===============================
BiocCheckGitClone('dnaEPICO')
===============================
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4097/572aa109bb5b4f50b8a3c397b858f9b5d4607d18/dnaEPICO
BiocVersion: 3.23
Package: dnaEPICO
PackageVersion: 0.99.6
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4097/572aa109bb5b4f50b8a3c397b858f9b5d4607d18/dnaEPICO.BiocCheck
BiocCheckVersion: 1.47.20
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4097/572aa109bb5b4f50b8a3c397b858f9b5d4607d18/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 v1.47.20 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/4097/572aa109bb5b4f50b8a3c397b858f9b5d4607d18/dnaEPICO.Rcheck
* using R Under development (unstable) (2026-03-05 r89546)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-03-24 04:12:21 UTC
* using option --no-vignettes
* checking for file dnaEPICO/DESCRIPTION ... OK
* this is package dnaEPICO version 0.99.6
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 28 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable. Move as many as possible to Suggests and
use conditionally.
* 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 ... [21s/21s] OK
* checking whether the package can be loaded with stated dependencies ... [20s/20s] OK
* checking whether the package can be unloaded cleanly ... [22s/22s] OK
* checking whether the namespace can be loaded with stated dependencies ... [21s/21s] OK
* checking whether the namespace can be unloaded cleanly ... [21s/21s] OK
* checking loading without being on the library search path ... [20s/20s] 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 ... [69s/69s] NOTE
Found the following assignments to the global environment:
File dnaEPICO/R/methylationGLMM_T1T2.R:
assign(paste0(pheno, "LME"), fitResult, envir = .GlobalEnv)
assign(paste0(pheno, "LME"), fitResult, envir = .GlobalEnv)
assign(paste0(pheno, "SummaryLME"), fitResult, envir = .GlobalEnv)
assign(paste0(pheno, "SummaryLME"), fitResult, envir = .GlobalEnv)
File dnaEPICO/R/methylationGLM_T1.R:
assign(paste0(pheno, "GLM"), fitResult, envir = .GlobalEnv)
assign(paste0(pheno, "GLM"), fitResult, envir = .GlobalEnv)
assign(paste0(pheno, "SummaryGLM"), fitResult, envir = .GlobalEnv)
assign(paste0(pheno, "SummaryGLM"), fitResult, envir = .GlobalEnv)
* checking Rd files ... [0s/0s] 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,\n MHCSF_TotalScore,BRS_TotalScore",
"Name,chr,pos,UCSC_RefGene_Group,UCSC_RefGene_Name,\n Relation_to_Island,GencodeV41_Group",
Rd file 'methylationGLM_T1.Rd':
\usage lines wider than 90 characters:
"DASS_Depression,DASS_Anxiety,DASS_Stress,PCL5_TotalScore,\n MHCSF_TotalScore,BRS_TotalScore",
"Name,chr,pos,UCSC_RefGene_Group,UCSC_RefGene_Name,\n 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 ... [33s/33s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running testthat.R [22s/22s]
[23s/23s] 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 ... [3s/3s] OK
* DONE
Status: 2 NOTEs
See
/home/pkgbuild/packagebuilder/workers/jobs/4097/572aa109bb5b4f50b8a3c397b858f9b5d4607d18/dnaEPICO.Rcheck/00check.log
for details.
===============================
BiocCheck('dnaEPICO_0.99.6.tar.gz')
===============================
Installing dnaEPICO
Package installed successfully
dnaEPICO session metadata
sourceDir: /tmp/Rtmpb9cq9y/file1db00722533222/dnaEPICO
BiocVersion: 3.23
Package: dnaEPICO
PackageVersion: 0.99.6
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4097/572aa109bb5b4f50b8a3c397b858f9b5d4607d18/dnaEPICO.BiocCheck
BiocCheckVersion: 1.47.20
sourceDir: /tmp/Rtmpb9cq9y/file1db00722533222/dnaEPICO
installDir: /tmp/Rtmpb9cq9y/file1db0076dfccb98
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 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 (19%).
* 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...
i NOTE: Avoid sapply(); use vapply()
Found in files:
R/estimateLC.R (line 438, column 12)
...
R/preprocessingMinfiEwasWater.R (line 798, column 14)
i NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
estimateLC.R (line 185, column 26)
...
svaEnmix.R (line 338, column 13)
i NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
cat() in R/methylationGLM_T1.R (line 165, column 1)
...
print() in R/svaEnmix.R (line 370, column 1)
i NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
R/estimateLC.R (line 55, column 16)
...
R/svaEnmix.R (line 301, column 17)
i NOTE: Avoid the use of 'paste' in condition signals
Found in files:
R/methylationGLM_T1.R (line 315, column 22)
...
R/preprocessingMinfiEwasWater.R (line 572, column 22)
* 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 15
functions greater than 50 lines.
The longest 5 functions are:
methylationGLM_T1() (R/methylationGLM_T1.R): 892 lines
...
svaEnmix() (R/svaEnmix.R): 315 lines
* Checking man page documentation...
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Registered S3 method overwritten by 'lme4':
method from
na.action.merMod car
No methods found in package 'RSQLite' for request: 'dbListFields' when loading 'lumi'
i NOTE: Usage of dontrun / donttest tags found in man page examples. 100% of
man pages use at least one of these tags.
Found in files:
dnamReport.Rd
...
svaEnmix.Rd
i NOTE: Use donttest instead of dontrun.
Found in files:
estimateLC.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; 257 lines (4%) are > 80 characters long.
First few lines:
R/DNAm.R#L8 #' @param preprocessingDir Character. Di ...
...
vignettes/dnaEPICO.Rmd#L1499 As package developers, we try to explain ...
i NOTE: Consider 4 spaces instead of tabs; 2 lines (0%) contain tabs.
First few lines:
R/methylationGLMM_T1T2.R#L863 subDf <- as.data.frame(subD ...
R/methylationGLMM_T1T2.R#L881 annDF$CpG <- rownames(annDF) ...
i NOTE: Consider multiples of 4 spaces for line indents; 703 lines (12%) are
not.
First few lines:
R/DNAm.R#L66 } ...
...
vignettes/dnaEPICO.Rmd#L1398 "N_CORES=1" ...
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 v1.47.20 results
0 ERRORS | 0 WARNINGS | i 14 NOTES
i See the dnaEPICO.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.