===============================
R CMD BUILD
===============================
* checking for file RBPEqBind/DESCRIPTION ... OK
* preparing RBPEqBind:
* 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 RBPEqBind_0.99.0.tar.gz
===============================
BiocCheckGitClone('RBPEqBind')
===============================
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4131/RBPEqBind_20260306190405/RBPEqBind
BiocVersion: 3.23
Package: RBPEqBind
PackageVersion: 0.99.0
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4131/RBPEqBind_20260306190405/RBPEqBind.BiocCheck
BiocCheckVersion: 1.47.18
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4131/RBPEqBind_20260306190405/RBPEqBind
installDir: NULL
isTarBall: FALSE
platform: unix
* Checking valid files...
ERROR: System files found that should not be Git tracked.
RBPEqBind.Rproj
* 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 v1.47.18 results
1 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/4131/RBPEqBind_20260306190405/RBPEqBind.Rcheck
* using R Under development (unstable) (2026-01-15 r89304)
* 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 RBPEqBind/DESCRIPTION ... OK
* this is package RBPEqBind version 0.99.0
* 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 RBPEqBind 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 ... [6s/6s] OK
* checking whether the package can be loaded with stated dependencies ... [6s/6s] OK
* checking whether the package can be unloaded cleanly ... [6s/6s] OK
* checking whether the namespace can be loaded with stated dependencies ... [6s/6s] OK
* checking whether the namespace can be unloaded cleanly ... [6s/6s] OK
* checking loading without being on the library search path ... [6s/6s] 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 ... [22s/22s] 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 ... [16s/16s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running testthat.R [9s/9s]
[9s/9s] 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 ... [3s/3s] OK
* DONE
Status: OK
===============================
BiocCheck('RBPEqBind_0.99.0.tar.gz')
===============================
Installing RBPEqBind
Package installed successfully
RBPEqBind session metadata
sourceDir: /tmp/RtmpZwNQTu/file1aeb113723bed/RBPEqBind
BiocVersion: 3.23
Package: RBPEqBind
PackageVersion: 0.99.0
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4131/RBPEqBind_20260306190405/RBPEqBind.BiocCheck
BiocCheckVersion: 1.47.18
sourceDir: /tmp/RtmpZwNQTu/file1aeb113723bed/RBPEqBind
installDir: /tmp/RtmpZwNQTu/file1aeb113ba83ca9
isTarBall: TRUE
platform: unix
Running BiocCheck on RBPEqBind
* 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 (30%).
* 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 RBPEqBind...
* Checking coding practice...
i NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
utils.R (line 70, column 13)
visualization.R (line 97, column 32)
visualization.R (line 252, column 32)
* 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 11
functions greater than 50 lines.
The longest 5 functions are:
plotBubble() (R/visualization.R): 239 lines
...
plotGrid() (R/visualization.R): 94 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; 130 lines (5%) are > 80 characters long.
First few lines:
R/data_loading.R#L8 #' @param rbp Optional character vector ...
...
vignettes/RBPEqBind-intro.Rmd#L425 fasta_file <- system.file("extdata", "te
...
i NOTE: Consider multiples of 4 spaces for line indents; 958 lines (40%) are
not.
First few lines:
R/data_loading.R#L21 if (!file.exists(file)) { ...
...
vignettes/RBPEqBind-intro.Rmd#L438 parallel = TRUE ...
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 502 Bad Gateway.
BiocCheck v1.47.18 results
1 ERRORS | 0 WARNINGS | i 5 NOTES
i See the RBPEqBind.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.