similar to: Incorrect permissions to edit database package

--Apple-Mail-1--963012407 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; format=flowed Hi, I get exactly the same error message as in report no 6920. Furthermore, starting "update Bioconducter" the following message appears (running Mac OS X 10.3.4 (7H63)) : > {library(reposTools);update.packages2(getAllDeps=TRUE)} Synching your local package

reposTools is part of Bioconductor not R. Please use the correct bug repository. Note that PR#6920 does not mention any `error message' whatsoever (nor does it claim to): the message quoted help.start() Making links in per-session dir ... If /usr/bin/open is already running, it is *not* restarted, and you must switch to its window. Otherwise, be patient ... is the standard

Sorry to ask a (probably) dumb question, but I am trying to install XML package on Windows XP, R 2.0.1, and I get the error: "This application has failed to start because libxml2.dll was not found. Re-installing the application may fix this problem" > library(XML) Error in dyn.load(x, as.logical(local), as.logical(now)) : unable to load shared library

Full_Name: H Deshmukh Version: 2.0 OS: 2000 Submission from: (NULL) (129.174.206.239) Can somebody tell me what is it that i am doing wrong,i was not sure whether to post BioConductor error here or not. Thanks >source("http://www.bioconductor.org/getBioC.R") > getBioC(libName = "all") Running getBioC version 1.2.65.... If you encounter problems, first make sure that

Quite a simple one really! When I run boxplot(), the labels on the X axis are horizontal, and I want them vertical. So I did: par(las=3) boxplot(...) And my labels just aren't there anymore.... Any help???

Hi Thanks once again for your help, I do appreciate it..... however.... Here is what I get with your test.... (under tcsh - i normally use bash, but I will keep everything the same) users/mwatson> env http_proxy=http://wwwcache.bbsrc.ac.uk:8080/ R >options(internet.info=0) >update.packages() trying URL `http://cran.r-project.org/src/contrib/PACKAGES' unable to connect to

Hi When I use plot(hclust(dist..)...)...) etc to create a dendrogram of a hierarchial cluster analysis, I end up with a vertical tree. What do I need to do to get a horizontal tree? Also, my users are used to seeing trees who's leaves all "end" at the same place (eg. Like in minitab). Is this possible in R? Thanks Mick Michael Watson Head of Informatics Institute for Animal

Hi I did a google search on this and came up with nothing. OK, in the latest release of R for windows, I want to change the gui to SDI mode. Edit -> GUI preferences Choose SDI Apply I get the message about properties not being able to be changed on a running console, and that I need to save. So I click Save, and am met with a "Save As" dialogue box with the default file called

Hi Forgive my ignorance. I am selecting a column of a data.frame using the column name, and I want to know what the resulting column "is". My data frame is called "submin" and the column name is held in a variable called "display.gname" Eg: > is.data.frame(submin) [1] TRUE > is.data.frame(submin[,display.gname]) [1] FALSE >

Hi When I give the command: > heatmap.2(as.matrix(d),Rowv=as.dendrogram(hc.gene),Colv=FALSE,scale="row ",trace="none",col=greenred.colors(79)) The resulting heatmap has re-ordered my columns! This is time-course data, and I don't want my columns re-ordered! Note from the help: Rowv: determines if and how the _row_ dendrogram should be reordered.

Hi Sorry to ask such a basic question. I have a list, each element of which is a vector of two values. What I actually want is a matrix with two columns, and one row per element of the list. Obviously I have tried as.matrix(), and as.vector() but I didn't expect the latter to work. I feel so lame asking this. Any suggestions? Mick

OK, I really am struggling with this one! Forgive me if I am being stupid.... I am running R 1.7.1 on Suse Linux 8.1. I connect to the internet through a proxy so I have: IAHC-LINUX03:~ # echo $http_proxy wwwcache.bbsrc.ac.uk:8080 IAHC-LINUX03:~ # echo $HTTP_PROXY wwwcache.bbsrc.ac.uk:8080 just in case ;-) SO, i go into R and I get: >

Hi I have data from 12 subjects. The measurement is log(expression) of a particular gene and can be assumed to be normally distributed. The 12 subjects are divided into the following groups: Infected, Vaccinated, Lesions - 3 measurements Infected, Vaccintaed, No Lesions - 2 measurements Infected, Not Vaccinated, Lesions - 4 measurements Uninfected, Not Vaccinated, No Lesions - 3 measurements

OK, dumb question, and it is probably in the docs somewhere, but after 12 months working with R and quite a while looking at the docs, I still don't know (or have forgotten) how to replace all NA values in a matrix at once with some other value. I can do it column by column using is.na(), but I can't figure out how to do it for the whole matrix. My apologies, I am ashamed ;-) Michael

I think that title makes sense... I hope it does... I have a data frame, one of the columns of which is a factor. I want the rows of data that correspond to the level in that factor which occurs the most times. I can get a list by doing: by(data,data$pattern,subset) And go through each element of the list counting the rows, to find the maximum.... BUT I can't help thinking there's

Hi I have seen a few posts to this list regarding problems accessing the x11() device over cgi - namely, when trying to create a graphic using the jpeg() function, everything is fine from the command line but it won't work over cgi, producing the error: "Unable to open connection to X11 display" Has anyone actually solved this particular problem satisfactorily? Please reply

Hi This is a difference between the way matrices and data frames work I guess. I want to replace the NA values in a data frame by 0, and the code works as long as the data frame in question actually includes an NA value. If it doesn't, there is an error: df <- data.frame(c1=c(1,1,1),c2=c(2,2,NA)) df[is.na(df)] <- 0 df df <- data.frame(c1=c(1,1,1),c2=c(2,2,2)) df[is.na(df)] <-

Hi I have a complicated plot which has a potentially large legend. What I want to do is actually create the legend in a new window. Has anyone done this before? I'd like to be able to create a window with just the legend in it, and have it so the window is just the right size etc. I'm sure someone must have done this already? If not, any tips would be welcome. Thanks Mick

Hi I am performing an analysis of variance with two factors, each with two levels. I have differing numbers of observations in each of the four combinations, but all four combinations *are* present (2 of the factor combinations have 3 observations, 1 has 4 and 1 has 5) I have used both anova(aov(...)) and anova(lm(...)) in R and it gave the same result - as expected. I then plugged this into

Hi I've been reading the help for by and aggregate but can't get my head round how to do this. I have a data frame - the first three columns are replicate measurements, then the next 3 are replicates etc up to 36 (so 12 variables with 3 replicate measurements each). I want to compute the mean for each of the 12 variables, so that, for each row, I have 12 means. A grouping variable