CRAN Package Check Results for Package dnapath

Last updated on 2020-07-09 05:47:38 CEST.

Check Details

Version: 0.6.3
Check: Rd cross-references
Result: NOTE
    Undeclared package ‘DGCA’ in Rd xrefs
Flavor: r-devel-linux-x86_64-fedora-clang

Version: 0.6.3
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: ‘reactome.db’
Flavor: r-patched-solaris-x86

Version: 0.6.3
Check: examples
Result: ERROR
    Running examples in ‘dnapath-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: get_reactome_pathways
    > ### Title: Obtain Reactome pathways
    > ### Aliases: get_reactome_pathways
    >
    > ### ** Examples
    >
    > # Obtaining a pathway list for human (Homo sapiens).
    > # In this example, overlapping pathways are not combined (this is
    > # specified by setting overlap_limit to NULL).
    > pathway_list <- get_reactome_pathways("Homo sapiens", overlap_limit = NULL,
    + min_size = 10, max_size = 20)
    Obtaining reactome pathway information for species: Homo sapiens
    Error in loadNamespace(name) : there is no package called ‘reactome.db’
    Calls: get_reactome_pathways ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
    Execution halted
Flavors: r-patched-solaris-x86, r-release-osx-x86_64, r-oldrel-osx-x86_64

Version: 0.6.3
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building ‘introduction_to_dnapath.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    --- finished re-building ‘introduction_to_dnapath.Rmd’
    
    --- re-building ‘package_data.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    Quitting from lines 30-31 (package_data.Rmd)
    Error: processing vignette 'package_data.Rmd' failed with diagnostics:
    there is no package called 'reactome.db'
    --- failed re-building ‘package_data.Rmd’
    
    SUMMARY: processing the following file failed:
     ‘package_data.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavors: r-patched-solaris-x86, r-oldrel-osx-x86_64

Version: 0.6.3
Check: package dependencies
Result: NOTE
    Packages suggested but not available for checking: 'GENIE3', 'reactome.db'
Flavors: r-release-osx-x86_64, r-oldrel-osx-x86_64

Version: 0.6.3
Check: Rd cross-references
Result: NOTE
    Package unavailable to check Rd xrefs: ‘GENIE3’
Flavor: r-release-osx-x86_64

Version: 0.6.3
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building ‘introduction_to_dnapath.Rmd’ using rmarkdown
    Quitting from lines 214-217 (introduction_to_dnapath.Rmd)
    Error: processing vignette 'introduction_to_dnapath.Rmd' failed with diagnostics:
    Timeout was reached: [useast.ensembl.org:8443] Connection timed out after 10727 milliseconds
    --- failed re-building ‘introduction_to_dnapath.Rmd’
    
    --- re-building ‘package_data.Rmd’ using rmarkdown
    Quitting from lines 30-31 (package_data.Rmd)
    Error: processing vignette 'package_data.Rmd' failed with diagnostics:
    there is no package called 'reactome.db'
    --- failed re-building ‘package_data.Rmd’
    
    SUMMARY: processing the following files failed:
     ‘introduction_to_dnapath.Rmd’ ‘package_data.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-release-osx-x86_64

Version: 0.6.3
Check: Rd cross-references
Result: NOTE
    Packages unavailable to check Rd xrefs: ‘DGCA’, ‘GENIE3’
Flavor: r-oldrel-osx-x86_64