===============================
R CMD BUILD
===============================
* checking for file ‘RFGeneRank/DESCRIPTION’ ... OK
* preparing ‘RFGeneRank’:
* 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 ‘RFGeneRank_0.99.3.tar.gz’
===============================
BiocCheckGitClone('RFGeneRank')
===============================
Error: package or namespace load failed for ‘BiocCheck’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
there is no package called ‘RBGL’
Execution halted
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/4041/f85576b0a04a3eb2056943c1dddd1cd2f3fea17b/RFGeneRank.Rcheck’
* using R version 4.6.0 alpha (2026-04-05 r89794)
* 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: 2026-04-06 19:38:18 UTC
* using option ‘--no-vignettes’
* checking for file ‘RFGeneRank/DESCRIPTION’ ... OK
* this is package ‘RFGeneRank’ version ‘0.99.3’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... ERROR
Package suggested but not available: ‘GEOquery’
The suggested packages are required for a complete check.
Checking can be attempted without them by setting the environment
variable _R_CHECK_FORCE_SUGGESTS_ to a false value.
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
* DONE
Status: 1 ERROR
See
‘/home/pkgbuild/packagebuilder/workers/jobs/4041/f85576b0a04a3eb2056943c1dddd1cd2f3fea17b/RFGeneRank.Rcheck/00check.log’
for details.
===============================
BiocCheck('RFGeneRank_0.99.3.tar.gz')
===============================
Registered S3 method overwritten by 'bit64':
method from
print.bitstring tools
── Installing RFGeneRank ───────────────────────────────────────────────────────
✔ Package installed successfully
── RFGeneRank session metadata ─────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpmGxlKU/file1fd50c7e7f4fd4/RFGeneRank
→ BiocVersion: 3.23
→ Package: RFGeneRank
→ PackageVersion: 0.99.3
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4041/f85576b0a04a3eb2056943c1dddd1cd2f3fea17b/RFGeneRank.BiocCheck
→ BiocCheckVersion: 1.47.23
→ sourceDir: /tmp/RtmpmGxlKU/file1fd50c7e7f4fd4/RFGeneRank
→ installDir: /tmp/RtmpmGxlKU/file1fd50c19ae2101
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on RFGeneRank ─────────────────────────────────────────────
* 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 4.5.0 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 (26%).
* 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...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of RFGeneRank...
* 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 19
functions greater than 50 lines.
The longest 5 functions are:
• validate_genes() (R/validate_genes.R): 382 lines
• ...
• rank_genes() (R/rank_genes.R): 235 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; 290 lines (6%) are > 80 characters long.
First few lines:
• R/accessors_public.R#L12 #' \item{`oof(x)`}{A list of out-of-fo ...
• ...
• vignettes/RFGeneRank.Rmd#L112 # Detect whether the matrix is count-lik ...
i NOTE: Consider multiples of 4 spaces for line indents; 1642 lines (34%) are
not.
First few lines:
• R/accessors_public.R#L80 .rfgr_imp_set(x, value) ...
• ...
• vignettes/RFGeneRank.Rmd#L184 top = 20 ...
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...
✖ ERROR: Unable to find your email in the Support Site: HTTP 504 Gateway
Timeout.
── BiocCheck v1.47.23 results ──────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 0 WARNINGS | i 5 NOTES
i See the RFGeneRank.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.