CRAN Package Check Results for Package dnapath

Last updated on 2022-04-27 06:53:39 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.6.11 38.71 180.89 219.60 ERROR
r-devel-linux-x86_64-debian-gcc 0.6.11 27.81 130.40 158.21 ERROR
r-devel-linux-x86_64-fedora-clang 0.6.11 263.91 ERROR
r-devel-linux-x86_64-fedora-gcc 0.6.11 271.20 ERROR
r-devel-windows-x86_64 0.6.11 62.00 335.00 397.00 OK
r-patched-linux-x86_64 0.6.11 33.30 164.80 198.10 ERROR
r-release-linux-x86_64 0.6.11 30.52 167.15 197.67 ERROR
r-release-macos-arm64 0.6.11 85.00 NOTE
r-release-macos-x86_64 0.6.11 229.00 OK
r-release-windows-x86_64 0.6.11 63.00 350.00 413.00 OK
r-oldrel-macos-arm64 0.6.11 145.00 OK
r-oldrel-macos-x86_64 0.6.11 185.00 OK
r-oldrel-windows-ix86+x86_64 0.6.11 86.00 474.00 560.00 OK

Check Details

Version: 0.6.11
Check: examples
Result: ERROR
    Running examples in 'dnapath-Ex.R' failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### 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 get_reactome_pathways("Homo sapiens", overlap_limit = NULL, min_size = 10, :
     Homo sapiens is not an available species. Use one of the following:
     1-diphosphate,
     Bos taurus
    ,
     Caenorhabditis elegans
    ,
     Canis familiaris
    ,
     Danio rerio
    ,
     Dictyostelium discoideum
    ,
     Drosophila melanogaster
    ,
     Gallus gallus
    ,
     Homo sapiens
    ,
     Mus musculus
    ,
     Mycobacterium tuberculosis
    ,
     Plasmodium falciparum
    ,
     Rattus norvegicus
    ,
     Saccharomyces cerevisiae
    ,
     Schizosaccharomyces pombe
    ,
     Sus scrofa
    Xenopus tropicalis
    .
    Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-linux-x86_64

Version: 0.6.11
Check: re-building of vignette outputs
Result: ERROR
    Error(s) in re-building vignettes:
     ...
    --- re-building 'introduction_to_dnapath.Rmd' using rmarkdown
    --- finished 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:
    Homo sapiens is not an available species. Use one of the following:
     1-diphosphate,
     Bos taurus
    ,
     Caenorhabditis elegans
    ,
     Canis familiaris
    ,
     Danio rerio
    ,
     Dictyostelium discoideum
    ,
     Drosophila melanogaster
    ,
     Gallus gallus
    ,
     Homo sapiens
    ,
     Mus musculus
    ,
     Mycobacterium tuberculosis
    ,
     Plasmodium falciparum
    ,
     Rattus norvegicus
    ,
     Saccharomyces cerevisiae
    ,
     Schizosaccharomyces pombe
    ,
     Sus scrofa
    Xenopus tropicalis
    .
    --- failed re-building 'package_data.Rmd'
    
    SUMMARY: processing the following file failed:
     'package_data.Rmd'
    
    Error: Vignette re-building failed.
    Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-linux-x86_64

Version: 0.6.11
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 get_reactome_pathways("Homo sapiens", overlap_limit = NULL, min_size = 10, :
     Homo sapiens is not an available species. Use one of the following:
     1-diphosphate,
     Bos taurus
    ,
     Caenorhabditis elegans
    ,
     Canis familiaris
    ,
     Danio rerio
    ,
     Dictyostelium discoideum
    ,
     Drosophila melanogaster
    ,
     Gallus gallus
    ,
     Homo sapiens
    ,
     Mus musculus
    ,
     Mycobacterium tuberculosis
    ,
     Plasmodium falciparum
    ,
     Rattus norvegicus
    ,
     Saccharomyces cerevisiae
    ,
     Schizosaccharomyces pombe
    ,
     Sus scrofa
    Xenopus tropicalis
    .
    Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 0.6.11
Check: re-building of vignette outputs
Result: ERROR
    Error(s) in re-building vignettes:
    --- re-building ‘introduction_to_dnapath.Rmd’ using rmarkdown
    --- finished 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:
    Homo sapiens is not an available species. Use one of the following:
     1-diphosphate,
     Bos taurus
    ,
     Caenorhabditis elegans
    ,
     Canis familiaris
    ,
     Danio rerio
    ,
     Dictyostelium discoideum
    ,
     Drosophila melanogaster
    ,
     Gallus gallus
    ,
     Homo sapiens
    ,
     Mus musculus
    ,
     Mycobacterium tuberculosis
    ,
     Plasmodium falciparum
    ,
     Rattus norvegicus
    ,
     Saccharomyces cerevisiae
    ,
     Schizosaccharomyces pombe
    ,
     Sus scrofa
    Xenopus tropicalis
    .
    --- failed re-building ‘package_data.Rmd’
    
    SUMMARY: processing the following file failed:
     ‘package_data.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 0.6.11
Check: package dependencies
Result: NOTE
    Packages suggested but not available for checking:
     'GENIE3', 'minet', 'AnnotationDbi', 'reactome.db', 'biomaRt'
Flavor: r-release-macos-arm64

Version: 0.6.11
Check: Rd cross-references
Result: NOTE
    Packages unavailable to check Rd xrefs: ‘minet’, ‘GENIE3’
Flavor: r-release-macos-arm64