Hi Eduardo & Ting-Wen,

ape 4.0 is not yet released. The available version is 3.5-0.10 and, you are right Eduardo, it fixes this issue. The instructions to install this new version of ape is here:


http://ape-package.ird.fr/ape_installation.html#versions

The issue (not really a bug, strictly speaking) is because NCBI servers do not accept HTTP requests anymore like many web services. The new version of read.GenBank() uses HTTPS in place of HTTP. The relevant information from NCBI can be found there:

https://www.ncbi.nlm.nih.gov/news/06-10-2016-ncbi-https/

Best,

Emmanuel

Le 11/11/2016 à 09:22, Eduardo Ascarrunz a écrit :
Hi Ting-Wen.

Are you using the latest version of ape? Emmanuel released ape v.4.0
yesterday with a bug fix for that function.

Best,

Eduardo

2016-11-11 0:35 GMT+01:00 Chen, Ting-Wen <
ting-wen.c...@biologie.uni-goettingen.de>:

Dear all,

recently I got an error when downloading sequences in R using MacOS 10.12
(but no problem when using WIndows 7). I was using the function
read.GenBank in package ape and pretty sure my laptop was connecting to the
internet. Following is how the error looks like:

R version 3.3.2 (2016-10-31) -- "Sincere Pumpkin Patch"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin13.4.0 (64-bit)
...
[R.app GUI 1.68 (7288) x86_64-apple-darwin13.4.0]

library(ape)
read.GenBank("U15717")
Error in file(file, "r") : cannot open the connection

Does anybody know how to solve this problem?

All the best
Ting-Wen

--
Ting-Wen Chen
J.F. Blumenbach Institute of Zoology and Anthropology
Georg August University Goettingen
Berliner Str. 28
D-37073 Goettingen, Germany
Tel: +49-55139-10943

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