===============================
R CMD BUILD
===============================
* checking for file ‘OmniAgeR/DESCRIPTION’ ... OK
* preparing ‘OmniAgeR’:
* 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 ‘OmniAgeR_0.99.4.tar.gz’
===============================
BiocCheckGitClone('OmniAgeR')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4158/OmniAgeR_20260518071433/OmniAgeR
→ BiocVersion: 3.23
→ Package: OmniAgeR
→ PackageVersion: 0.99.4
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4158/OmniAgeR_20260518071433/OmniAgeR.BiocCheck
→ BiocCheckVersion: 1.49.6
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4158/OmniAgeR_20260518071433/OmniAgeR
→ 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...
i NOTE: (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()'.
── BiocCheck v1.49.6 results ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 1 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/4158/OmniAgeR_20260518071433/OmniAgeR.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: 2026-05-18 11:17:17 UTC
* using option ‘--no-vignettes’
* checking for file ‘OmniAgeR/DESCRIPTION’ ... OK
* this is package ‘OmniAgeR’ 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 ‘OmniAgeR’ 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 ... [5s/5s] OK
* checking whether the package can be loaded with stated dependencies ... [4s/4s] OK
* checking whether the package can be unloaded cleanly ... [4s/4s] OK
* checking whether the namespace can be loaded with stated dependencies ... [4s/4s] OK
* checking whether the namespace can be unloaded cleanly ... [5s/5s] OK
* checking loading without being on the library search path ... [5s/5s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
‘BiocFileCache’ ‘OmniAgeRData’
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 ... [19s/19s] OK
* checking Rd files ... [1s/1s] 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 ... ERROR
TIMEOUT: R CMD check exceeded 15 mins
===============================
BiocCheck('OmniAgeR_0.99.4.tar.gz')
===============================
── Installing OmniAgeR ─────────────────────────────────────────────────────────
✔ Package installed successfully
── OmniAgeR session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmpkrz6kf/file10e1ea174423ba/OmniAgeR
→ BiocVersion: 3.23
→ Package: OmniAgeR
→ PackageVersion: 0.99.4
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4158/OmniAgeR_20260518071433/OmniAgeR.BiocCheck
→ BiocCheckVersion: 1.49.6
→ sourceDir: /tmp/Rtmpkrz6kf/file10e1ea174423ba/OmniAgeR
→ installDir: /tmp/Rtmpkrz6kf/file10e1ea7dad27ef
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on OmniAgeR ───────────────────────────────────────────────
* 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 4.5.0 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...
* 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 (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...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of OmniAgeR...
* 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 25
functions greater than 50 lines.
The longest 5 functions are:
• .dispatchClockWeights() (R/GetFeature.R): 182 lines
• ...
• systemsAge() (R/SystemsAge.R): 101 lines
* Checking man page documentation...
[12m/14m] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
bernabeuCAge 21.147 0.908 24.276
compEpiScores 20.265 0.684 22.927
zhangClock 19.914 1.011 21.966
corticalClock 18.117 0.428 23.352
grimAge2 17.522 0.363 19.378
compCHIP 17.263 0.421 18.663
grimAge1 17.058 0.351 18.749
retroAge 17.008 0.362 18.553
stochClocks 17.060 0.304 19.541
pipekRetrainedh 16.950 0.321 18.533
causalClock 16.829 0.398 18.614
knightGa 16.875 0.324 18.406
compSmokeIndex 16.728 0.352 18.269
horvath2018Clock 16.745 0.331 18.315
compCRP 16.777 0.295 18.068
horvath2013Clock 16.668 0.400 18.081
phenoAge 16.683 0.354 18.561
zhang10 16.691 0.345 18.346
pedBEClock 16.656 0.378 18.247
intrinClock 16.662 0.369 18.238
pipekElasticNet 16.704 0.311 18.290
centenarianClock 16.662 0.335 18.170
leeExtendedABEC 16.712 0.285 18.346
leeABEC 16.687 0.307 18.430
icClock 16.643 0.350 18.252
pipekFilteredh 16.659 0.314 18.150
hepatoXuRisk 16.607 0.352 18.201
mayneGa 16.609 0.311 18.068
linClock 16.603 0.299 18.165
dnamTL 16.587 0.312 17.881
epicGa 16.607 0.291 18.140
garagnaniClock 16.575 0.307 18.086
bohlinGa 16.191 0.505 17.964
compIL6 16.260 0.308 17.787
weidnerClock 16.244 0.287 17.712
wuClock 16.210 0.318 17.682
vidalBraloClock 16.203 0.307 17.690
hannumClock 16.142 0.327 17.374
epiMarker 13.216 0.560 18.175
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’i NOTE: Consider adding runnable examples to man pages that document exported
objects.
• ctsClocks.Rd
• ...
• universalPanMammalianClocks.Rd
i NOTE: Usage of dontrun / donttest tags found in man page examples. 21% of man
pages use at least one of these tags.
Found in files:
• brainCtClock.Rd
• ...
• universalPanMammalianClocks.Rd
i NOTE: Use donttest instead of dontrun.
Found in files:
• brainCtClock.Rd
• ...
• universalPanMammalianClocks.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; 476 lines (3%) are > 80 characters long.
First few lines:
• R/ABEC.R#L78 return(.calLinearClock(betaM, eabecC ...
• ...
• vignettes/OmniAgeR.Rmd#L814 plot_df <- data.frame(ActualAge = phenoT ...
i NOTE: Consider multiples of 4 spaces for line indents; 308 lines (2%) are
not.
First few lines:
• R/ABEC.R#L106 minCoverage = ...
• ...
• man/universalPanMammalianClocks.Rd#L12 verbose = TRUE ...
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 v1.49.6 results ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 8 NOTES
i See the OmniAgeR.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.