Package suggested but not available for checking: ‘msa’
checkRd: (-1) is_datelife_query.Rd:17: Lost braces; missing escapes or markup?
    17 | First, that \code{input} is of class {datelifeQuery}.
       |                                      ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  clean_taxon_info_children.Rd: taxonomy_taxon_info
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following HTML validation problems:
get_dated_otol_induced_subtree.html:53:1 (get_dated_otol_induced_subtree.Rd:19): Warning: trimming empty <dt>
get_otol_synthetic_tree.html:67:1 (get_otol_synthetic_tree.Rd:29): Warning: trimming empty <dt>
summary_matrix_to_phylo.html:89:1 (summary_matrix_to_phylo.Rd:42): Warning: trimming empty <dt>
checkRd: (-1) is_datelife_query.Rd:17: Lost braces; missing escapes or markup?
    17 | First, that \code{input} is of class {datelifeQuery}.
       |                                      ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  clean_taxon_info_children.Rd: taxonomy_taxon_info
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following HTML validation problems:
get_dated_otol_induced_subtree.html:53:1 (get_dated_otol_induced_subtree.Rd:19): Warning: trimming empty <dt>
get_otol_synthetic_tree.html:67:1 (get_otol_synthetic_tree.Rd:29): Warning: trimming empty <dt>
summary_matrix_to_phylo.html:89:1 (summary_matrix_to_phylo.Rd:42): Warning: trimming empty <dt>
Imports includes 22 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
checkRd: (-1) is_datelife_query.Rd:17: Lost braces; missing escapes or markup?
    17 | First, that \code{input} is of class {datelifeQuery}.
       |                                      ^
Note: found 2596 marked UTF-8 strings
Running examples in ‘datelife-Ex.R’ failed
The error most likely occurred in:

> ### Name: get_ott_children
> ### Title: Use this instead of 'rotl::tol_subtree()' when taxa are not in
> ###   synthesis tree and you still need to get all species or an induced
> ###   OpenTree subtree
> ### Aliases: get_ott_children
> 
> ### ** Examples
> 
> # An example with the dog genus:
> 
> # It is currently not possible to get an OpenTree subtree of a taxon that is
> #  missing from the OpenTree synthetic tree.
> # The dog genus is not monophyletic in the OpenTree synthetic tree, so in
> #  practice, it has no node to extract a subtree from.
> tnrs <- tnrs_match("Canis")
---> Runnning TNRS to match input names to reference taxonomy (OTT).
Error in curl::curl_fetch_memory(url, handle = handle) : 
  SSL peer certificate or SSH remote key was not OK: [api.opentreeoflife.org] SSL certificate problem: certificate has expired
Calls: tnrs_match -> tnrs_match.default
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘Getting_started_with_datelife.Rmd’ using rmarkdown
--- finished re-building ‘Getting_started_with_datelife.Rmd’

--- re-building ‘fringiliidae.Rmd’ using rmarkdown
--- finished re-building ‘fringiliidae.Rmd’

--- re-building ‘make_datelife_query.Rmd’ using rmarkdown

Quitting from lines 30-31 [unnamed-chunk-2] (make_datelife_query.Rmd)
Error: processing vignette 'make_datelife_query.Rmd' failed with diagnostics:
SSL peer certificate or SSH remote key was not OK: [api.opentreeoflife.org] SSL certificate problem: certificate has expired
--- failed re-building ‘make_datelife_query.Rmd’

--- re-building ‘making_bold_trees.Rmd’ using rmarkdown
--- finished re-building ‘making_bold_trees.Rmd’

SUMMARY: processing the following file failed:
  ‘make_datelife_query.Rmd’

Error: Vignette re-building failed.
Execution halted
Found the following HTML validation problems:
get_dated_otol_induced_subtree.html:53:1 (get_dated_otol_induced_subtree.Rd:19): Warning: trimming empty <dt>
get_otol_synthetic_tree.html:67:1 (get_otol_synthetic_tree.Rd:29): Warning: trimming empty <dt>
summary_matrix_to_phylo.html:89:1 (summary_matrix_to_phylo.Rd:42): Warning: trimming empty <dt>
checkRd: (-1) is_datelife_query.Rd:17: Lost braces; missing escapes or markup?
    17 | First, that \code{input} is of class {datelifeQuery}.
       |                                      ^
Note: found 2596 marked UTF-8 strings
Running examples in ‘datelife-Ex.R’ failed
The error most likely occurred in:

> ### Name: get_ott_children
> ### Title: Use this instead of 'rotl::tol_subtree()' when taxa are not in
> ###   synthesis tree and you still need to get all species or an induced
> ###   OpenTree subtree
> ### Aliases: get_ott_children
> 
> ### ** Examples
> 
> # An example with the dog genus:
> 
> # It is currently not possible to get an OpenTree subtree of a taxon that is
> #  missing from the OpenTree synthetic tree.
> # The dog genus is not monophyletic in the OpenTree synthetic tree, so in
> #  practice, it has no node to extract a subtree from.
> tnrs <- tnrs_match("Canis")
---> Runnning TNRS to match input names to reference taxonomy (OTT).
Error in curl::curl_fetch_memory(url, handle = handle) : 
  SSL peer certificate or SSH remote key was not OK: [api.opentreeoflife.org] SSL certificate problem: certificate has expired
Calls: tnrs_match -> tnrs_match.default
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘Getting_started_with_datelife.Rmd’ using rmarkdown
--- finished re-building ‘Getting_started_with_datelife.Rmd’

--- re-building ‘fringiliidae.Rmd’ using rmarkdown
--- finished re-building ‘fringiliidae.Rmd’

--- re-building ‘make_datelife_query.Rmd’ using rmarkdown

Quitting from lines 30-31 [unnamed-chunk-2] (make_datelife_query.Rmd)
Error: processing vignette 'make_datelife_query.Rmd' failed with diagnostics:
SSL peer certificate or SSH remote key was not OK: [api.opentreeoflife.org] SSL certificate problem: certificate has expired
--- failed re-building ‘make_datelife_query.Rmd’

--- re-building ‘making_bold_trees.Rmd’ using rmarkdown
--- finished re-building ‘making_bold_trees.Rmd’

SUMMARY: processing the following file failed:
  ‘make_datelife_query.Rmd’

Error: Vignette re-building failed.
Execution halted
Found the following HTML validation problems:
get_dated_otol_induced_subtree.html:53:1 (get_dated_otol_induced_subtree.Rd:19): Warning: trimming empty <dt>
get_otol_synthetic_tree.html:67:1 (get_otol_synthetic_tree.Rd:29): Warning: trimming empty <dt>
summary_matrix_to_phylo.html:89:1 (summary_matrix_to_phylo.Rd:42): Warning: trimming empty <dt>
checkRd: (-1) is_datelife_query.Rd:17: Lost braces; missing escapes or markup?
    17 | First, that \code{input} is of class {datelifeQuery}.
       |                                      ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  clean_taxon_info_children.Rd: taxonomy_taxon_info
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following HTML validation problems:
get_dated_otol_induced_subtree.html:53:1 (get_dated_otol_induced_subtree.Rd:19): Warning: trimming empty <dt>
get_otol_synthetic_tree.html:67:1 (get_otol_synthetic_tree.Rd:29): Warning: trimming empty <dt>
summary_matrix_to_phylo.html:89:1 (summary_matrix_to_phylo.Rd:42): Warning: trimming empty <dt>
checkRd: (-1) is_datelife_query.Rd:17: Lost braces; missing escapes or markup?
    17 | First, that \code{input} is of class {datelifeQuery}.
       |                                      ^
Found the following HTML validation problems:
get_dated_otol_induced_subtree.html:53:1 (get_dated_otol_induced_subtree.Rd:19): Warning: trimming empty <dt>
get_otol_synthetic_tree.html:67:1 (get_otol_synthetic_tree.Rd:29): Warning: trimming empty <dt>
summary_matrix_to_phylo.html:89:1 (summary_matrix_to_phylo.Rd:42): Warning: trimming empty <dt>
checkRd: (-1) is_datelife_query.Rd:17: Lost braces; missing escapes or markup?
    17 | First, that \code{input} is of class {datelifeQuery}.
       |                                      ^
Found the following HTML validation problems:
get_dated_otol_induced_subtree.html:53:1 (get_dated_otol_induced_subtree.Rd:19): Warning: trimming empty <dt>
get_otol_synthetic_tree.html:67:1 (get_otol_synthetic_tree.Rd:29): Warning: trimming empty <dt>
summary_matrix_to_phylo.html:89:1 (summary_matrix_to_phylo.Rd:42): Warning: trimming empty <dt>
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
checkRd: (-1) is_datelife_query.Rd:17: Lost braces; missing escapes or markup?
    17 | First, that \code{input} is of class {datelifeQuery}.
       |                                      ^
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
checkRd: (-1) is_datelife_query.Rd:17: Lost braces; missing escapes or markup?
    17 | First, that \code{input} is of class {datelifeQuery}.
       |                                      ^
checkRd: (-1) is_datelife_query.Rd:17: Lost braces; missing escapes or markup?
    17 | First, that \code{input} is of class {datelifeQuery}.
       |                                      ^
Found the following HTML validation problems:
get_dated_otol_induced_subtree.html:53:1 (get_dated_otol_induced_subtree.Rd:19): Warning: trimming empty <dt>
get_otol_synthetic_tree.html:67:1 (get_otol_synthetic_tree.Rd:29): Warning: trimming empty <dt>
summary_matrix_to_phylo.html:89:1 (summary_matrix_to_phylo.Rd:42): Warning: trimming empty <dt>
Package suggested but not available for checking: ‘msa’
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
Package suggested but not available for checking: ‘msa’
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   3.5Mb