search for: getbioc

...I am trying to install R/Bioconductor on a G4 Mac running OS X. I have successfully installed R so that a command window opens, but installation of the downloaded Bioconductor package is giving me trouble. After copying/pasting the Bioconductor installation script in to the window and typing getBioC(), I get the following error message. "Error in getBioC(): R not currently configured to allow HTTP connections, which is required for getBioC to work properly." Any suggestions would be greatly appreciated. Sincerely, Carol Foster -- Carol M. Foster, Ph.D. Postdoctoral Resea...

Full_Name: H Deshmukh Version: 2.0 OS: 2000 Submission from: (NULL) (129.174.206.239) Can somebody tell me what is it that i am doing wrong,i was not sure whether to post BioConductor error here or not. Thanks >source("http://www.bioconductor.org/getBioC.R") > getBioC(libName = "all") Running getBioC version 1.2.65.... If you encounter problems, first make sure that you are running the latest version of getBioC() which can be found at: www.bioconductor.org/getBioC.R Please direct any concerns or questions to bioconductor@stat.m...

...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] "" [3] "biocLite <- function(pkgs, groupName=\"lite\", ...)" [4] "{" [5] " if (missing(pkgs))"...

Hi, I am trying to install the BioC package from bioconductor onto a Windows Server 2003 machine. I can connect to bioconductor and when I run the getBioC("affy","release") function it starts to download but then it stops with the following error: Error: unable to create temporary directory 'C:\Program Files\R\R-2.2.1\release\file1eb26e9' The download just ends there. Does anyone have any idea what the problem is? Tha...

...ning R 1.7.1 on Suse Linux 8.1. I connect to the internet through a proxy so I have: IAHC-LINUX03:~ # echo $http_proxy wwwcache.bbsrc.ac.uk:8080 IAHC-LINUX03:~ # echo $HTTP_PROXY wwwcache.bbsrc.ac.uk:8080 just in case ;-) SO, i go into R and I get: > source("http://www.bioconductor.org/getBioC.R") unable to connect to 'www.bioconductor.org' on port 80. Error in file(file, "r") : cannot open URL `http://www.bioconductor.org/getBioC.R' OK so is R just not picking up my proxy setting? It seems to be trying port 80 on something, and I have specifically set it to...

...C-LINUX03:~ # echo $http_proxy > > wwwcache.bbsrc.ac.uk:8080 > > IAHC-LINUX03:~ # echo $HTTP_PROXY > > wwwcache.bbsrc.ac.uk:8080 > > > > just in case ;-) > > > > SO, i go into R and I get: > > > > > source("http://www.bioconductor.org/getBioC.R") > > unable to connect to 'www.bioconductor.org' on port 80. > > Error in file(file, "r") : cannot open URL `http://www.bioconductor.org/getBioC.R' > > > > OK so is R just not picking up my proxy setting? > > Your setting is wrong, so...

dear all, I try to update my Rversion fro 1.7.1 to 1.8.1 on linux. I have a problem when I try to install pacakges from Bioconductors with : source("http://www.bioconductor.org/getBioC.R") and getBioC(relLevel="release") somme errors append and when I make a library(affy) for example I obtain : > library(affy) Error in setIs("character", "characterORMIAME", where = where) : Class "character" is sealed; new superc...

Hi, I am new to using R and Bioconductor. My first attempt at installing R seemed successful. Then while attempting to getBioC() I had to force quit the R application since I had to attend to something else urgently. When i returned and tried to getBioC, I am getting errors indicating that there is a lock on some files. So i would like to uninstall/remove all R components and Bioconductor components and then start afresh a...

...ot;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. I place the address "http://www.bioconductor.org/getBioC.R" in my browser (MOZILLA-LINUX SERVER) the output is below. source("http://bioconductor.org/getBioC.R") biocLite <- function(pkgs, groupName="lite", ...) { if (missing(pkgs)) getBioC(groupName=groupName, ...) else getBioC(pkgs=pkgs...

I am receiving the following errors when trying to install gcrma and a number of other Bioconductor packages when the installWithVers flag is set to be TRUE. >source("http://www.bioconductor.org/getBioC.R"); >getBioC("gcrma", installWithVers=T); Running biocinstall version 2.0.7 with R version 2.5.0 Your version of R requires version 2.0 of Bioconductor. Loading required package: affy Loading required package: Biobase Loading required package: affy Loading required package: Bio...

...ot;="http...:8080") >Sys.getenv("http_proxy") http_proxy "http://...:8080" http://by-cache.bayer-ag.com:8080/ but than by try to use the source command to download the bioC.R script I'm getting the message: >source("http:/bioconductor.org/getBioC.R") Error in file(file, "r", encoding = encoding) : unable to open connection In addition: Warning message: cannot open file 'http:/bioconductor.org/getBioC.R' Is there a possibility to change the proxy setting after the programm is already running or do i need to d...

Dear All, I installed R on linux red-hat 7.3. I tried to run getBioC() script, which download R packages from bioconductor site, but I get the followin error message: Error in getBioC() : Your R is not currently configured to allow HTTP connections, which is required for getBioC to work properly. How do I configure R correctly? Thanks, Ron

Dear all! I had installed R 1.6.2. and I tried to download Bioconductor using Bioconductor install script. However, when I run the script in R it reports following: Error in getBioC(all) : Your R is not currently configured to allow HTTP connections, which is required for getBioC to work properly. Can you help me how to solve this problem and successfully download Bioconductor packages. Thank you very much in advance. Sincerely, Berislav Bosnjak, BSc

>I just installed bioconductor via getBioC.R but there >is 3 problems: apparently some libraries are missing >and I don't know which one, and even the XML package >add a error message like : >1:Installation of package Rgraphviz had non-zero exit >status in: installPkg(fileName, pkg, pkgVer, type, >lib, repEntry, versF...

...yast to install it -we did not have these environment variables set: setenv LD_LIBRARY_PATH /geninf/prog/VIZ64/lib/graphviz setenv PKG_CONFIG_PATH /geninf/prog/VIZ64/lib/pkgconfig/ we installed graphvix 2.6 and rgraphviz 1.8 we installed in R using: source("http://bioconductor.org/getBioC.R") getBioC("Rgraphviz") and then: library(Rgraphviz) works fine Harm Nijveen Harm.nijveen@wur.nl Wageningen [[alternative HTML version deleted]]

...onductor 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 : Running getBioC version 0.1.8 with R version 2.4.0 Running biocinstall version 1.9.9 with R version 2.4.0 Your version of R requires version 1.9 of Bioconductor. Avis dans install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies,...

Dear list, I have a lot of troubles installing Rgraphviz. I installed graphviz 2.13 from "graphviz-2.13.20061222.0540.tar" I installed the library Rgraphviz > getBioC("Rgraphviz") Running biocinstall version 2.0.8 with R version 2.5.0 Your version of R requires version 2.0 of Bioconductor. trying URL ' http://bioconductor.org/packages/2.0/bioc/src/contrib/Rgraphviz_1.14.0.tar.gz ' Content type 'application/x-gzip' length 1522949 bytes...

Hi , there: I used function source to download the package but found > source("http://www.bioconductor.org/getBioC.R") Error in file(file, "r") : unable to open connection In addition: Warning message: unable to resolve 'www.bioconductor.org'. Then I downloaded the packages from CRAN and found > local({a <- CRAN.packages() + install.packages(select.list(a[,1],,TRUE), .libPath...

...I have also installed Biobase using the same command successfully but when i go into R and type library() to see all the available packages, I dont see Biobase package there. Am i missing something here? Since I am using Bioconductor, I also try to install packages using getBioC() but I still get errors like: Error in file(file, "r") unable to connect to 'www.bioconductor.org' on port 80. If anyone has any advice on this, I will greatly appreciate. Thanks, Saran [[alternative HTML version deleted]]

I would like to use the getBioC.R script from http://www.bioconductor.org/getBioC.R to install the biobase packages. Unfortunately, url() and download.file() die when trying to talk to my proxy: > getBioC("exprs") connect: Cannot assign requested address unable to connect to 'gproxy1.pfizer.com'. connect...