search for: biocinstall

...nductor library. > sessionInfo() R version 3.4.2 (2017-09-28) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 7 x64 (build 7601) Service Pack 1 When I try to useDevel it fails. I've removed packages and again loaded but I get the same error message. remove.packages("BiocInstaller") source("https://bioconductor.org/biocLite.R") library(BiocInstaller) Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help > useDevel() Error: 'devel' version requires a more recent R I'm running into this error for few days now. I close R after...

...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 'lib' is missing: using '\Users\dbickel/R/win-library/2.11' Error in if (ok) { : missing value where TRUE/FALSE ne...

Hi I am trying to install a package (bioconductor) but every time I try to install it I get this message: source("http://bioconductor.org/biocLite.R") Warning in install.packages("BiocInstaller", repos = a["BioCsoft", "URL"]) : 'lib = "C:/Program Files/R/R-3.0.0/library"' is not writable Error in install.packages("BiocInstaller", repos = a["BioCsoft", "URL"]) : unable to install packages > biocLite(&quo...

...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(lib, fields) 6: installed.packages(lib.loc = libpath, fields = c("Package", "Version")) 5: getDependencies(pkgs,...

...ite.R") Fehler in file(filenaReme, "r", encoding = encoding) : 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 u...

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, 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: 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/K...

...tors 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 > source("http://bioconductor.org/biocLite.R") Warning messages: 1: In safeSource() : Redefining ‘biocinstall’ 2: In safeSource() : Redefining ‘biocinstallPkgGroups’ 3: In safeSource() : Redefining ‘biocinstallRepos’ > > biocLite("biomaRt") Running biocinstall version 2.4.11 with R version 2.9.0 Your version of R requires version 2.4 of Bioconductor. Warning in install.packages(pkgs = pkgs...

Hi all, I'm just tried to start analysing some micro-array chips. And R was asking for this package. When I tried to install it it says that: Using R version 2.10.1, biocinstall version 2.5.10. Installing Bioconductor version 2.5 packages: [1] "hugene10stv1cdf" Please wait... Warning message: In getDependencies(pkgs, dependencies, available, lib) : package ?hugene10stv1cdf? is not available What do I wrong and where can I get this package from? Thanks Chris...

...d base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] tools_2.10.1 > source("http://bioconductor.org/biocLite.R") biocLite("GenomeGraphs")Warning messages: 1: In safeSource() : Redefining 'biocinstall' 2: In safeSource() : Redefining 'biocinstallPkgGroups' 3: In safeSource() : Redefining 'biocinstallRepos' > biocLite("GenomeGraphs") Using R version 2.10.1, biocinstall version 2.5.11. Installing Bioconductor version 2.5 packages: [1] "GenomeGraphs" P...

...tallation. ERROR: configuration failed for package 'Rgraphviz' ** Removing '/home/laura/R/i486-pc-linux-gnu-library/2.8/Rgraphviz' I specify the directory /usr/share because there is where graphviz was installed (or at least is located there). I also get this warning in R: Running biocinstall version 2.3.13 with R version 2.8.1 Your version of R requires version 2.3 of Bioconductor. But even if I download manually and try to install R 2.9, the version taht it runs is 2.8. Well, two problems in one: Rgraphviz package and R update. I appreciate any help. I'm sorry if I'm skipp...

..., 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" Please wait... Warning: unable to access index for repository http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/universal/contrib/2.9 trying URL 'http://bioconductor.org/packages/2.4/bioc/bin/macosx/universa...

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 'http://bioconductor.org/packages/2.1/bioc/bin/windows/contrib/2.6/MassSpecWavelet_1.4.0.zip' Content type 'application/zip' length 2129961 bytes (2.0 Mb) opened URL downloaded 2....

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 install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, : argument 'lib' is missing: using '/usr/local/lib/R/site-library' Please advise. THanks. [[a...

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 ' http://www.bioconductor.org/packages/2.5/data/annotation/bin/windows/contrib/2.10/hgu133acdf_2.5.0.zip ' Error in download.file(url, destfile, method, mode = "wb",...

I am trying to install or load pasilla package on R. i am getting the following error. Please let me know how to install pasilla on R. biocLite("pasilla") Using R version 2.13.2, biocinstall version 2.8.4. Installing Bioconductor version 2.8 packages: [1] "pasilla" Please wait... Installing package(s) into ‘C:/Users/Sridhar/Documents/R/win-library/2.13’ (as ‘lib’ is unspecified) Warning message: In getDependencies(pkgs, dependencies, available, lib) : package ‘pasilla’ is no...

...losest thing I find is the method MLearn_new() under MLInterfaces. I've tried replacing MLearn() with MLearn_new() in my script, but I still get the same error, this time: Error: could not find function "MLearn_new" Any ideas what I'm doing wrong here? Thanks. R version 2.13.4, Biocinstall version 2.8.4, on Ubuntu 10.04 -- View this message in context: http://r.789695.n4.nabble.com/Error-could-not-find-function-MLearn-tp3998805p3998805.html Sent from the R help mailing list archive at Nabble.com.

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 etc etc.... but when I do: library(Rgraphv...

...conductor 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 requires version 2.2 of BioConductor. Will install the following packages: [1] "affy" "affydata" "affyPLM" "annaffy" "annotate" [6] "Biobase" "Bios...

...ly. 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’ (as ‘lib’ is unspecified) Mensajes de aviso perdidos In getDependencies(pkgs, dependencies, available, lib) : package ‘SJava’ is...