search for: bioc_mirror

...es(ind=1:10) r <- getOption("repos") r <- r[!is.na(r)] options(repos=r) Is there a simpler way? I've searched for quite a while without finding an answer. Incidentally, the help page for "options" says: A Bioconductor mirror can be selected by setting options("BioC_mirror"): the default value is "http://www.bioconductor.org". The word "default" is a bit confusing here, because when I start R, I see: R> options()$BioC_mirror NULL -- Kevin Wright

...ystem. 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 = http://www.bioconductor.org Change using chooseBioCmirror(). > biocLite("ALL") Using R version 2.11.1, biocinstall version 2.6.7. Installing Bioconductor version 2.6 packages: [1] "ALL" Please wait... Warning in install.packages(pkgs = pkgs, repos = repos, ...) : argument...

...kann Verbindung nicht öffnen Zusätzlich: Warnmeldung: In file(filename, "r", encoding = encoding) : kann 'bioconductur.org' nicht auflösen > source ("http://bioconductor.org/biocLite.R") BiocInstaller version 1.2.1, ?biocLite for help > biocLite("lumi") BioC_mirror: 'http://www.bioconductor.org' Using R version 2.14, BiocInstaller version 1.2.1. Installing package(s) 'lumi' Installing package(s) into ‘/home/hnorpois/R/i686-pc- linux-gnu-library/2.14’ (as ‘lib’ is unspecified) Warnung: dependency ‘hdrcde’ is not available versuche URL ' htt...

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 version 2.7.7. Installing Bioconductor version 2.7 packages: [1] "SJava" Please wait... Installing package(s) into ‘C:\Users\Hp\Documents/R/win-library/2.12...

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 Bioconductor version 2.6 packages: [1] "SSPA" Please wait... trying URL 'http://www.bioconductor.org/packages/2.6/bioc/bin/...

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 'http://www.bioconductor.org/packages/2.9/bioc/src/contrib/DESeq_1.6.1.tar...

...States.1252 LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base > source("http://www.bioconductor.org/biocLite.R") BioC_mirror = http://www.bioconductor.org Change using chooseBioCmirror(). > biocLite("Biobase") Using R version 2.12.0, biocinstall version 2.7.4. Installing Bioconductor version 2.7 packages: [1] "Biobase" Please wait... Error: subscript out of bounds > traceback() 7: .readPkgDesc...

...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: http://bioconductor.org Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15. Installing package(s) 'KEGGSOAP' trying URL 'http://bioconductor.org/packages/2.11/bioc/bin/windows/contrib/2.15/KEGGSOAP_1.32.0.zip' Content type 'application/zip' length 69037 b...

...e method described for this installation on the Bioconductor website: source("http://bioconductor.org/biocLite.R") biocLite("globaltest") I get and the following result, which I can't find an reference to on the list archives: > biocLite("globaltest") BioC_mirror: 'http://www.bioconductor.org' Using R version 2.14, BiocInstaller version 1.2.1. Installing package(s) 'globaltest' trying URL 'http://www.bioconductor.org/packages/2.9/bioc/src/contrib/globaltest_5.8.1.tar.gz' Content type 'application/x-gzip' length 956376 bytes (...

...o The documented line-length limit of 4095 bytes when reading from the console now also applies also to parse(file="") (which previously had a limit of around 1024 bytes). o A Bioconductor mirror can be set for use by setRepositories() via the option "BioC_mirror", e.g. the European mirror can be selected by options(BioC_mirror="http://bioconductor.statistik.tu-dortmund.de") o Double-clicking in a tk_select.list() list box now selects the item and closes the list box (as happens on the Windows select.lis...

...o The documented line-length limit of 4095 bytes when reading from the console now also applies also to parse(file="") (which previously had a limit of around 1024 bytes). o A Bioconductor mirror can be set for use by setRepositories() via the option "BioC_mirror", e.g. the European mirror can be selected by options(BioC_mirror="http://bioconductor.statistik.tu-dortmund.de") o Double-clicking in a tk_select.list() list box now selects the item and closes the list box (as happens on the Windows select.lis...

Hello, I'm trying to install KEGGSOAP with bioconductor but i'm facing this problem: /> biocLite("KEGGSOAP") BioC_mirror: http://bioconductor.org Using R version 2.15, BiocInstaller version 1.4.4. Installing package(s) 'KEGGSOAP' trying URL 'http://www.bioconductor.org/packages/2.10/bioc/src/contrib/KEGGSOAP_1.30.0.tar.gz' Content type 'application/x-gzip' length 11324 bytes (11 Kb) opened URL...

...o edit the paths described in /etc/ldpaths but without any success. Any hints how I can tell the system where to search for libgvc ? Thank's in advance, Wolfgang Below the complete commands & error message and sessionInfo : > source("http://www.bioconductor.org/biocLite.R") BioC_mirror = http://bioconductor.org Change using chooseBioCmirror(). > biocLite("Rgraphviz") Using R version 2.13.0, biocinstall version 2.8.4. Installing Bioconductor version 2.8 packages: [1] "Rgraphviz" Please wait... trying URL 'http://bioconductor.org/packages/2.8/bioc/src/co...

Hi, On a fresh install of R on mac os x 10.6.4 (snow leopard) RSQLite did not install while running biocLite() $ R R version 2.11.1 (2010-05-31) Copyright (C) 2010 The R Foundation for Statistical Computing ISBN 3-900051-07-0 [...] Loading required package: utils BioC_mirror = http://www.bioconductor.org Change using chooseBioCmirror(). [Previously saved workspace restored] > biocLite("RSQLite") Using R version 2.11.1, biocinstall version 2.6.7. Installing Bioconductor version 2.6 packages: [1] "RSQLite" Please wait... Warning in install.packag...

...ext interface. This changes the > behaviour of new.packages(ask=TRUE) to be like > update.packages(ask=TRUE) on those platforms in using a text > menu: use ask="graphics" for a graphical menu. > > o New function chooseBioCmirror() to set the "BioC_mirror" option. > > o The R grammar prevents using the argument 'name' in signatures > of S4 methods for '$' and '$<-', since they will always be > called with a character string value for 'name'. The implicit > S4 generic f...

...sers to choose the text interface. This changes the behaviour of new.packages(ask=TRUE) to be like update.packages(ask=TRUE) on those platforms in using a text menu: use ask="graphics" for a graphical menu. o New function chooseBioCmirror() to set the "BioC_mirror" option. o The R grammar prevents using the argument 'name' in signatures of S4 methods for '$' and '$<-', since they will always be called with a character string value for 'name'. The implicit S4 generic functions have been c...

...sers to choose the text interface. This changes the behaviour of new.packages(ask=TRUE) to be like update.packages(ask=TRUE) on those platforms in using a text menu: use ask="graphics" for a graphical menu. o New function chooseBioCmirror() to set the "BioC_mirror" option. o The R grammar prevents using the argument 'name' in signatures of S4 methods for '$' and '$<-', since they will always be called with a character string value for 'name'. The implicit S4 generic functions have been c...