Re: [R-sig-phylo] error when using function read.GenBank in ape

2016-11-22 Thread Vojtěch Zeisek 
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 :
> > 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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Re: [R-sig-phylo] error when using function read.GenBank in ape

2016-11-21 Thread Emmanuel Paradis 
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 :

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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Re: [R-sig-phylo] error when using function read.GenBank in ape

2016-11-21 Thread Vojtěch Zeisek 
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 :
> >>> 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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Re: [R-sig-phylo] error when using function read.GenBank in ape

2016-11-21 Thread Emmanuel Paradis 

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 :

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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Re: [R-sig-phylo] error when using function read.GenBank in ape

2016-11-12 Thread Eduardo Ascarrunz 
Hi Emmanuel,

Right! Sorry I misspoke.

Best,

Eduardo

2016-11-11 23:32 GMT+01:00 Emmanuel Paradis :

> 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/
>>>
>>>
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>>
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>>
>>
>>
>>
>>
>>

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Re: [R-sig-phylo] error when using function read.GenBank in ape

2016-11-11 Thread Emmanuel Paradis 

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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Re: [R-sig-phylo] error when using function read.GenBank in ape

2016-11-11 Thread Eduardo Ascarrunz 
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/
>

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[R-sig-phylo] error when using function read.GenBank in ape

2016-11-10 Thread Chen, Ting-Wen 
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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