Hi Rinku, The R scripts in my Taverna 2 workflows are executed on an ubuntu server that has Rserve version 0.4 and R version 2.7.1 installed.
I don¹t know what the most up to date combination of R and Rserve that works with Taverna 2 is though. Peter. On 30/04/2010 01:15, "Rinku Saha" <[email protected]> wrote: > Hi Paul > My local host 6311 was not connecting.Its solved now and i am able to run > the R scripts.Thank you and thanks to all. > I had one more question,when we switch to Taverna 2,which R version and Rserve > combination would you suggest. > Kind Regards > Rinku > > On Thu, 29 Apr 2010 18:31:16 +0530 wrote >> >Sounds like your server is not running properly. >> >The RServe window should give you some errors. Run the exe file by >> >accessing it from within a command prompt. That way you should still see >> >some errors, even if it does close. >> > >> >Check: >> > >> > * that your firewall permissions are not blocking that port >> > * the port is open for communication >> > * you can run the R-script without it being run through RServe >> > * someone else can try your workflow >> > >> >Paul. >> > >> >Rinku Saha wrote: >>> >> Hi Alan >>> >> When i try to telnet for 6311 it says "Could not not open connection >>> >> to host at 6311". >>> >> Also when i start the R serv from with R and create and run a r script >>> >> through Taverna the Rserv crashes and the workflow fails to run.Thus >>> >> need some help with this. >>> >> >>> >> Kind Regards >>> >> Rinku >>> >> >>> >> On Thu, 29 Apr 2010 17:38:01 +0530 wrote >>>> >> >Rinku Saha wrote: >>>>> >> >> Hi Stian >>>>> >> >> I have taverna 1.7.1 .Then installed the Rshell plugin. Then >>>>> >> >> installed R2.8.0 with Rserv installation from within R.Also then >>>>> >> >> rebooted the machine and started R serv from with R .Rserv opened and >>>>> >> >> then started Taverna . >>>> >> > >>>>> >> >> But its giving me error as in the "tavernaerror" >>>>> >> >> when i try to create a new workflow using a small script(as in >>>>> >> >> "rr.xml"). >>>> >> > >>>> >> >The error indicates that the plugin cannot "talk" to your R server. You >>>> >> >could try telneting to the port e.g. >>>> >> > >>>> >> >telnet localhost 6311 >>>> >> > >>>> >> >to see if it can be contacted. >>>> >> > >>>>> >> >> Also in this R script when i try to add a input port i only >>>>> >> >> have 4 options in the dropdown numeric,string,numeric vector and >>> >> string >>>>> >> >> vector whereas in the Taverna tutorial i see some additional ones such >>>>> >> >> as integer,double R ex-pression >>>>> >> >> e.t.c(http://www.mygrid.org.uk/usermanual1.7/rshell_processor.html). >>>> >> > >>>> >> >That tutorial is for the standard R support within 1.7 not the R plugin >>>> >> >that you've added. >>>> >> > >>>>> >> >> So then i went back and searched if this combination of 1.7.1+R2.8.0 >>>>> >> >> +Rserv would work.I found from taverna user forum that another user >>> >> had >>>>> >> >> similar problem.So i followed his combination of >>>>> >> >> >>> >> >>> Taverna1.7.1+R2.4.1+Rser_0.4-7(http://ftp5.gwdg.de/pub/misc/cran/bin/windows >>> /contrib/2.4). >>> >> >>>>> >> >> <http://ftp5.gwdg.de/pub/misc/cran/bin/windows/contrib/2.4 >>>>> <http://www.rediffmail.com/cgi-bin/red.cgi?red=http%3A%2F%2Fftp5%2Egwdg%2E >>>>> de%2Fpub%2Fmisc%2Fcran%2Fbin%2Fwindows%2Fcontrib%2F2%2E4> >>> >> >>> <http://www.rediffmail.com/cgi-bin/red.cgi?red=http%3A%2F%2Fftp5%2Egwdg%2Ede >>> %2Fpub%2Fmisc%2Fcran%2Fbin%2Fwindows%2Fcontrib%2F2%2E4 >>> <http://www.rediffmail.com/cgi-bin/red.cgi?red=http%3A%2F%2Fwww%2Erediffmail >>> %2Ecom%2Fcgi%2Dbin%2Fred%2Ecgi%3Fred%3Dhttp%253A%252F%252Fftp5%252Egwdg%252E >>> de%252Fpub%252Fmisc%252Fcran%252Fbin%252Fwindows%252Fcontrib%252F2%252E4> >> >>>>> >> >> I still end up getting same error and also when i enter the input and >>>>> >> >> run the workflow ,R serve window closes. >>>> >> > >>>> >> >I don't understand what you mean by "R serve window closes". Do you >>>> >> >mean that Rserv crashed? >>>> >> > >>>>> >> >> There is one more thing when i run some R workflows in this >>>>> >> >> >>>>> linkhttp://janus.cs.utwente.nl:8000/twiki/bin/view/BioRange/RshellHelp >>>>> >> >> (such as PlotTest.xml or the others) they run succesfully without any >>>>> >> >> errors.Thus i am wondering where is it that something is going >>>>> >> >> wrong.Please let me know. >>>>> >> >> >>>>> >> >> Besides i have java1.6 on my machine. >>>>> >> >> >>>>> >> >> I am so thankful to all you for helping with this and really >>> >> appreciate it. >>>>> >> >> >>>>> >> >> Kind Regards >>>>> >> >> Rinku >>>> >> > >>>> >> >Alan >>>> >> > >>>> >> > >>>> >> >>>> >-------------------------------------------------------------------------->>>> ---- >>>> >> >_______________________________________________ >>>> >> >taverna-users mailing list >>>> >> >[email protected] >>>> </prism/writemail?&mode=mail_to_individual&[email protected] >>>> forge.net&output=web&els=06d591ecf60aa926f2920567fd70081d> >>> >> >>> prism/writemail?&mode=mail_to_individual&[email protected] >>> ge.net&output=web&els=3e66e78b73f0bc7b7a716ab08c8ef099 >>> </prism/writemail?&mode=mail_to_individual&email=prism/writemail?&mode=mail_ >>> to_individual&[email protected]&output=web&els=3e66e >>> 78b73f0bc7b7a716ab08c8ef099&output=web&els=06d591ecf60aa926f2920567fd70081d> > >>>> >> >[email protected] >>>> </prism/writemail?&mode=mail_to_individual&[email protected] >>>> forge.net&output=web&els=06d591ecf60aa926f2920567fd70081d> >>> >> >>> prism/writemail?&mode=mail_to_individual&[email protected] >>> ge.net&output=web&els=3e66e78b73f0bc7b7a716ab08c8ef099 >>> </prism/writemail?&mode=mail_to_individual&email=prism/writemail?&mode=mail_ >>> to_individual&[email protected]&output=web&els=3e66e >>> 78b73f0bc7b7a716ab08c8ef099&output=web&els=06d591ecf60aa926f2920567fd70081d> > >>>> >> >Web site: http://www.taverna.org.uk >>>> <http://www.rediffmail.com/cgi-bin/red.cgi?red=http%3A%2F%2Fwww%2Etaverna%2 >>>> Eorg%2Euk> >>> >> >>> <http://www.rediffmail.com/cgi-bin/red.cgi?red=http%3A%2F%2Fwww%2Etaverna%2E >>> org%2Euk >>> <http://www.rediffmail.com/cgi-bin/red.cgi?red=http%3A%2F%2Fwww%2Erediffmail >>> %2Ecom%2Fcgi%2Dbin%2Fred%2Ecgi%3Fred%3Dhttp%253A%252F%252Fwww%252Etaverna%25 >>> 2Eorg%252Euk> > >>>> >> >Mailing lists: http://www.taverna.org.uk/about/contact-us/ >>>> <http://www.rediffmail.com/cgi-bin/red.cgi?red=http%3A%2F%2Fwww%2Etaverna%2 >>>> Eorg%2Euk%2Fabout%2Fcontact%2Dus%2F> >>> >> >>> <http://www.rediffmail.com/cgi-bin/red.cgi?red=http%3A%2F%2Fwww%2Etaverna%2E >>> org%2Euk%2Fabout%2Fcontact%2Dus%2F >>> <http://www.rediffmail.com/cgi-bin/red.cgi?red=http%3A%2F%2Fwww%2Erediffmail >>> %2Ecom%2Fcgi%2Dbin%2Fred%2Ecgi%3Fred%3Dhttp%253A%252F%252Fwww%252Etaverna%25 >>> 2Eorg%252Euk%252Fabout%252Fcontact%252Dus%252F> > >>>> >> > >>> >> >>> <http://sigads.rediff.com/RealMedia/ads/click_nx.ads/www.rediffmail.com/sign >>> atureline....@middle >>> <http://www.rediffmail.com/cgi-bin/red.cgi?red=http%3A%2F%2Fsigads%2Erediff% >>> 2Ecom%2FRealMedia%2Fads%2Fclick%5Fnx%2Eads%2Fwww%2Erediffmail%2Ecom%2Fsignat >>> ureline%2Ehtm%40Middle> ?> >>> >> >>> >> ------------------------------------------------------------------------ >>> >> >>> >> >>> ------------------------------------------------------------------------------ >>> >> >>> >> ------------------------------------------------------------------------ >>> >> >>> >> _______________________________________________ >>> >> taverna-users mailing list >>> >> [email protected] >>> </prism/writemail?&mode=mail_to_individual&[email protected] >>> orge.net&output=web&els=06d591ecf60aa926f2920567fd70081d> >>> >> [email protected] >>> </prism/writemail?&mode=mail_to_individual&[email protected] >>> orge.net&output=web&els=06d591ecf60aa926f2920567fd70081d> >>> >> Web site: http://www.taverna.org.uk >>> <http://www.rediffmail.com/cgi-bin/red.cgi?red=http%3A%2F%2Fwww%2Etaverna%2E >>> org%2Euk> >>> >> Mailing lists: http://www.taverna.org.uk/about/contact-us/ >>> <http://www.rediffmail.com/cgi-bin/red.cgi?red=http%3A%2F%2Fwww%2Etaverna%2E >>> org%2Euk%2Fabout%2Fcontact%2Dus%2F> >>> >> >> > >> >---------------------------------------------------------------------------->> -- >> >_______________________________________________ >> >taverna-users mailing list >> >[email protected] >> </prism/writemail?&mode=mail_to_individual&[email protected] >> rge.net&output=web&els=06d591ecf60aa926f2920567fd70081d> >> >[email protected] >> </prism/writemail?&mode=mail_to_individual&[email protected] >> rge.net&output=web&els=06d591ecf60aa926f2920567fd70081d> >> >Web site: http://www.taverna.org.uk >> <http://www.rediffmail.com/cgi-bin/red.cgi?red=http%3A%2F%2Fwww%2Etaverna%2Eo >> rg%2Euk> >> >Mailing lists: http://www.taverna.org.uk/about/contact-us/ >> <http://www.rediffmail.com/cgi-bin/red.cgi?red=http%3A%2F%2Fwww%2Etaverna%2Eo >> rg%2Euk%2Fabout%2Fcontact%2Dus%2F> >> > > > <http://sigads.rediff.com/RealMedia/ads/click_nx.ads/www.rediffmail.com/signat > ureline....@middle?> > > ------------------------------------------------------------------------------ > > _______________________________________________ > taverna-users mailing list > [email protected] > [email protected] > Web site: http://www.taverna.org.uk > Mailing lists: http://www.taverna.org.uk/about/contact-us/
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