From guy.lionel at gmail.com  Thu Sep 12 10:03:56 2013
From: guy.lionel at gmail.com (Lionel Guy)
Date: Thu, 12 Sep 2013 10:03:56 +0200
Subject: [genoPlotR-help] could not find function
	\"read_comparison_from_file
In-Reply-To: <BLU169-W11656065624A5131069A613BD3A0@phx.gbl>
References: <BLU169-W11656065624A5131069A613BD3A0@phx.gbl>
Message-ID: <DF4C949A-48B6-44A1-858A-407392DF7DE8@gmail.com>

Hi Wing,

Have you loaded the library? 

> library(genoPlotR)

Can you mail the result of

> sessionInfo()

so that I can see which version of genoPlotR you are using?
It's strange that it can perform the two first commands but breaks on the third one...

Cheers,

Lionel

On 12 Sep 2013, at 9:51 , wing sze ho <howingsze86 at hotmail.com> wrote:

> Dear Dr. Lionel,
> 
> Was trying to work on the examples in section 7.2.3 (Getting started with genoPlotR) and encountered some problem.
> 
> Below are the commands that i followed exactly according to the manual. However, it seems that "read_comparison_from_blast" couldn't be found. Please advice.
> 
> 
> Loading Tcl/Tk interface ... done
> Loading required package: stats
> Loading required package: graphics
> Loading required package: MASS
> Loading required package: nnet
> Loading required package: survival
> Loading required package: splines
> > BH <- try(read_dna_seg_from_file("NC_005956.gbk"))
> > BQ <- try(read_dna_seg_from_file("NC_005955.gbk"))
> > BH_vs_BQ <- try(read_comparison_from_blast("NC_005956_vs_NC_005955.blast"))
> > xlims <- list(c(1,50000), c(1,50000))
> > plot_gene_map(dna_segs=list(BH, BQ),
> + comparisons=list(BH_vs_BQ),
> + xlims=xlims,
> + main="BH vs BQ, comparison of the first 50 kb",
> + gene_type="side_blocks",
> + dna_seg_scale=TRUE, scale=FALSE)
> > BH_vs_BQ
> [1] "Error in try(read_comparison_from_blast(\"NC_005956_vs_NC_005955.blast\")) : \n  could not find function \"read_comparison_from_blast\"\n"
> attr(,"class")
> [1] "try-error"
> attr(,"condition")
> <simpleError in doTryCatch(return(expr), name, parentenv, handler): could not find function "read_comparison_from_blast">
> 
> 
> many thanks.
> 
> best wishes,
> wing sze
> 

--
Lionel Guy
Petterslundsgatan 24B, SE-75328 Uppsala
email: guy.lionel at gmail.com, mobile: +46 (0)73 9760618, phone: +46 (0)18 410 7398


From howingsze86 at hotmail.com  Fri Sep 13 02:33:18 2013
From: howingsze86 at hotmail.com (wing sze ho)
Date: Fri, 13 Sep 2013 08:33:18 +0800
Subject: [genoPlotR-help] genoPlotR-help Digest, Vol 13, Issue 1
In-Reply-To: <mailman.15.1378980008.25183.genoplotr-help@lists.r-forge.r-project.org>
References: <mailman.15.1378980008.25183.genoplotr-help@lists.r-forge.r-project.org>
Message-ID: <BLU169-W242CBC87DFCF4472053E13BD3B0@phx.gbl>

Dear Dr. Lionel,
The questions that I'm going to ask might be too simple as I'm a newbie to R.
would like to ask how am I going to check where R was started?  (Provided that the Genbank 
les and their comparison have been saved underthe correct names in the directory where R was started). I'm using linux. 
I did not load the library(genoPlotR) at the first place. this is what I get after loading the library.
> sessionInfo()R version 2.14.1 (2011-12-22)Platform: i686-pc-linux-gnu (32-bit)
locale: [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    [7] LC_PAPER=C                 LC_NAME=C                  [9] LC_ADDRESS=C               LC_TELEPHONE=C            [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
attached base packages:[1] stats     graphics  grDevices utils     datasets  methods   base     > library(genoPlotR)Loading required package: gridLoading required package: ade4
Attaching package: ?ade4?
The following object(s) are masked from ?package:base?:
    within
> BH <- try(read_dna_seg_from_file("NC_005956.gbk"))Error in file(con, "r") : cannot open the connectionIn addition: Warning message:In file(con, "r") :  cannot open file 'NC_005956.gbk': No such file or directory

Sorry for asking such simple questions. please advice.
best regards,wing sze




> From: genoplotr-help-request at lists.r-forge.r-project.org
> Subject: genoPlotR-help Digest, Vol 13, Issue 1
> To: genoplotr-help at lists.r-forge.r-project.org
> Date: Thu, 12 Sep 2013 12:00:08 +0200
> 
> Send genoPlotR-help mailing list submissions to
> 	genoplotr-help at lists.r-forge.r-project.org
> 
> To subscribe or unsubscribe via the World Wide Web, visit
> 	https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genoplotr-help
> 
> or, via email, send a message with subject or body 'help' to
> 	genoplotr-help-request at lists.r-forge.r-project.org
> 
> You can reach the person managing the list at
> 	genoplotr-help-owner at lists.r-forge.r-project.org
> 
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of genoPlotR-help digest..."
> 
> 
> Today's Topics:
> 
>    1. Re: could not find function	\"read_comparison_from_file
>       (Lionel Guy)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Thu, 12 Sep 2013 10:03:56 +0200
> From: Lionel Guy <guy.lionel at gmail.com>
> To: wing sze ho <howingsze86 at hotmail.com>
> Cc: Help for genoPlotR <genoplotr-help at lists.r-forge.r-project.org>
> Subject: Re: [genoPlotR-help] could not find function
> 	\"read_comparison_from_file
> Message-ID: <DF4C949A-48B6-44A1-858A-407392DF7DE8 at gmail.com>
> Content-Type: text/plain; charset=iso-8859-1
> 
> Hi Wing,
> 
> Have you loaded the library? 
> 
> > library(genoPlotR)
> 
> Can you mail the result of
> 
> > sessionInfo()
> 
> so that I can see which version of genoPlotR you are using?
> It's strange that it can perform the two first commands but breaks on the third one...
> 
> Cheers,
> 
> Lionel
> 
> On 12 Sep 2013, at 9:51 , wing sze ho <howingsze86 at hotmail.com> wrote:
> 
> > Dear Dr. Lionel,
> > 
> > Was trying to work on the examples in section 7.2.3 (Getting started with genoPlotR) and encountered some problem.
> > 
> > Below are the commands that i followed exactly according to the manual. However, it seems that "read_comparison_from_blast" couldn't be found. Please advice.
> > 
> > 
> > Loading Tcl/Tk interface ... done
> > Loading required package: stats
> > Loading required package: graphics
> > Loading required package: MASS
> > Loading required package: nnet
> > Loading required package: survival
> > Loading required package: splines
> > > BH <- try(read_dna_seg_from_file("NC_005956.gbk"))
> > > BQ <- try(read_dna_seg_from_file("NC_005955.gbk"))
> > > BH_vs_BQ <- try(read_comparison_from_blast("NC_005956_vs_NC_005955.blast"))
> > > xlims <- list(c(1,50000), c(1,50000))
> > > plot_gene_map(dna_segs=list(BH, BQ),
> > + comparisons=list(BH_vs_BQ),
> > + xlims=xlims,
> > + main="BH vs BQ, comparison of the first 50 kb",
> > + gene_type="side_blocks",
> > + dna_seg_scale=TRUE, scale=FALSE)
> > > BH_vs_BQ
> > [1] "Error in try(read_comparison_from_blast(\"NC_005956_vs_NC_005955.blast\")) : \n  could not find function \"read_comparison_from_blast\"\n"
> > attr(,"class")
> > [1] "try-error"
> > attr(,"condition")
> > <simpleError in doTryCatch(return(expr), name, parentenv, handler): could not find function "read_comparison_from_blast">
> > 
> > 
> > many thanks.
> > 
> > best wishes,
> > wing sze
> > 
> 
> --
> Lionel Guy
> Petterslundsgatan 24B, SE-75328 Uppsala
> email: guy.lionel at gmail.com, mobile: +46 (0)73 9760618, phone: +46 (0)18 410 7398
> 
> 
> 
> ------------------------------
> 
> _______________________________________________
> genoPlotR-help mailing list
> genoPlotR-help at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genoplotr-help
> 
> End of genoPlotR-help Digest, Vol 13, Issue 1
> *********************************************
 		 	   		  
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From howingsze86 at hotmail.com  Fri Sep 13 10:46:25 2013
From: howingsze86 at hotmail.com (wing sze ho)
Date: Fri, 13 Sep 2013 16:46:25 +0800
Subject: [genoPlotR-help] genoPlotR-help Digest, Vol 13, Issue 1
In-Reply-To: <BLU169-W242CBC87DFCF4472053E13BD3B0@phx.gbl>
References: <mailman.15.1378980008.25183.genoplotr-help@lists.r-forge.r-project.org>,
 <BLU169-W242CBC87DFCF4472053E13BD3B0@phx.gbl>
Message-ID: <BLU169-W99BDB56FC32B6F8A69242BBD3B0@phx.gbl>

Dear Dr. Lionel,
I have figured out the way and had generated the diagram. Thanks. 

Best regards,wing sze
From: howingsze86 at hotmail.com
To: genoplotr-help at lists.r-forge.r-project.org
Subject: RE: genoPlotR-help Digest, Vol 13, Issue 1
Date: Fri, 13 Sep 2013 08:33:18 +0800




Dear Dr. Lionel,
The questions that I'm going to ask might be too simple as I'm a newbie to R.
would like to ask how am I going to check where R was started?  (Provided that the Genbank 
les and their comparison have been saved underthe correct names in the directory where R was started). I'm using linux. 
I did not load the library(genoPlotR) at the first place. this is what I get after loading the library.
> sessionInfo()R version 2.14.1 (2011-12-22)Platform: i686-pc-linux-gnu (32-bit)
locale: [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    [7] LC_PAPER=C                 LC_NAME=C                  [9] LC_ADDRESS=C               LC_TELEPHONE=C            [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
attached base packages:[1] stats     graphics  grDevices utils     datasets  methods   base     > library(genoPlotR)Loading required package: gridLoading required package: ade4
Attaching package: ?ade4?
The following object(s) are masked from ?package:base?:
    within
> BH <- try(read_dna_seg_from_file("NC_005956.gbk"))Error in file(con, "r") : cannot open the connectionIn addition: Warning message:In file(con, "r") :  cannot open file 'NC_005956.gbk': No such file or directory

Sorry for asking such simple questions. please advice.
best regards,wing sze




> From: genoplotr-help-request at lists.r-forge.r-project.org
> Subject: genoPlotR-help Digest, Vol 13, Issue 1
> To: genoplotr-help at lists.r-forge.r-project.org
> Date: Thu, 12 Sep 2013 12:00:08 +0200
> 
> Send genoPlotR-help mailing list submissions to
> 	genoplotr-help at lists.r-forge.r-project.org
> 
> To subscribe or unsubscribe via the World Wide Web, visit
> 	https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genoplotr-help
> 
> or, via email, send a message with subject or body 'help' to
> 	genoplotr-help-request at lists.r-forge.r-project.org
> 
> You can reach the person managing the list at
> 	genoplotr-help-owner at lists.r-forge.r-project.org
> 
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of genoPlotR-help digest..."
> 
> 
> Today's Topics:
> 
>    1. Re: could not find function	\"read_comparison_from_file
>       (Lionel Guy)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Thu, 12 Sep 2013 10:03:56 +0200
> From: Lionel Guy <guy.lionel at gmail.com>
> To: wing sze ho <howingsze86 at hotmail.com>
> Cc: Help for genoPlotR <genoplotr-help at lists.r-forge.r-project.org>
> Subject: Re: [genoPlotR-help] could not find function
> 	\"read_comparison_from_file
> Message-ID: <DF4C949A-48B6-44A1-858A-407392DF7DE8 at gmail.com>
> Content-Type: text/plain; charset=iso-8859-1
> 
> Hi Wing,
> 
> Have you loaded the library? 
> 
> > library(genoPlotR)
> 
> Can you mail the result of
> 
> > sessionInfo()
> 
> so that I can see which version of genoPlotR you are using?
> It's strange that it can perform the two first commands but breaks on the third one...
> 
> Cheers,
> 
> Lionel
> 
> On 12 Sep 2013, at 9:51 , wing sze ho <howingsze86 at hotmail.com> wrote:
> 
> > Dear Dr. Lionel,
> > 
> > Was trying to work on the examples in section 7.2.3 (Getting started with genoPlotR) and encountered some problem.
> > 
> > Below are the commands that i followed exactly according to the manual. However, it seems that "read_comparison_from_blast" couldn't be found. Please advice.
> > 
> > 
> > Loading Tcl/Tk interface ... done
> > Loading required package: stats
> > Loading required package: graphics
> > Loading required package: MASS
> > Loading required package: nnet
> > Loading required package: survival
> > Loading required package: splines
> > > BH <- try(read_dna_seg_from_file("NC_005956.gbk"))
> > > BQ <- try(read_dna_seg_from_file("NC_005955.gbk"))
> > > BH_vs_BQ <- try(read_comparison_from_blast("NC_005956_vs_NC_005955.blast"))
> > > xlims <- list(c(1,50000), c(1,50000))
> > > plot_gene_map(dna_segs=list(BH, BQ),
> > + comparisons=list(BH_vs_BQ),
> > + xlims=xlims,
> > + main="BH vs BQ, comparison of the first 50 kb",
> > + gene_type="side_blocks",
> > + dna_seg_scale=TRUE, scale=FALSE)
> > > BH_vs_BQ
> > [1] "Error in try(read_comparison_from_blast(\"NC_005956_vs_NC_005955.blast\")) : \n  could not find function \"read_comparison_from_blast\"\n"
> > attr(,"class")
> > [1] "try-error"
> > attr(,"condition")
> > <simpleError in doTryCatch(return(expr), name, parentenv, handler): could not find function "read_comparison_from_blast">
> > 
> > 
> > many thanks.
> > 
> > best wishes,
> > wing sze
> > 
> 
> --
> Lionel Guy
> Petterslundsgatan 24B, SE-75328 Uppsala
> email: guy.lionel at gmail.com, mobile: +46 (0)73 9760618, phone: +46 (0)18 410 7398
> 
> 
> 
> ------------------------------
> 
> _______________________________________________
> genoPlotR-help mailing list
> genoPlotR-help at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genoplotr-help
> 
> End of genoPlotR-help Digest, Vol 13, Issue 1
> *********************************************
 		 	   		   		 	   		  
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