===============================
R CMD BUILD
===============================
* checking for file ‘enrichmet/DESCRIPTION’ ... OK
* preparing ‘enrichmet’:
* checking DESCRIPTION meta-information ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
WARNING: directory ‘enrichmet/vignettes’ is empty
Omitted ‘LazyData’ from DESCRIPTION
* building ‘enrichmet_0.99.9.tar.gz’
===============================
BiocCheckGitClone('enrichmet')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3845/3cc659d6098512d5cbf77ae116782dd5e78eee83/enrichmet
→ BiocVersion: 3.23
→ Package: enrichmet
→ PackageVersion: 0.99.9
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3845/3cc659d6098512d5cbf77ae116782dd5e78eee83/enrichmet.BiocCheck
→ BiocCheckVersion: 1.47.6
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3845/3cc659d6098512d5cbf77ae116782dd5e78eee83/enrichmet
→ 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...
i NOTE: (Optional) CITATION file not found. Only include a CITATION file if
there is a preprint or publication for this Bioconductor package. Note that
Bioconductor packages are not required to have a CITATION file but it is useful
both for users and for tracking Bioconductor project-wide metrics. When
including a CITATION file, add the publication using the 'doi' argument of
'bibentry()'.
── BiocCheck v1.47.6 results ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 1 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3845/3cc659d6098512d5cbf77ae116782dd5e78eee83/enrichmet.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* 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 ‘enrichmet/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘enrichmet’ 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 serialization versions ... OK
* checking whether package ‘enrichmet’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... 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 ... [4s/4s] OK
* checking whether the package can be loaded with stated dependencies ... [3s/3s] OK
* checking whether the package can be unloaded cleanly ... [3s/3s] OK
* checking whether the namespace can be loaded with stated dependencies ... [3s/3s] OK
* checking whether the namespace can be unloaded cleanly ... [4s/4s] OK
* checking loading without being on the library search path ... [3s/3s] 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 ... [13s/13s] 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 ... [19s/18s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
enrichmet 4.8 0.242 4.996
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [164s/36s]
[164s/36s] OK
* checking package vignettes ... NOTE
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
* checking PDF version of manual ... [4s/4s] OK
* DONE
Status: 1 NOTE
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3845/3cc659d6098512d5cbf77ae116782dd5e78eee83/enrichmet.Rcheck/00check.log’
for details.
===============================
BiocCheck('enrichmet_0.99.9.tar.gz')
===============================
── Installing enrichmet ────────────────────────────────────────────────────────
✔ Package installed successfully
── enrichmet session metadata ──────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpWiKRhU/file25724c40a4b6e4/enrichmet
→ BiocVersion: 3.23
→ Package: enrichmet
→ PackageVersion: 0.99.9
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3845/3cc659d6098512d5cbf77ae116782dd5e78eee83/enrichmet.BiocCheck
→ BiocCheckVersion: 1.47.6
→ sourceDir: /tmp/RtmpWiKRhU/file25724c40a4b6e4/enrichmet
→ installDir: /tmp/RtmpWiKRhU/file25724c779685d6
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on enrichmet ──────────────────────────────────────────────
* 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 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 (25%).
* Checking for pinned package versions in DESCRIPTION...
* Checking for 'fnd' role in Authors@R...
* Checking NAMESPACE...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
✖ ERROR: No vignette sources in vignettes/ directory.
* Checking whether vignette is built with 'R CMD build'...
✖ ERROR: Vignette must be built by 'R CMD build'. Please see the `Vignette
Checks` section of the BiocCheck vignette.
* Checking package installation calls in R code...
* Checking for library/require of enrichmet...
* 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 13
functions greater than 50 lines.
The longest 5 functions are:
• enrichmet() (R/enrichmet.R): 338 lines
• ...
• perform_enrichment_analysis() (R/perform_enrichment_analysis.R): 236 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; 254 lines (7%) are > 80 characters long.
First few lines:
• R/calculate_metabolite_centrality.R#L6 #' @param PathwayVsMetabolites A data
fr ...
• ...
• R/run_de.R#L331 # Original method - take first K ...
i NOTE: Consider multiples of 4 spaces for line indents; 112 lines (3%) are
not.
First few lines:
• R/calculate_metabolite_centrality.R#L40 !is.na(Metabolites ...
• ...
• R/run_de.R#L210 alpha = .da ...
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 v1.47.6 results ───────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 0 WARNINGS | i 3 NOTES
i See the enrichmet.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.