similar to: ANN: 'weaver' package, caching for Sweave

Hi Seth, The possibility of caching computations would be a great boon when one is iteratively refining a paper; so I'm most grateful for your work on this. Unfortunately I have a problem to report: ******************installing****************** > source("http://bioconductor.org/biocLite.R") > biocLite("weaver") Running getBioC version 0.1.8 with R version

Does anybody have a workable system to run an Rnw document through R-Sweave when necessary, but to just run it through LaTeX if no new R calculations are needed? I.e., the figures already exist, I do not need R to do more work for me, so I send the document straight to LaTeX. I want to leave open the option that I might need to run the document through Sweave in the future, so I don't want

The warnings from make.packages.html() on the Apple Mac OS X platform can be dealt with as follows: ------------------------------------------------ (1) make.packages.html() uses the function tempdir() and attempts to create a temporary directory in the default location /tmp/ which fails due to the /tmp directory architecture on the Mac. I set up a .Renviron file in my user account

I have recently upgraded to Ubuntu Gutsy and, for the first time, am using a 64-bit installation. After failing miserably to install R from source, not a problem for me in the past with a 32-bit install, I went the route of using the Debian Etch build. This went smoothly, but I am unable to update my numerous R and BioConductor packages, getting non-zero exit status errors on each package. Is

In the context of installing a Bioconductor package using our biocLite() function, install.packages() warns > install.packages("RUVSeq", repos="http://bioconductor.org/packages/2.14/bioc") Installing package into '/home/mtmorgan/R/x86_64-unknown-linux-gnu-library/3.1-2.14' (as 'lib' is unspecified) Warning message: package 'RUVSeq' is not available

To whom it may concern. As I would like to analyse some array data I was keen on downloading the lumi package that depends obviously on hdrcde that is not available for r 2.12.1. I did not find instructions to solve or circumvent this problem. Installing hdrcde by hand did not work either. It was not detected by > (.packages(all.available=TRUE)) if installed in the R library. Thanks Hermann

Hello, I'm looking for a way to extract objects from what gets created when I Sweave with driver = weaver(). I found where the .Rdata objects are, but when I load one into R, I don't see anything that looks like the objects that were created in that code chunk. > load("/home/darstr/r_env_cache/2.11.0/AbsMeth_5/ac047940aaa9cf1a1ec09f1628b13381.RData") > ls() [1]

HI, I would like to update my DESeq package version on R-2-14 using bioclite() and get this message, could somebody help please? > biocLite("DESeq") BioC_mirror: 'http://www.bioconductor.org' Using R version 2.14, BiocInstaller version 1.2.1. Installing package(s) 'DESeq' Installing package(s) into ?/nfs/team82/nac/R-modules? (as ?lib? is unspecified) trying URL

--- On Tue, 15/7/08, haani hanni <maaryam_khan@yahoo.com> wrote: From: haani hanni <maaryam_khan@yahoo.com> Subject: how i can install Rgraphviz in R2.7.1 To: "Nabble" <support@nabble.com> Cc: r-help-request@r-project.org Date: Tuesday, 15 July, 2008, 1:39 PM hello i am a new user of R.i have window XP Proffessional in my P.C.i wanted to make the graphs of my

Hi, I am trying to install GenomeGraphs package from bioconductor, but failed by a non-zero exit error. From the error message, it seems that there is a shared library problem. Any suggestion on fixing it? Thanks so much. > sessionInfo() R version 2.10.1 (2009-12-14) x86_64-unknown-linux-gnu locale: [1] LC_CTYPE=en_US.iso885915 LC_NUMERIC=C [3] LC_TIME=en_US.iso885915

Hi, Reading help("Documentation"), I'm led to believe that a help call like: ?myFun(x, sqrt(wt)) Will search for help on the appropriate method in the case that myFun is generic. This isn't working for me. Here is an example using the Biobase package: ## If Biobase is not installed source("http://bioconductor.org/biocLite.R") biocLite("Biobase")

Hi All, I posted this on the bioconductor list and didn't get a response there, so I'm hoping someone here can help. I don't know a heck of a lot about R, so I apologize if this seems like a trivial issue. This error comes up when trying to install the bioconductor globaltest package. Any clues? Thanks! Rusty -----Original Message----- From: bioconductor-bounces at r-project.org

Hi Patrick, Greetings from !(sunny) Pittsburgh. What's the scoop on RCurl on windows (XP)? I've tried to install RCurl_0.92-0.zip and RCurl_0.9-3.zip, with both R 2.7.2 and R 2.8.0 from the RGUI (utils:::menuInstallLocal), and get the error "Windows binary packages in zipfiles are not supported". which (according to google's one and only hit) comes from a perl script.

Hello, I have the fellowing problem and I am thankful for any advice! Regards, Samuel ################################################################ >   source("http://bioconductor.org/biocLite.R") BioC_mirror = http://www.bioconductor.org Change using chooseBioCmirror(). >     biocLite("SSPA") Using R version 2.11.0, biocinstall version 2.6.7. Installing

Hi again, I have been playing around with the order of loading packages, and as far as I can tell, there's nothing specific with affycoretools that's causing my Rgui to crash (i.e., shuts down and the Microsoft 'please send error report' box pops up). Instead, it has something to do with the order & type of packages that are loaded that add items to the menu bar by

Dear experts I installed Rgraphviz with the following command: source("http://www.bioconductor.org/biocLite.R") biocLite("Rgraphviz") But had a problem when I tried to load it. This says that libcdt-4.dll is missing in your computer and the following message in R window: > library("Rgraphviz") Loading required package: graph Loading required package:

I found a package on www.bioconductor.com that allows me to install using this line: source("http://bioconductor.org/biocLite.R") biocLite("MassSpecWavelet") The prompt showed me the following message: Running biocinstall version 2.1.10 with R version 2.6.2 Your version of R requires version 2.1 of Bioconductor. trying URL

Hi, I get an error indicating a missing library from the package 'Ruuid'. I suppose this means I should install RGtk. I just thought I'd document the error. Maybe a dependency entry is missing? R 2.9.0 OS X 10.5.8 Thanks, - chris > biocLite('Ruuid') Using R version 2.9.0, biocinstall version 2.4.12. Installing Bioconductor version 2.4 packages: [1] "Ruuid"

I am running the last R version on SuSE 11.1. I installed the Bioconductor environment following the instructions on the web. As a consequence some core packages from Bioconductors were installed. I need to add some more packages. So I tried biomaRt as follows. It does not get installed correctly. Please see the following sequence. Thank you in advance. Maura >

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: