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R CMD BUILD
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* 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
* looking to see if a ‘data/datalist’ file should be added
* building ‘OmniAgeR_0.99.6.tar.gz’
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BiocCheckGitClone('OmniAgeR')
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── Running Git clone checks on OmniAgeR ────────────────────────────────────────
* 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
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* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/4158/e27811aa579184f7ed8f81ff93057fe6bb4c63d1/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: 2026-06-26 17:33:54 UTC
* using option ‘--no-vignettes’
* checking for file ‘OmniAgeR/DESCRIPTION’ ... OK
* this is package ‘OmniAgeR’ version ‘0.99.6’
* 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 ... INFO
installed size is 8.3Mb
sub-directories of 1Mb or more:
data 7.8Mb
* 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 ... [6s/6s] OK
* checking whether the package can be loaded with stated dependencies ... [5s/5s] OK
* checking whether the package can be unloaded cleanly ... [5s/5s] OK
* checking whether the namespace can be loaded with stated dependencies ... [6s/6s] OK
* checking whether the namespace can be unloaded cleanly ... [6s/6s] OK
* checking loading without being on the library search path ... [6s/6s] 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 ... [23s/23s] 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [7s/7s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [196s/262s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
epiMarker 13.470 0.787 19.741
brainCtClock 6.652 0.843 7.939
pastaScores 6.648 0.425 8.467
ctsClocks 6.279 0.436 9.600
universalPanMammalianClocks 5.606 0.237 7.598
panMammalianBlood 5.436 0.327 26.924
panMammalianSkin 5.187 0.203 6.964
dnamCTFClock 4.086 0.267 5.615
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [7s/7s]
[7s/7s] 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 ... [7s/7s] OK
* DONE
Status: OK
===============================
BiocCheck('OmniAgeR_0.99.6.tar.gz')
===============================
── Installing OmniAgeR ─────────────────────────────────────────────────────────
✔ Package installed successfully
── OmniAgeR session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/RtmplKhDnw/file203e502e239fcb/OmniAgeR
→ BiocVersion: 3.23
→ Package: OmniAgeR
→ PackageVersion: 0.99.6
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4158/e27811aa579184f7ed8f81ff93057fe6bb4c63d1/OmniAgeR.BiocCheck
→ BiocCheckVersion: 1.49.21
→ sourceDir: /tmp/RtmplKhDnw/file203e502e239fcb/OmniAgeR
→ installDir: /tmp/RtmplKhDnw/file203e50b8a21fd/lib
→ 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...
i NOTE: Consider adding these automatically suggested biocViews: Normalization
i Search 'biocViews' at https://contributions.bioconductor.org
* 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...
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 (40%).
* 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 33
functions greater than 50 lines.
The longest 5 functions are:
• .getDfBrainCt() (R/Brain_CT_clock.R): 215 lines
• ...
• .extractScInput() (R/utils.R): 123 lines
* Checking man page documentation...
i NOTE: Consider adding runnable examples to man pages that document exported
objects.
• dot-scImmuAgingMakePseudocells.Rd
• ...
• systemsAge.Rd
i NOTE: Usage of dontrun / donttest tags found in man page examples. 74% of man
pages use at least one of these tags.
Found in files:
• bernabeuCAge.Rd
• ...
• zhangClock.Rd
i NOTE: Use donttest instead of dontrun.
Found in files:
• bernabeuCAge.Rd
• ...
• zhangClock.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; 565 lines (3%) are > 80 characters long.
First few lines:
• R/Bernabeu_cAge.R#L72 bernabeuCAgeInterceptLog <- bernabeu ...
• ...
• vignettes/OmniAgeR.Rmd#L766 plot_df <- data.frame(ActualAge = phenoT ...
i NOTE: Consider multiples of 4 spaces for line indents; 1673 lines (10%) are
not.
First few lines:
• R/ABEC.R#L71 .runEpiClockPipeline( ...
• ...
• vignettes/OmniAgeR.Rmd#L759 assays = list(ctf=t(ctfExample[[2]])) ...
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...
! WARNING: Unable to retrieve email info from the Support Site: Failed to
perform HTTP request. Caused by error in `curl::curl_fetch_memory()`: ! Timeout
was reached [support.bioconductor.org]: Operation timed out after 15002
milliseconds with 0 bytes received
── BiocCheck v1.49.21 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 1 WARNINGS | i 9 NOTES
i See the OmniAgeR.BiocCheck folder and run
`browseVignettes(package = 'BiocCheck')`
for details.