Running ‘testthat.R’ [1923s/453s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(respR)
  > data("urchins.rd")
  > data("sardine.rd")
  > data("squid.rd")
  > data("intermittent.rd")
  > data("flowthrough.rd")
  > data("flowthrough_mult.rd")
  > 
  > test_check("respR")

Running examples in 'refseqR-Ex.R' failed
The error most likely occurred in:

> ### Name: refseq_geneSymbol
> ### Title: Get the gene symbol
> ### Aliases: refseq_geneSymbol
> 
> ### ** Examples
> 
> # Get the gene symbol from a set of XM accessions
> xm = c("XM_004487701", "XM_004488493")
> sapply(xm, function(x) refseq_geneSymbol (x, db = "nuccore"), USE.NAMES = FALSE)
[1] "LOC101512347" "LOC101506901"
> 
> # Get the gene symbol from a set of XP accessions
> xp = c("XP_004487758")
> sapply(xp, function(x) refseq_geneSymbol (x, db = "protein"), USE.NAMES = FALSE)
Warning in check_xml_errors(x) : BLOB ID IS NOT IMPLEMENTED
Warning in check_xml_errors(x) : NCBI C++ Exception:
    Error: UNK_MODULE(CException::eInvalid) "UNK_FILE", line 18446744073709551615: UNK_FUNC --- 

Error: Must specify either (not both) 'id' or 'web_history' arguments
Execution halted
Running examples in ‘refseqR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: refseq_XPlength
> ### Title: Get the protein length from an XP accession
> ### Aliases: refseq_XPlength
> 
> ### ** Examples
> 
>  # Get the XM ids from a set of XP accessions
>  xp = c("XP_004487758", "XP_004488550")
>  sapply(xp, function(x) refseq_XPlength(x), USE.NAMES = FALSE)
Warning: Esummary includes error message: Invalid uid XP_004488550 at position= 0
Error: No esummary records found in file
Execution halted

Package required but not available: ‘biocViews’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.

Error(s) in re-building vignettes:
--- re-building ‘UserManualPRANA.Rmd’ using rmarkdown

Quitting from lines  at lines 108-109 [unnamed-chunk-11] (UserManualPRANA.Rmd)
Error: processing vignette 'UserManualPRANA.Rmd' failed with diagnostics:
Can't join `x$entrezgene_id` with `y$entrezgene_id` due to incompatible
types.
ℹ `x$entrezgene_id` is a <double>.
ℹ `y$entrezgene_id` is a <character>.
--- failed re-building ‘UserManualPRANA.Rmd’

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

Error: Vignette re-building failed.
Execution halted