===============================
R CMD BUILD
===============================
* checking for file ‘ctdR/DESCRIPTION’ ... OK
* preparing ‘ctdR’:
* 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 ‘ctdR_0.99.9.tar.gz’
===============================
BiocCheckGitClone('ctdR')
===============================
── Running Git clone checks on ctdR ────────────────────────────────────────────
* Checking valid files...
* Checking for inst/doc folders...
* Checking DESCRIPTION readability...
* Checking for valid use of maintainer fields...
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/4232/ctdR_20260918075722/ctdR.Rcheck’
* using R version 4.6.1 (2026-06-24)
* 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: 2026-09-18 11:59:02 UTC
* using option ‘--no-vignettes’
* checking for file ‘ctdR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ctdR’ version ‘0.99.9’
* 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 ‘ctdR’ 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 ... [8s/8s] OK
* checking whether the package can be loaded with stated dependencies ... [7s/7s] OK
* checking whether the package can be unloaded cleanly ... [7s/7s] OK
* checking whether the namespace can be loaded with stated dependencies ... [7s/7s] OK
* checking whether the namespace can be unloaded cleanly ... [7s/7s] OK
* checking loading without being on the library search path ... [7s/7s] 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 ... [25s/25s] OK
* checking Rd files ... [0s/0s] 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 files in ‘vignettes’ ... OK
* checking examples ... [26s/26s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
enrichment_CTD 7.637 0.205 7.842
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [16s/16s]
[16s/16s] 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 ... [4s/4s] OK
* DONE
Status: OK
===============================
BiocCheck('ctdR_0.99.9.tar.gz')
===============================
── Installing ctdR ─────────────────────────────────────────────────────────────
✔ Package installed successfully
── ctdR session metadata ───────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpiQlOFi/file2e2885c2e1a28/ctdR
→ BiocVersion: 3.23
→ Package: ctdR
→ PackageVersion: 0.99.9
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4232/ctdR_20260918075722/ctdR.BiocCheck
→ BiocCheckVersion: 1.49.31
→ sourceDir: /tmp/RtmpiQlOFi/file2e2885c2e1a28/ctdR
→ installDir: /tmp/RtmpiQlOFi/file2e28854b06b391/lib
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on ctdR ───────────────────────────────────────────────────
* 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...
* 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 if 'Package:' field matches directory / tarball...
* Checking for Version: field...
* Checking DESCRIPTION readability...
* Checking validity of DESCRIPTION fields...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for whitespace in DESCRIPTION field names...
* Checking for proper Description: field...
* Checking for Bioconductor software dependencies...
i Bioconductor dependencies found in Imports & Depends (62%).
* Checking for pinned package versions in DESCRIPTION...
* Checking for 'fnd' role in Authors@R...
i 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 CITATION...
* Checking that provided CITATION file is correctly formatted...
* 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 ctdR...
* Checking coding practice...
i NOTE: Avoid the use of 'paste' in condition signals
Found in files:
• R/enrichment_analysis.R (line 265, column 17)
• R/enrichment_analysis.R (line 421, column 13)
• R/ora.R (line 144, column 13)
i NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
• R/gsea.R (line 53, column 13)
* Checking parsed R code in R directory, examples, vignettes...
i NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 7 times)
• suppressWarnings() in R/enrichment_analysis.R (line 539, column 32)
• ...
• suppressMessages() in R/import_CTD.R (line 207, column 16)
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 7
functions greater than 50 lines.
The longest 5 functions are:
• plot_CTD() (R/plot_CTD.R): 106 lines
• ...
• .plot_camera() (R/plot_CTD.R): 71 lines
* Checking man page documentation...
i NOTE: Usage of dontrun / donttest tags found in man page examples. 2% of man
pages use at least one of these tags.
Found in files:
• as_genesets_CTD.Rd
i NOTE: Use donttest instead of dontrun.
Found in files:
• as_genesets_CTD.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; 20 lines (0%) are > 80 characters long.
First few lines:
• R/CTDFile.R#L34 #' @return \code{CTDFile()} returns a \c ...
• ...
• vignettes/ctdR.Rmd#L811 | **Best for** | DEG lists | Exploratory ...
i NOTE: Consider multiples of 4 spaces for line indents; 289 lines (5%) are
not.
First few lines:
• R/enrichment_analysis.R#L279 interaction_types ...
• ...
• vignettes/ctdR.Rmd#L954 Comparing the effects of PFAS and dexa ...
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 'ctdr' is already in your 'Watched Tags' on the Support Site.
── BiocCheck v1.49.31 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 8 NOTES
i See the ctdR.BiocCheck folder and run
`browseVignettes(package = 'BiocCheck')`
for details.