similar to: issue with base:::namespaceImportMethods

Hi Everybody I need to "transport" some data and results to use another application (Sweave via LyX - where debugging is very difficult) in order to build a report. Is it possible to store a collection of variables of different types (like named integers, matricies, data frames and two lists) all in one list and save it and then simply load it again later and "unpack" the

Hi all, I have a problem with a package that imports two other packages which both export a method for the `[` primitive function. I set up a reproducible example here: https://github.com/kforner/namespaceImportFrom_problem.git Basically, the testPrimitiveImport package imports testPrimitiveExport1 and testPrimitiveExport2, which both export a S4 class and a `[` method for the class. Then: R

Hi, namespaceImportFrom in base/R/namespace.R has the following: fdef <- methods:::getGeneric(genName, impenv) The definition of getGeneric is in methods/R/RMethodUtils.R starts with: getGeneric <- ## return the definition of the function named f as a generic. ## ## If there is no definition, throws an error or returns ## NULL according to the value of

I have followed the instructions on how to build a Windows package and everything seems to work EXCEPT that I can't see the data files that I have loaded into the data directory. I have placed the appropriate data in the data directory (as in the instructions). There are 3 data sets, which I can see when I use the command in R. Details below. I have searched everywhere to try to fix this, but

Dear list, It seems that a package (pkgB) using another package (pkgA) with S4 generics formed by taking existing functions (for example 'plot') must not import the existing functions ('plot') in its namespace to avoid the warning "replacing previous import: plot". Suppose we use the simple 'import' directive in the name space of pkgB. pkgA and pkgB files would

Dear All, Thank you kindly for such detailed replies. I was looking to overlay data using algorithms so that i am able to tell which genes are differentially expressed due to changes in copy number. I did a pubmed search and found only 7 literature pieces all of which use in-house algorithms. I am yet to explore Gviz since it wouldn't work on R 2.14, would try it after upgrading to R 2.15.

I assigned a class the first problem in Pinheiro & Bates, which uses the data set PBIB from the SASmixed package. I have recently downloaded 2.0.1 and its associated packages. On trying library(SASmixed) data(PBIB) library(nlme) plot(PBIB) I get a warning message Warning message: replacing previous import: coef in: namespaceImportFrom(self, asNamespace(ns)) after library(nlme) and a

Hello, Can anyone please suggest any packages in R that can be used to overlay gene expression data on SNP (affymetrix) copy number ? Thanks, Ekta Senior Research Associate Bioinformatics Department Jubilant Biosys Pvt Ltd, #96, Industrial Suburb, 2nd Stage Yeshwantpur, Bangalore 560 022 Ph No : +91-80-66628346 The information contained in this electronic message and in any attachments to this

[I think I've seen this reported before but can't locate it any more. I believe this oddity (glitch? feature?) is behind a query that Jean-Baptiste Ferdy asked a year ago <http://finzi.psych.upenn.edu/Rhelp08/2008-October/176449.html>] It appears that glmmPQL looks in the global workspace, not within the data frame specified by the "data" argument, for the variables

Dear members, I can't install "nser" package. It is not in cran but install_version and install_github both are not working: > install_version("nser",version = "1.4.0") Downloading package from url: https://cran.rstudio.com//src/contrib/Archive/nser/nser_1.4.0.tar.gz These packages have more recent versions available. It is

Dear all, I have a dataset that looks like id var1 var2 var4 var7 var8 1 0.0 0.1 0.3 0.9 0.0 2 0.4 0.6 0.0 0.0 0.2 3 0.0 0.0 0.0 0.8 0.7 Some columns are missed, for example, here the fourth (var3), sixth(var5) and seventh (var6) columns. I want to first determine which columns are missed in a huge dataset and then add the missed

It says that nser requires the most recent version of magrittr that you do not have installed. You must update magrittr before attempting to install nser: update.packages(oldPkgs = "magrittr") or at the prompt you were presented before, choose to update magrittr before installing nser. On Sun, Apr 9, 2023, 17:55 akshay kulkarni <akshay_e4 at hotmail.com> wrote: > Dear

Hi, I vaguely recall this was discussed in the past, but I cannot remember the context. The code below shows the problem: ---<---------------cut here---------------start-------------->--- R> library(stats4) R> library(lme4) Loading required package: Matrix Attaching package: 'Matrix' The following object(s) are masked from package:stats : xtabs

Hello all, I just wanted to share a small perl script that generates a dot file from the result of the R profiler. The dot file can than be used to create a graphical display of the profiling. You can save this file in the bin directory of your R installation and then create a graph, for example an SVG by piping the output of the script to dot: $ R CMD Rprof2dot Rprof.out | dot -Tsvg >

Hi, further down from the problem I asked about yesterday I encounter the following problem (please appologize for the lengthy mail - I have not found a brief example making the issue clear): - using R packages making use of namespaces & - S4 classes when using --with-package-versions in the install call: Pkgs install ok and the first pkg 'base' can be loaded in R

Hello, I am trying to create a simple Manhattan plot for a small list of 200 SNPs spread out in the genome in different genes. I have tried different functions (using ggplot2 and a function created by Stephen Turner, mhtplot etc.)-none of them work smoothly. Does anyone have a simple way to create the plot (not for all 22 chromosomes)- with the x axis showing the genes name and not the

Hi, There seems to be a problem with setGroupGeneric() from package 'methods'. The symptoms are somewhat erratic, in the sense that small changes may lead to any of the following behaviours. 1.Package works without problems on Windows and installs on Linux but gives error when loaded with library(). 2.Package installs on both systems and gives error when loaded on any of them. 3.

Hello there, I am having trouble installing R-2.6.1 on GNU/linux. Here is how I configure and run it: ./configure --with-x=no --enable-R-shlib make The configure step is uneventful, the tail end of make follows. Does anyone have any experience with that? Thanks a lot in advance for any suggestions. gcc -std=gnu99 -shared -L/usr/local/lib -o stats.so init.o kmeans.o ansari.o bandwidths.o

Folks, I am finding problems with using "dse": > library(dse1) Loading required package: tframe Error: c("package '%s' required by '%s' could not be found", "setRNG", "dse1") > library(dse2) Loading required package: setRNG Error: package 'setRNG' could not be loaded In addition: Warning message: there is no package called

Hi, I am currently preparing a new version of my package papeR. When I run R CMD check using the development version of R I get the following note: Package in Depends field not imported from: ?nlme?, ?lme4?, ?survival? These packages needs to imported from for the case when this namespace is loaded but not attached. I now have problems to fix this issue. It is easy to get rid of two of the