CRAN Package Check Results for Package rbioapi

Last updated on 2021-10-22 05:59:57 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.7.4 8.42 67.76 76.18 OK
r-devel-linux-x86_64-debian-gcc 0.7.4 5.97 51.63 57.60 OK
r-devel-linux-x86_64-fedora-clang 0.7.4 98.73 OK
r-devel-linux-x86_64-fedora-gcc 0.7.4 88.46 OK
r-devel-windows-x86_64 0.7.4 13.00 169.00 182.00 OK
r-devel-windows-x86_64-gcc10-UCRT 0.7.4 OK
r-patched-linux-x86_64 0.7.4 8.95 69.82 78.77 OK
r-patched-solaris-x86 0.7.4 103.80 OK
r-release-linux-x86_64 0.7.4 7.36 69.11 76.47 OK
r-release-macos-arm64 0.7.4 OK
r-release-macos-x86_64 0.7.4 WARN
r-release-windows-ix86+x86_64 0.7.4 11.00 177.00 188.00 OK
r-oldrel-macos-x86_64 0.7.4 WARN
r-oldrel-windows-ix86+x86_64 0.7.4 13.00 176.00 189.00 OK

Check Details

Version: 0.7.4
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building ‘rbioapi.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
    Retrieving taxonomic nodes that their scientific name field contain adenovirus (page 1).
    Iterating from page 1 to page 3.
    Retrieving taxonomic nodes that their scientific name field contain adenovirus (page 1).
    Retrieving taxonomic nodes that their scientific name field contain adenovirus (page 2).
    Retrieving taxonomic nodes that their scientific name field contain adenovirus (page 3).
    --- finished re-building ‘rbioapi.Rmd’
    
    --- re-building ‘rbioapi_enrichr.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
    Retrieving List of available libraries and statistics from Enrichr human.
    PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
    PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
    Quitting from lines 57-67 (rbioapi_enrichr.Rmd)
    Error: processing vignette 'rbioapi_enrichr.Rmd' failed with diagnostics:
    invalid 'path' argument
    --- failed re-building ‘rbioapi_enrichr.Rmd’
    
    --- re-building ‘rbioapi_jaspar.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
    Retrieving a list of all releases of JASPAR database.
    Retrieving a details of JASPAR database release number 7.
    Retrieving a list of collections available in JASPAR release 2020.
    Retrieving a list of matrix profiles available in JASPAR CORE collection release 2020 (page 1).
    Retrieving a list of taxonomic groups available in JASPAR release 2020.
    Retrieving a list of matrix profiles of taxonomic group insects available in JASPAR release 2020 (page 1).
    Retrieving a list of species available in JASPAR release 2020.
    Retrieving a list of matrix profiles of species 9606 available in JASPAR release 2020 (page 1).
    Retrieving details of matrix profile with ID MA0600.2.
    Retrieving details of TFFM profile with ID TFFM0056.3.
    --- finished re-building ‘rbioapi_jaspar.Rmd’
    
    --- re-building ‘rbioapi_mieaa.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
    PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
    PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
    Quitting from lines 91-102 (rbioapi_mieaa.Rmd)
    Error: processing vignette 'rbioapi_mieaa.Rmd' failed with diagnostics:
    invalid 'path' argument
    --- failed re-building ‘rbioapi_mieaa.Rmd’
    
    --- re-building ‘rbioapi_panther.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
    --- finished re-building ‘rbioapi_panther.Rmd’
    
    --- re-building ‘rbioapi_reactome.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
    Retrieving Reactome Analysis Results of your supplied Identifiers.
    PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
    PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
    Quitting from lines 75-86 (rbioapi_reactome.Rmd)
    Error: processing vignette 'rbioapi_reactome.Rmd' failed with diagnostics:
    invalid 'path' argument
    --- failed re-building ‘rbioapi_reactome.Rmd’
    
    --- re-building ‘rbioapi_string.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
    Mapping 14 Input Identifiers to STRING Identifiers.
    Retrieving STRING Network interaction of 14 Input Identifiers.
    PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
    PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
    Quitting from lines 95-105 (rbioapi_string.Rmd)
    Error: processing vignette 'rbioapi_string.Rmd' failed with diagnostics:
    invalid 'path' argument
    --- failed re-building ‘rbioapi_string.Rmd’
    
    --- re-building ‘rbioapi_uniprot.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
    Retrieving UniProt Entity with accession number P29965.
    Searching UniProt and retrieving proteins that match your supplied inputs.
    Searching UniProt and retrieving proteins that match your supplied inputs.
    Searching UniProt and retrieving proteins that match your supplied inputs.
    Searching UniProt and retrieving proteins that match your supplied inputs.
    Searching UniProt and retrieving proteins that match your supplied inputs.
    --- finished re-building ‘rbioapi_uniprot.Rmd’
    
    SUMMARY: processing the following files failed:
     ‘rbioapi_enrichr.Rmd’ ‘rbioapi_mieaa.Rmd’ ‘rbioapi_reactome.Rmd’
     ‘rbioapi_string.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavors: r-release-macos-x86_64, r-oldrel-macos-x86_64