===============================
R CMD BUILD
===============================
* checking for file ‘RBPSpecificity/DESCRIPTION’ ... OK
* preparing ‘RBPSpecificity’:
* 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 ‘RBPSpecificity_0.99.5.tar.gz’
===============================
BiocCheckGitClone('RBPSpecificity')
===============================
── Running Git clone checks on RBPSpecificity ──────────────────────────────────
* Checking valid files...
* Checking for inst/doc folders...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
* Checking that provided CITATION file is correctly formatted...
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/4132/d97abdd0d5a43b86e88c37def9b83945787f586c/RBPSpecificity.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: 2026-07-05 00:21:48 UTC
* using option ‘--no-vignettes’
* checking for file ‘RBPSpecificity/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RBPSpecificity’ version ‘0.99.5’
* 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 ‘RBPSpecificity’ 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 ... [10s/10s] OK
* checking whether the package can be loaded with stated dependencies ... [10s/10s] OK
* checking whether the package can be unloaded cleanly ... [10s/10s] OK
* checking whether the namespace can be loaded with stated dependencies ... [10s/10s] OK
* checking whether the namespace can be unloaded cleanly ... [10s/10s] OK
* checking loading without being on the library search path ... [10s/10s] 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 ... [33s/33s] 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/19s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘manual_check_rbps.R’ [189s/189s]
Running ‘testthat.R’ [14s/14s]
[203s/203s] 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('RBPSpecificity_0.99.5.tar.gz')
===============================
── Installing RBPSpecificity ───────────────────────────────────────────────────
✔ Package installed successfully
── RBPSpecificity session metadata ─────────────────────────────────────────────
→ sourceDir: /tmp/RtmpJy2Yw8/file8b4c82d73228e/RBPSpecificity
→ BiocVersion: 3.23
→ Package: RBPSpecificity
→ PackageVersion: 0.99.5
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4132/d97abdd0d5a43b86e88c37def9b83945787f586c/RBPSpecificity.BiocCheck
→ BiocCheckVersion: 1.49.21
→ sourceDir: /tmp/RtmpJy2Yw8/file8b4c82d73228e/RBPSpecificity
→ installDir: /tmp/RtmpJy2Yw8/file8b4c85d2ea6d7/lib
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on RBPSpecificity ─────────────────────────────────────────
* 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 for whitespace in DESCRIPTION field names...
* Checking if 'Package:' field matches directory / tarball...
* 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 (50%).
* 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...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of RBPSpecificity...
* 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 8
functions greater than 50 lines.
The longest 5 functions are:
• countKmersBkg() (R/enrichment.R): 161 lines
• ...
• generateBkgSet() (R/utility.R): 83 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/data.R#L9 #' Lam, B., Myers, Z., Sud, P., Jou, J ...
• ...
• vignettes/RBPSpecificity.Rmd#L302 Cellular_Sensitivity = sapply(cellul
...
i NOTE: Consider multiples of 4 spaces for line indents; 169 lines (5%) are
not.
First few lines:
• R/enrichment.R#L48 bkg_min_dist = ...
• ...
• vignettes/RBPSpecificity.Rmd#L47 greater sensitivity to sequence chang
...
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...
! WARNING: Unable to retrieve email info from the Support Site: Failed to
perform HTTP request. Caused by error in `curl::curl_fetch_memory()`: ! Timeout
was reached [support.bioconductor.org]: Operation timed out after 15001
milliseconds with 0 bytes received
── BiocCheck v1.49.21 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 1 WARNINGS | i 3 NOTES
i See the RBPSpecificity.BiocCheck folder and run
`browseVignettes(package = 'BiocCheck')`
for details.