similar to: Can´t start help and update on Mac (PR (PR#6964)

--Apple-Mail-1--963012407 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; format=flowed Hi, I get exactly the same error message as in report no 6920. Furthermore, starting "update Bioconducter" the following message appears (running Mac OS X 10.3.4 (7H63)) : > {library(reposTools);update.packages2(getAllDeps=TRUE)} Synching your local package

Hi I am running R 2.0 on Suse Linux 8.2. I get an error message when loading a library: "Incorrect permissions to edit the package database, /usr/lib/R/library/liblisting.Rda: save.locLib(locLibList, curLib)" However, when I look at that file, the user I am running R as has r and w permissions on it.... So firstly - any ideas why I get this error message? And secondly, does it

Dear List, I tested the example in the reposTools vignette: library(reposTools); Loading required package: tools genRepos("Test Repository", "http://biowww.dfci.harvard.edu/~jgentry/","newRepos"); Error in rep.int(colnames(x), nr) : unimplemented type 'NULL' in 'rep' Could someone help me out with this one? I'd appreciate all help.... I am

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

Dear list, I face some problems installing gpclib_1.0-1.tar.gz: R-161 R : Copyright 2002, The R Development Core Team Version 1.6.1 (2002-11-01) [...] system("R CMD INSTALL gpclib_1.0-1.tar.gz") WARNING: ignoring environment value of R_HOME ERROR: This R is version 1.5.0 package 'gpclib' depends on R 1.6.1 The same happens with http://www.bioconductor.org/getBioC.R

Full_Name: Hans Kestler Version: 2.2.0 OS: 10.4.3 Submission from: (NULL) (84.156.184.101) > sam1.out<-sam(raw1[,2:23],raw1.cl,B=0,rand=124) We're doing 319770 complete permutations Error: cannot allocate vector of size 575586 Kb R(572,0xa000ed68) malloc: *** vm_allocate(size=589402112) failed (error code=3) R(572,0xa000ed68) malloc: *** error: can't allocate region

Full_Name: Dr. Hans A. Kestler Version: 1.8.1. OS: Linux, Win, Mac OSX Submission from: (NULL) (134.60.73.116) The code below produces after a different number of iterations i the following error: Error in optim(par = rep(0.5, length(edges)), loglik, method = "L-BFGS-B", : non-finite value supplied by optim This was reproducible on different machines (Mac G4 OSX, AMD Opteron

Hi, I want to automatically fit variograms to a large number of different sample data sets, and call the funtion "likfit" (in package geoR) from within a for-loop. "likfit" does again call "optim". After ssuccessfully fitting variograms to some of the data sets, the procedure crashes and I get the error message: Error in optim(par = ini, fn = negloglik.GRF,

Hi again, I have been playing around with the order of loading packages, and as far as I can tell, there's nothing specific with affycoretools that's causing my Rgui to crash (i.e., shuts down and the Microsoft 'please send error report' box pops up). Instead, it has something to do with the order & type of packages that are loaded that add items to the menu bar by

Hi, I have built R (current development version) and BioConductor 1.7 with portland group compiler on a AMD Opteron. When I ran qc assessment on Affymetrix latin square data set, I got the following output, Loading required package: affy Loading required package: Biobase Loading required package: tools Welcome to Bioconductor Vignettes contain introductory material. To view,

The Bioconductor development team announces release 1.1 of the Bioconductor packages for the analysis of genomic data. Bioconductor is an open source bioinformatics software project based on R. Version 1.1 features: ===================== * All packages from the 1.0 release are included. All current bug fixes have been applied, and most have upgraded and provide enhanced functionality. *

The Bioconductor development team announces release 1.1 of the Bioconductor packages for the analysis of genomic data. Bioconductor is an open source bioinformatics software project based on R. Version 1.1 features: ===================== * All packages from the 1.0 release are included. All current bug fixes have been applied, and most have upgraded and provide enhanced functionality. *

CRAN (and crantastic) updates this week New packages ------------ * DCGL (1.0) Bao-Hong Liu http://crantastic.org/packages/DCGL Functions for basic differential coexpression analyses: gene filtering, link filtering, DCG (Differentially-Coexpressed Gene) identification and DCL (Differentially-Coexpressed Links) identification.Two algorithms,named DCP and DCe, are provided for

Hi! How to write PIDs to syslog? Example: Sep 19 00:57:00 hostname dovecot: pop3-login: Login: user=< username at domainname.com >, method=PLAIN, rip=XXX.XXX.XXX.XXX, lip=XXX.XXX.XXX.XXX, mpid=14407, TLS, session=<6LYlcmYDAQC4reGs> Sep 19 00:57:00 hostname dovecot: pop3( username at domainname.com ): Disconnected: Logged out top=0/0, retr=0/0, del=0/0, size=0 Sep 19 00:57:09 hostname

Hi! Stata is available for Mac (native) according to http://s281191135.onlinehome.us/2008/20080427-stata.html and rundo and rundolines are open source, and come with the source code. You might be able to compile rundo and rundolines for Mac from that source code. There is also Macpad++, a Notepad++ for Mac. You'd think those four would get it done all Mac native. Have you considered using

Hi everyone, I've searched the mail archives and I haven't been able to find a solution to this. I want to subclass a MatchSpy in the Python bindings and have Enquire use it. However, when I try to do so, I get a TypeError raised. The following example illustrates this: >>> import xapian >>> database = xapian.Database(dbpath) >>> class

Hi, is it possible to generate differently colored error bars in one plot? Thx in advance, Heinrich [[alternative HTML version deleted]]

...unless its me missing something... > help.search("prompt", agrep=F) Error: couldn't find function ".class1" > traceback() 12: initialize(value, ...) 11: initialize(value, ...) 10: new("ObjectsWithPackage", value, package = pkg) 9: metaNameUndo(unique(these), prefix = "M", searchForm = searchForm) 8: methods:::getGenerics(ns) 7:

Hi everyone, My purpose is to read a .CEL file into R. The .CEL file was created from a .CAB by using DTT software found on Affymetrix website I read the .CEL file in R using ReadAffy as follows: > d2=ReadAffy(widget=T) and I complete the fields as required. It does not complain. For example I could find the description: > description(d2) Experimenter name: BB Laboratory: FFL Contact

doveadm(mrm): Debug: http-client: conn 127.0.0.1:9998 [1]: Got 200 response for request [Req38: PUT http://localhost:9998/tika/] (took 296 ms + 8 ms in queue) doveadm(mrm): Panic: kevent(): Invalid argument Program received signal SIGABRT, Aborted. 0x00000008014e6f7a in thr_kill () from /lib/libc.so.7 (gdb) fr 6 #6 0x00000008011a3e49 in io_loop_handler_run_internal (ioloop=0x801c214e0) at