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Arek Kasprzyk, MD. MSc. Ph.D.
Head of Data Management
Center for Translational Genomics and Bioinformatics
San Raffaele Scientific Institute
Via Olgettina 58
20132 Milano
Italy
Error in value[[3L]](cond) :
Request to BioMart web service failed. Verify if you are still connected to the internet. Alternatively the BioMart web service is temporarily down.
-- Steven Rosanoff Software Engineer EMBL-European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD, UK Phone: +44 (0)1223 494565 Email: sros...@ebi.ac.uk Learn more about EBI at: http://www.ebi.ac.uk
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sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US LC_NUMERIC=C LC_TIME=en_US
[4] LC_COLLATE=en_US LC_MONETARY=en_US LC_MESSAGES=en_US
[7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_US LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] R.utils_1.33.0 R.oo_1.18.0 R.methodsS3_1.6.1 Roleswitch_1.4.0
[5] DBI_0.3.0 Biobase_2.22.0 Biostrings_2.30.1 XVector_0.2.0
[9] IRanges_1.20.7 BiocGenerics_0.8.0 biomaRt_2.18.0 microRNA_1.24.0
[13] plotrix_3.5-7 reshape_0.8.5 pracma_1.7.0
loaded via a namespace (and not attached):
[1] GenomicRanges_1.14.4 plyr_1.8.1 Rcpp_0.11.2
[4] RCurl_1.95-4.3 stats4_3.0.1 tools_3.0.1
[7] XML_3.98-1.1
The one not working in local:
R version 3.1.1 (2014-07-10)
Platform: x86_64-apple-darwin13.1.0 (64-bit)
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] biomaRt_2.22.0 limma_3.22.1 R.utils_1.34.0 R.oo_1.18.0 R.methodsS3_1.6.1 vimcom.plus_0.9-93 setwidth_1.0-3
[8] colorout_1.0-2
loaded via a namespace (and not attached):
[1] acepack_1.3-3.3 annotate_1.44.0 AnnotationDbi_1.28.0 base64enc_0.1-2 BatchJobs_1.4
[6] BBmisc_1.7 Biobase_2.26.0 BiocGenerics_0.12.0 BiocParallel_1.0.0 bitops_1.0-6
[11] brew_1.0-6 caTools_1.17.1 checkmate_1.5.0 cluster_1.15.3 codetools_0.2-9
[16] colorspace_1.2-4 DBI_0.3.1 DESeq2_1.6.1 digest_0.6.4 fail_1.2
[21] foreach_1.4.2 foreign_0.8-61 Formula_1.1-2 gdata_2.13.3 genefilter_1.48.1
[26] geneplotter_1.44.0 GenomeInfoDb_1.2.0 GenomicRanges_1.18.1 ggplot2_1.0.0 gplots_2.14.2
[31] grid_3.1.1 gtable_0.1.2 gtools_3.4.1 Hmisc_3.14-5 IRanges_2.0.0
[36] iterators_1.0.7 KernSmooth_2.23-13 lattice_0.20-29 latticeExtra_0.6-26 locfit_1.5-9.1
[41] MASS_7.3-35 munsell_0.4.2 nnet_7.3-8 parallel_3.1.1 plyr_1.8.1
[46] proto_0.3-10 RColorBrewer_1.0-5 Rcpp_0.11.3 RcppArmadillo_0.4.450.1.0 RCurl_1.95-4.3
[51] reshape2_1.4 rpart_4.1-8 RSQLite_0.11.4 S4Vectors_0.4.0 scales_0.2.4
[56] sendmailR_1.2-1 splines_3.1.1 stats4_3.1.1 stringr_0.6.2 survival_2.37-7
[61] tools_3.1.1 XML_3.98-1.1 xtable_1.7-4 XVector_0.6.0
Thanks in advance for your help.
Jose
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at some level the firewall filters were not defined properly. They have now opened the right ports, we have access and it is working fine from local and from the cluster without any modification of the R script.
e-mail: garciamanteiga.josem...@hsr.it
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e-mail: garciamantei...@hsr.it
(host="grch37.ensembl.org", path="/biomart/martservice") doesn't work!
Hello!
I seem to be having the same problem here since about 18 hours. I tried the "wget -O registry_test.xml http://www.biomart.org/biomart/martservice?type=registry" command and got "404 Not Found
2016-04-28 18:06:58 ERROR 404: Not Found."
Within R environment, listMarts gives me no result,
> library('biomaRt')
> listMarts()
[1] biomart version
<0 rows> (or 0-length row.names)
whereas specifying host aslistMarts(host="grch37.ensembl.org", path="/biomart/martservice") works. Yet for host = ensembl.org and biomart.org, it fails. I want to use chr38.
Please help!
> sessionInfo()
R version 3.2.5 (2016-04-14)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu precise (12.04.2 LTS)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=C
[4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=C LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] biomaRt_2.26.1
loaded via a namespace (and not attached):
[1] IRanges_2.4.8 parallel_3.2.5 DBI_0.3.1
[4] RCurl_1.95-4.8 Biobase_2.30.0 AnnotationDbi_1.32.3
[7] RSQLite_1.0.0 S4Vectors_0.8.11 BiocGenerics_0.16.1
[10] stats4_3.2.5 bitops_1.0-6 XML_3.98-1.4
Hello!
I seem to be having the same problem here since about 18 hours. I tried the "wget -O registry_test.xml http://www.biomart.org/biomart/martservice?type=registry" command and got "404 Not Found
2016-04-28 18:06:58 ERROR 404: Not Found."
Within R environment, listMarts gives me no result,
> library('biomaRt')
> listMarts()
[1] biomart version
<0 rows> (or 0-length row.names)
whereas specifying host aslistMarts(host="grch37.ensembl.org", path="/biomart/martservice") works. Yet for host = ensembl.org and biomart.org, it fails. I want to use chr38.
Please help!
> sessionInfo()
R version 3.2.5 (2016-04-14)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu precise (12.04.2 LTS)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=C
[4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=C LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] biomaRt_2.26.1
loaded via a namespace (and not attached):
[1] IRanges_2.4.8 parallel_3.2.5 DBI_0.3.1
[4] RCurl_1.95-4.8 Biobase_2.30.0 AnnotationDbi_1.32.3
[7] RSQLite_1.0.0 S4Vectors_0.8.11 BiocGenerics_0.16.1
[10] stats4_3.2.5 bitops_1.0-6 XML_3.98-1.4
On Wednesday, October 29, 2014 at 6:06:54 PM UTC+9, Arek Kasprzyk wrote:
Visit this group at https://groups.google.com/group/biomart-users.
<snptrial2.txt>
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> mart <- useMart(biomart = "ensembl", dataset = "hsapiens_gene_ensembl")
Request to BioMart web service failed. Verify if you are still connected to the internet. Alternatively the BioMart web service is temporarily down. Check http://www.biomart.org and verify if this website is available. Error: XML content does not seem to be XML: