similar to: packages MANOR, qvalue, and tkWidgets fail install on Fedora 7 with latest R-beta build

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

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]]

Good Morning Everyone, I was going through my list of FTBFS packages today and I fixed all my R packages but 2: qvalue and xtable. qvalue requires ggplot2 xtable requires: lsmeans, spdep, splm, sphet, plm I am not doing any R anymore these days and in fact spot has been the one maintaining most of my R packages these days (thanks spot!!), so I am not really interested in maintaining more R

Dear colleagues, This is not strictly a R question, but I hope it is ok to ask on the list. I fed a vector of p-values from about 20 million anova tests to the package q-value and obtained this output: > qsummary(asso_p.qvalue) Call: qvalue(p = asso_p.vec) pi0: 1 Cumulative number of significant calls: <1e-04 <0.001 <0.01 <0.025 <0.05 <0.1 <1

Dear All, In Storey's estimator of the proportion of true nulls, the estimator depends on the tuning parameter lamda. Suppose now that an estimator of this proportion has been obtained by the qvalue package, what is the lamda that corresponds to the estimate? How to get this lamda? Thanks, -Chee [[alternative HTML version deleted]]

Hello, I'm apologize to have made failure before. I wrote this : p<-scan("teststat.txt") on R and R returns Error in scan ("teststat.txt") : "scan" expected a real, got "x". I don't really understand,because teststat has been created, so........ Thanks a lot. Sandrine

Greetings! The Bioconductor core group would like to announce the 5th release of Bioconductor, version 1.4. There are many new packages as well as several major upgrades and fixes in older packages, and users are encouraged to upgrade existing tools and check out the new packages. Release 1.4 is intended to be operated with R version 1.9.x, which can be obtained at CRAN

Hello, I took me very long to find out how to set the initial value in the combobox widget in tk (see the example below). My question is now : Why does "textvariable" has to be a tclVar while "values" can be a normal vector? My next question is: How could I have known this much earlier? Is there a documentation for the tcl/tk usage in R? I know a lot of website with example.

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, 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

Hi, I recently updated to R 3.0.1. I'm running linux ubuntu 12.04. I realized that I have to update all the installed packages so I run > update.packages(checkBuilt=TRUE) as described here http://www.r-bloggers.com/r-3-0-0-is-released-whats-new-and-how-to-upgrade/ . The first thing it did was telling me that it will not update several packages. When it was finished I used the warnings

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"

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, I have a huge dataset (53 million records). I have to calculate the p and q values of my data. How can I do it in R or perl? I have downloaded R (I'm completely new to R). and the package qvalue but I don't understand how can I call/use qvalue package with R. When I type library(qvalue), it gives me an error that this package doesn't exist. What should I do? Thanks! -- View this

Hi! As per Thomas' advice, I upgraded R by using "update.packages()" and got the following warning messages: Warning messages: 1: installation of package 'lmtest' had non-zero exit status in: install.packages(update[, "Package"], instlib, contriburl = contriburl, 2: installation of package 'quadprog' had non-zero exit status in: install.packages(update[,

When trying to update packages after the sysadmin updated R on my unix box I got errors on some packages. For example for chron: * DONE (chron) mkdir: cannot create directory `/usr/lib/R/library/00LOCK': Permission denied ERROR: failed to lock directory '/usr/lib/R/library' for modifying I got similar messages for spatial and cluster and warnings for other packages. Finally I got:

I am moving from windoze on a Dell laptop to Debian but I seem to have hit a snag for R. I managed to find the information to point an /etc/apt/sources.list entry at my local CRAN repository and have installed R 2.13.1 for squeeze from the Bristol UK repository. I installed a number of the additional R packages using synaptic which reported no errors but when I run my first

Dear R-list, I have encountered the following error message trying to update R packages: > update.packages(ask='graphics') Warning in install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, : 'lib' is not writable Error in install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, : unable to

Hello! I've just installed R 2.11.1 on my new home PC. Just the base R. My PC has Windows 7. R was installed in C / Program Files (x86) / R - R-2.11.1 Then - through the menue - I went to Update packages, chose the mirror and R detected the few packages that needed to be updated. After I clicked on OK I got the following error message: > update.packages(ask='graphics') --- Please

Hi all, apologies if this has been answered before, I didn't find the answer in the archives. I am putting together a package that I would like to have optional functionality if another package is installed. In normal, non-package code, I would simply write something like if (require(qvalue)) { # use package qvalue } else { # do not use package qvalue } If I do something like that in a