===============================
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_0.99.15.tar.gz
===============================
BiocCheckGitClone('dnaEPICO')
===============================
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4097/2dbd9067dff3c6871717c688c176c6d426cdaed5/dnaEPICO
BiocVersion: 3.23
Package: dnaEPICO
PackageVersion: 0.99.15
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4097/2dbd9067dff3c6871717c688c176c6d426cdaed5/dnaEPICO.BiocCheck
BiocCheckVersion: 1.49.4
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4097/2dbd9067dff3c6871717c688c176c6d426cdaed5/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 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/4097/2dbd9067dff3c6871717c688c176c6d426cdaed5/dnaEPICO.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: 2026-05-11 04:20:26 UTC
* using option --no-vignettes
* checking for file dnaEPICO/DESCRIPTION ... OK
* this is package dnaEPICO version 0.99.15
* 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 ... [11s/11s] 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 ... [317s/313s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
preprocessingMinfiEwasWater 46.347 1.163 47.513
extractMetricsMinfiEwasWater 34.175 1.870 36.058
analyzeSvaEnmix 17.594 0.725 18.321
dnamReport 15.618 1.723 13.704
annotateMethylationGLMM_T1T2Summaries 14.521 0.887 15.418
assessSamplesMinfiEwasWater 12.683 0.448 13.132
plotAssessmentMinfiEwasWater 12.391 0.416 12.808
readRGSetMinfiEwasWater 10.032 0.431 10.465
svaEnmix 9.793 0.061 9.855
filterProbesMinfiEwasWater 8.949 0.273 9.294
normalizeMinfiEwasWater 8.124 0.362 8.486
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running testthat.R [292s/287s]
[292s/288s] 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/4097/2dbd9067dff3c6871717c688c176c6d426cdaed5/dnaEPICO.Rcheck/00check.log
for details.
WARNING: R CMD check exceeded 10 min requirement
===============================
BiocCheck('dnaEPICO_0.99.15.tar.gz')
===============================
Installing dnaEPICO
Package installed successfully
dnaEPICO session metadata
sourceDir: /tmp/RtmpgX6GGk/file105890229994ee/dnaEPICO
BiocVersion: 3.23
Package: dnaEPICO
PackageVersion: 0.99.15
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4097/2dbd9067dff3c6871717c688c176c6d426cdaed5/dnaEPICO.BiocCheck
BiocCheckVersion: 1.49.4
sourceDir: /tmp/RtmpgX6GGk/file105890229994ee/dnaEPICO
installDir: /tmp/RtmpgX6GGk/file1058902bc6abd3
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...
* 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...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
i Bioconductor dependencies found in Imports & Depends (32%).
* 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-local.Rmd
dnaEPICO-pipeline.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...
i NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 2 times)
suppressWarnings() in R/dnamReport.R (line 1093, column 21)
suppressWarnings() in R/dnamReport.R (line 1396, column 17)
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 59
functions greater than 50 lines.
The longest 5 functions are:
dnamReport() (R/dnamReport.R): 2503 lines
...
methylationGLMM_T1T2() (R/methylationGLMM_T1T2.R): 221 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; 468 lines (3%) are > 80 characters long.
First few lines:
R/dnamReport.R#L23 if (is.null(path) || !length(path) || ...
...
vignettes/dnaEPICO-pipeline.Rmd#L896 steps compatible with this route
because ...
i NOTE: Consider multiples of 4 spaces for line indents; 4424 lines (30%) are
not.
First few lines:
R/dnamReport.R#L10 gsub("\\\\", "/", normalizePath(path, ...
...
vignettes/dnaEPICO-pipeline.Rmd#L1106 configuration has been defined. ...
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 7 NOTES
i See the dnaEPICO.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.