Re: [R] use AnnBuilderSourceUrls with local path insted of ftp adress
I want to build my own GO package using the function GOPkgBuilder of AnnBuilder. It uses AnnBuilderSourceUrls to collect data from different ftp sites. These data are not complete for my organism, so I would like to change the ftp adresses to a local one. The changing itself is working but when I run the script I get the following Error: Error in loadFromUrl(file.path(sourceURLs[[EG]], gene2go.gz)) : URL /path/to/file/gene2go.gz is incorrect or the target site is not responding! First of all, please post questions about BioConductor packages in BioConductor mailing list instead of R. Is /path/to/file a real local path? If so, you may also need to modify GOPkgBuilder a little. Try to change the line eg = EG(srcUrl = sourceURLs[[EG]]) to eg = EG(srcUrl = sourceURLs[[EG]], fromWeb = FALSE) The full code of the script is this: library(AnnBuilder) list-options(AnnBuilderSourceUrls) list$AnnBuilderSourceUrls$EG-/path/to/file/ options(AnnBuilderSourceUrls=list$AnnBuilderSourceUrls) GOPkgBuilder(pkgName = GO, pkgPath = ., filename = go_200706-termdb.obo-xml.gz, version = v.1.0, author = list(author = author, maintainer = maintainer [EMAIL PROTECTED]) ) Thanks in advance for any help. Daniela Albrecht -- Pt! Schon vom neuen GMX MultiMessenger gehört? Der kanns mit allen: http://www.gmx.net/de/go/multimessenger __ R-help@stat.math.ethz.ch mailing list 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. Jianhua Zhang Department of Medical Oncology Dana-Farber Cancer Institute 44 Binney Street Boston, MA 02115-6084 __ R-help@stat.math.ethz.ch mailing list 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] tcltk programming guide
Go to http://bioinf.wehi.edu.au/~wettenhall/RTclTkExamples/. There are good examples. X-Original-To: [EMAIL PROTECTED] Delivered-To: [EMAIL PROTECTED] X-Virus-Scanned: by amavisd-new at stat.math.ethz.ch Mime-Version: 1.0 (Apple Message framework v733) To: R-help@stat.math.ethz.ch From: Simone Gabbriellini [EMAIL PROTECTED] Date: Thu, 11 Aug 2005 14:04:58 +0200 Subject: [R] tcltk programming guide X-BeenThere: r-help@stat.math.ethz.ch X-Mailman-Version: 2.1.6 List-Id: Main R Mailing List: Primary help r-help.stat.math.ethz.ch List-Unsubscribe: https://stat.ethz.ch/mailman/listinfo/r-help, mailto:[EMAIL PROTECTED] List-Archive: https://stat.ethz.ch/pipermail/r-help List-Post: mailto:r-help@stat.math.ethz.ch List-Help: mailto:[EMAIL PROTECTED] List-Subscribe: https://stat.ethz.ch/mailman/listinfo/r-help, mailto:[EMAIL PROTECTED] Content-Transfer-Encoding: 7bit X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on pascal.dfci.harvard.edu X-Spam-Level: X-Spam-Status: No, score=-2.6 required=3.0 tests=BAYES_00 autolearn=ham version=3.0.1 Dear List, I'm looking for some documentation about the R tcltk package The one I found in the help doesn't look exaustive, I need information on the use of the single tk widget, maybe with some examples thank you, simone gabbriellini __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Jianhua Zhang Department of Medical Oncology Dana-Farber Cancer Institute 44 Binney Street Boston, MA 02115-6084 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Re: datalist
Hi, The following is a cut/paste from http://developer.r-project.org/200update.txt: ... 3) When a package is installed, all the data sets are loaded to see what they produce. If this is undesirable (because they are enormous, or depend on other packages that need to be installed later, ...), add a `datalist' file to the data subdirectory as described in `Writing R Extensions'. ... I only saw a mentioning of 00Index in the description about the data subdirectory in Writing R Extensions/Package Subdirectories. Could someone point me to the right place or tell me what a 'datalist' file is supposed to be? Thanks. JZ __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Regexpr with .
Try regexpr(\\., Female.Alabama) and gsub(\\., ,, Female.Alabama) X-Sybari-Trust: 9293cd92 d90ef28b 235e1558 093d From: Thompson, Trevor [EMAIL PROTECTED] To: [EMAIL PROTECTED] Date: Wed, 13 Aug 2003 10:46:45 -0400 MIME-Version: 1.0 X-Virus-Scanned: by amavisd-milter (http://amavis.org/) X-Virus-Scanned: by amavisd-milter (http://amavis.org/) X-Spam-Status: No, hits=0.6 required=5.0 tests=HTML_30_40 version=2.54 X-Spam-Level: X-Spam-Checker-Version: SpamAssassin 2.54 (1.174.2.17-2003-05-11-exp) Content-Disposition: inline Content-Transfer-Encoding: 7bit Subject: [R] Regexpr with . X-BeenThere: [EMAIL PROTECTED] X-Mailman-Version: 2.1.2 List-Id: Main R Mailing List: Primary help r-help.stat.math.ethz.ch List-Help: mailto:[EMAIL PROTECTED] List-Post: mailto:[EMAIL PROTECTED] List-Subscribe: https://www.stat.math.ethz.ch/mailman/listinfo/r-help, mailto:[EMAIL PROTECTED] List-Archive: https://www.stat.math.ethz.ch/pipermail/r-help List-Unsubscribe: https://www.stat.math.ethz.ch/mailman/listinfo/r-help, mailto:[EMAIL PROTECTED] I'm trying to use the regexpr function to locate the decimal in a character string. Regardless of the position of the decimal, the function returns 1. For example, regexpr(., Female.Alabama) [1] 1 attr(,match.length) [1] 1 In trying to figure out what was going on here, I tried the below command: gsub(., ,, Female.Alabama) [1] ,, It looks like R is treating every character in the string as if it were decimal. I didn't see anything in the help file about . being some kind of special character. Any idea why R is treating a decimal this way in these functions? Any suggestions how to get around this? Thanks for any suggestions. -Trevor [[alternative HTML version deleted]] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help Jianhua Zhang Department of Biostatistics Dana-Farber Cancer Institute 44 Binney Street Boston, MA 02115-6084 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] rbind question
How about foo - c(1,2,3) bar - matrix(rep(foo, 5), ncol = length(foo), byrow = TRUE) Date: 8 Jul 2003 15:58:25 +0200 From: David Andel [EMAIL PROTECTED] To: [EMAIL PROTECTED] MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Virus-Scanned: by amavisd-milter (http://amavis.org/) X-Virus-Scanned: by amavisd-milter (http://amavis.org/) X-Spam-Status: No, hits=-5.3 required=5.0 tests=BAYES_01, HAS_ORGANIZATION version=2.54 X-Spam-Level: X-Spam-Checker-Version: SpamAssassin 2.54 (1.174.2.17-2003-05-11-exp) Subject: [R] rbind question X-BeenThere: [EMAIL PROTECTED] X-Mailman-Version: 2.1.2 List-Id: Main R Mailing List: Primary help r-help.stat.math.ethz.ch List-Help: mailto:[EMAIL PROTECTED] List-Post: mailto:[EMAIL PROTECTED] List-Subscribe: https://www.stat.math.ethz.ch/mailman/listinfo/r-help, mailto:[EMAIL PROTECTED] List-Archive: https://www.stat.math.ethz.ch/pipermail/r-help List-Unsubscribe: https://www.stat.math.ethz.ch/mailman/listinfo/r-help, mailto:[EMAIL PROTECTED] Hi I am trying to replicate a vector in n rows for comparison purposes with another matrix. foo - c(1,2,3) bar - rbind(foo,foo) # does the trick for 2 rows bar - rbind(rep(foo,2)) # does something else How do I generate a matrix with all rows=foo without writing 'foo' n times as arg? Thanks, David __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help Jianhua Zhang Department of Biostatistics Dana-Farber Cancer Institute 44 Binney Street Boston, MA 02115-6084 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] tkexit
Would tkdestroy() work for you? Date: Thu, 6 Mar 2003 11:33:05 -0300 (ART) From: [EMAIL PROTECTED] To: [EMAIL PROTECTED] MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Virus-Scanned: by amavisd-milter (http://amavis.org/) X-Virus-Scanned: by amavisd-milter (http://amavis.org/) X-Virus-Scanned: by amavisd-milter (http://amavis.org/) X-Spam-Status: No, hits=2.1 required=5.0 tests=NO_REAL_NAME,SPAM_PHRASE_00_01 version=2.43 X-Spam-Level: ** Subject: [R] tkexit X-BeenThere: [EMAIL PROTECTED] X-Mailman-Version: 2.1.1 List-Id: Main R Mailing List: Primary help r-help.stat.math.ethz.ch List-Help: mailto:[EMAIL PROTECTED] List-Post: mailto:[EMAIL PROTECTED] List-Subscribe: https://www.stat.math.ethz.ch/mailman/listinfo/r-help, mailto:[EMAIL PROTECTED] List-Archive: https://www.stat.math.ethz.ch/pipermail/r-help List-Unsubscribe: https://www.stat.math.ethz.ch/mailman/listinfo/r-help, mailto:[EMAIL PROTECTED] Sorry, my question is if exists a command tkexit in R, i need a command how exit of tcl for close an aplication. How to use him. Thank __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help Jianhua Zhang Department of Biostatistics Dana-Farber Cancer Institute 44 Binney Street Boston, MA 02115-6084 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
[R] Re: A tcltk question
Hi, I am trying to create a light-weight window with no border and title bar. The following code does not work for me. base - tktoplevel() tkwm.overrideredirect(base, TRUE) (or FALSE) Could someone help me out? Thanks. Jianhua Zhang Department of Biostatistics Dana-Farber Cancer Institute 44 Binney Street Boston, MA 02115-6084 __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] Tcl/Tk support is not available on this system.
You probably do not have the tcl/tk libraries on which R tcltk package relies. tcl/tk can be downloaded from the web. From: Forbeck, Doug (NIH/NCI) [EMAIL PROTECTED] To: '[EMAIL PROTECTED]' [EMAIL PROTECTED] MIME-Version: 1.0 X-Virus-Scanned: by amavisd-milter (http://amavis.org/) X-Virus-Scanned: by amavisd-milter (http://amavis.org/) X-Spam-Status: No, hits=0.7 required=5.0 tests=EXCHANGE_SERVER,SPAM_PHRASE_00_01 version=2.43 X-Spam-Level: Subject: [R] Tcl/Tk support is not available on this system. X-BeenThere: [EMAIL PROTECTED] X-Mailman-Version: 2.0.13 List-Help: mailto:[EMAIL PROTECTED]?subject=help List-Post: mailto:[EMAIL PROTECTED] List-Subscribe: http://www.stat.math.ethz.ch/mailman/listinfo/r-help, mailto:[EMAIL PROTECTED]?subject=subscribe List-Id: Main R Mailing List: Primary help r-help.stat.math.ethz.ch List-Unsubscribe: http://www.stat.math.ethz.ch/mailman/listinfo/r-help, mailto:[EMAIL PROTECTED]?subject=unsubscribe List-Archive: http://www.stat.math.ethz.ch/pipermail/r-help/ X-Original-Date: Tue, 11 Feb 2003 09:39:30 -0500 Date: Tue, 11 Feb 2003 09:39:30 -0500 I am trying to get R to run on a Red Hat 8 system, I am running R version 1.6.2 with Tcl/Tk version 8.3.5 installed. When I try to test R from the data_sets directory I get the error message; Error in firstlib(which.lib.loc, package) : Tcl/Tk support is not available on this system Error in fileBrowser(textToShow = Choose one CDF file , nSelect = 1, : tcl/tk library not available Execution halted. Any help would be appreciated. Doug Forbeck __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help Jianhua Zhang Department of Biostatistics Dana-Farber Cancer Institute 44 Binney Street Boston, MA 02115-6084 __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] Built-in R GUI type features
Tow packages (widgetTools and tkWidgets) in www.bioconductor.org web site may be of interest to you. widgetTools allows users to build widgets using R (without having to know any tcl/tk or R tcltk command). tkWidgets contains widgets for data import, file/object selection All: The select.list() command brings up a modal dialog box with a (scrollable) list of items ... etc. -- i.e., a GUI control. I also know about winDialog, file.choose and the winMenu commands. What other such GUIisms are built into ** base ** R (I know about the tcltk package)? Or, better yet, how can I search on or list them? Many thanks. Bert Gunter Biometrics Research RY 84-16 Merck Company P.O. Box 2000 Rahway, NJ 07065-0900 Phone: (732) 594-7765 mailto: [EMAIL PROTECTED] The business of the statistician is to catalyze the scientific learning process. -- George E.P. Box -- __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] installing the XML package
You need to install libxml. Read the doc for XML package for more information. From: Susan J. Miller [EMAIL PROTECTED] X-Accept-Language: en MIME-Version: 1.0 To: [EMAIL PROTECTED] Content-Transfer-Encoding: 7bit X-Virus-Scanned: by amavisd-milter (http://amavis.org/) X-Virus-Scanned: by amavisd-milter (http://amavis.org/) X-Spam-Status: No, hits=0.0 required=5.0 tests=NOSPAM_INC,SIGNATURE_LONG_SPARSE,SPAM_PHRASE_00_01, USER_AGENT_MOZILLA_XM,X_ACCEPT_LANG version=2.43 X-Spam-Level: Subject: [R] installing the XML package X-BeenThere: [EMAIL PROTECTED] X-Mailman-Version: 2.0.13 List-Help: mailto:[EMAIL PROTECTED]?subject=help List-Post: mailto:[EMAIL PROTECTED] List-Subscribe: http://www.stat.math.ethz.ch/mailman/listinfo/r-help, mailto:[EMAIL PROTECTED]?subject=subscribe List-Id: Main R Mailing List: Primary help r-help.stat.math.ethz.ch List-Unsubscribe: http://www.stat.math.ethz.ch/mailman/listinfo/r-help, mailto:[EMAIL PROTECTED]?subject=unsubscribe List-Archive: http://www.stat.math.ethz.ch/pipermail/r-help/ X-Original-Date: Thu, 16 Jan 2003 14:03:16 -0700 Date: Thu, 16 Jan 2003 14:03:16 -0700 I'm trying to install the XML package in R 1.6.1 (install.packages(XML)). The download is OK, but during configuration the file parser.h cannot be found (it looks in libxml/ and gnome-xml/ then gives up). What is missing from my system? -- Thanks, -susan Susan J. Miller Biotechnology Computing Facility Arizona Research Laboratories Bio West 228 University of Arizona Tucson, AZ 85721 (520) 626-2597 __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help
[R] Re: Embedding windows in a text widget
Could someone tell me how to embed windows in a text box using tkcreate command of R tcltk package? I tried the following and was not successful; base - tktoplevel() text - tktext(base, width = 30, height = 10) tkpack(text) button - tkbutton(text, text = try) tkcreate(text, window, end, window = button) Thanks. JZ __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help
