[Bioc-devel] tokay2 error with httr

Martin Morgan martin.morgan at roswellpark.org
Sun Apr 15 18:37:30 CEST 2018

Hi Klara --

You have code structured like

   out <- tryCatch({
       response = httr::GET(url)
    }, error = function(cond) {
       ... htr::http_status(response)$message

so if GET() fails, response is undefined; I guess this is what happened, 
the "why" is a mystery but could be as simple as transient internet 

It seems like you could instead report conditionMessage(cond) in the 
error function (catching the GET() error), and use 
httr::stop_for_status() to check for invalid status response from the 

FWIW your code in utils.R is not consistently indented (sometimes tabs, 
sometimes spaces); I'd strongly suggest 4 spaces and no tabs. Also 
message(paste(...)) can usually be represented simply as message(..., 
including multiline messages.


On 04/15/2018 12:25 PM, Klara Kaleb wrote:
> Hi Bioc team,
> I am one of the maintainers the roma package in the devel version.  The package is building fine on mac and linux, however I am experience an error on tokay2 that I have been so far unable to solve. The problem seems to be in receiving the responses from the API. which fails in the first vignette with the following error message:
> "
> Error: processing vignette 'exploring_hogs.Rmd' failed with diagnostics:
> object 'response' not found
> "
> I have checked the relevant end point and it works as it is suppose to do. Furthermore, the same error does not show up in mac and linux servers. Would you happen to have any pointers to what might be causing this error?
> Thank you in advance,
> Klara
> 	[[alternative HTML version deleted]]
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