===============================
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_0.99.5.tar.gz’
===============================
BiocCheckGitClone('OmniAgeR')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4158/dba85006e4f6e09da4f7318ef97e7cd1930229a6/OmniAgeR
→ BiocVersion: 3.23
→ Package: OmniAgeR
→ PackageVersion: 0.99.5
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4158/dba85006e4f6e09da4f7318ef97e7cd1930229a6/OmniAgeR.BiocCheck
→ BiocCheckVersion: 1.49.6
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4158/dba85006e4f6e09da4f7318ef97e7cd1930229a6/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/dba85006e4f6e09da4f7318ef97e7cd1930229a6/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 15:46:36 UTC
* using option ‘--no-vignettes’
* checking for file ‘OmniAgeR/DESCRIPTION’ ... OK
* this is package ‘OmniAgeR’ version ‘0.99.5’
* 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 ... OK
* 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 ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'bohlinGa.Rd':
\examples lines wider than 100 characters:
if (length(requiredCpGs) == 0) requiredCpGs <- allFeatures # Fallback if features do not use 'cg' prefix
Rd file 'causalClock.Rd':
\examples lines wider than 100 characters:
if (length(requiredCpGs) == 0) requiredCpGs <- allFeatures # Fallback if features do not use 'cg' prefix
Rd file 'centenarianClock.Rd':
\examples lines wider than 100 characters:
if (length(requiredCpGs) == 0) requiredCpGs <- allFeatures # Fallback if features do not use 'cg' prefix
Rd file 'compCHIP.Rd':
\examples lines wider than 100 characters:
if (length(requiredCpGs) == 0) requiredCpGs <- allFeatures # Fallback if features do not use 'cg' prefix
Rd file 'compCRP.Rd':
\examples lines wider than 100 characters:
if (length(requiredCpGs) == 0) requiredCpGs <- allFeatures # Fallback if features do not use 'cg' prefix
Rd file 'compEpiScores.Rd':
\examples lines wider than 100 characters:
if (length(requiredCpGs) == 0) requiredCpGs <- allFeatures # Fallback if features do not use 'cg' prefix
Rd file 'compIL6.Rd':
\examples lines wider than 100 characters:
if (length(requiredCpGs) == 0) requiredCpGs <- allFeatures # Fallback if features do not use 'cg' prefix
Rd file 'compSmokeIndex.Rd':
\examples lines wider than 100 characters:
if (length(requiredCpGs) == 0) requiredCpGs <- allFeatures # Fallback if features do not use 'cg' prefix
Rd file 'corticalClock.Rd':
\examples lines wider than 100 characters:
if (length(requiredCpGs) == 0) requiredCpGs <- allFeatures # Fallback if features do not use 'cg' prefix
Rd file 'dnamTL.Rd':
\examples lines wider than 100 characters:
if (length(requiredCpGs) == 0) requiredCpGs <- allFeatures # Fallback if features do not use 'cg' prefix
Rd file 'epicGa.Rd':
\examples lines wider than 100 characters:
if (length(requiredCpGs) == 0) requiredCpGs <- allFeatures # Fallback if features do not use 'cg' prefix
Rd file 'garagnaniClock.Rd':
\examples lines wider than 100 characters:
if (length(requiredCpGs) == 0) requiredCpGs <- allFeatures # Fallback if features do not use 'cg' prefix
Rd file 'hannumClock.Rd':
\examples lines wider than 100 characters:
if (length(requiredCpGs) == 0) requiredCpGs <- allFeatures # Fallback if features do not use 'cg' prefix
Rd file 'hepatoXuRisk.Rd':
\examples lines wider than 100 characters:
if (length(requiredCpGs) == 0) requiredCpGs <- allFeatures # Fallback if features do not use 'cg' prefix
Rd file 'horvath2013Clock.Rd':
\examples lines wider than 100 characters:
if (length(requiredCpGs) == 0) requiredCpGs <- allFeatures # Fallback if features do not use 'cg' prefix
Rd file 'horvath2018Clock.Rd':
\examples lines wider than 100 characters:
if (length(requiredCpGs) == 0) requiredCpGs <- allFeatures # Fallback if features do not use 'cg' prefix
Rd file 'icClock.Rd':
\examples lines wider than 100 characters:
if (length(requiredCpGs) == 0) requiredCpGs <- allFeatures # Fallback if features do not use 'cg' prefix
Rd file 'intrinClock.Rd':
\examples lines wider than 100 characters:
if (length(requiredCpGs) == 0) requiredCpGs <- allFeatures # Fallback if features do not use 'cg' prefix
Rd file 'knightGa.Rd':
\examples lines wider than 100 characters:
if (length(requiredCpGs) == 0) requiredCpGs <- allFeatures # Fallback if features do not use 'cg' prefix
Rd file 'leeABEC.Rd':
\examples lines wider than 100 characters:
if (length(requiredCpGs) == 0) requiredCpGs <- allFeatures # Fallback if features do not use 'cg' prefix
Rd file 'leeCommonABEC.Rd':
\examples lines wider than 100 characters:
if (length(requiredCpGs) == 0) requiredCpGs <- allFeatures # Fallback if features do not use 'cg' prefix
Rd file 'leeExtendedABEC.Rd':
\examples lines wider than 100 characters:
if (length(requiredCpGs) == 0) requiredCpGs <- allFeatures # Fallback if features do not use 'cg' prefix
Rd file 'linClock.Rd':
\examples lines wider than 100 characters:
if (length(requiredCpGs) == 0) requiredCpGs <- allFeatures # Fallback if features do not use 'cg' prefix
Rd file 'mayneGa.Rd':
\examples lines wider than 100 characters:
if (length(requiredCpGs) == 0) requiredCpGs <- allFeatures # Fallback if features do not use 'cg' prefix
Rd file 'pedBEClock.Rd':
\examples lines wider than 100 characters:
if (length(requiredCpGs) == 0) requiredCpGs <- allFeatures # Fallback if features do not use 'cg' prefix
Rd file 'phenoAge.Rd':
\examples lines wider than 100 characters:
if (length(requiredCpGs) == 0) requiredCpGs <- allFeatures # Fallback if features do not use 'cg' prefix
Rd file 'pipekElasticNet.Rd':
\examples lines wider than 100 characters:
if (length(requiredCpGs) == 0) requiredCpGs <- allFeatures # Fallback if features do not use 'cg' prefix
Rd file 'pipekFilteredh.Rd':
\examples lines wider than 100 characters:
if (length(requiredCpGs) == 0) requiredCpGs <- allFeatures # Fallback if features do not use 'cg' prefix
Rd file 'pipekRetrainedh.Rd':
\examples lines wider than 100 characters:
if (length(requiredCpGs) == 0) requiredCpGs <- allFeatures # Fallback if features do not use 'cg' prefix
Rd file 'retroAge.Rd':
\examples lines wider than 100 characters:
if (length(requiredCpGs) == 0) requiredCpGs <- allFeatures # Fallback if features do not use 'cg' prefix
Rd file 'vidalBraloClock.Rd':
\examples lines wider than 100 characters:
if (length(requiredCpGs) == 0) requiredCpGs <- allFeatures # Fallback if features do not use 'cg' prefix
Rd file 'weidnerClock.Rd':
\examples lines wider than 100 characters:
if (length(requiredCpGs) == 0) requiredCpGs <- allFeatures # Fallback if features do not use 'cg' prefix
Rd file 'wuClock.Rd':
\examples lines wider than 100 characters:
if (length(requiredCpGs) == 0) requiredCpGs <- allFeatures # Fallback if features do not use 'cg' prefix
Rd file 'zhang10.Rd':
\examples lines wider than 100 characters:
if (length(requiredCpGs) == 0) requiredCpGs <- allFeatures # Fallback if features do not use 'cg' prefix
Rd file 'zhangClock.Rd':
\examples lines wider than 100 characters:
if (length(requiredCpGs) == 0) requiredCpGs <- allFeatures # Fallback if features do not use 'cg' prefix
These lines will be truncated in the PDF manual.
* 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 ... [193s/247s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
epiMarker 12.630 0.618 17.633
bohlinGa 6.873 0.487 8.860
corticalClock 4.751 0.138 6.253
vidalBraloClock 2.784 0.120 5.009
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [5s/5s]
[5s/5s] 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: 1 NOTE
See
‘/home/pkgbuild/packagebuilder/workers/jobs/4158/dba85006e4f6e09da4f7318ef97e7cd1930229a6/OmniAgeR.Rcheck/00check.log’
for details.
===============================
BiocCheck('OmniAgeR_0.99.5.tar.gz')
===============================
── Installing OmniAgeR ─────────────────────────────────────────────────────────
✔ Package installed successfully
── OmniAgeR session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpPfwFbr/file2226fa66b06acf/OmniAgeR
→ BiocVersion: 3.23
→ Package: OmniAgeR
→ PackageVersion: 0.99.5
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4158/dba85006e4f6e09da4f7318ef97e7cd1930229a6/OmniAgeR.BiocCheck
→ BiocCheckVersion: 1.49.6
→ sourceDir: /tmp/RtmpPfwFbr/file2226fa66b06acf/OmniAgeR
→ installDir: /tmp/RtmpPfwFbr/file2226fa6f904676
→ 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 (21%).
* 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...
i NOTE: Consider adding runnable examples to man pages that document exported
objects.
• bernabeuCAge.Rd
• ...
• universalPanMammalianClocks.Rd
i NOTE: Usage of dontrun / donttest tags found in man page examples. 23% of man
pages use at least one of these tags.
Found in files:
• bernabeuCAge.Rd
• ...
• universalPanMammalianClocks.Rd
i NOTE: Use donttest instead of dontrun.
Found in files:
• bernabeuCAge.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; 515 lines (4%) are > 80 characters long.
First few lines:
• R/ABEC.R#L103 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#L142 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.