Hi Emmanuel, Right! Sorry I misspoke.
Best, Eduardo 2016-11-11 23:32 GMT+01:00 Emmanuel Paradis <emmanuel.para...@ird.fr>: > 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 >>> >>> _______________________________________________ >>> R-sig-phylo mailing list - R-sig-phylo@r-project.org >>> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo >>> Searchable archive at http://www.mail-archive.com/r- >>> sig-ph...@r-project.org/ >>> >>> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> R-sig-phylo mailing list - R-sig-phylo@r-project.org >> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo >> Searchable archive at http://www.mail-archive.com/r- >> sig-ph...@r-project.org/ >> >> >> >> >> >> [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
