at least one of these tags.
Found in files:
• getGLIPHreference.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; 312 lines (5%) are > 80 characters long.
First few lines:
• R/clusterScoring.R#L101 #' "Identifying specificity groups in th ...
• ...
• vignettes/immGLIPH.Rmd#L600 7. **Choose the right reference**: For m ...
i NOTE: Consider multiples of 4 spaces for line indents; 2377 lines (36%) are
not.
First few lines:
• R/clustering.R#L33 sequences, ...
• ...
• vignettes/immGLIPH.Rmd#L601 For specialized repertoires, provide ...
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 v1.49.4 results ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 10 NOTES
i See the immGLIPH.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.