CRAN Package Check Results for Maintainer ‘Junhui Li <ljh.biostat at gmail.com>’

Last updated on 2026-04-27 13:51:58 CEST.

Package	ERROR	OK
gtWAS		13
ProbeDeveloper	4	9
TmCalculator	6	7
ZetaSuite		13

Package gtWAS

Current CRAN status: OK: 13

Package ProbeDeveloper

Current CRAN status: ERROR: 4, OK: 9

Version: 1.1.1
Check: package dependencies
Result: ERROR Package required and available but unsuitable version: ‘TmCalculator’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. Flavors: r-release-macos-arm64, r-release-macos-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64

Package TmCalculator

Current CRAN status: ERROR: 6, OK: 7

Version: 1.0.4
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘TmCalculator.Rmd’ using rmarkdown Quitting from TmCalculator.Rmd:125-181 [tm_viz] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `[.XMLInternalDocument`: ! No method for subsetting an XMLInternalDocument with numeric --- Backtrace: ▆ 1. └─TmCalculator::plot_tm_genome_tracks(...) 2. └─TmCalculator (local) create_chr_plot(chromosome_to_plot) 3. └─Gviz::IdeogramTrack(genome = genome_assembly, chromosome = chr) 4. └─methods::new(...) 5. ├─methods::initialize(value, ...) 6. └─Gviz::initialize(value, ...) 7. └─Gviz (local) .local(.Object, ...) 8. └─Gviz:::.cacheGenomes(genome = genome) 9. └─Gviz::.doCache(...) 10. ├─BiocGenerics::eval(expression, envir = callEnv) 11. ├─base::eval(expression, envir = callEnv) 12. │ └─base::eval(expression, envir = callEnv) 13. └─rtracklayer::ucscGenomes() 14. ├─response[[5]] 15. └─XML:::`[[.XMLInternalDocument`(response, 5) 16. ├─x[i, addFinalizer = addFinalizer] 17. └─XML:::`[.XMLInternalDocument`(x, i, addFinalizer = addFinalizer) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'TmCalculator.Rmd' failed with diagnostics: No method for subsetting an XMLInternalDocument with numeric --- failed re-building ‘TmCalculator.Rmd’ SUMMARY: processing the following file failed: ‘TmCalculator.Rmd’ Error: Vignette re-building failed. Execution halted Flavor: r-devel-linux-x86_64-debian-gcc

Version: 1.0.4
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: --- re-building 'TmCalculator.Rmd' using rmarkdown Quitting from TmCalculator.Rmd:125-181 [tm_viz] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `[.XMLInternalDocument`: ! No method for subsetting an XMLInternalDocument with numeric --- Backtrace: ▆ 1. └─TmCalculator::plot_tm_genome_tracks(...) 2. └─TmCalculator (local) create_chr_plot(chromosome_to_plot) 3. └─Gviz::IdeogramTrack(genome = genome_assembly, chromosome = chr) 4. └─methods::new(...) 5. ├─methods::initialize(value, ...) 6. └─Gviz::initialize(value, ...) 7. └─Gviz (local) .local(.Object, ...) 8. └─Gviz:::.cacheGenomes(genome = genome) 9. └─Gviz::.doCache(...) 10. ├─BiocGenerics::eval(expression, envir = callEnv) 11. ├─base::eval(expression, envir = callEnv) 12. │ └─base::eval(expression, envir = callEnv) 13. └─rtracklayer::ucscGenomes() 14. ├─response[[5]] 15. └─XML:::`[[.XMLInternalDocument`(response, 5) 16. ├─x[i, addFinalizer = addFinalizer] 17. └─XML:::`[.XMLInternalDocument`(x, i, addFinalizer = addFinalizer) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'TmCalculator.Rmd' failed with diagnostics: No method for subsetting an XMLInternalDocument with numeric --- failed re-building 'TmCalculator.Rmd' SUMMARY: processing the following file failed: 'TmCalculator.Rmd' Error: Vignette re-building failed. Execution halted Flavor: r-devel-windows-x86_64

Version: 1.0.4
Check: package dependencies
Result: ERROR Package required but not available: ‘karyoploteR’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. Flavors: r-release-macos-arm64, r-release-macos-x86_64

Version: 1.0.4
Check: package dependencies
Result: ERROR Packages required but not available: 'ggbio', 'karyoploteR' Package suggested but not available for checking: ‘BSgenome.Hsapiens.UCSC.hg38’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64

Package ZetaSuite

Current CRAN status: OK: 13