search for: bioclite

...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 still got the following errors: (1) I tried biocLite() and then library ("TailRank"), I got the following errors. > biocLite() Error in biocLite() : could not find function "biocLite" > library("TailRank") Loading required package: oompaBase Error: package or namespace load failed for ?TailRank? in loadNamespace(i...

Hi, I did a quick search for other packages that provide the beta binomial distribution and found "rmutil". > install.packages("rmutil") The package has the CDF (pbetabinom) and inverse CDF (qbetabinom) among other functions. HTH, Eric On Wed, Nov 1, 2017 at 7:50 AM, MCGUIRE, Rhydwyn < rmcgu at doh.health.nsw.gov.au> wrote: > Hi there, > > It looks like

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: source("http://www.bioconductor.org/biocLite.R") biocLite("DESeq") Thank you

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 if(is.element(annotpkg, installed.packages()[,1]) == "FALSE"){ source("http://www.bioconductor.org/biocLite.R")...

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(&...

...ex), recursive = TRUE)) && file.create(searchindex))) { warning("cannot create HTML search index") return(FALSE) } useUTF8 <- capabilities("iconv") When I run this redefined version, it runs to completion without warning. However, when biocLite() runs, it does not access my redefined make.packages.html() in .Globalenv - the bioclite() call appears to always call the package:utils copy of this function. Perhaps such modifications could be done by package:utils developers? Thanks to Herve Pages for his excellent summarization of the issue...

...structions 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 Norpois This was my try to install the lumi package: > source ("http://bioconductur.org/biocLite.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") Bio...

...unwilling to do that. If I have to do something as root, it has to be something more focused like running a particular R command (install.packages(), for example). It seems insane to me that they expect (http://www.bioconductor.org/install) a root user to run source("http://bioconductor.org/biocLite.R") biocLite("limma") If I could do the installs as me with their script, and then copy the install folder into the system, then it would be OK, if the packages would work. Or perhaps post-processing is required to fiddle some paths inside package files? pj -- Paul E. Johnson Pro...

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 library("Rgraphviz"), and got the same err...

...PE=English_United 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 > traceb...

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

...ot to do with L drive, which I don't know how to fix > it. Please help. Any suggestions will be greatly appreciated. > > Thank you very much, > Nguyen > You don't specify what commands you are using to install these packages. Bioconductor recommends installing packages with biocLite(), like so: source("http://bioconductor.org/biocLite.R") biocLite(c("multtest", "preprocessCore")) Please send the output of those commands, as well as the output of sessionInfo() so we can help solve your problem. Thanks Dan > _______________________________...

...Tuesday, 15 July, 2008, 1:39 PM hello i am a new user of R.i have window XP Proffessional in my P.C.i wanted to make the graphs of my data in Rgraphviz.the version of R which i am using is 2.7.1.when i try to install Rgraphviz in R by usinr the commands > /source(http://bioconductor.org/biocLite.R) > biocLite("Rgraphviz") > source("http://bioconductor.org/biocLite.R") > biocLite("Rgraphviz") Running biocinstall version 2.2.9 with R version 2.7.1 Your version of R requires version 2.2 of BioConductor. trying URL 'http://bioconductor.org/packages/2...

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 uns...

...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 removing biocInstaller and proceed with following steps....

I meet lots of problem when installing the package ROCR, do you have meet such problems? 1, biocLite("ROCR") 2, biocLite("gplots") 3, biocLite("Rgraphviz") 4, sudo apt-get install graphviz oh, no, unlimited question, what's wrong with R in ROCR or gplots or et al Error : object ‘nobs’ is not exported by 'namespace:gdata' installation of package ‘gplots_2...

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 downloaded the source files and installed in the directory /usr/lib64/R/library but when i try using those files, they show as not installed. Anybody encounter this problem before OR is there somethin...

...t;) Error in lowess(log(abs(t(res))), log(abs(t(synthesised)))) :?? NA/NaN/Inf in foreign function call (arg 1) Then I thought to use your Limma package for background correction. Do you think it's a right choice ? However, I installed Limma using > source("http://www.bioconductor.org/biocLite.R") > biocLite("limma") > biocLite("statmod") > library(limma) and then used the commands which generated the error as follows -- > system.time(fit <- loessFit( log(abs(t(res))), log(abs(t(synthesised))))) Error in loessFit(log(abs(t(res))), log(abs(t(synth...

...g install.packages() > well is a bit of a, err, "setback". Maybe I need to add it again at the end > of .libPath() ? If I might chime in, I'd like to add my vote to the "users should be able to use install.packages and should be able to install bioconductor packages with biocLite". Longer story ============ Two cases (I've just faced this morning), where /usr/local/lib/R/site-library/ was not user-writeable: 1. Students using Debian or Ubuntu on their laptops, where these students are not particularly knowledgeable about Linux. 2. Sys admins that install an...

...s 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'm wrong!) CRAN uses bioconductor packages in another version than biocLite would install. For example: Our package gMCP depends on the package graph that has recently switched to the bioconductor repositories. But even the following commands will fail (i.e. install incompatible versions) for R 2.12 under Windows (and most likely MacOS): source("http://www.bioconduc...