===============================
BiocCheckGitClone('STADyUM')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3916/cfca0687f860642790d4808c36509538a62db99c/STADyUM
→ BiocVersion: 3.22
→ Package: STADyUM
→ PackageVersion: 0.99.3
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3916/cfca0687f860642790d4808c36509538a62db99c/STADyUM.BiocCheck
→ BiocCheckVersion: 1.45.18
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3916/cfca0687f860642790d4808c36509538a62db99c/STADyUM
→ 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...
* Checking that provided CITATION file is correctly formatted...
── BiocCheck v1.45.18 results ──────────────────────────────────────────────────
✖ 0 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/3916/cfca0687f860642790d4808c36509538a62db99c/STADyUM.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* 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 ‘STADyUM/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘STADyUM’ version ‘0.99.3’
* 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 ‘STADyUM’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* 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 ... [9s/9s] OK
* checking whether the package can be unloaded cleanly ... [9s/9s] OK
* checking whether the namespace can be loaded with stated dependencies ... [9s/9s] OK
* checking whether the namespace can be unloaded cleanly ... [9s/9s] OK
* checking loading without being on the library search path ... [9s/9s] 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 ... [34s/34s] 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 line endings in C/C++/Fortran sources/headers ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... NOTE
Compilation used the following non-portable flag(s):
‘-Werror=format-security’
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... [83s/83s] ERROR
Running examples in ‘STADyUM-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: TranscriptionRates-class
> ### Title: Base class for TranscriptionRates objects
> ### Aliases: TranscriptionRates-class plotMeanPauseDistrib
> ### plotMeanPauseDistrib,TranscriptionRates-method
> ### plotExpectedVsActualPauseSiteCounts
> ### plotExpectedVsActualPauseSiteCounts,TranscriptionRates-method
> ### plotChiDistrib plotChiDistrib,TranscriptionRates-method plotBetaVsChi
> ### plotBetaVsChi,TranscriptionRates-method plotPauseSiteContourMap
> ### plotPauseSiteContourMap,TranscriptionRates-method
>
> ### ** Examples
>
> # Create an ExperimentTranscriptionRates object
> load(system.file("extdata", "granges_for_read_counting_DLD1_chr21.RData",
+ package = "STADyUM"))
> expRates <- estimateTranscriptionRates(system.file("extdata",
+ "PROseq-DLD1-aoi-NELFC_Auxin_Ctrl-SE_plus_chr21.bw", package = "STADyUM"),
+ bigwigMinus = system.file("extdata",
+ "PROseq-DLD1-aoi-NELFC_Auxin_Ctrl-SE_minus_chr21.bw", package = "STADyUM"),
+ pauseRegions = bw_pause_filtered,
+ geneBodyRegions = bw_gb_filtered,
+ name = "Control"
+ )
Importing bigwig files...
Processing plus and minus strands bigwig...
Summarizing pause and gene body regions...
Generating read counts table...
estimating rates...
> plotPauseSiteContourMap(expRates, file="pause_sites_contour_map.png")
Error in `geom_density_2d()`:
! Problem while computing stat.
i Error occurred in the 1st layer.
Caused by error in `compute_layer()`:
! The package "MASS" is required for calculating 2D density.
Backtrace:
▆
1. ├─STADyUM::plotPauseSiteContourMap(expRates, file = "pause_sites_contour_map.png")
2. ├─STADyUM::plotPauseSiteContourMap(expRates, file = "pause_sites_contour_map.png")
3. │ └─ggplot2::ggsave(file, p, width = width, height = height, dpi = dpi)
4. │ └─base::lapply(plot, grid.draw)
5. │ ├─grid (local) FUN(X[[i]], ...)
6. │ └─ggplot2 (local) `grid.draw.ggplot2::ggplot`(X[[i]], ...)
7. │ ├─base::print(x)
8. │ └─ggplot2 (local) `print.ggplot2::ggplot`(x)
9. │ ├─ggplot2::ggplot_build(x)
10. │ └─ggplot2 (local) `ggplot_build.ggplot2::ggplot`(x)
11. │ └─ggplot2:::by_layer(...)
12. │ ├─rlang::try_fetch(...)
13. │ │ ├─base::tryCatch(...)
14. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
15. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
16. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
17. │ │ └─base::withCallingHandlers(...)
18. │ └─ggplot2 (local) f(l = layers[[i]], d = data[[i]])
19. │ └─l$compute_statistic(d, layout)
20. │ └─ggplot2 (local) compute_statistic(..., self = self)
21. │ └─self$stat$compute_layer(data, self$computed_stat_params, layout)
22. │ └─ggplot2 (local) compute_layer(..., self = self)
23. │ └─rlang::check_installed("MASS", reason = "for calculating 2D density.")
24. │ └─base::stop(cnd)
25. └─rlang (local) `<fn>`(`<rlb_r___>`)
26. └─handlers[[1L]](cnd)
27. └─cli::cli_abort(...)
28. └─rlang::abort(...)
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
SimulationTranscriptionRates-class 28.079 3.931 32.015
ExperimentTranscriptionRates-class 27.641 0.355 27.998
SimulatePolymerase-class 7.443 0.078 7.521
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [88s/88s]
[89s/89s] 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: 1 ERROR, 2 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3916/cfca0687f860642790d4808c36509538a62db99c/STADyUM.Rcheck/00check.log’
for details.
===============================
BiocCheck('STADyUM_0.99.3.tar.gz')
===============================
── Installing STADyUM ──────────────────────────────────────────────────────────
✔ Package installed successfully
── STADyUM session metadata ────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpWrOywW/file3138c064d14f54/STADyUM
→ BiocVersion: 3.22
→ Package: STADyUM
→ PackageVersion: 0.99.3
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3916/cfca0687f860642790d4808c36509538a62db99c/STADyUM.BiocCheck
→ BiocCheckVersion: 1.45.18
→ sourceDir: /tmp/RtmpWrOywW/file3138c064d14f54/STADyUM
→ installDir: /tmp/RtmpWrOywW/file3138c06da1f2be
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on STADyUM ────────────────────────────────────────────────
* 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 4.4.0 to 4.5.0
* 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 (38%).
* 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 STADyUM...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* 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; 46 lines (1%) are > 80 characters long.
First few lines:
• R/base-transcription-rates-class.R#L170 plot.title = element_tex ...
• ...
• vignettes/STADyUM.Rmd#L188 This uses the same core Expectation Maxi ...
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 v1.45.18 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 3 NOTES
i See the STADyUM.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.