similar to: Error in GDCprepare step of TCGAbiolinks

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",

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 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 Forum my machine runs Ubuntu 9.04. I am trying to install Biomart, what I realize is that something is missing and it can't install XML, RCurl but I don't know what more to do, I looked in previous posts but I did not find infoprmation that helped. Thanks Andreia biocLite("biomaRt") Running biocinstall version 2.3.14 with R version 2.8.1 Your version of R requires version

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

Hi everybody: Below is the plain text version of this week's Ogg Traffic. The HTML version is due to be posted on vorbis.com sometime later tonight. Enjoy, Carsten. <p>Ogg Traffic for Tuesday, March 11, 2003 [1]Carsten "Purple" Haese March 11, 2003 _________________________________________________________________ Table of Contents 1. Status Updates

Hello everyone, I just thought I would let people here know that ldc (llvm backend for the D Programming Language) is getting pretty usable (a few larger libraries compile) and it now has x86-64 support added. I decided to run some timings on some D and C++ code to compare ldc to dmd (the mainline compiler), gdc (the gcc based D compiler) and g++. I used a ray tracing program found in this

On Oct 27, 2008, at 11:03 PM, Kelly W wrote: > Hello everyone, > > I just thought I would let people here know that ldc (llvm backend > for the D Programming Language) is getting pretty usable (a few > larger libraries compile) and it now has x86-64 support added. I > decided to run some timings on some D and C++ code to compare ldc to > dmd (the mainline compiler),

R-BiocFileCache is now branched for f32 (finally). You should be able to build it if/when the PDC comes back up. Lotta random outages right now. Tom On Mon, Jul 6, 2020 at 10:40 AM Jos? Ab?lio Matos <jamatos at fc.up.pt> wrote: > On Tuesday, 9 June 2020 03.40.52 WEST Tom Callaway wrote: > > Over the last several days, I've been working hard to get all of the > Fedora >

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

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]]

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]]

On Tue, 9 Jun 2020 at 04:42, Tom Callaway <tcallawa at redhat.com> wrote: > > 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

On Tuesday, 9 June 2020 03.40.52 WEST Tom Callaway wrote: > 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

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

On 18/09/2018 2:16 PM, Marcel Ramos wrote: > Dear R-devs, > > > Scenario: > > When checking a package via `R CMD check package_tar.ball`, required / suggested packages may be missing. R subsequently returns a list of packages that are missing (delimited by spaces). > > Example: > > ``` > R CMD check glmSparseNet_0.99.13.tar.gz > * using log directory

Hallo, I just installed all needed packages for my project on my PC. But I cannot load all at one time. I now want to load limma. How can I realize the following plan: I want to install for example limma inclusive all needed other sub packages (add-on). Can anyone tell me the corresponding command? Thanks, Corinna Here is the result of the command library(): Pakete in Library

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 =