[R] problem formatting and positioning title in heatmap
I am using heatmap with the arguments below. The title size stays the same no matter what I set cex.main to. Is this expected? Can I adjust the title size in heatmap? Also, the position of the main title is at the very upper edge of the output and if I use a \n to stack the title the upper line is out of bounds and doesn't show up. I am outputting to pdf. Any help? Thanks, Mark heatmap(x = dataM, RowSideColors = RowSideColors, ColSideColors=ColSideColors, main = title, margins = c(50,50), scale= do.scale ,labRow=geneNames, labCol=colLabels, col = hmcol, cex.main = 1, cexRow = row.lab.mag, cexCol = col.lab.mag) sessionInfo() R version 2.6.0 Under development (unstable) (2007-08-29 r42686) i686-pc-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C attached base packages: [1] splines tools stats graphics grDevices utils datasets [8] methods base other attached packages: [1] RColorBrewer_1.0-1 MergeMaid_2.9.0MASS_7.2-36 [4] rat2302_1.17.0 rat2302cdf_1.17.0 affycoretools_1.9.4 [7] annaffy_1.9.1 KEGG_1.17.1GO_1.99.1 [10] xtable_1.5-1 gcrma_2.9.1matchprobes_1.9.10 [13] biomaRt_1.11.4 RCurl_0.8-3XML_1.92-1 [16] GOstats_2.3.16 Category_2.3.30genefilter_1.15.11 [19] survival_2.32 RBGL_1.13.6annotate_1.15.6 [22] GO.db_1.99.1 AnnotationDbi_0.1.12 RSQLite_0.6-0 [25] DBI_0.2-3 limma_2.11.11 affy_1.15.7 [28] preprocessCore_0.99.12 affyio_1.5.8 Biobase_1.15.30 [31] graph_1.15.14 loaded via a namespace (and not attached): [1] cluster_1.11.7 -- --- Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work, Mobile VoiceMail (317) 663-0513 Home (no voice mail please) __ 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.
[R] problem with recursive unlink on Linux Fedora 7
I am trying to delete a directory and its contents using unlink. The help page says this is not supported on some platforms but that if ignored a warning will be given. On Fedora 7 it is seemingly ignored but no warning is given. My command and sessionInfo() are below. Is this expected behavior? If it will not work on my platform, is there an alternative set of commands that will accomplish the same thing? Thanks, Mark unlink(x = tmp.dir, recursive = TRUE) sessionInfo() R version 2.6.0 Under development (unstable) (2007-08-29 r42686) i686-pc-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C attached base packages: [1] tools stats graphics grDevices utils datasets methods [8] base other attached packages: [1] affy_1.15.7preprocessCore_0.99.12 affyio_1.5.8 [4] Biobase_1.15.29graph_1.15.14 loaded via a namespace (and not attached): [1] cluster_1.11.7 -- --- Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work, Mobile VoiceMail (317) 663-0513 Home (no voice mail please) __ 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.
[R] trouble extracting R code from vignette using example from www.bioconductor.org
Not sure if this is an R or BioC question so will cross-post. I cannot extract R code from vignettes because system.file(doc, my.bioc.package) returns . I got this code directly off of http://www.bioconductor.org/docs/vignettes.html. A specific example using siggenes follows but I have tested this using multiple packages, including those for which I can clearly see the vignette *.Rnw in the doc directory. One thing in my setup that I have customized, and which I wonder if is causing this problem, is that I am using a site-library as directed in the R install manual. I have this in my .Rprofile .libPaths(new= ~/R_HOME/site-library) #tell R where site-library is In all other respects, however, my packages are working correctly. Example and sessionInfo() follows. thanks, Mark require(siggenes) Loading required package: siggenes Loading required package: multtest Latest major changes in siggenes: Version 1.9.27: EBAM update completed. Added new vignette. Version 1.11.7: Improved version of EBAM for categorical data. Version 1.11.9: Added findDelta for determining the number of genes called differentially expressed for a given FDR, and vice versa. Attaching package: 'siggenes' The following object(s) are masked _by_ .GlobalEnv : list.siggenes system.file(doc, siggenes) [1] sessionInfo() R version 2.6.0 Under development (unstable) (2007-08-08 r42441) i686-pc-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C attached base packages: [1] splines tools stats graphics grDevices utils datasets [8] methods base other attached packages: [1] siggenes_1.11.13 multtest_1.16.1affycoretools_1.9.4 [4] annaffy_1.9.1 KEGG_1.17.0xtable_1.5-1 [7] gcrma_2.9.1matchprobes_1.9.10 biomaRt_1.11.4 [10] RCurl_0.8-3XML_1.9-0 GOstats_2.3.9 [13] RBGL_1.13.4GO_1.17.0 limma_2.11.10 [16] affy_1.15.7preprocessCore_0.99.12 affyio_1.5.8 [19] Category_2.3.26genefilter_1.15.10 survival_2.32 [22] annotate_1.15.6AnnotationDbi_0.0.90 RSQLite_0.6-0 [25] DBI_0.2-3 Biobase_1.15.26graph_1.15.10 loaded via a namespace (and not attached): [1] cluster_1.11.7 -- --- Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work, Mobile VoiceMail (317) 663-0513 Home (no voice mail please) __ 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 error on Linux
Seth and Brian, Today and downloaded and installed the latest R-devel and tcltk now works. My suspicion is that Tcl was not on my path when R-devel was installed previously. BTW, I had though that is was a courtesy to cc: the maintainers of a package when writing either R-devel or R-help about a specific package. For tcltk, I see: Maintainer:R Core Team [EMAIL PROTECTED] If it is not appropriate to write R-core regarding packages they maintain, would it perhaps not be better to remove them as maintainers or, not suggest that people cc: maintainers of packages? Just an idea. As for the suggestion that I not use R-devel, I do that because I sometimes use BioC packages that have just been published and are only available in the devel versions of BioC. Are you suggesting that only people who can debug things themselves, and thus who do not need to write to R-devel, use R-devel? As an open-source user, I thought the philosophy was that it was useful to have users willing to test beta versions of software and have those users report problems to developers. If that is not the case, please put a stronger warning on R-devel and warn users not to use it unless they are willing to debug and take care of all problems themselves. Thanks, Mark --- Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work, Mobile VoiceMail (317) 663-0513 Home (no voice mail please) ** Seth Falcon wrote: Hi Mark, Prof Brian Ripley [EMAIL PROTECTED] writes: On Thu, 9 Aug 2007, Mark W Kimpel wrote: I am having trouble getting tcltk package to load on openSuse 10.2 running R-devel. I have specifically put my /usr/share/tcl directory in my PATH, but R doesn't seem to see it. I also have installed tk on my system. Any ideas on what the problem is? Any chance you are running R on a remote server using an ssh session? If that is the case, you may have an ssh/X11 config issue that prevents using tcl/tk from such a session. Rerun the configure script for R and verify that tcl/tk support is listed in the summary. Also, note that I have some warning messages on starting up R, not sure what they mean or if they are pertinent. Those are coming from a Bioconductor package: again you must be using development versions with R-devel and those are not stable (last time I looked even Biobase would not install, and the packages change daily). BioC devel tracks R-devel, but not on a daily basis -- because R changes daily. The recent issues with Biobase are a result of changes to R and have already been fixed. If you have all those packages in your startup, please don't -- there will be a considerable performance hit so only load them when you need them. Presumably, that's why they are there in the first place. The warning messages are a problem and suggest some needed improvements to the methods packages. These are being worked on. + seth __ 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.
[R] tcltk error on Linux
I am having trouble getting tcltk package to load on openSuse 10.2 running R-devel. I have specifically put my /usr/share/tcl directory in my PATH, but R doesn't seem to see it. I also have installed tk on my system. Any ideas on what the problem is? Also, note that I have some warning messages on starting up R, not sure what they mean or if they are pertinent. Thanks, Mark Warning messages: 1: In .updateMethodsInTable(fdef, where, attach) : Couldn't find methods table for conditional, package Category may be out of date 2: In .updateMethodsInTable(fdef, where, attach) : Methods list for generic conditional not found require(tcltk) Loading required package: tcltk Error in firstlib(which.lib.loc, package) : Tcl/Tk support is not available on this system sessionInfo() R version 2.6.0 Under development (unstable) (2007-08-01 r42387) i686-pc-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C attached base packages: [1] splines tools stats graphics grDevices utils datasets [8] methods base other attached packages: [1] affycoretools_1.9.3annaffy_1.9.1 xtable_1.5-0 [4] gcrma_2.9.1matchprobes_1.9.10 biomaRt_1.11.4 [7] RCurl_0.8-1XML_1.9-0 GOstats_2.3.8 [10] Category_2.3.19genefilter_1.15.9 survival_2.32 [13] KEGG_1.17.0RBGL_1.13.3annotate_1.15.3 [16] AnnotationDbi_0.0.88 RSQLite_0.6-0 DBI_0.2-3 [19] GO_1.17.0 limma_2.11.9 affy_1.15.7 [22] preprocessCore_0.99.12 affyio_1.5.6 Biobase_1.15.23 [25] graph_1.15.10 loaded via a namespace (and not attached): [1] cluster_1.11.7 rcompgen_0.1-15 -- --- Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work, Mobile VoiceMail (317) 663-0513 Home (no voice mail please) __ 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] Reading time/date string
Look at some of these functions... DateTimeClasses(base) Date-Time Classes as.POSIXct(base)Date-time Conversion Functions cut.POSIXt(base)Convert a Date or Date-Time Object to a Factor format.Date(base) Date Conversion Functions to and from Character Mark --- Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work, Mobile VoiceMail (317) 663-0513 Home (no voice mail please) ** Matthew Walker wrote: Hello everyone, Can anyone tell me what function I should use to read time/date strings and turn them into a form such that I can easily calculate the difference of two? The strings I've got look like 10:17:07 02 Aug 2007. If I could calculate the number of seconds between them I'd be very happy! Cheers, Matthew __ 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. __ 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] RSPython won't load in R 2.6.0 under Linux
Duncan, Thanks for the update on the update. I downloaded and installed it and receive the following messages on installation and require(RSPython). Also, checked to make sure python was on my path and working and it is (also below). I am running openSuse 10.2. sessionInfo() follows as well. Mark * DONE (RSPython) The downloaded packages are in /tmp/Rtmp4QozuD/downloaded_packages Warning message: In install.packages(pkgs = RSPython, repos = http://www.omegahat.org/R;) : dependency ‘Python’ is not available require(RSPython) Loading required package: RSPython Attaching package: 'RSPython' The following object(s) are masked from package:base : .Call Warning message: In .Call(InitPython) : the Python callback manager has been registered implicitly using the defaults (referenceManager())! Python is installed on my system and can be invoked from the command line: [EMAIL PROTECTED]:~ python Python 2.5 (r25:51908, May 25 2007, 16:14:04) [GCC 4.1.2 20061115 (prerelease) (SUSE Linux)] on linux2 Type help, copyright, credits or license for more information. quit() [EMAIL PROTECTED]:~ whereis python python: /usr/bin/python2.5 /usr/bin/python2.5-config /usr/bin/python /usr/lib/python2.5 /usr/lib/python /usr/bin/X11/python2.5 /usr/bin/X11/python2.5-config /usr/bin/X11/python /usr/include/python2.5 /usr/include/python /usr/share/man/man1/python.1.gz [EMAIL PROTECTED]:~ sessionInfo() R version 2.6.0 Under development (unstable) (2007-08-01 r42387) i686-pc-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C attached base packages: [1] splines tools stats graphics grDevices utils datasets [8] methods base other attached packages: [1] RSPython_0.8-0 affycoretools_1.9.3annaffy_1.9.1 [4] xtable_1.5-0 gcrma_2.9.1matchprobes_1.9.10 [7] biomaRt_1.11.4 RCurl_0.8-1XML_1.9-0 [10] GOstats_2.3.8 Category_2.3.18genefilter_1.15.9 [13] survival_2.32 KEGG_1.17.0RBGL_1.13.3 [16] annotate_1.15.3AnnotationDbi_0.0.88 RSQLite_0.6-0 [19] DBI_0.2-3 GO_1.17.0 limma_2.11.9 [22] affy_1.15.7preprocessCore_0.99.12 affyio_1.5.6 [25] Biobase_1.15.23graph_1.15.10 loaded via a namespace (and not attached): [1] cluster_1.11.7 Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work, Mobile VoiceMail (317) 663-0513 Home (no voice mail please) ** Duncan Temple Lang wrote: Mark, Just thought I'd let you know that I did get a chance to make the changes and some others besides and there is a new RSPython release on the Omegahat web site. Thanks, D. Mark W Kimpel wrote: I can compile RSPython without difficulty, been when I try to load it, I get the error messages below. Also below are some cryptic warnings I get on R boot (in case these are pertinent) and my sessionInfo(). Any help is appreciated. Thanks, Mark Warning messages: 1: In .updateMethodsInTable(fdef, where, attach) : Couldn't find methods table for conditional, package Category may be out of date 2: In .updateMethodsInTable(fdef, where, attach) : Methods list for generic conditional not found require(RSPython) Loading required package: RSPython Error in dyn.load(file, ...) : unable to load shared library '/home/mkimpel/R_HOME/site-library/RSPython/libs/RSPython.so': /home/mkimpel/R_HOME/site-library/RSPython/libs/RSPython.so: undefined symbol: Rf_initEmbeddedR sessionInfo() R version 2.6.0 Under development (unstable) (2007-08-01 r42387) i686-pc-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C attached base packages: [1] splines tools stats graphics grDevices utils datasets [8] methods base other attached packages: [1] affycoretools_1.9.3annaffy_1.9.1 xtable_1.5-0 [4] gcrma_2.9.1matchprobes_1.9.10 biomaRt_1.11.4 [7] RCurl_0.8-1XML_1.9-0 GOstats_2.3.8 [10] Category_2.3.18genefilter_1.15.9 survival_2.32 [13] KEGG_1.17.0RBGL_1.13.3annotate_1.15.3 [16] AnnotationDbi_0.0.88 RSQLite_0.6-0 DBI_0.2-3 [19] GO_1.17.0 limma_2.11.9 affy_1.15.7 [22] preprocessCore_0.99.12 affyio_1.5.6 Biobase_1.15.23 [25] graph_1.15.10 loaded via a namespace (and not attached): [1] cluster_1.11.7 rcompgen_0.1
[R] RSPython won't load in R 2.6.0 under Linux
I can compile RSPython without difficulty, been when I try to load it, I get the error messages below. Also below are some cryptic warnings I get on R boot (in case these are pertinent) and my sessionInfo(). Any help is appreciated. Thanks, Mark Warning messages: 1: In .updateMethodsInTable(fdef, where, attach) : Couldn't find methods table for conditional, package Category may be out of date 2: In .updateMethodsInTable(fdef, where, attach) : Methods list for generic conditional not found require(RSPython) Loading required package: RSPython Error in dyn.load(file, ...) : unable to load shared library '/home/mkimpel/R_HOME/site-library/RSPython/libs/RSPython.so': /home/mkimpel/R_HOME/site-library/RSPython/libs/RSPython.so: undefined symbol: Rf_initEmbeddedR sessionInfo() R version 2.6.0 Under development (unstable) (2007-08-01 r42387) i686-pc-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C attached base packages: [1] splines tools stats graphics grDevices utils datasets [8] methods base other attached packages: [1] affycoretools_1.9.3annaffy_1.9.1 xtable_1.5-0 [4] gcrma_2.9.1matchprobes_1.9.10 biomaRt_1.11.4 [7] RCurl_0.8-1XML_1.9-0 GOstats_2.3.8 [10] Category_2.3.18genefilter_1.15.9 survival_2.32 [13] KEGG_1.17.0RBGL_1.13.3annotate_1.15.3 [16] AnnotationDbi_0.0.88 RSQLite_0.6-0 DBI_0.2-3 [19] GO_1.17.0 limma_2.11.9 affy_1.15.7 [22] preprocessCore_0.99.12 affyio_1.5.6 Biobase_1.15.23 [25] graph_1.15.10 loaded via a namespace (and not attached): [1] cluster_1.11.7 rcompgen_0.1-15 --- Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work, Mobile VoiceMail (317) 663-0513 Home (no voice mail please) __ 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.
[R] X11 font issue on Linux when creating a jpeg or png from a graphNEL object
I am trying to write a png or jpeg file from a plot (graphNEL.object) on a cluster running Suse Linux and get the following error using either device: jpeg(filename = fileName, width = width, height = height, pointsize = 12, bg = white) plot(result.gN, layout.param, nodeAttrs = nAttrs, edgeAttrs = eAttrs, main=Title) dev.off() Error during wrapup: could not find any X11 fonts Check that the Font Path is correct. When I do xset -q I get: Keyboard Control: auto repeat: onkey click percent: 0LED mask: auto repeat delay: 500repeat rate: 30 auto repeating keys: 00ffdbbf fadfffdfffdfe5ef bell percent: 50bell pitch: 400bell duration: 100 Pointer Control: acceleration: 2/1threshold: 4 Screen Saver: prefer blanking: yesallow exposures: yes timeout: 0cycle: 0 Colors: default colormap: 0x20BlackPixel: 0WhitePixel: 16777215 Font Path: /usr/share/fonts/misc,/usr/share/fonts/truetype,/usr/share/fonts/Type1,/usr/share/fonts/100dpi,/usr/share/fonts/75dpi Bug Mode: compatibility mode is disabled DPMS (Energy Star): Standby: 0Suspend: 0Off: 0 DPMS is Enabled Monitor is On Font cache: Server does not have the FontCache Extension It looks to me like the fonts I need are on the font path per http://cran.r-project.org/doc/manuals/R-admin.html, but I am not sure what the message about Font cache means. Here is my sessionInfo(): R version 2.6.0 Under development (unstable) (2007-05-19 r41638) powerpc64-unknown-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C attached base packages: [1] tools stats graphics grDevices utils datasets [7] methods base other attached packages: Rgraphviz geneplotter latticeannotate Biobase graph 1.14.01.14.00.15-51.14.11.14.01.14.1 Advice? Thanks, Mark -- --- Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work, Mobile VoiceMail (317) 663-0513 Home (no voice mail please) __ 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.
[R] help with executing instruction every i-th run of loop
I am running a very long loop and would like to save intermediate
results in case of a system or program crash. Here is the skeleton of
what my code would be:
for (i in 1:zillion)
{
results[[i]]-do.something.function()
if (logical.test(i)) {save(results, results.tmp)}
}
logical.test would test to see if i/1000 has no remainder. What R
function would test that?
Is there an even better way to address my need?
Thanks,
Mark
--
---
Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry
Indiana University School of Medicine
15032 Hunter Court, Westfield, IN 46074
(317) 490-5129 Work, Mobile VoiceMail
(317) 663-0513 Home (no voice mail please)
__
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] can't load just saved R object ReadItem: unknown type 65
Luke, I'll be gone for about 2 weeks but will work on getting you a reproducible example when I get back. If this topic comes up with anyone else, please copy me on your responses as I may miss it in the 600 emails I'll have to delete on my return :) Mark Luke Tierney wrote: According to the logs nothing at all has changed in the serialization code in a month and nothing of consequence for much longer than that. To track this down we will need a complete, reproducible, and preferably minimal example. Best, luke On Thu, 22 Mar 2007, Mark W Kimpel wrote: I have run into a problem loading a just saved R object using R-devel. I have been saving and loading this particular type of R object for a long while and never ran into this problem. I save, then immediately reload (to test save) and get ReadItem: unnknown type 65. This error is reproducible after logout from server and restart of emacs and R. Below is my output and sessionInfo(). Thanks, Mark setwd(~/Genomics/Experiments.Genomic/BB01/acb.shell) local(save(affy.object.preprocessed, file =affy.object.preprocessed.R )) load(affy.object.preprocessed.R) Error in load(affy.object.preprocessed.R) : ReadItem: unknown type 65, perhaps written by later version of R sessionInfo() R version 2.5.0 Under development (unstable) (2007-03-11 r40824) powerpc64-unknown-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C attached base packages: [1] splines stats graphics grDevices datasets utils [7] tools methods base other attached packages: multtestrat2302cdf affycoretools annaffyxtable 1.13.1 1.15.0 1.7.8 1.7.3 1.4-3 gcrma matchprobes biomaRt RCurl XML 2.7.3 1.7.4 1.9.21 0.8-0 1.6-0 GOstats CategoryMatrix latticegenefilter 2.1.13 2.1.20 0.9975-11 0.14-16 1.13.8 survival KEGG RBGL annotateGO 2.31 1.15.12 1.11.4 1.13.6 1.15.12 graph limma affyaffyio Biobase 1.13.6 2.9.13 1.13.14 1.3.3 1.13.39 -- Mark W. Kimpel MD Neuroinformatics Department of Psychiatry Indiana University School of Medicine __ 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.
[R] can't load just saved R object ReadItem: unknown type 65
I have run into a problem loading a just saved R object using R-devel. I have been saving and loading this particular type of R object for a long while and never ran into this problem. I save, then immediately reload (to test save) and get ReadItem: unnknown type 65. This error is reproducible after logout from server and restart of emacs and R. Below is my output and sessionInfo(). Thanks, Mark setwd(~/Genomics/Experiments.Genomic/BB01/acb.shell) local(save(affy.object.preprocessed, file =affy.object.preprocessed.R )) load(affy.object.preprocessed.R) Error in load(affy.object.preprocessed.R) : ReadItem: unknown type 65, perhaps written by later version of R sessionInfo() R version 2.5.0 Under development (unstable) (2007-03-11 r40824) powerpc64-unknown-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C attached base packages: [1] splines stats graphics grDevices datasets utils [7] tools methods base other attached packages: multtestrat2302cdf affycoretools annaffyxtable 1.13.1 1.15.0 1.7.8 1.7.3 1.4-3 gcrma matchprobes biomaRt RCurl XML 2.7.3 1.7.4 1.9.21 0.8-0 1.6-0 GOstats CategoryMatrix latticegenefilter 2.1.13 2.1.20 0.9975-11 0.14-16 1.13.8 survival KEGG RBGL annotateGO 2.31 1.15.12 1.11.4 1.13.6 1.15.12 graph limma affyaffyio Biobase 1.13.6 2.9.13 1.13.14 1.3.3 1.13.39 -- Mark W. Kimpel MD Neuroinformatics Department of Psychiatry Indiana University School of Medicine __ 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.
[R] can't load just saved R object using R-devel ReadItem: unknown type 65
I am unable to load a just saved R object. Get message ReadItem: unknown type 65 I am using R-devel and the problem is reproducible after logout and restarting R. Output and sessionInfo() below. Mark setwd(~/Genomics/Experiments.Genomic/BB01/acb.shell) local(save(affy.object.preprocessed, file =affy.object.preprocessed.R )) load(affy.object.preprocessed.R) Error in load(affy.object.preprocessed.R) : ReadItem: unknown type 65, perhaps written by later version of R sessionInfo() R version 2.5.0 Under development (unstable) (2007-03-11 r40824) powerpc64-unknown-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C attached base packages: [1] splines stats graphics grDevices datasets utils [7] tools methods base other attached packages: multtestrat2302cdf affycoretools annaffyxtable 1.13.1 1.15.0 1.7.8 1.7.3 1.4-3 gcrma matchprobes biomaRt RCurl XML 2.7.3 1.7.4 1.9.21 0.8-0 1.6-0 GOstats CategoryMatrix latticegenefilter 2.1.13 2.1.20 0.9975-11 0.14-16 1.13.8 survival KEGG RBGL annotateGO 2.31 1.15.12 1.11.4 1.13.6 1.15.12 graph limma affyaffyio Biobase 1.13.6 2.9.13 1.13.14 1.3.3 1.13.39 -- Mark W. Kimpel MD Neuroinformatics Department of Psychiatry Indiana University School of Medicine __ 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.
[R] problem with RCurl install on Unix
I am having trouble getting an install of RCurl to work properly on a Unix server. The steps I have taken are: 1. installed cUrl from source without difficulty 2. installed RCurl from source using the command ~/R_HOME/R-devel/bin/R CMD INSTALL -l ~/R_HOME/R-devel/library ~/RCurl_0.8-0.tar.gz I received no errors during this install 3. when I go back to R and require(RCurl), I get require(RCurl) Loading required package: RCurl Error in dyn.load(x, as.logical(local), as.logical(now)) : unable to load shared library '/N/u/mkimpel/BigRed/R_HOME/R-devel/library/RCurl/libs/RCurl.so': libcurl.so.4: cannot open shared object file: No such file or directory °1§ FALSE Outside of R I get mkimpelàBigRed:¨/R_HOME/R-devel/library/RCurl/libs ls RCurl.so I can cat into RCurl and I have even done chmod a+x RCurl.so in case there was a problem with permission for R to open the file. Below is my sessionInfo. Thanks, Mark sessionInfo() R version 2.5.0 Under development (unstable) (2007-03-11 r40824) powerpc64-unknown-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C attached base packages: °1§ stats graphics grDevices datasets utils tools °7§ methods base other attached packages: limma affyaffyio Biobase 2.9.13 1.13.14 1.3.3 1.13.39 -- Mark W. Kimpel MD Neuroinformatics Department of Psychiatry Indiana University School of Medicine __ 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.
[R] getting ess/emacs to link with a remote instance of R
I am running ess/emacs on Linux and have an R instance running on a remote Unix server. I would like to be able to direct input from my ess buffer to R (hope I am using the right lingo, I am new to emacs). The ess manual contains a section describing how to do just that, but a prerequisite is to install a lisp file ssh.el , which can be found at ftp://ftp.splode.com/pub/users/friedman/emacs-lisp/ssh . I have downloaded the file but can nowhere find exactly what directory I should put the file into and, what, if any, entry I might need to make in my .emacs file. One reference says to put the file in the lisp emacs directory, but there are actually several directories that have names similar to this. I tried them all without success. Whenever I try M-x ssh, I get [no match]. Can an experienced ess/emacs Unix user give me a hand? As a client, I am running openSuse 10.2 Linux and the latest versions of both ess and emacs, which both installed without problems. Thanks, Mark -- Mark W. Kimpel MD Neuroinformatics Official Business Address: Department of Psychiatry Indiana University School of Medicine PR M116 Institute of Psychiatric Research 791 Union Drive Indianapolis, IN 46202 Preferred Mailing Address: 15032 Hunter Court Westfield, IN 46074 (317) 490-5129 Work, Mobile VoiceMail (317) 663-0513 Home (no voice mail please) 1-(317)-536-2730 FAX __ 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] getting ess/emacs to link with a remote instance of R
Seth, Thank you for your response, every worked exactly as you described it, even the fact that ?help does not work very well with a remote session. I will probably open up a separate emacs window with a local R process to access help functions. I didn't know about the ess-help, I had checked out emacs-help but, looking at an archive, it looked like it had very little activity over the past two years. Maybe I was mistaken? Thanks, Mark Mark W. Kimpel MD Neuroinformatics Official Business Address: Department of Psychiatry Indiana University School of Medicine PR M116 Institute of Psychiatric Research 791 Union Drive Indianapolis, IN 46202 Preferred Mailing Address: 15032 Hunter Court Westfield, IN 46074 (317) 490-5129 Work, Mobile VoiceMail (317) 663-0513 Home (no voice mail please) 1-(317)-536-2730 FAX Seth Falcon wrote: Hi Mark, [I've cc'd the ess-help list and any further discussion should probably happen there with r-help removed] Mark W Kimpel [EMAIL PROTECTED] writes: I am running ess/emacs on Linux and have an R instance running on a remote Unix server. I would like to be able to direct input from my ess buffer to R (hope I am using the right lingo, I am new to emacs). The ess manual contains a section describing how to do just that, but a prerequisite is to install a lisp file ssh.el , which can be found at ftp://ftp.splode.com/pub/users/friedman/emacs-lisp/ssh . In my experience, ssh.el doesn't do anything all that great. Instead I would try: 1. Start a shell inside Emacs using 'M-x shell'. In this shell, ssh to your remote host and start R. 2. In the remote R session do: 'M-x ess-remote'. At the Emacs mini-buffer prompt type 'r'. 3. In a buffer containing R code, you should be able to send code to the remote session as usual (choose the shell buffer when prompted). Note: * C-c C-c will kill your ssh session (and R). IOW, you can't easily interrupt an R process running remotely. * I have never had success getting help to work via ESS when running R remotely. YMMV. * You may find that sending commands to the remote session without echoing is much faster. So you might try C-u C-c C-r to send a region. + seth __ 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] Off topic:Spam on R-help increase?
me too. Over 50% of messages are spam. I also noted the same thing on ESS-help. Carlos Guerra wrote: Dear Gunter, I am having the same problem at my email box. Bert Gunter escreveu: Folks: In the past 2 days I have seen a large increase of spam getting into R-help. Are others experiencing this problem? If so, has there been some change to the spam filters on the R-servers? If not, is the problem on my end? Feel free to reply privately. Thanks. Bert Gunter Genentech Nonclinical Statistics South San Francisco, CA 94404 650-467-7374 __ 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. -- Mark W. Kimpel MD Neuroinformatics Department of Psychiatry Indiana University School of Medicine __ 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] merge words=data name
Duncan, Both yours and Gabor's methods were far superior to mine. I am curious why you like Gabor's better than yours. From the perspective of someone who uses R regularly but has only read about C, yours seems more R-like. Would Gabor's be more computationally efficient if the loop was big enough? I ask this because it made me ask myself, are the C-like functions of R 'better' (computationally) than the more R-like ones? Am I making sense? Mark Duncan Murdoch wrote: On 2/11/2007 4:17 PM, Robert McFadden wrote: -Original Message- From: Duncan Murdoch [mailto:[EMAIL PROTECTED] eval(parse(text=my.data)) I would like to thank everybody very much for help, but especially for Duncan - it works wonderful. You're welcome, but I have to say I like Gabor's solution better than mine, assuming that M3 is fixed. Duncan Murdoch __ 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. -- Mark W. Kimpel MD Neuroinformatics Department of Psychiatry Indiana University School of Medicine __ 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] This web site make writing R easier
When I visited the site it seems to be a work in the pre-alpha testing phase. Nothing is functional. Mark semgogo sem wrote: Hello, I sugguest you try a web site, www.mycodegarden.org. It offer many functionalities such as autocomplete, intellisense and syntax highlighting that will save you lots of time on writing R procedure. Open http://www.mycodegarden.org/index.php?title=PlayPageaction=edit, press intellisense button and select R language, enjoy it. best regard! _ 享用世界上最大的电子邮件系统― MSN Hotmail。 http://www.hotmail.com __ 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. -- Mark W. Kimpel MD Neuroinformatics Department of Psychiatry Indiana University School of Medicine __ 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] [BioC] Outlook does threading [Broadcast]
To close out this thread... I have solved my problem with Outlook not displaying threads by creating a Gmail account for all my R and BioC needs and am viewing that with Mozilla Thunderbird. Seems to be working nicely and I now have the benefit of viewing by threads like to many of you have been doing all along. I continue to use Outlook for my other needs. I thought I would share this in case other Outlook users search the archives and wonder how the problem was ever solved. Thanks again, Mark Kimpel IU School of Medicine Liaw, Andy wrote: This is really off-topic for both BioC and R-help, so I'll keep it short. From: Kimpel, Mark William See below for Bert Gunter's off list reply to me (which I do appreciate). I'm putting it back on the list because it seems there is still confusion regarding the difference between threading and sorting by subject. I thought the example I will give below will serve as instructional for other Outlook users who may be similarly confused as I was (am?). Per Bert's instructions, I just set up my inbox to sort by subject. I sent one email to myself with the subject test1 and then replied to it without changing the subject. The reply correctly went to test1 in the inbox sorter. I then changed the subject heading in the test1 reply to test2 and sent it to myself. This time Outlook re-categorized it and put it in a separate compartment in the view called test2. If Outlook can do threading the way the R mail server does, I don't think this is the way to do it. AFAIK there's no proper way to get the correct threading in Outlook. What I do is group by conversation topic, but that doesn't solve the problem. This is only problem on your (and all Outlook users'?) end, though. The bigger problem that affects the lists is that some versions of MS Exchange Server do not include the In-reply-to header field that many mailing lists rely on for proper threading. As a result, when I reply to other people's post, it may show up in Outlook as having been threaded properly (because the subject is fine), but it throws everything else that does proper threading off. Unless someone has an idea of how to correctly set up Outlook to do threading in the manner that the R mail server does, Maybe some VBA coding can be done to get it right, but short of that, I very much doubt it. I think the message for us Outlook users is to just create, from scratch, a new message when initiating a new subject. That message ought to be clear for everyone. You should never reply to a message when you really mean to start a new topic, regardless what you are using. Andy Thanks for all your help. Mark -Original Message- From: Bert Gunter [mailto:[EMAIL PROTECTED] Sent: Wednesday, January 31, 2007 7:03 PM To: Kimpel, Mark William Subject: Outlook does threading Mark: No need to bother the R list with this. Outlook does threading. Just sort on Subject in the viewer. Bert Gunter Genentech Nonclinical Statistics South San Francisco, CA 94404 650-467-7374 -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Kimpel, Mark William Sent: Wednesday, January 31, 2007 3:36 PM To: Peter Dalgaard Cc: r-help@stat.math.ethz.ch; [EMAIL PROTECTED] Subject: Re: [R] possible spam alert Peter, Thanks you for your explanation, I had taken Mr. Connolly's message to me to imply that I was not changing the subject line. I use MS Outlook 2007 and, unless I am just not seeing it, Outlook does not normally display the in reply to header, I was under the mistaken impression that that was what the Subject line was for. See, for example, the header to your message to me below. Outlook will, however, sort messages by Subject, and that is what I thought was meant by threading. Well, I learned something today and apologize for any inconvenience my posts may have caused. BTW, I use Outlook because it is supported by my university server and will synch my appointments and contacts with my PDA, which runs Windows CE. If anyone has a suggestion for me of a better email program that will provide proper threading AND work with a MS email server and synch with Windows CE, I'd love to hear it. Thanks again, Mark Mark W. Kimpel MD (317) 490-5129 Work, Mobile (317) 663-0513 Home (no voice mail please) 1-(317)-536-2730 FAX -Original Message- From: Peter Dalgaard [mailto:[EMAIL PROTECTED] Sent: Wednesday, January 31, 2007 6:25 PM To: Kimpel, Mark William Cc: [EMAIL PROTECTED]; r-help@stat.math.ethz.ch Subject: Re: [R] possible spam alert Kimpel, Mark William wrote: The last two times I have originated message threads on R or Bioconductor I have received the message included below from someone named Patrick Connolly. Both times I was the originator
