===============================
R CMD BUILD
===============================
* checking for file ‘dnaEPICO/DESCRIPTION’ ... OK
* preparing ‘dnaEPICO’:
* 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 ‘dnaEPICO_0.99.11.tar.gz’
===============================
BiocCheckGitClone('dnaEPICO')
===============================
Registered S3 method overwritten by 'bit64':
method from
print.bitstring tools
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4097/0e1b0ede73ffd49fc81536b6ccec4e8795f8127b/dnaEPICO
→ BiocVersion: 3.23
→ Package: dnaEPICO
→ PackageVersion: 0.99.11
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4097/0e1b0ede73ffd49fc81536b6ccec4e8795f8127b/dnaEPICO.BiocCheck
→ BiocCheckVersion: 1.47.25
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4097/0e1b0ede73ffd49fc81536b6ccec4e8795f8127b/dnaEPICO
→ 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 NAMESPACE...
* Checking for valid maintainer...
* Checking CITATION...
* Checking that provided CITATION file is correctly formatted...
── BiocCheck v1.47.25 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/4097/0e1b0ede73ffd49fc81536b6ccec4e8795f8127b/dnaEPICO.Rcheck’
* using R version 4.6.0 alpha (2026-04-05 r89794)
* 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: 2026-04-14 09:29:44 UTC
* using option ‘--no-vignettes’
* checking for file ‘dnaEPICO/DESCRIPTION’ ... OK
* this is package ‘dnaEPICO’ version ‘0.99.11’
* 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 ‘dnaEPICO’ 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 ... [0s/0s] OK
* checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the package can be unloaded cleanly ... [0s/0s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
* checking loading without being on the library search path ... [0s/0s] 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 ... [9s/9s] OK
* checking Rd files ... [1s/1s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'methylationGLMM_T1T2.Rd':
\usage lines wider than 90 characters:
"DASS_Depression,DASS_Anxiety,DASS_Stress,PCL5_TotalScore,MHCSF_TotalScore,BRS_TotalScore",
"Name,chr,pos,UCSC_RefGene_Group,UCSC_RefGene_Name,Relation_to_Island,GencodeV41_Group",
Rd file 'methylationGLM_T1.Rd':
\usage lines wider than 90 characters:
"DASS_Depression,DASS_Anxiety,DASS_Stress,PCL5_TotalScore,MHCSF_TotalScore,BRS_TotalScore",
"Name,chr,pos,UCSC_RefGene_Group,UCSC_RefGene_Name,Relation_to_Island,GencodeV41_Group",
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 ... [273s/273s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
preprocessingMinfiEwasWater 41.568 0.944 42.512
extractMetricsMinfiEwasWater 35.880 0.575 36.465
analyzeSvaEnmix 15.240 0.695 15.937
annotateMethylationGLMM_T1T2Summaries 13.336 0.707 14.043
assessSamplesMinfiEwasWater 11.643 0.364 12.014
plotAssessmentMinfiEwasWater 10.735 0.308 11.044
svaEnmix 9.470 0.067 9.536
readRGSetMinfiEwasWater 8.876 0.125 9.002
normalizeMinfiEwasWater 7.906 0.300 8.208
filterProbesMinfiEwasWater 7.854 0.107 7.962
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [241s/241s]
[241s/241s] 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 ... [6s/6s] OK
* DONE
Status: 1 NOTE
See
‘/home/pkgbuild/packagebuilder/workers/jobs/4097/0e1b0ede73ffd49fc81536b6ccec4e8795f8127b/dnaEPICO.Rcheck/00check.log’
for details.
===============================
BiocCheck('dnaEPICO_0.99.11.tar.gz')
===============================
Registered S3 method overwritten by 'bit64':
method from
print.bitstring tools
── Installing dnaEPICO ─────────────────────────────────────────────────────────
✔ Package installed successfully
── dnaEPICO session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp4sbyJe/file1a50d218b92ce1/dnaEPICO
→ BiocVersion: 3.23
→ Package: dnaEPICO
→ PackageVersion: 0.99.11
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4097/0e1b0ede73ffd49fc81536b6ccec4e8795f8127b/dnaEPICO.BiocCheck
→ BiocCheckVersion: 1.47.25
→ sourceDir: /tmp/Rtmp4sbyJe/file1a50d218b92ce1/dnaEPICO
→ installDir: /tmp/Rtmp4sbyJe/file1a50d265a8553b
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on dnaEPICO ───────────────────────────────────────────────
* 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 4.4 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: ChipOnChip
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 that Package field matches directory/tarball name...
* Checking for Version: field...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
i Bioconductor dependencies found in Imports & Depends (30%).
* 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:
• dnaEPICO.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of dnaEPICO...
* 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 52
functions greater than 50 lines.
The longest 5 functions are:
• preprocessingMinfiEwasWater() (R/preprocessingMinfiEwasWater.R): 541
lines
• ...
• summarizeMethylationGLM_T1Models() (R/methylationGLM_T1_steps.R): 186
lines
* Checking man page documentation...
* 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; 399 lines (3%) are > 80 characters long.
First few lines:
• R/dnamReport.R#L8 #' Internal helper that normalizes paths ...
• ...
• vignettes/dnaEPICO.Rmd#L1447 As package developers, we try to explain ...
i NOTE: Consider multiples of 4 spaces for line indents; 2996 lines (25%) are
not.
First few lines:
• R/dnamReport.R#L14 gsub("\\\\", "/", normalizePath(path, ...
• ...
• vignettes/dnaEPICO.Rmd#L960 - your working directory contains a va ...
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 v1.47.25 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 7 NOTES
i See the dnaEPICO.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.