similar to: garbage collection & memory leaks in 'R', it seems...

I am trying to analyse a mouse dataset with 45000 genes and 24 or 48 timpoints to find cycling genes using GeneCycle. However the function fisher.g.test never runs. I am pasting the input/output summary below. I would be grateful if someone could provide any insight. I 've run GeneCycle successfully in the past on similar data, but I had to reinstall R and the packages again, so this version

Hi, I've just started using R and fdrtool, and I'm not sure if the qvalues I'm receiving back are accurate. I performed fdrtool on pvalues obtained from a two way anova on proteomics data. So I have 266 data values (protein spots) for two factors (ft, vr, and the interaction) for each biological sample. One of the two factors (vr) has a highly significant effect with 119 protein

Hi, I am new to bioconductor, trying to install KEGGSOAP package, but got warnings() when installing and error message when trying to load the package, can anyone suggest what went wrong? many thanks John > source("http://bioconductor.org/biocLite.R") Bioconductor version 2.11 (BiocInstaller 1.8.3), ?biocLite for help > biocLite("KEGGSOAP") BioC_mirror:

Hello, I am using fdrtool(x, statistic="pvalue") where x is a vector of chisq p-values. I can get this command to work with some x, but not with others. When it does NOT work, I get the following screen output: > fdrtool(pvals$Chi2.pval, statistic="pvalue") Step 1... determine cutoff point Step 2... estimate parameters of null distribution and eta0 Step 3... compute p-values

Hi, I am trying to load into R a MATLAB format file (actually, as saved by octave). The file is about 300kB but R complains with a memory allocation error: > library(Rcompression) > library(R.matlab) Loading required package: R.oo Loading required package: R.methodsS3 R.methodsS3 v1.2.0 (2010-03-13) successfully loaded. See ?R.methodsS3 for help. R.oo v1.7.2 (2010-04-13) successfully

Hi, All I got trouble on installing the qvalue package. Error message: package 'tcltk' does not have a name space [cchen1 at ibibmem Yale_CB]$ R CMD INSTALL qvalue.tar.gz * installing to library '/cchome/cchen1/R/x86_64-unknown-linux-gnu-library/2.10' * installing *source* package 'qvalue' ... ** R ** data ** inst ** preparing package for lazy loading Error : package

There was mention of this [r-sig-fedora at r-project.org] mailing list on one of the other R lists overnight. I thought the list needed a bit of posting, as I could not recall seeing content recently on it. I cross post to the Red Hat hosted list as well, it raises issues relevant there as well I have been packaging in support of many of the financial packages at CRAN and in R-Forge [

Hello all, I'm trying to use the package qvalue. Upon trying to install it I'm running into trouble. I re-downloaded and installed the most recent CRAN distribution of R which announced itself to have tcltk included. Now when I try to load qvalue I'm getting errors that seem to indicate that I need tcltk2. I tried going to get that package and loading it but both qvalue and tcltk seem

Hi. I am using R 2.3.1 on Windows XP. I had installed a library package into my first session and wanted the same package in my second session, so I went out to the CRAN mirror and tried to install the package, and got the following message: ********************************************************************* >utils:::menuInstallPkgs() trying URL

I got the following warnings when I install R.oo. Are these warnings normal? Should I reinstall the package as mentioned in the warnings? How to reinstall? The sessionInfo() is at the end. > install.packages("R.oo", dependencies=T) Warning in install.packages("R.oo", dependencies = T) : argument 'lib' is missing: using '/utility/R' also installing the

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>

After installing R 2.10 under RHEL5, whenever I attempt to install packages I get the error message: "Warning: R include directory is empty -- perhaps need to install R-devel.rpm or similar" Bioconductor did manage to install, but I do get this message when using install.packages() for anything. Suggestions for a fix would be appreciated! installation info: > version

Dear list, I have been trying to run the function "qvalue" under the package qvalue on a vector with about 20 million values. > asso_p.qvalue<-qvalue(asso_p.vector) Error: cannot allocate vector of size 156513 Kb > sessionInfo() Version 2.3.1 (2006-06-01) i686-pc-linux-gnu attached base packages: [1] "methods" "stats" "graphics"

I am creating covariance matrices from sets of points, and I am having frequent problems where I create matrices that are non-positive definite. I've started using the corpcor package, which was specifically designed to address these types of problems. It has solved many of my problems, but I still have one left. One of the matrices I need to calculate is a cross-covariance matrix. In other

Hi Guys, I am new to R and just trying to write a small script to automate a couple commands. But I run into the setwd(): cannot change working directory. I googled a little bit and tried all fixes/suggestions with no success. Basically I have a script that works from inside a directory with my data (/home/sean/Rtest/Data01). Now I want to modify the script to make it run from the upper directory

Hi, I have a data.frame(zscores) that looks like this: gA gB g1 0.2 0.6 g2 0.3 Na My problem is that I need to use a function and the output is a vector of only the non NA values, so shorter than the list I would obtain dropping the data.frame. What is the cleanest way to keep row and column names or putting the values back into the same data frame format? The function

I noticed about a couple weeks ago that my R start up script starting showing the below errors, following the line "Type 'q()' to quit R" Not sure what I did different and so far it hasn't caused major problems but kind of fear that it will. Can you please help? I also posted my Rprofile below. Attempting to load the environment 'package:R.utils' R.methodsS3 v1.2.2

Hi, I am trying to install qvalue, however its giving installation error -> Error : package 'tcltk' does not have a name space ERROR: lazy loading failed for package ?qvalue? * removing ?/home/sbw/R/x86_64-unknown-linux-gnu-library/2.12/qvalue? The downloaded packages are in ?/tmp/RtmpKnS1X4/downloaded_packages? Warning message: In install.packages(pkgs = pkgs, repos = repos, ...)

Hi all, I'm trying to do some object-oriented programming in R using the R.oo package. Right from the start I encountered a strange (at least for me) problem. I define a new class/constructor based on the R.oo documentation. However the first attempt to create an object fails: === Code: === library(R.oo); setConstructorS3("MyClass",function(param) { print(param);

I am using storey's qvalue package but I keep on getting errors. Why is this? > qvalue(p, lambda=0.5)$pi0 [1] "ERROR: p-values not in valid range." Error in qvalue(p, lambda = 0.5)$pi0 : $ operator is invalid for atomic vectors -- Thanks, Jim. [[alternative HTML version deleted]]