similar to: labels and counting

Hello, I am using R 2.11.0. I have a curious problem where I get a warning in R CMD check which is seemingly not relevant to my Rd file. The warning says : * checking Rd \usage sections ... WARNING Bad \usage lines found in documentation object 'enrichmentCalc': <unescaped bksl>S4method{enrichmentCalc}{GenomeDataList, BSgenome}(rs, organism, seqLen=NULL, ...) <unescaped

Hello, I am using R 2.11.0. I have a curious problem where I get a warning in R CMD check which is seemingly not relevant to my Rd file. The warning says : * checking Rd \usage sections ... WARNING Bad \usage lines found in documentation object 'enrichmentCalc': <unescaped bksl>S4method{enrichmentCalc}{GenomeDataList, BSgenome}(rs, organism, seqLen=NULL, ...) <unescaped

I'm in the process of converting some S3 methods to S4 methods. I have this function : setGeneric("enrichmentCalc", function(rs, organism, seqLen, ...){standardGeneric("enrichmentCalc")}) setMethod("enrichmentCalc", c("GenomeDataList", "BSgenome"), function(rs, organism, seqLen, ...) { ... ... ... })

Dear list, I ran into a strange behaviour of the pnbinom function - or maybe I just made a stupid mistake. First thing is that pnbinom seems to be very slow. The other - more interesting one - is that I get two different curves when I plot the estimated density and the density given by pnbinom. Shouldn't it be the same? This is only the case, I think, if I use the parameter size = 1. I

Hi, I am sorry for this simple question, but... How do I extract something from a data.frame? The following is my Problem: I have got a dataframe "a" with various columns. One of those columns is called V3 and contains elements of the following levels: > levels(a$V3) [1] "C" "CA" "CB" "CD" "CD1" "CD2"

Dear all, I am trying to calculate a score for a string sequence consisting of the following four letters: ACGT. I have got a matrix giving the scores for each pair of letters. So for example the string ACCT has got the pairs: AC, CC and CT. The matrix has got the following form: names<-c("A","C","G","T"); mscore<-matrix(0,4,4);

Dear list, I would like to extract from a matrix all those rows, that are unique. By unique, I don't mean the unique that is accomplished by the function unique(), though... Consider the following example: > h [,1] [,2] [1,] 4 4 [2,] 1 4 [3,] 4 1 Now unique(h) returns exactly the same - because 1 4 and 4 1 is not the same for that function. What I would like to

Dear list, I have got an array with observational values t and I would like to fit a geometric distribution to it. As I understand the geometric distribution, there is only one parameter, the probability p. I estimated it by 1/mean(t). Now I plotted the estimated density function by plot(ecdf(t),do.points=FALSE,col.h="blue"); and I would like to add the geometric distribution. This

All, I have just returned to R after a decade of absence, and it is good to see that R has become such a great success! I'm trying to bring Design of Experiments into some aspects of software performance evaluation, and to teach myself that, I picked up "Experiments: Planning, Analysis and Optimization" by Wu and Hamada. I try to reproduce an analysis in the book using lm, but

Hi All. I have R code whose functionality is being replicated within a C+ program. The outputs are to be compared to validate the conversion somewhat - however (as is always the case) I have stuffed my code with random number calls. Random uniform numbers in C+ are being produced using the (Boost) mersenne-twister generators (mt11213b & mt19937) - which is the default type of generator

I have grades data. I read them from a csv in letter-grade format. I then converted them to levels levels(grades$grade)=c('A+','A','A-','B+','B','B-','C+','C','C-','D+','D','D-') And then to numbers grades$gp=grades$grade levels(grades$gp)=c(4.3,4.0,3.7, 3.3,3.0,2.7, 2.3,2.0,1.7, 1.3,1.0,0.7)

Hi, I came into a crash when using 32-bit `speexdec` and found that there's an address overflow in function `print_comments()`: static void print_comments(char *comments, int length) { char *c=comments; int len, i, nb_fields; char *end; if (length<8) { fprintf (stderr, "Invalid/corrupted comments\n"); return; } end = c+length;

Hi: I noticed a bug in the realloc error checking code in the QEMU backend for RealTek8139. However, what''s worse is that there is no cap on the total size of the transmit buffer at all. So a guest can keep extending it until memory runs out. CP_TX_BUFFER_SIZE is already 64K. So it seems to me that we don''t need the while loop to extend the buffer at all since no transmitted

Hi again, thanks a lot for the quick answer. I just forgot the comma, always these stupid mistakes... Anyways, as I said before, I have two data.frames containing about 1000 rows and I would like to avoid looping through all of them... In each data.frame are coordinates (x,y,z), so every row is giving the information on one single point. I would like to calculate the distance from each point

Hi all, I am trying to make a script that prints all possible models from a model I've created using nls(). It is a logisitc model which in total includes 13 variables. So its >8000 models I need to create, which I don't want to do manually. I've tried modify scripts made for linear models with no results. I've tried these scripts on a two variable model (c,a1 and a2 is what I

Hi All, I'm using the TermGenerator::index_text() on version 1.0.4 with the FLAG_SPELLING turned on, because the new spelling suggestion stuff seems awesome, but I'm getting a segv. (gdb) bt #0 0xb7ae153c in Xapian::WritableDatabase::add_spelling (this=0xa553988, word=@0xbff97724, freqinc=1) at ./include/xapian/ base.h:154 #1 0xb7becf47 in

The VMI ROM detection and code patching mechanism is illustrated in setup.c. There ROM is a binary block published by the hypervisor, and and there are certainly implications of this. ROMs certainly have a history of being proprietary, very differently licensed pieces of software, and mostly under non-free licenses. Before jumping to the conclusion that this is a bad thing, let us consider more

The VMI ROM detection and code patching mechanism is illustrated in setup.c. There ROM is a binary block published by the hypervisor, and and there are certainly implications of this. ROMs certainly have a history of being proprietary, very differently licensed pieces of software, and mostly under non-free licenses. Before jumping to the conclusion that this is a bad thing, let us consider more

David Vandevoorde a écrit : > > I don't think those are _good_ reasons though: If one doesn't want a C+ > + function to be inlined, one shouldn't define it inline. > > You must not have written a lot of C++ template then. You don't have the choice in this case, just check your STL header. > > FWIW, I've been involved in a couple of attempts by

Hello, I'm trying to learn R (for fun!), and I've tried to find any previous discussion of this problem (or something like it) and haven't found one. When I run the following command, R seems to simply stop. I get no error message, but I also have no ">" or "+" to type after (although I can type). The only solution seems to be restarting the program.