similar to: problems in installing biomart

I am running the last R version on SuSE 11.1. I installed the Bioconductor environment following the instructions on the web. As a consequence some core packages from Bioconductors 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 >

Dear list members, I encountered this problem and the solution pointed out in a previous thread did not work for me. (e.g. install.packages("RCurl", repos = "http://www.omegahat.org/R") I work with Ubuntu Hardy, and installed R 2.6.2 via apt-get. I really need RCurl in order to use biomaRt ... any help would be greatly appreciated. Best wishes, Emmanuel

Dear all, I am trying to install a package from bioconductor (biomaRt) for which I need the RCurl package. I get the following main error message when I try to install RCurl (and its dependencies). configure: error: no acceptable C compiler found in $PATH See `config.log' for more details. ERROR: configuration failed for package ‘RCurl’ I searched for possible solutions and read in some

Hi Patrick, Greetings from !(sunny) Pittsburgh. What's the scoop on RCurl on windows (XP)? I've tried to install RCurl_0.92-0.zip and RCurl_0.9-3.zip, with both R 2.7.2 and R 2.8.0 from the RGUI (utils:::menuInstallLocal), and get the error "Windows binary packages in zipfiles are not supported". which (according to google's one and only hit) comes from a perl script.

Steffen, When the new biomaRt tries to load it errors out because I do not have RMySQL installed. There is not a Windows binary for RMySQL and it does contain C code that I do not know how to build. I do not use the MySQL option in biomaRt. Does RMySQL need to be a required dependency? Below is my screen output and sessionINfo. require(biomaRt) Loading required package: biomaRt Loading required

I'm trying to identify the positions of all genes within a specific chromosomal region using biomart. When using the current biomart database I'm able to do this without issue. However, I need to use build 36 of the mouse genome which was last included in ensembl mart 46. I selected this mart and the mouse dataset as follows: mart<-useMart(biomart="ensembl_mart_46",

I recently updated R 2.10.1 Patched (2010-02-20 r51163) This morning I reinstalled biomaRt using biocLite. Now I can no more connect to biomaRt and even the following instruction is hanging for a while until the same error message pops up. > listMarts() Error in value[[3L]](cond) : Request to BioMart web service failed. Verify if you are still connected to the internet. Alternatively the

Hi !  Facing problem with " getSequence" commend .  when only biomaRt package loaded the following example working well  >mart <- useMart("ensembl",dataset="hsapiens_gene_ensembl") >seq = getSequence(id="BRCA1", type="hgnc_symbol", seqType="peptide", mart = mart) show(seq) but when i have loaded the seqinr, i got problem

Can biomaRt connect to data base "http://mirecords.umn.edu" or a branch of it ... for instance the validated miRNAs list ..? Thank you very much. Maura tutti i telefonini TIM! [[alternative HTML version deleted]]

I have run into a problem loading a just saved R object using R-devel. I have been saving and loading this particular type of R object for a long while and never ran into this problem. I save, then immediately reload (to test save) and get "ReadItem: unnknown type 65". This error is reproducible after logout from server and restart of emacs and R. Below is my output and

I have run into a problem loading a just saved R object using R-devel. I have been saving and loading this particular type of R object for a long while and never ran into this problem. I save, then immediately reload (to test save) and get "ReadItem: unnknown type 65". This error is reproducible after logout from server and restart of emacs and R. Below is my output and

Hi, I can run the code some days ago . But cant run now.  Problem 1: Output is ok ensembl = useDataset("hsapiens_gene_ensembl",mart=ensembl) utr5 = getSequence(chromosome=3, start=185514033, end=185535839, type="entrezgene",seqType="5utr", mart=ensembl)  Output :                                                                                                5utr

I'm using 'getBM' function in Bioconductor package 'biomaRt' to retrieve gene ids based on known chromosome locations. The question is getBM just only return one gene id once a time, even a query is mapped to multiple genes. What's the criteria for picking that special one? [[alternative HTML version deleted]]

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("http://bioconductor.org/biocLite.R") BioC_mirror =

Hi, I'm trying to get data from web page and modify it in R. I have a problem with encoding. I'm not able to get encoding right in htmlTreeParse command. See below > library(RCurl) > library(XML) > > site <- getURL("http://www.aarresaari.net/jobboard/jobs.html") > txt <- readLines(tc <- textConnection(site)); close(tc) > txt <- htmlTreeParse(txt,

I executed the following lines several times from a script as well as pasting them in an R shell. Systematically biomaRt is failing. The problem is to extract the 3UTR sequences corresponding to a vector containing 1941 Ensembl Transcript numbers (some are duplicated ... is this s problem ?) Please, find the failing instructions in the following including the ENST vector Any suggestion is

Hi, I am trying to install GenomeGraphs package from bioconductor, but failed by a non-zero exit error. From the error message, it seems that there is a shared library problem. Any suggestion on fixing it? Thanks so much. > sessionInfo() R version 2.10.1 (2009-12-14) x86_64-unknown-linux-gnu locale: [1] LC_CTYPE=en_US.iso885915 LC_NUMERIC=C [3] LC_TIME=en_US.iso885915

I have recently upgraded to Ubuntu Gutsy and, for the first time, am using a 64-bit installation. After failing miserably to install R from source, not a problem for me in the past with a 32-bit install, I went the route of using the Debian Etch build. This went smoothly, but I am unable to update my numerous R and BioConductor packages, getting non-zero exit status errors on each package. Is

Over the last several days, I've been working hard to get all of the Fedora R packages rebuilt against R 4.0 in rawhide (in the F33-R-4 side tag). With the exception of R-biomaRt, R-BSgenome, R-GenomicAlignments, and R-rtracklayer, I believe everything is built and updated to the latest versions. And of those packages, they're all ready to go when Fedora infrastructure is working reliably

Martin, Well, thanks for jumping in! We need all the help we can get ;) I changed the execute bit as you suggested and recompiled, no luck, still the same error message. Below is the output you wanted me to look at, its a bit beyond me so I include both a brief grep summary and then the whole enchilada. I do note that my output is different from yours, but I'm not sure how to interpret. I