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
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
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
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
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
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
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
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
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
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
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
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
Packages suggested but not available for checking:
  'GENIE3', 'minet', 'AnnotationDbi', 'reactome.db', 'biomaRt'
Packages unavailable to check Rd xrefs: ‘minet’, ‘GENIE3’