Ah, OK, it makes sense then. Thank You for this key point. :-) Yours, V. Dne pondělí 21. listopadu 2016 19:03:03 CET jste napsal(a): > Maybe I can clarify this point... The testing versions of ape are not > intended to be on CRAN. That's why they have version numbers with four > parts, so that they are always larger than the current version number on > CRAN but less than the upcoming one. Thus, the update mechanism of R > should work properly if you installed a testing version. > > Best, > > Emmanuel > > Le 21/11/2016 à 17:59, Vojtěch Zeisek a écrit : > > Hello, > > Emmanuel, the problem was/is, that CRAN has version 3.5 (further > > subversion > > not specified) and there read.GenBank is broken. Installation from Your > > web > > went fine. i was wondering if 3.5.10 or above is/should be in CRAN. The > > fix() is nice trick, thank You. Anyway, I'm looking forward 4.0. > > Sincerely, > > V. > > > > Dne pondělí 21. listopadu 2016 13:25:12 CET jste napsal(a): > >> Hi Vojtěch, > >> > >> ape 4.0 is not yet on CRAN. We are running more tests. > >> > >> You could use the testing version: there won't be substantial changes > >> once it is on CRAN. > >> > >> If you cannot install the testing version from ape-package.ird.fr (maybe > >> mostly for users of MacOS with no compiling tools), a simple fix to this > >> issue is to run: > >> > >> fix(read.GenBank) > >> > >> and replace "http:...." by "https:....", save and close. > >> > >> Best, > >> > >> Emmanuel > >> > >> Le 19/11/2016 à 09:48, Vojtěch Zeisek a écrit : > >>> 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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