CRAN Package Check Results for Maintainer ‘Matthew Daniel Young <my4 at sanger.ac.uk>’

Last updated on 2020-08-07 01:50:28 CEST.

Package SoupX

Current CRAN status: WARN: 2, NOTE: 6, OK: 4

Version: 1.4.5
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: ‘DropletUtils’
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-solaris-x86, r-release-macos-x86_64, r-oldrel-macos-x86_64

Version: 1.4.5
Check: installed package size
Result: NOTE
     installed size is 11.7Mb
     sub-directories of 1Mb or more:
     data 9.8Mb
     doc 1.1Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-windows-ix86+x86_64, r-patched-solaris-x86, r-release-macos-x86_64, r-release-windows-ix86+x86_64, r-oldrel-macos-x86_64, r-oldrel-windows-ix86+x86_64

Version: 1.4.5
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building ‘pbmcTutorial.Rmd’ using rmarkdown
    Warning in block_exec(params) :
     Failed to tidy R code in chunk 'quick_start'. Reason:
    Error in loadNamespace(name) : there is no package called 'formatR'
    
    Warning in block_exec(params) :
     Failed to tidy R code in chunk 'install_CRAN'. Reason:
    Error in loadNamespace(name) : there is no package called 'formatR'
    
    Warning in block_exec(params) :
     Failed to tidy R code in chunk 'install'. Reason:
    Error in loadNamespace(name) : there is no package called 'formatR'
    
    Warning in block_exec(params) :
     Failed to tidy R code in chunk 'load'. Reason:
    Error in loadNamespace(name) : there is no package called 'formatR'
    
    Warning in block_exec(params) :
     Failed to tidy R code in chunk 'download'. Reason:
    Error in loadNamespace(name) : there is no package called 'formatR'
    
    Warning in block_exec(params) :
     Failed to tidy R code in chunk 'load_data'. Reason:
    Error in loadNamespace(name) : there is no package called 'formatR'
    
    Warning in block_exec(params) :
     Failed to tidy R code in chunk 'load_data_manual'. Reason:
    Error in loadNamespace(name) : there is no package called 'formatR'
    
    Warning in block_exec(params) :
     Failed to tidy R code in chunk 'load_saved'. Reason:
    Error in loadNamespace(name) : there is no package called 'formatR'
    
    Warning in block_exec(params) :
     Failed to tidy R code in chunk 'estimateSoup'. Reason:
    Error in loadNamespace(name) : there is no package called 'formatR'
    
    Warning in block_exec(params) :
     Failed to tidy R code in chunk 'estimateNoDrops'. Reason:
    Error in loadNamespace(name) : there is no package called 'formatR'
    
    Warning in block_exec(params) :
     Failed to tidy R code in chunk 'set_clustering'. Reason:
    Error in loadNamespace(name) : there is no package called 'formatR'
    
    Warning in block_exec(params) :
     Failed to tidy R code in chunk 'add_DR'. Reason:
    Error in loadNamespace(name) : there is no package called 'formatR'
    
    Warning in block_exec(params) :
     Failed to tidy R code in chunk 'plot_annot'. Reason:
    Error in loadNamespace(name) : there is no package called 'formatR'
    
    Warning in block_exec(params) :
     Failed to tidy R code in chunk 'plot_IGKC'. Reason:
    Error in loadNamespace(name) : there is no package called 'formatR'
    
    Warning in block_exec(params) :
     Failed to tidy R code in chunk 'sanity_check'. Reason:
    Error in loadNamespace(name) : there is no package called 'formatR'
    
    Warning in block_exec(params) :
     Failed to tidy R code in chunk 'set_rho'. Reason:
    Error in loadNamespace(name) : there is no package called 'formatR'
    
    Warning in block_exec(params) :
     Failed to tidy R code in chunk 'genes1'. Reason:
    Error in loadNamespace(name) : there is no package called 'formatR'
    
    Warning in block_exec(params) :
     Failed to tidy R code in chunk 'genes2'. Reason:
    Error in loadNamespace(name) : there is no package called 'formatR'
    
    Warning in block_exec(params) :
     Failed to tidy R code in chunk 'auto_est'. Reason:
    Error in loadNamespace(name) : there is no package called 'formatR'
    
    Warning in block_exec(params) :
     Failed to tidy R code in chunk 'auto_est_unif_prior'. Reason:
    Error in loadNamespace(name) : there is no package called 'formatR'
    
    Warning in block_exec(params) :
     Failed to tidy R code in chunk 'topSoupGenes'. Reason:
    Error in loadNamespace(name) : there is no package called 'formatR'
    
    Warning in block_exec(params) :
     Failed to tidy R code in chunk 'inferNonExpressed'. Reason:
    Error in loadNamespace(name) : there is no package called 'formatR'
    
    Warning in block_exec(params) :
     Failed to tidy R code in chunk 'igGenes'. Reason:
    Error in loadNamespace(name) : there is no package called 'formatR'
    
    Warning in block_exec(params) :
     Failed to tidy R code in chunk 'calculateNullMatrix'. Reason:
    Error in loadNamespace(name) : there is no package called 'formatR'
    
    Warning in block_exec(params) :
     Failed to tidy R code in chunk 'visNullMatrix'. Reason:
    Error in loadNamespace(name) : there is no package called 'formatR'
    
    Warning in block_exec(params) :
     Failed to tidy R code in chunk 'calcNullMatrixWithClustering'. Reason:
    Error in loadNamespace(name) : there is no package called 'formatR'
    
    Warning in block_exec(params) :
     Failed to tidy R code in chunk 'calcContamination'. Reason:
    Error in loadNamespace(name) : there is no package called 'formatR'
    
    Warning in block_exec(params) :
     Failed to tidy R code in chunk 'viewCont'. Reason:
    Error in loadNamespace(name) : there is no package called 'formatR'
    
    Warning in block_exec(params) :
     Failed to tidy R code in chunk 'decontaminate'. Reason:
    Error in loadNamespace(name) : there is no package called 'formatR'
    
    Warning in block_exec(params) :
     Failed to tidy R code in chunk 'mostZeroed'. Reason:
    Error in loadNamespace(name) : there is no package called 'formatR'
    
    Warning in block_exec(params) :
     Failed to tidy R code in chunk 'mostReduced'. Reason:
    Error in loadNamespace(name) : there is no package called 'formatR'
    
    Warning in block_exec(params) :
     Failed to tidy R code in chunk 'IGKC_change'. Reason:
    Error in loadNamespace(name) : there is no package called 'formatR'
    
    Warning in block_exec(params) :
     Failed to tidy R code in chunk 'change_plots'. Reason:
    Error in loadNamespace(name) : there is no package called 'formatR'
    
    Warning in block_exec(params) :
     Failed to tidy R code in chunk 'writeOut'. Reason:
    Error in loadNamespace(name) : there is no package called 'formatR'
    
    ! LaTeX Error: File `framed.sty' not found.
    
    ! Emergency stop.
    <read *>
    
    Error: processing vignette 'pbmcTutorial.Rmd' failed with diagnostics:
    LaTeX failed to compile /data/gannet/ripley/R/packages/tests-clang/SoupX.Rcheck/vign_test/SoupX/vignettes/pbmcTutorial.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See pbmcTutorial.log for more info.
    --- failed re-building ‘pbmcTutorial.Rmd’
    
    SUMMARY: processing the following file failed:
     ‘pbmcTutorial.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang

Version: 1.4.5
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building ‘pbmcTutorial.Rmd’ using rmarkdown
    ! LaTeX Error: File `framed.sty' not found.
    
    ! Emergency stop.
    <read *>
    
    Error: processing vignette 'pbmcTutorial.Rmd' failed with diagnostics:
    LaTeX failed to compile /data/gannet/ripley/R/packages/tests-devel/SoupX.Rcheck/vign_test/SoupX/vignettes/pbmcTutorial.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See pbmcTutorial.log for more info.
    --- failed re-building ‘pbmcTutorial.Rmd’
    
    SUMMARY: processing the following file failed:
     ‘pbmcTutorial.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc