similar to: Documenting S4 Methods

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

Hello i have some trouble getting my webservice to run . I have the following webservice : class DirectSpoolAPI < ActionWebService::API::Base api_method :add, :expects => [{:html=>:string},{:from=>:string}], :returns => [Customer] end class DirectSpoolService < ActionWebService::Base web_service_api DirectSpoolAPI def add(html,from) Customer.find(:first) end

Hello, Everyone, how to use "loop" to make the process automatic and fast? When compute each sample, the script type in R almost the same, just the input and output file's name is changed(chr1 change to chr2, chr3,chr4...). The first sample's script like this: >chr1=MEDIPS.readAlignedSeqences(BSgenome="hg19", file="chr1",numrows= )

Over the last several days, I've been working hard to get all of the Fedora R packages rebuilt against R 4.0 in rawhide (in the F33-R-4 side tag). With the exception of R-biomaRt, R-BSgenome, R-GenomicAlignments, and R-rtracklayer, I believe everything is built and updated to the latest versions. And of those packages, they're all ready to go when Fedora infrastructure is working reliably

I originally posted this to the xenapi mailing list but i dont think many are on there... here''s my question. My first attempt at this, trying to get php to interface with /var/run/xend/xen-api.sock (or even 127.0.0.1:9363 for that matter). I can make a connection to both the unix socket and the inet socket and write/read data. The problem is i always get the same responce back, also

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

Hi, I am currently building an R package and I am facing a peculiar problem where some of the functions does not work within the package. However, if I source the script the function works. For example, in a method for parallelization of analysis on each chromosome simultaneously I am receiving error at the following position of the code: # this profile the information chromosome wise and

Hi, I was installing hundreds of packages on a machine with a single call to install.packages() and after a long time the call to install.packages() finally returned with the following warnings and errors: Warning messages: 1: packages ?hgu133aprobe?, ?hgu95av2.db?, ?BSgenome.Celegans.UCSC.ce2?, ?BSgenome.Mmusculus.UCSC.mm10?, ?BSgenome.Dmelanogaster.UCSC.dm3.masked?,

Hi, Found in the man page for update.packages: repos: character vector, the base URL(s) of the repositories to use, i.e., the URL of the CRAN master such as ?"http://cran.r-project.org"? or its Statlib mirror, ?"http://lib.stat.cmu.edu/R/CRAN"?.Can be ?NULL? to install from local files (?.tar.gz? for source packages). - Using

Hi, I was wondering I'm going about this in the correct way. I need to test if there are coding sequences or exons in hg19 which match a string of 100bp "D" i.e. [A,G or T]. However I'm getting a strange result. I get a hit on chr7, using the 100bp search however when I search with 60bp sequence of "D" I don't get any hits. library("BSgenome")

Hi all - I have a Player model. The database looks like this: +-------------------+--------------+------+-----+---------+----------------+ | Field | Type | Null | Key | Default | Extra | +-------------------+--------------+------+-----+---------+----------------+ | id | int(11) | NO | PRI | NULL | auto_increment | | fname |

Hi Folks, I''m having trouble with setting up web services with layered dispatching. I''ve defined my controller (backend_controller.rb) as: class BackendController < ApplicationController web_service_dispatching_mode :layered web_service_scaffold :invoke web_service (:car) {CarService.new} end and my service (node_service.rb) as:

This is a correction to my previous message, I forgot to swap two lines in the body of setMakeGenericMethod. Sorry about that. The correct (full message) reads like this: Hi, This works > setGeneric("clear", function(obj) standardGeneric("clear")) [1] "clear" but this doesn't. Why? > funName <- "clear" > setGeneric(funName,

hi ,I am writing a soft package based on R. But when I try to read a configure file showed as below. How can I read the parameter in this text file. How can I read the parameter into each variable in this file ? configinfo<-scan(file(configfile),ok=TRUE,n=-1) scan seems need every line have same column ? configinfo <- readLines(configfile,ok=TRUE,n=-1) methodnum <-

Hi, I am using XEN-4.1.2 and linux-2.6.32 as dom0. After I upgraded stackless python from 2.5 to 2.7 (and rebuilt xen). XenAPI became unusable, I spent some time to investigate XenAPI,py, it looks fine. So, I guess xend has problem with python 2.7, because it always returned method unknown. Do I have to tweak xend to let it support python 2.7? Thanks, Eric /root # python Python 2.7.5 Stackless

Hello, I have got the following problem: given is a large string sequence consisting of the four letters "A" "C" "G" and "T" (as before). Additionally, I have got a second string sequence of the same length giving a label for each character. The labels are "+" and "-". Now I would like to create an 8x8 matrix which contains the

Dear xen-users, I''m using Xen Cloud platform 1.1 with cloudstack. I have this situation, not sure if it''s a bug or intended behavior. I''ve setup 2 servers: A hosts NFS server, B is installed XCP 1.1. I''ve mounted NFS shared directory from A to B, to make a SR for virtual guest disk image. (which in cloudstack, is called primary storage). But when I stop the

I have created the function prototype with the following code: const uintmax_t methodNameSize = 1024; const char methodNameTemplate[] = "llvm.memcpy.p0i%llu.p0i%llu.i%llu"; char methodName[methodNameSize]; // Create the methodName. memset(methodName, 0, methodNameSize); sprintf(methodName, methodNameTemplate, dstSize, srcSize, lengthSize); // Search for the

On Sep 7, 2010, at 8:03 AM, F van der Meeren wrote: > Hello, > > I have a question, what is wrong with the following code? > > declare void @llvm.memcpy.p0i64.p0i64.i8(i64*, i64*, i8, i32, i1) nounwind > > ... > > call void @llvm.memcpy.p0i64.p0i64.i8(i64* %19, i64* %21, i8 %17, i32 0, i1 false) > > ... > > > According to the compiler this is the