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wejlab / animalcules

R shiny app for interactive microbiome analysis
https://wejlab.github.io/animalcules-docs/
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linux check error related to Entrez #37

Closed jasonzhao0307 closed 5 years ago

jasonzhao0307 commented 5 years ago

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

base::assign(".ptime", proc.time(), pos = "CheckExEnv")

Name: find_taxonomy

Title: Find the taxonomy for unlimited tids

Aliases: find_taxonomy

** Examples

taxonLevels <- find_taxonomy(tids=1200) Error in curl::curl_fetch_memory(url, handle = handle) : Error in the HTTP2 framing layer Calls: find_taxonomy ... request_fetch -> request_fetch.write_memory ->

ref: https://github.com/ropensci/rentrez/issues/127

jasonzhao0307 commented 5 years ago

https://github.com/ropensci/rentrez/issues/127 seems useful

jasonzhao0307 commented 5 years ago

pushed a commit: https://github.com/compbiomed/animalcules/commit/1ff88c4f87bd1ebddc98493711a369f8953ef11f

not sure if this will affect speed, will probably change back later.

dwinter commented 5 years ago

Hi @jasonzhao0307 , in case this is still relevant, the latest version of rentrez (v.1.2.2 on CRAN now) has addressed the bug that was throwing these errors