[BioC] problems when trying to use biomaRt
Jenny Drnevich
drnevich at illinois.edu
Wed Mar 17 14:39:42 CET 2010
Hi Juan,
This won't be much help, other to say that I have the exact same
problem on my machine, and I've never been able to figure out exactly
what the problem is. I think it has something to do with our system's
firewall or something, because once this happens, I can't even get
biomart.org up on a browser!! It's like they are blocking the
connection or something. Here's the start of the thread from before:
https://stat.ethz.ch/pipermail/bioconductor/2009-November/030579.html.
I confess I haven't spent much time since then trying to resolve the
problem because I haven't really needed to use biomaRt. It is very
inconvenient, and I'd like to figure it out at some point...
Good luck,
Jenny
> sessionInfo()
R version 2.10.1 (2009-12-14)
i386-pc-mingw32
locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] grid stats graphics grDevices datasets utils methods
[8] base
other attached packages:
[1] biomaRt_2.2.0 limma_3.2.1 affyQCReport_1.24.0
[4] lattice_0.17-26 xtable_1.5-6 simpleaffy_2.22.0
[7] genefilter_1.28.2 made4_1.20.0 scatterplot3d_0.3-29
[10] gplots_2.7.4 caTools_1.10 bitops_1.0-4.1
[13] gdata_2.6.1 gtools_2.6.1 RColorBrewer_1.0-2
[16] ade4_1.4-14 affyPLM_1.22.0 preprocessCore_1.8.0
[19] gcrma_2.18.1 affycoretools_1.18.0 KEGG.db_2.3.5
[22] GO.db_2.3.5 RSQLite_0.8-0 DBI_0.2-5
[25] AnnotationDbi_1.8.1 affy_1.24.2 Biobase_2.6.1
[28] RWinEdt_1.8-2
loaded via a namespace (and not attached):
[1]
affyio_1.14.0 annaffy_1.18.0 annotate_1.24.0 Biostrings_2.14.10
[5]
Category_2.12.0 GOstats_2.12.0 graph_1.24.1 GSEABase_1.8.0
[9]
IRanges_1.4.9 RBGL_1.22.0 RCurl_1.2-1 splines_2.10.1
[13] survival_2.35-7 tools_2.10.1 XML_2.6-0
>
At 06:00 AM 3/17/2010, Juan Pablo Fededa wrote:
>Dear bioconductor-help contributors,
>
>
>I'm trying to use biomaRt package in R, and when I run the next line, the R
>GUI crashes:
>
>ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
>
>Theres is no error message at all, simply R is not responding anymore.
>when loading library(biomaRt) the prompt sign appears again, and you can
>already run basic things like:
>listMarts()
>
>When I run sessionInfo() I get this:
>
>R version 2.10.1 (2009-12-14)
>i386-pc-mingw32
>
>locale:
>[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United
>States.1252
>[3] LC_MONETARY=English_United States.1252
>LC_NUMERIC=C
>[5] LC_TIME=English_United States.1252
>
>attached base packages:
>[1] stats graphics grDevices utils datasets methods base
>
>other attached packages:
>[1] biomaRt_2.2.0
>
>loaded via a namespace (and not attached):
>[1] RCurl_1.3-1 XML_2.6-0
>
>Do you have any idea of what can I change to make it work?
>Thanks in advance,
>
> [[alternative HTML version deleted]]
>
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Jenny Drnevich, Ph.D.
Functional Genomics Bioinformatics Specialist
W.M. Keck Center for Comparative and Functional Genomics
Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign
330 ERML
1201 W. Gregory Dr.
Urbana, IL 61801
USA
ph: 217-244-7355
fax: 217-265-5066
e-mail: drnevich at illinois.edu
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