===============================
R CMD BUILD
===============================
* checking for file ‘epiSeeker/DESCRIPTION’ ... OK
* preparing ‘epiSeeker’:
* checking DESCRIPTION meta-information ... OK
* installing the package 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 ‘epiSeeker_0.99.1.tar.gz’
===============================
BiocCheckGitClone('epiSeeker')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3952/epiSeeker_20251003162239/epiSeeker
→ BiocVersion: 3.22
→ Package: epiSeeker
→ PackageVersion: 0.99.1
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3952/epiSeeker_20251003162239/epiSeeker.BiocCheck
→ BiocCheckVersion: 1.45.18
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3952/epiSeeker_20251003162239/epiSeeker
→ installDir: NULL
→ isTarBall: FALSE
→ platform: unix
* Checking valid files...
Warning in readLines(gitignore) :
incomplete final line found on '/home/pkgbuild/packagebuilder/workers/jobs/3952/epiSeeker_20251003162239/epiSeeker/.gitignore'
* 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 v1.45.18 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/3952/epiSeeker_20251003162239/epiSeeker.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* 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 24.04.3 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘epiSeeker/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘epiSeeker’ version ‘0.99.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... ERROR
Namespace dependencies missing from DESCRIPTION Imports/Depends entries:
'RSQLite', 'UpSetR', 'gridBase'
Imports includes 31 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.
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
* DONE
Status: 1 ERROR
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3952/epiSeeker_20251003162239/epiSeeker.Rcheck/00check.log’
for details.
===============================
BiocCheck('epiSeeker_0.99.1.tar.gz')
===============================
── Installing epiSeeker ────────────────────────────────────────────────────────
✔ Package installed successfully
── epiSeeker session metadata ──────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpmTHyfR/file3b7ee2b6fe1ee/epiSeeker
→ BiocVersion: 3.22
→ Package: epiSeeker
→ PackageVersion: 0.99.1
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3952/epiSeeker_20251003162239/epiSeeker.BiocCheck
→ BiocCheckVersion: 1.45.18
→ sourceDir: /tmp/RtmpmTHyfR/file3b7ee2b6fe1ee/epiSeeker
→ installDir: /tmp/RtmpmTHyfR/file3b7ee2d9f4fd9
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on epiSeeker ──────────────────────────────────────────────
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
i NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or removed
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R version dependency...
i NOTE: Update R version dependency from 4.1.0 to 4.5.0
* 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: GeneRegulation
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 (38%).
* 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:
• epiSeeker.rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of epiSeeker...
* Checking coding practice...
i NOTE: Avoid sapply(); use vapply()
Found in files:
• R/enrichOverlap.R (line 221, column 18)
• ...
• R/utilities.R (line 495, column 27)
i NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
• annotateSeq.R (line 175, column 38)
• ...
• utilities.R (line 1184, column 36)
i NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
• cat() in R/annotateSeq.R (line 116, column 9)
• ...
• cat() in R/utilities.R (line 648, column 21)
i NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
• R/dplyr-verb.R (line 5, column 16)
• ...
• R/utilities.R (line 543, column 18)
* Checking parsed R code in R directory, examples, vignettes...
i Found @ in man/bmData.Rd
i NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
i NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 5 times)
• suppressWarnings() in R/addGeneAnno.R (line 31, column 9)
• ...
• suppressMessages() in R/utilities.R (line 436, column 25)
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 45
functions greater than 50 lines.
The longest 5 functions are:
• plotBmProf.internal() (R/plotBmProf.R): 394 lines
• ...
• getGenomicAnnotation() (R/getGenomicAnnotation.R): 185 lines
* Checking man page documentation...
i NOTE: Consider adding runnable examples to man pages that document exported
objects.
• getPromoters.Rd
• ...
• plotAnnoPie-methods.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; 561 lines (6%) are > 80 characters long.
First few lines:
• R/addGeneAnno.R#L24 message("geneID type is not supp ...
• ...
• vignettes/epiSeeker.rmd#L781 Here is the output of `sessionInfo()` on ...
i NOTE: Consider 4 spaces instead of tabs; 5 lines (0%) contain tabs.
First few lines:
• R/epiSeeker-package.R#L40 #' \item{areaStat}{ The sum of the tes ...
• ...
• R/getGenomicAnnotation.R#L195 annotation[j] <- lbs ...
i NOTE: Consider multiples of 4 spaces for line indents; 1938 lines (21%) are
not.
First few lines:
• R/AllGenerics.R#L15 function(x, r = 0.2, cex = 1.2, ...) ...
• ...
• vignettes/epiSeeker.rmd#L689 verbose = FALSE) ...
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 v1.45.18 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 16 NOTES
i See the epiSeeker.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.