similar to: unedited copy/paste from install.packages man page to update.packages man page

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

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?,

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, ...) { ... ... ... })

Hi, I received a bug report from a French user who told me there was something wrong with the function packageVersion(), but packageDescription() worked well. Below is the session info; I'm not sure if other French users can reproduce the error message: > packageVersion('base') Erreur : sp?cification de version incorrecte base > sessionInfo() R version 2.12.1 (2010-12-16)

Matthew Dowle wrote: > Hi, > > Try package 'data.table'. It has a concept of keys which allows you to do > exactly that. > > http://datatable.r-forge.r-project.org/ > > Matthew > > Hi Matthew, Unfortunately, the load of that library fails (it builds successfully). I'm currently looking into why. Error output looks something similar to: >

I'm running R 2.11.1 on 64 bit Debian. I've had no problem installing any other CRAN packages, but installing package "gbm" fails due to: *** installing help indices ** building package indices ... ** testing if installed package can be loaded Error : .onAttach failed in attachNamespace() for 'gbm', details: call: NULL error: 'packageVersion' is not an

FYI, I plan on implementing this for F31 if no issues arise. ---------- Forwarded message --------- From: Ben Cotton <bcotton at redhat.com> Date: Tue, 2 Jul 2019 at 10:55 Subject: Fedora 31 System-Wide change proposal: Automatic R runtime dependencies To: <devel-announce at lists.fedoraproject.org>, Development discussions related to Fedora <devel at lists.fedoraproject.org>

I apologize in advance for not having done more homework in advance, but thought I would send this along to see if anyone else was seeing this. I am having some sort of ggplot2/plyr/very-recent-R-devel dependency issues. Just installed R Under development (unstable) (2014-09-01 r66509) -- "Unsuffered Consequences" from source. > packageVersion("ggplot2") [1]

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= )

hello, if i load the RSQLite package in addition to the RPostgreSQL package, i get various errors when trying to use RPostgreSQL functions. here is an example transcript showing one such error: ========================================================== R version 2.15.0 (2012-03-30) [...] > packageVersion('RPostgreSQL') [1] 0.3.2 > packageVersion('RSQLite') [1] 0.11.1

Hi, While reading about the new 'recycle0' argument of paste/paste0, I spotted a mysterious "cd" floating in the air in the man page: recycle0: ?logical? indicating if zero-length character arguments (and all zero-length or no arguments when ?collapse? is not ?NULL?) should lead to the zero-length ?character(0)?. cd ^^ This is in R

Thanks, fixed. Tomas On 5/13/20 5:14 AM, Dirk Eddelbuettel wrote: > On 12 May 2020 at 19:59, Herv? Pag?s wrote: > | While reading about the new 'recycle0' argument of paste/paste0, I > | spotted a mysterious "cd" floating in the air in the man page: > | > | recycle0: ?logical? indicating if zero-length character arguments (and > | all

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

CRAN, by relying on the powerful package management system that is part of R, provides an unparalleled framework for extending R with nearly 20k packages. We recently encountered an issue that highlights a missing element in the otherwise outstanding package management system. So we would like to start a discussion about enhancing its feature set. As shown below, a mechanism to force

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

On 12 May 2020 at 19:59, Herv? Pag?s wrote: | While reading about the new 'recycle0' argument of paste/paste0, I | spotted a mysterious "cd" floating in the air in the man page: | | recycle0: ?logical? indicating if zero-length character arguments (and | all zero-length or no arguments when ?collapse? is not | ?NULL?) should lead to the zero-length

Hi i need use these 2 librarys? ( vctrs ) and ( ggplot2 ) , and the 2 librarys are installed in my Rstudio? RStudio Version 1.2.5033 ? 2009-2019 RStudio, Inc. "Orange Blossom" (330255dd, 2019-12-04) but i got all times thesse messages....please help-me...thanks lot of > library ( vctrs ) Error: package or namespace load failed for ?vctrs? in loadNamespace(i, c(lib.loc, .libPaths()),

I've made a small enhancement to R that would help developers better control what versions of code we're using where. Basically, to load a package in R, one currently does: library(whateverPackage) and with the enhancement, you can ensure that you're getting at least version X of the package: library(whateverPackage, version=3.14) Reasons one might

Hello, I wrote a class like so: > rcfdpsuperclass <- setRefClass( > Class="rcfdpsuperclass", > fields = list( > RcfpdVersion = "character"), > methods = list( > initialize = function(){ > 'Populates fields with defaults and lock as appropriate' > initFields( > RcfpdVersion =