similar to: Unexpected source() behavior in R-devel

Hi, I am trying to install Bioconductor software on our server with Red Hat Linux Enterprise (Server) edition version 4, 32GB Ram and automatic proxy configuration (http://www.ntu.edu.sg/proxy.pac) setting. from http://www.bioconductor.org <http://www.bioconductor.org/> website but couldn't install. I encounter the following errors highlighted in RED when I try to download from

Hi, I am unable to install packages on my R 2.12.0 Windows 7 machine. Here are the relevant lines: sessionInfo() R version 2.12.0 (2010-10-15) Platform: x86_64-pc-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C LC_TIME=English_United States.1252

Neither biocLite nor the GUI menus can install packages on my system. Here is relevant output: > version _ platform i386-pc-mingw32 arch i386 os mingw32 system i386, mingw32 status major 2 minor 11.1 year 2010 month 05 day 31 svn rev 52157 language R version.string R version 2.11.1 (2010-05-31) > source("http://bioconductor.org/biocLite.R") BioC_mirror =

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

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 >

I was trying to install R on a unix server. Because of a firewall i can't install biocLite for working with Bioconductor. With windows it wasn't a problem. I used the option '--internet2' to bypass the firewall. I don't have any idea, how to do it with unix. I tried to set my proxy >Sys.putenv("http_proxy"="http...:8080")

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

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

Hi All, I tried to install AnnotationDBI like so: source("http://bioconductor.org/biocLite.R") biocLite("AnnotationDbi") and got this error: .... Loading required package: RSQLite Error in dyn.load(file, ...) : unable to load shared library '/RHEL3/local/lib64/R/library/ RSQLite/libs/RSQLite.so': /RHEL3/local/lib64/R/library/RSQLite/libs/RSQLite.so: undefined

Hi, I am trying to install the “impute” package in unix. but I get the following error message. I followed the following steps. Do you know what is causing this and how I can solve this problem? source("http://www.bioconductor.org/biocLite.R") biocLite("impute") Using R version 2.11.1, biocinstall version 2.6.10. Installing Bioconductor version 2.6 packages: [1]

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

Hi, Recently I try to install Biobase component using the tutorials from cran.r-project.org/doc/Rnews/Rnews_2006-5.pdf I tried u <- "http://bioconductor.org/biocLite.R" > source(u) > biocLite("pkgDepTools", dependencies=TRUE) Running biocinstall version 2.0.8 with R version 2.5.1 Your version of R requires version 2.0 of Bioconductor. Warning in

I always followed http://cran.r-project.org/bin/linux/ubuntu/ to install R on Ubuntu 8.1. I had no errors before! > install.packages("XML") Warning in install.packages("XML") : argument 'lib' is missing: using '/usr/local/lib/R/site-library' --- Please select a CRAN mirror for use in this session --- Loading Tcl/Tk interface ... done trying URL

Hello useRs, I'm trying to install bioconductor on ubuntu edgy eft and R 2.4.0. I have some error messages during installation, in particular for the package "affy" : "Error: package 'affy' required by 'makecdfenv' could not be found" I have tryed to install 'makecdfenv' with the command : getBioC("makecdfenv") But I have this message

Hi, While trying to install hgu133acdf- windows package in R im getting the following error and unable to install the same. > source("http://bioconductor.org/biocLite.R") > biocLite("hgu133acdf") Using R version 2.10.0, biocinstall version 2.5.10. Installing Bioconductor version 2.5 packages: [1] "hgu133acdf" Please wait... trying URL '

Hello, I am trying to install SJava but I haven't been able to complete it successfully. I have tried to install it from bioconductor using the followin code and got the following output: > source("http://www.bioconductor.org/biocLite.R") BioC_mirror = http://bioconductor.org Change using chooseBioCmirror(). > biocLite("SJava") Using R version 2.12.2, biocinstall

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

Hi All, I tried to install the package of Rgraphviz in the following two ways successfully: source("http://bioconductor.org/biocLite.R") biocLite("Rgraphviz") install.packages(pkgs="C:/Progra~1/R/lib_download/Rgraphviz_1.24.0.zip", lib="C:/Progra~1/R/R-2.10.1/library", repos=NULL) but when I loaded the package though library(Rgraphviz) or

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

Dear Forum my machine runs Ubuntu 9.04. I am trying to install Biomart, what I realize is that something is missing and it can't install XML, RCurl but I don't know what more to do, I looked in previous posts but I did not find infoprmation that helped. Thanks Andreia biocLite("biomaRt") Running biocinstall version 2.3.14 with R version 2.8.1 Your version of R requires version