Hello, is it already in CRAN? read.GenBank for me failed with newest version from CRAN, I had to update directly from Ape's website... Sincerely, V.
Dne sobota 12. listopadu 2016 13:16:47 CET, Eduardo Ascarrunz napsal(a): > 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 -- Vojtěch Zeisek https://trapa.cz/en/ Department of Botany Faculty of Science, Charles University Benátská 433/2, Prague, 12801, CZ https://www.natur.cuni.cz/biology/botany/ Institute of Botany, Academy of Sciences Zámek 1, Průhonice, 25243, CZ http://www.ibot.cas.cz/en/ Czech Republic
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