similar to: S4 Method Rd Warning

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 members, I have defined a binary operator %append% with methods for some S4 classes. In my documentation file, I want to list the methods explicitly by using e.g.: \S4method{\%append\%}{RecLinkData,RecLinkData}(x, y) In the HTML documentation this comes out right as ## S4 method for signature 'RecLinkResult,RecLinkResult' x %append% y , but R CMD check

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

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

I would like to add a class to the SparseM package. I have a class "matrix.csr" that describes a matrix in compressed sparse row format, now I would like a class matrix.diag.csr that describes such objects when they happen to be diagonal. The idea is that matrix.diag.csr objects should behave (later in life) exactly like matrix.csr objects, the distinction is only needed in order to

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?,

Dear developers, We want to use "\S4method" to document new S4-methods for "[" and "[<-". We use this for other functions/methods and it works without any problem, but in case of "[" and "[<-" we didn't manage to bring this to work. The problem occurs in the development version of our package "distrSim" which can be found

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")

On Wed, 9 Oct 2013 10:44:27 +0000 (UTC) Thorsten Glaser <tg at mirbsd.de> wrote: > Anil Singhar dixit: > > >Manual testing as provided within the package has been done with all > >tests passing. This includes the units tests available under > >usr/klibc/tests, usr/utils, usr/dash and usr/gzip. For dash and > >gzip, only sanity testing has been done. > >

Given S4 methods [ and [<-, how do I write the Rd-file usage clause for the latter one? What I have now is: \S4method{[}{TimeSeries,TimeDate,missing}(x, i, j, ..., drop) \S4method{[<-}{TimeSeries,TimeDate,missing,ANY}(x, i, j, ..., value) which results in the following output: ## S4 method for signature 'TimeSeries, TimeDate, missing': x[i, j, ..., drop]

Hi, this is perhaps not so much an issue, but as you are currently working on the Rd parser anyway... When you want to document specific S4 methods for an S4 generic by \S4method{} within a \usage{} environment, and the second (signature_list) argument is "long", be it because you use multiple dispatch, be it because you use long class-names, (or both), one would probably like to be

Dear R Developers, the new simplify argument in apply causes that my package (hsdar) does not pass the checks in R-devel. The workaround, Kurt Hornik send me, is working for the R-code: if("simplify" %in% names(formals(base::apply))) do something else do something else Unfortunately, I cannot conditionalize the man pages of the functions. I get the message that

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

Interesting problem. I'm very rusty on S4 but would one solution be to, already now, add 'simplify = TRUE' to the S4 method and document it; setMethod("apply", signature(X = "Speclib"), function(X, FUN, bySI = NULL, ..., simplify = TRUE) { ? Henrik On Fri, May 22, 2020 at 6:26

What is the Rd file alias and usage syntax for an S4 assignment method? I have been trying variations on \alias{TSdoc<-,default-method} \usage{ \S4method{TSdoc}{default}(x) <- value but so far I have not got it right according to various codoc, etc, checks. Paul Gilbert ==================================================================================== La version fran?aise

Ein eingebundener Text mit undefiniertem Zeichensatz wurde abgetrennt. Name: nicht verf?gbar URL: <https://stat.ethz.ch/pipermail/r-help/attachments/20101220/d04ff621/attachment.pl>

Hi, I want to analyse DNA sequence data (mtDNA) in R as in calculate Fst, Heterozygosity and such summary statistics. Package Adagenet converts the DNA sequence into retaining only retaining the polymorphic sites and then calcuates Fst.. but is there any other way to do this? I mean analyse the DNA sequence as it is.. and calculate the statistics? Thanks! [[alternative HTML version deleted]]