Re: [R] Diff'ing 2 strings
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. > __ 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.
Re: [R] Diff'ing 2 strings
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]] __ 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.
Re: [R] Diff'ing 2 strings
> 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]] __ 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.
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. __ 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.
Re: [R] Diff'ing 2 strings
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 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.
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 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.
Re: [R] Diff'ing 2 strings
>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.
Re: [R] Diff'ing 2 strings
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]] __ 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.
Re: [R] Diff'ing 2 strings
?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]] __ 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. __ 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.
Re: [R] Diff'ing 2 strings
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]] __ 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. __ 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.
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]] __ 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.
Re: [R] Diff'ing 2 strings
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 __ [ mailto:R-help@r-project.org | R-help@r-project.org ] mailing list -- To UNSUBSCRIBE and more, see [ https://stat.ethz.ch/mailman/listinfo/r-help | https://stat.ethz.ch/mailman/listinfo/r-help ] PLEASE do read the posting guide [ http://www.r-project.org/posting-guide.html | http://www.R-project.org/posting-guide.html ] and provide commented, minimal, self-contained, reproducible code. [[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.
Re: [R] Diff'ing 2 strings
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]] __ 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.
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 < 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]] __ 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.