Hi,
 

I am trying to work with biomaRt. When i try to create a mart object, I get this error massage:

> library("biomaRt")
> ensembl = useMart("ensembl",dataset="mmusculus_gene_ensembl")
Space required after the Public Identifier
SystemLiteral " or ' expected
SYSTEM or PUBLIC, the URI is missing
Opening and ending tag mismatch: hr line 7 and body
Opening and ending tag mismatch: body line 4 and html
Premature end of data in tag html line 2
Error: 1: Space required after the Public Identifier
2: SystemLiteral " or ' expected
3: SYSTEM or PUBLIC, the URI is missing
4: Opening and ending tag mismatch: hr line 7 and body
5: Opening and ending tag mismatch: body line 4 and html
6: Premature end of data in tag html line 2

I have updated to the newest version, but still the error pop up each time.

any ideas why this is or what I'm doing wrong??

Assa

> sessionInfo()
R version 3.2.1 (2015-06-18)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.10.5 (Yosemite)

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_2.8.1

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.1               RColorBrewer_1.1-2        futile.logger_1.4.1       plyr_1.8.3               
 [5] GenomeInfoDb_1.4.3        XVector_0.8.0             bitops_1.0-6              futile.options_1.0.0     
 [9] tools_3.2.1               rpart_4.1-10              digest_0.6.8              RSQLite_1.0.0            
[13] annotate_1.46.1           gtable_0.1.2              lattice_0.20-33           DBI_0.3.1                
[17] parallel_3.2.1            proto_0.3-10              RcppArmadillo_0.6.200.2.0 gridExtra_2.0.0          
[21] genefilter_1.50.0         stringr_1.0.0             cluster_2.0.3             S4Vectors_0.6.6          
[25] IRanges_2.2.9             locfit_1.5-9.1            nnet_7.3-11               stats4_3.2.1             
[29] grid_3.2.1                Biobase_2.28.0            AnnotationDbi_1.30.1      XML_3.98-1.3             
[33] survival_2.38-3           BiocParallel_1.2.22       foreign_0.8-66            latticeExtra_0.6-26      
[37] Formula_1.2-1             geneplotter_1.46.0        DESeq2_1.8.2              ggplot2_1.0.1            
[41] reshape2_1.4.1            lambda.r_1.1.7            magrittr_1.5              scales_0.3.0             
[45] Hmisc_3.17-0              BiocGenerics_0.14.0       GenomicRanges_1.20.8      MASS_7.3-44              
[49] splines_3.2.1             xtable_1.8-0              colorspace_1.2-6          stringi_1.0-1            
[53] acepack_1.3-3.3           RCurl_1.95-4.7            munsell_0.4.2            
 

Eventually, you might have already got to that solution yourself, but apparently you have to switch to the biomart host to ensembl:

> ensembl = useMart("ENSEMBL_MART_ENSEMBL",dataset="mmusculus_gene_ensembl", host="www.ensembl.org")

cheers, jo