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<body class='hmmessage'><div dir='ltr'>Dear Dr. Lionel,<div><br></div><div>The questions that I'm going to ask might be too simple as I'm a newbie to R.</div><div><br></div><div>would like to ask how am I going to check <b style="font-size: 12pt;">where R was started? </b><span style="font-size: 12pt;">(Provided that the Genbank les and their comparison have been saved under</span></div><div>the correct names<b> in the directory where R was started).</b> I'm using linux. </div><div><br></div><div>I did not load the <span style="font-size: 12pt;">library(genoPlotR) </span><span style="font-size: 12pt;">at the first place. this is what I get after loading the library.</span></div><div><span style="font-size: 12pt;"><br></span></div><div><div>> sessionInfo()</div><div>R version 2.14.1 (2011-12-22)</div><div>Platform: i686-pc-linux-gnu (32-bit)</div><div><br></div><div>locale:</div><div> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C </div><div> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 </div><div> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 </div><div> [7] LC_PAPER=C LC_NAME=C </div><div> [9] LC_ADDRESS=C LC_TELEPHONE=C </div><div>[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C </div><div><br></div><div>attached base packages:</div><div>[1] stats graphics grDevices utils datasets methods base </div><div>> library(genoPlotR)</div><div>Loading required package: grid</div><div>Loading required package: ade4</div><div><br></div><div>Attaching package: ‘ade4’</div><div><br></div><div>The following object(s) are masked from ‘package:base’:</div><div><br></div><div> within</div><div><br></div><div>> BH <- try(read_dna_seg_from_file("NC_005956.gbk"))</div><div>Error in file(con, "r") : cannot open the connection</div><div>In addition: Warning message:</div><div>In file(con, "r") :</div><div> cannot open file 'NC_005956.gbk': No such file or directory</div><div><br></div><div><br></div><div>Sorry for asking such simple questions. please advice.</div><div><br></div><div>best regards,</div><div>wing sze</div><div><br></div><div style="font-size: 12pt;"><br></div></div><div><span style="font-size: 12pt;"><br></span></div><div><span style="font-size: 12pt;"><br></span></div><div><br><div>> From: genoplotr-help-request@lists.r-forge.r-project.org<br>> Subject: genoPlotR-help Digest, Vol 13, Issue 1<br>> To: genoplotr-help@lists.r-forge.r-project.org<br>> Date: Thu, 12 Sep 2013 12:00:08 +0200<br>> <br>> Send genoPlotR-help mailing list submissions to<br>> genoplotr-help@lists.r-forge.r-project.org<br>> <br>> To subscribe or unsubscribe via the World Wide Web, visit<br>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genoplotr-help<br>> <br>> or, via email, send a message with subject or body 'help' to<br>> genoplotr-help-request@lists.r-forge.r-project.org<br>> <br>> You can reach the person managing the list at<br>> genoplotr-help-owner@lists.r-forge.r-project.org<br>> <br>> When replying, please edit your Subject line so it is more specific<br>> than "Re: Contents of genoPlotR-help digest..."<br>> <br>> <br>> Today's Topics:<br>> <br>> 1. Re: could not find function \"read_comparison_from_file<br>> (Lionel Guy)<br>> <br>> <br>> ----------------------------------------------------------------------<br>> <br>> Message: 1<br>> Date: Thu, 12 Sep 2013 10:03:56 +0200<br>> From: Lionel Guy <guy.lionel@gmail.com><br>> To: wing sze ho <howingsze86@hotmail.com><br>> Cc: Help for genoPlotR <genoplotr-help@lists.r-forge.r-project.org><br>> Subject: Re: [genoPlotR-help] could not find function<br>> \"read_comparison_from_file<br>> Message-ID: <DF4C949A-48B6-44A1-858A-407392DF7DE8@gmail.com><br>> Content-Type: text/plain; charset=iso-8859-1<br>> <br>> Hi Wing,<br>> <br>> Have you loaded the library? <br>> <br>> > library(genoPlotR)<br>> <br>> Can you mail the result of<br>> <br>> > sessionInfo()<br>> <br>> so that I can see which version of genoPlotR you are using?<br>> It's strange that it can perform the two first commands but breaks on the third one...<br>> <br>> Cheers,<br>> <br>> Lionel<br>> <br>> On 12 Sep 2013, at 9:51 , wing sze ho <howingsze86@hotmail.com> wrote:<br>> <br>> > Dear Dr. Lionel,<br>> > <br>> > Was trying to work on the examples in section 7.2.3 (Getting started with genoPlotR) and encountered some problem.<br>> > <br>> > 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.<br>> > <br>> > <br>> > Loading Tcl/Tk interface ... done<br>> > Loading required package: stats<br>> > Loading required package: graphics<br>> > Loading required package: MASS<br>> > Loading required package: nnet<br>> > Loading required package: survival<br>> > Loading required package: splines<br>> > > BH <- try(read_dna_seg_from_file("NC_005956.gbk"))<br>> > > BQ <- try(read_dna_seg_from_file("NC_005955.gbk"))<br>> > > BH_vs_BQ <- try(read_comparison_from_blast("NC_005956_vs_NC_005955.blast"))<br>> > > xlims <- list(c(1,50000), c(1,50000))<br>> > > plot_gene_map(dna_segs=list(BH, BQ),<br>> > + comparisons=list(BH_vs_BQ),<br>> > + xlims=xlims,<br>> > + main="BH vs BQ, comparison of the first 50 kb",<br>> > + gene_type="side_blocks",<br>> > + dna_seg_scale=TRUE, scale=FALSE)<br>> > > BH_vs_BQ<br>> > [1] "Error in try(read_comparison_from_blast(\"NC_005956_vs_NC_005955.blast\")) : \n could not find function \"read_comparison_from_blast\"\n"<br>> > attr(,"class")<br>> > [1] "try-error"<br>> > attr(,"condition")<br>> > <simpleError in doTryCatch(return(expr), name, parentenv, handler): could not find function "read_comparison_from_blast"><br>> > <br>> > <br>> > many thanks.<br>> > <br>> > best wishes,<br>> > wing sze<br>> > <br>> <br>> --<br>> Lionel Guy<br>> Petterslundsgatan 24B, SE-75328 Uppsala<br>> email: guy.lionel@gmail.com, mobile: +46 (0)73 9760618, phone: +46 (0)18 410 7398<br>> <br>> <br>> <br>> ------------------------------<br>> <br>> _______________________________________________<br>> genoPlotR-help mailing list<br>> genoPlotR-help@lists.r-forge.r-project.org<br>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genoplotr-help<br>> <br>> End of genoPlotR-help Digest, Vol 13, Issue 1<br>> *********************************************<br></div></div> </div></body>
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