similar to: error installing bioconductor

Hi Nguyen, > Subject: [R] install "multtest" and "preprocessCore" packages in > Bioconductor library > Date: Wed, 30 Nov 2011 09:57:36 -0800 > From: UyenThao Nguyen <unguyen at tethysbio.com> > To: r-help <r-help at r-project.org> > CC: uth.nguyen at ucdavis.edu <uth.nguyen at ucdavis.edu> > > Hi All, > > I've tried to

Dear all, for a CRAN-package that depends on another Bioconductor-package I find two things annoying and would like to know whether there are some workarounds: 1) Is there some inevitable problem that install.packages does not install uninstalled packages (on which the specified package depends) also from Bioconductor (in the correct version)? 2) In my understanding (please correct me if

I am having problem installing the affycoretools package. When I do it through biocLite, I get error messages saying the package XML cannot be installed and that I need a more recent version of libxml2. When I try to install the tar.gz file, I get the message /usr/local/R/2.4.0/lib/R/bin/exec/R: error while loading shared libraries: libg2c.so.0: cannot open shared object ERROR: installing

I've asked a question in the BioConductor list about package management. My solution depends on your answer to the following question. Are installed R packages "relocatable"? I mean relocatable in the same sense that files in a RedHat RPM file might be "relocatable" after compiling (http://www.rpm.org/max-rpm/ch-rpm-reloc.html). This allows one to build a package as the

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.

Hi, I am trying to install Bioconductor onto R version 2.7.0 for Windows. I installed R, then followed the instructions on http://www.bioconductor.org/download, which state that you should type the following: source("http://bioconductor.org/biocLite.R") biocLite() When I do that, I get the following error: Running biocinstall version 2.2.9 with R version 2.7.0 Your version of R

Hi together, we received a question about the bioconductor package, maybe anybody could help the guy and I will deliver the message over our forum to him. If this way is allowed ... Regards Knut Here the question: Hello, I have installed R on a linux machine. I have then installed the biocLite.R package from bioconductor. I wanted to install a few other packages - hgu133plus2cdf, rma . I

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 currently set the Bioconductor repository in my .Rprofile using this code (which needs editing for every version number change of Bioconductor): # Choose repositories repos <- structure(c(CRAN="http://streaming.stat.iastate.edu/CRAN", CRANextra="http://www.stats.ox.ac.uk/pub/RWin",

hi all, Am new to R. I am having problems installing Bioconductor package in R on fedora core 4 running on AMD64 bit machine. this is the error message I get : gcc -shared -L/usr/local/lib -o affyPLM.so avg_log.o biweight.o chipbackground.o common_types.o do_PLMrlm.o do_PLMrma.o do_PLMthreestep.o idealmismatch.o LESN.o lm.o lm_threestep.o log_avg.o matrix_functions.o

No se bien si hacer la pregunta aca, pero en la lista de correo de bioconductor he tenido algunos problemas para hacer la consulta. Por un error actualice R de la version 15.0.3 a la 3.0.2, y ahora no me corren las librerias de bioconductor. Al intentar usar alguna me aparece el mensaje : Your Bioconductor is out-of-date, upgrade to version 2.13 by following instructions at

Hi, I been trying to install bioconducter into R using the script on the bioconductor home page. However, I get this error message: > source("http://www.bioconductor.org/biocLite.R") Error in file(file, "r", encoding = encoding) : unable to open connection In addition: Warning message: unable to connect to 'www.bioconductor.org' on port 80. It is maybe

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

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 =

Dear list, How can I detect a package is installed or not? If not, then install it. For example, in a script, I want to check the package DESeq is installed or not. If not, then I will using this script to install it. source("http://www.bioconductor.org/biocLite.R") biocLite("DESeq") The pseudo script would be like this: try: library("DESeq") catch:

Hello, Thank you for your response. I need to install RankTail package since it contains the beta binomial distribution, CDF and inverse CDF in the usual form which I need to use. However rmutil package contain unusual forms for these functions. So it is easier for me to deal with the forms are contained in RankTail. I tried to install bioconductor package, using the following commands but I

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

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

Why am I seeing the following in R-devel (sept 2, 2006 build) on opensuse 10.1? I'm sure it is something simple I am missing, but I just don't see it (output below). Thanks, Sean > readLines(url("http://www.bioconductor.org/biocLite.R")) [1] "source(\"http://bioconductor.org/getBioC.R\")" [2] ""

Dear All, I am trying to build a package for a set of functions. I am able to build the package and its working fine. When I check it with R CMD check I get a following warning : no visible global function definition for ‘biocLite’ I have used biocLite to load a user defined library from within a function if that library is not pre-installed