Re: [R] Diff'ing 2 strings

2019-01-10 Thread Sebastien Bihorel


Thanks for the clarification.

- Original Message -
From: "Duncan Murdoch" 
To: "Sebastien Bihorel" , "Jeff Newmiller" 

Cc: r-help@r-project.org
Sent: Thursday, January 10, 2019 11:43:14 AM
Subject: Re: [R] Diff'ing 2 strings

On 10/01/2019 11:38 a.m., Sebastien Bihorel wrote:
> Yep, I did. Got nothing. It does not come with R 3.4.3, which is the version 
> I can use.
> 
> R CMD Rdiff comes with this version, but it is a shell command not a R 
> function. It is meant for diff'ing R output.

It's in the tools package, so ?tools::Rdiff should get what you want 
even in that version.  But as you note, it isn't a general purpose diff 
for character vectors, it is targeted at comparing R output files.

Duncan Murdoch

> 
> 
> - Original Message -
> From: "Jeff Newmiller" 
> To: r-help@r-project.org, "Sebastien Bihorel" 
> , "Martin Møller Skarbiniks Pedersen" 
> 
> Cc: "R mailing list" 
> Sent: Thursday, January 10, 2019 10:49:15 AM
> Subject: Re: [R] Diff'ing 2 strings
> 
> Just type
> 
> ?Rdiff
> 
> it is in the preinstalled packages that come with R.
> 
> On January 10, 2019 7:35:42 AM PST, Sebastien Bihorel 
>  wrote:
>>From which the diffobj package? 
>>
>>
>> From: "Martin Møller Skarbiniks Pedersen" 
>> To: "Sebastien Bihorel" 
>> Cc: "R mailing list" 
>> Sent: Thursday, January 10, 2019 2:35:15 AM
>> Subject: Re: [R] Diff'ing 2 strings
>>
>>
>>
>> On Sat, Jan 5, 2019, 14:58 Sebastien Bihorel < [
>> mailto:sebastien.biho...@cognigencorp.com |
>> sebastien.biho...@cognigencorp.com ] wrote:
>>
>>
>> Hi,
>>
>> Does R include an equivalent of the linux diff command?
>>
>>
>>
>>
>> yes.
>> ?rdiff
>>
>> /martin
>>
>>
>>  [[alternative HTML version deleted]]
>>
>> __
>> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>

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Re: [R] Diff'ing 2 strings

2019-01-10 Thread Bert Gunter
It's the same thing. From ?Rdiff:

"Given two *R* output files, compute differences ignoring headers, footers
and some other differences."

Bert

Bert Gunter

"The trouble with having an open mind is that people keep coming along and
sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )


On Thu, Jan 10, 2019 at 8:39 AM Sebastien Bihorel <
sebastien.biho...@cognigencorp.com> wrote:

> Yep, I did. Got nothing. It does not come with R 3.4.3, which is the
> version I can use.
>
> R CMD Rdiff comes with this version, but it is a shell command not a R
> function. It is meant for diff'ing R output.
>
>
> - Original Message -
> From: "Jeff Newmiller" 
> To: r-help@r-project.org, "Sebastien Bihorel" <
> sebastien.biho...@cognigencorp.com>, "Martin Møller Skarbiniks Pedersen" <
> traxpla...@gmail.com>
> Cc: "R mailing list" 
> Sent: Thursday, January 10, 2019 10:49:15 AM
> Subject: Re: [R] Diff'ing 2 strings
>
> Just type
>
> ?Rdiff
>
> it is in the preinstalled packages that come with R.
>
> On January 10, 2019 7:35:42 AM PST, Sebastien Bihorel <
> sebastien.biho...@cognigencorp.com> wrote:
> >From which the diffobj package?
> >
> >
> >From: "Martin Møller Skarbiniks Pedersen" 
> >To: "Sebastien Bihorel" 
> >Cc: "R mailing list" 
> >Sent: Thursday, January 10, 2019 2:35:15 AM
> >Subject: Re: [R] Diff'ing 2 strings
> >
> >
> >
> >On Sat, Jan 5, 2019, 14:58 Sebastien Bihorel < [
> >mailto:sebastien.biho...@cognigencorp.com |
> >sebastien.biho...@cognigencorp.com ] wrote:
> >
> >
> >Hi,
> >
> >Does R include an equivalent of the linux diff command?
> >
> >
> >
> >
> >yes.
> >?rdiff
> >
> >/martin
> >
> >
> >   [[alternative HTML version deleted]]
> >
> >__
> >R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> >https://stat.ethz.ch/mailman/listinfo/r-help
> >PLEASE do read the posting guide
> >http://www.R-project.org/posting-guide.html
> >and provide commented, minimal, self-contained, reproducible code.
>
> --
> Sent from my phone. Please excuse my brevity.
>
> __
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

[[alternative HTML version deleted]]

__
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Re: [R] Diff'ing 2 strings

2019-01-10 Thread William Dunlap via R-help
> args(tools::Rdiff)
function (from, to, useDiff = FALSE, forEx = FALSE, nullPointers = TRUE,
Log = FALSE)
NULL
> version$version.string
[1] "R version 3.4.3 (2017-11-30)"

(The 'tools' package is not attached by default, so use ::.)
Bill Dunlap
TIBCO Software
wdunlap tibco.com


On Thu, Jan 10, 2019 at 8:39 AM Sebastien Bihorel <
sebastien.biho...@cognigencorp.com> wrote:

> Yep, I did. Got nothing. It does not come with R 3.4.3, which is the
> version I can use.
>
> R CMD Rdiff comes with this version, but it is a shell command not a R
> function. It is meant for diff'ing R output.
>
>
> - Original Message -
> From: "Jeff Newmiller" 
> To: r-help@r-project.org, "Sebastien Bihorel" <
> sebastien.biho...@cognigencorp.com>, "Martin Møller Skarbiniks Pedersen" <
> traxpla...@gmail.com>
> Cc: "R mailing list" 
> Sent: Thursday, January 10, 2019 10:49:15 AM
> Subject: Re: [R] Diff'ing 2 strings
>
> Just type
>
> ?Rdiff
>
> it is in the preinstalled packages that come with R.
>
> On January 10, 2019 7:35:42 AM PST, Sebastien Bihorel <
> sebastien.biho...@cognigencorp.com> wrote:
> >From which the diffobj package?
> >
> >
> >From: "Martin Møller Skarbiniks Pedersen" 
> >To: "Sebastien Bihorel" 
> >Cc: "R mailing list" 
> >Sent: Thursday, January 10, 2019 2:35:15 AM
> >Subject: Re: [R] Diff'ing 2 strings
> >
> >
> >
> >On Sat, Jan 5, 2019, 14:58 Sebastien Bihorel < [
> >mailto:sebastien.biho...@cognigencorp.com |
> >sebastien.biho...@cognigencorp.com ] wrote:
> >
> >
> >Hi,
> >
> >Does R include an equivalent of the linux diff command?
> >
> >
> >
> >
> >yes.
> >?rdiff
> >
> >/martin
> >
> >
> >   [[alternative HTML version deleted]]
> >
> >__
> >R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> >https://stat.ethz.ch/mailman/listinfo/r-help
> >PLEASE do read the posting guide
> >http://www.R-project.org/posting-guide.html
> >and provide commented, minimal, self-contained, reproducible code.
>
> --
> Sent from my phone. Please excuse my brevity.
>
> __
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

[[alternative HTML version deleted]]

__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.


Re: [R] Diff'ing 2 strings

2019-01-10 Thread Duncan Murdoch

On 10/01/2019 11:38 a.m., Sebastien Bihorel wrote:

Yep, I did. Got nothing. It does not come with R 3.4.3, which is the version I 
can use.

R CMD Rdiff comes with this version, but it is a shell command not a R 
function. It is meant for diff'ing R output.


It's in the tools package, so ?tools::Rdiff should get what you want 
even in that version.  But as you note, it isn't a general purpose diff 
for character vectors, it is targeted at comparing R output files.


Duncan Murdoch




- Original Message -
From: "Jeff Newmiller" 
To: r-help@r-project.org, "Sebastien Bihorel" , 
"Martin Møller Skarbiniks Pedersen" 
Cc: "R mailing list" 
Sent: Thursday, January 10, 2019 10:49:15 AM
Subject: Re: [R] Diff'ing 2 strings

Just type

?Rdiff

it is in the preinstalled packages that come with R.

On January 10, 2019 7:35:42 AM PST, Sebastien Bihorel 
 wrote:
From which the diffobj package? 



From: "Martin Møller Skarbiniks Pedersen" 
To: "Sebastien Bihorel" 
Cc: "R mailing list" 
Sent: Thursday, January 10, 2019 2:35:15 AM
Subject: Re: [R] Diff'ing 2 strings



On Sat, Jan 5, 2019, 14:58 Sebastien Bihorel < [
mailto:sebastien.biho...@cognigencorp.com |
sebastien.biho...@cognigencorp.com ] wrote:


Hi,

Does R include an equivalent of the linux diff command?




yes.
?rdiff

/martin


[[alternative HTML version deleted]]

__
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https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.




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and provide commented, minimal, self-contained, reproducible code.


Re: [R] Diff'ing 2 strings

2019-01-10 Thread Sebastien Bihorel
Yep, I did. Got nothing. It does not come with R 3.4.3, which is the version I 
can use.

R CMD Rdiff comes with this version, but it is a shell command not a R 
function. It is meant for diff'ing R output.


- Original Message -
From: "Jeff Newmiller" 
To: r-help@r-project.org, "Sebastien Bihorel" 
, "Martin Møller Skarbiniks Pedersen" 

Cc: "R mailing list" 
Sent: Thursday, January 10, 2019 10:49:15 AM
Subject: Re: [R] Diff'ing 2 strings

Just type

?Rdiff

it is in the preinstalled packages that come with R.

On January 10, 2019 7:35:42 AM PST, Sebastien Bihorel 
 wrote:
>From which the diffobj package? 
>
>
>From: "Martin Møller Skarbiniks Pedersen"  
>To: "Sebastien Bihorel"  
>Cc: "R mailing list"  
>Sent: Thursday, January 10, 2019 2:35:15 AM 
>Subject: Re: [R] Diff'ing 2 strings 
>
>
>
>On Sat, Jan 5, 2019, 14:58 Sebastien Bihorel < [
>mailto:sebastien.biho...@cognigencorp.com |
>sebastien.biho...@cognigencorp.com ] wrote: 
>
>
>Hi, 
>
>Does R include an equivalent of the linux diff command? 
>
>
>
>
>yes. 
>?rdiff 
>
>/martin 
>
>
>   [[alternative HTML version deleted]]
>
>__
>R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>https://stat.ethz.ch/mailman/listinfo/r-help
>PLEASE do read the posting guide
>http://www.R-project.org/posting-guide.html
>and provide commented, minimal, self-contained, reproducible code.

-- 
Sent from my phone. Please excuse my brevity.

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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and provide commented, minimal, self-contained, reproducible code.


Re: [R] Diff'ing 2 strings

2019-01-10 Thread Jeff Newmiller
Just type

?Rdiff

it is in the preinstalled packages that come with R.

On January 10, 2019 7:35:42 AM PST, Sebastien Bihorel 
 wrote:
>From which the diffobj package? 
>
>
>From: "Martin Møller Skarbiniks Pedersen"  
>To: "Sebastien Bihorel"  
>Cc: "R mailing list"  
>Sent: Thursday, January 10, 2019 2:35:15 AM 
>Subject: Re: [R] Diff'ing 2 strings 
>
>
>
>On Sat, Jan 5, 2019, 14:58 Sebastien Bihorel < [
>mailto:sebastien.biho...@cognigencorp.com |
>sebastien.biho...@cognigencorp.com ] wrote: 
>
>
>Hi, 
>
>Does R include an equivalent of the linux diff command? 
>
>
>
>
>yes. 
>?rdiff 
>
>/martin 
>
>
>   [[alternative HTML version deleted]]
>
>__
>R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>https://stat.ethz.ch/mailman/listinfo/r-help
>PLEASE do read the posting guide
>http://www.R-project.org/posting-guide.html
>and provide commented, minimal, self-contained, reproducible code.

-- 
Sent from my phone. Please excuse my brevity.

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.


Re: [R] Diff'ing 2 strings

2019-01-10 Thread Sebastien Bihorel
>From which the diffobj package? 


From: "Martin Møller Skarbiniks Pedersen"  
To: "Sebastien Bihorel"  
Cc: "R mailing list"  
Sent: Thursday, January 10, 2019 2:35:15 AM 
Subject: Re: [R] Diff'ing 2 strings 



On Sat, Jan 5, 2019, 14:58 Sebastien Bihorel < [ 
mailto:sebastien.biho...@cognigencorp.com | sebastien.biho...@cognigencorp.com 
] wrote: 


Hi, 

Does R include an equivalent of the linux diff command? 




yes. 
?rdiff 

/martin 


[[alternative HTML version deleted]]

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and provide commented, minimal, self-contained, reproducible code.


Re: [R] Diff'ing 2 strings

2019-01-10 Thread Martin Møller Skarbiniks Pedersen
On Thu, 10 Jan 2019 at 09:23, Gerrit Eichner <
gerrit.eich...@math.uni-giessen.de> wrote:

> Don't you mean ?Rdiff ?
>
>
Oh yes.
The unix/linux command diff uses the rdiff-algorithme and it seems that
Rdiff in R uses the exactly same algorithme.

Regards
Martin

[[alternative HTML version deleted]]

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Re: [R] Diff'ing 2 strings

2019-01-10 Thread Troels Ring
?Rdiff perhaps??
Troels

-Oprindelig meddelelse-
Fra: R-help  På vegne af Martin Møller
Skarbiniks Pedersen
Sendt: 10. januar 2019 08:35
Til: Sebastien Bihorel 
Cc: R mailing list 
Emne: Re: [R] Diff'ing 2 strings

On Sat, Jan 5, 2019, 14:58 Sebastien Bihorel <
sebastien.biho...@cognigencorp.com wrote:

> Hi,
>
> Does R include an equivalent of the linux diff command?
>

yes.
?rdiff

/martin

[[alternative HTML version deleted]]

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and provide commented, minimal, self-contained, reproducible code.

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and provide commented, minimal, self-contained, reproducible code.


Re: [R] Diff'ing 2 strings

2019-01-10 Thread Gerrit Eichner

Don't you mean ?Rdiff ?

 Hth  --  Gerrit

-
Dr. Gerrit Eichner   Mathematical Institute, Room 212
gerrit.eich...@math.uni-giessen.de   Justus-Liebig-University Giessen
Tel: +49-(0)641-99-32104  Arndtstr. 2, 35392 Giessen, Germany
http://www.uni-giessen.de/eichner
-

Am 10.01.2019 um 08:35 schrieb Martin Møller Skarbiniks Pedersen:

On Sat, Jan 5, 2019, 14:58 Sebastien Bihorel <
sebastien.biho...@cognigencorp.com wrote:


Hi,

Does R include an equivalent of the linux diff command?



yes.
?rdiff

/martin

[[alternative HTML version deleted]]

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and provide commented, minimal, self-contained, reproducible code.



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and provide commented, minimal, self-contained, reproducible code.


Re: [R] Diff'ing 2 strings

2019-01-09 Thread Martin Møller Skarbiniks Pedersen
On Sat, Jan 5, 2019, 14:58 Sebastien Bihorel <
sebastien.biho...@cognigencorp.com wrote:

> Hi,
>
> Does R include an equivalent of the linux diff command?
>

yes.
?rdiff

/martin

[[alternative HTML version deleted]]

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and provide commented, minimal, self-contained, reproducible code.


Re: [R] Diff'ing 2 strings

2019-01-09 Thread Sebastien Bihorel
Thanks 

Sorry my mention of "fairly complex strings" was indeed a bit vague, indeed. My 
code is building strings that contain \n characters so something that could be 
thought about as multiline strings. 

For comparing these strings, I was hoping to use something like the linux diff 
command which is smart enough to recognize these line chunks you mentioned and 
not just to a simple line-by-line comparison. 

I saw a few thread mentioning ?adist. I will look into that. 

Sebastien 


From: "Bert Gunter"  
To: "Sebastien Bihorel"  
Cc: "R-help"  
Sent: Saturday, January 5, 2019 10:19:42 AM 
Subject: Re: [R] Diff'ing 2 strings 

I do not know what you mean in your string context, as diff in Linux finds 
lines in files that differ. A reproducible example -- posting guide! -- would 
be most useful here. 

However, maybe something of the following strategy might be useful: 

1. Break up your strings into lists of string "chunks" relevant for your 
context via strspit() . Using "" (empty character) as the "sep" string would 
break your strings into individual characters; "\n" would break it into "lines" 
separated by the return 
character; etc. 

2. Compare your lists using e.g. lapply() and probably ?match and friends like 
?setdiff 

You should also probably check out the stringr package to see if it contains 
what you need. Also, if this is gene sequence related, posting on the 
Bioconductor list rather than here is likely to be more fruitful. 

Cheers, 
Bert 

Bert Gunter 

"The trouble with having an open mind is that people keep coming along and 
sticking things into it." 
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip ) 


On Sat, Jan 5, 2019 at 5:58 AM Sebastien Bihorel < [ 
mailto:sebastien.biho...@cognigencorp.com | sebastien.biho...@cognigencorp.com 
] > wrote: 


Hi, 

Does R include an equivalent of the linux diff command? 

Ideally I would like to diff 2 fairly complex strings and extract the 
differences without having to save them on disk and using a system('diff file1 
file2') command. 

Thanks 

Sebastien 

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| http://www.R-project.org/posting-guide.html ] 
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Re: [R] Diff'ing 2 strings

2019-01-05 Thread Bert Gunter
It's the "split" string not the "sep" string, as you and probably everyone
else already realizes.
And, of course, it could be a regular expression, not literally a character
string.

-- Bert

Bert Gunter

"The trouble with having an open mind is that people keep coming along and
sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )


On Sat, Jan 5, 2019 at 7:19 AM Bert Gunter  wrote:

> I do not know what you mean in your string context, as diff in Linux finds
> lines in files that differ. A reproducible example -- posting guide! --
> would be most useful here.
>
> However, maybe something of the following strategy might be useful:
>
> 1. Break up your strings into lists of string "chunks" relevant for your
> context via strspit() . Using "" (empty character) as the "sep" string
> would break your strings into individual characters; "\n" would break it
> into "lines" separated by the return
> character; etc.
>
> 2. Compare your lists using e.g. lapply() and probably ?match and friends
> like ?setdiff
>
> You should also probably check out the stringr package to see if it
> contains what you need. Also, if this is gene sequence related, posting on
> the Bioconductor list rather than here is likely to be more fruitful.
>
> Cheers,
> Bert
>
> Bert Gunter
>
> "The trouble with having an open mind is that people keep coming along and
> sticking things into it."
> -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )
>
>
> On Sat, Jan 5, 2019 at 5:58 AM Sebastien Bihorel <
> sebastien.biho...@cognigencorp.com> wrote:
>
>> Hi,
>>
>> Does R include an equivalent of the linux diff command?
>>
>> Ideally I would like to diff 2 fairly complex strings and extract the
>> differences without having to save them on disk and using a system('diff
>> file1 file2') command.
>>
>> Thanks
>>
>> Sebastien
>>
>> __
>> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
>

[[alternative HTML version deleted]]

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Re: [R] Diff'ing 2 strings

2019-01-05 Thread Bert Gunter
I do not know what you mean in your string context, as diff in Linux finds
lines in files that differ. A reproducible example -- posting guide! --
would be most useful here.

However, maybe something of the following strategy might be useful:

1. Break up your strings into lists of string "chunks" relevant for your
context via strspit() . Using "" (empty character) as the "sep" string
would break your strings into individual characters; "\n" would break it
into "lines" separated by the return
character; etc.

2. Compare your lists using e.g. lapply() and probably ?match and friends
like ?setdiff

You should also probably check out the stringr package to see if it
contains what you need. Also, if this is gene sequence related, posting on
the Bioconductor list rather than here is likely to be more fruitful.

Cheers,
Bert

Bert Gunter

"The trouble with having an open mind is that people keep coming along and
sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )


On Sat, Jan 5, 2019 at 5:58 AM Sebastien Bihorel <
sebastien.biho...@cognigencorp.com> wrote:

> Hi,
>
> Does R include an equivalent of the linux diff command?
>
> Ideally I would like to diff 2 fairly complex strings and extract the
> differences without having to save them on disk and using a system('diff
> file1 file2') command.
>
> Thanks
>
> Sebastien
>
> __
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

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[R] Diff'ing 2 strings

2019-01-05 Thread Sebastien Bihorel
Hi,

Does R include an equivalent of the linux diff command?

Ideally I would like to diff 2 fairly complex strings and extract the 
differences without having to save them on disk and using a system('diff file1 
file2') command.

Thanks

Sebastien

__
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https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.