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
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