===============================
BiocCheckGitClone('RBPSpecificity')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4132/RBPSpecificity_20260306190419/RBPSpecificity
→ BiocVersion: 3.23
→ Package: RBPSpecificity
→ PackageVersion: 0.99.0
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4132/RBPSpecificity_20260306190419/RBPSpecificity.BiocCheck
→ BiocCheckVersion: 1.47.18
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4132/RBPSpecificity_20260306190419/RBPSpecificity
→ installDir: NULL
→ isTarBall: FALSE
→ platform: unix
* Checking valid files...
✖ ERROR: System files found that should not be Git tracked.
• RBPSpecificity.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/4132/RBPSpecificity_20260306190419/RBPSpecificity.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 ‘RBPSpecificity/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RBPSpecificity’ 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 serialization versions ... 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 ... [17s/17s] OK
* checking for unstated dependencies in ‘tests’ ... WARNING
'::' or ':::' imports not declared from:
‘BSgenome.Hsapiens.UCSC.hg38’ ‘IRanges’
'library' or 'require' call not declared from: ‘BSgenome.Hsapiens.UCSC.hg38’
* checking tests ...
Running ‘testthat.R’ [8s/8s]
[8s/8s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(RBPSpecificity)
Error: package or namespace load failed for 'RBPSpecificity' in namespaceExport(ns, exports):
undefined exports: Assays, SummarizedExperiment, .DollarNames.SummarizedExperiment, .DollarNames.RangedSummarizedExperiment, makeSummarizedExperimentFromExpressionSet, makeSummarizedExperimentFromDataFrame, makeSummarizedExperimentFromLoom, naiveRangeMapper, probeRangeMapper, geneRangeMapper, rowRanges<-, rowData, rowData<-, colData, colData<-, assayNames, assayNames<-, assays, assays<-, assay, assay<-
In addition: Warning message:
S3 methods '.DollarNames.SummarizedExperiment', '.DollarNames.RangedSummarizedExperiment' were declared in NAMESPACE but not found
Execution halted
* 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 ...Warning in system2(file.path(R.home("bin"), "R"), c("CMD", args), out, out, :
error in running command
[0s/0s] WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
* checking PDF version of manual without index ...Warning in system2(file.path(R.home("bin"), "R"), c("CMD", args), out, out, :
error in running command
ERROR
Re-running with no redirection of stdout/stderr.
sh: 1: /home/biocbuild/bbs-3.23-bioc/R/bin/R: not found
Warning in system2(file.path(R.home("bin"), "R"), c("CMD", args), out, out, :
error in running command
* DONE
Status: 2 ERRORs, 2 WARNINGs, 1 NOTE
See
‘/home/pkgbuild/packagebuilder/workers/jobs/4132/RBPSpecificity_20260306190419/RBPSpecificity.Rcheck/00check.log’
for details.
===============================
BiocCheck('RBPSpecificity_0.99.0.tar.gz')
===============================
/bin/sh: 1: /home/biocbuild/bbs-3.23-bioc/R/bin/Rscript: not found