OPEN NEW CONNECTION ON FILE: hsa-miR-31_V_MirBase_FastaFiles.txt **** WRITE 3UTR SEQUENCE TO FILE: hsa-miR- 31_V_MirBase_FastaFiles.txt **** Error in getBM(attributes = c("hgnc_symbol", "ensembl_gene_id", "refseq_dna", : Query ERROR: caught BioMart::Exception::Database: Could not connect to mysql database ensembl_mart_56: DBI connect('database=ensembl_mart_ 56;host=martdb.ensembl.org;port=5316','anonymous',...) failed: Can't connect to MySQL server on 'martdb.ensembl.org' (110) at /srv/biomart_server/biomart.org/biomart- perl/lib/BioMart/Configuration/DBLocation.pm line 98 > sessionInfo() R version 2.9.0 (2009-04-17) x86_64-unknown-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US .UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_N AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTI FICATION=C attached base packages: [1] tools stats graphics grDevices utils datasets methods [8] base other attached packages: [1] microRNA_1.2.0 Rlibstree_0.3-2 gdata_2.4.2 CORNA_1.2 [5] XML_2.5-1 GEOquery_2.8.0 RCurl_0.98-1 bitops_1.0-4.1 [9] Biostrings_2.12.7 IRanges_1.2.3 biomaRt_2.0.0 Biobase_2.4.1 [13] JGR_1.6-7 iplots_1.1-3 JavaGD_0.5-2 rJava_0.6-3 loaded via a namespace (and not attached): [1] gtools_2.6.1 tutti i telefonini TIM! [[alternative HTML version deleted]]

Hi, Would it be possible to include the query you were attempting that generated this error? Steffen > > OPEN NEW CONNECTION ON FILE: hsa-miR-31_V_MirBase_FastaFiles.txt > > **** WRITE 3UTR SEQUENCE TO FILE: hsa-miR- 31_V_MirBase_FastaFiles.txt > **** > > Error in getBM(attributes = c("hgnc_symbol", "ensembl_gene_id", > "refseq_dna", : > Query ERROR: caught BioMart::Exception::Database: Could not connect to > mysql database ensembl_mart_56: DBI > connect('database=ensembl_mart_56;host=martdb.ensembl.org;port=5316' ,'anonymous',...) > failed: Can't connect to MySQL server on 'martdb.ensembl.org' (110) at > /srv/biomart_server/biomart.org/biomart- perl/lib/BioMart/Configuration/DBLocation.pm > line 98 > >> sessionInfo() > R version 2.9.0 (2009-04-17) > x86_64-unknown-linux-gnu > > locale: > LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_ US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC _NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDEN TIFICATION=C > > attached base packages: > [1] tools stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] microRNA_1.2.0 Rlibstree_0.3-2 gdata_2.4.2 CORNA_1.2 > [5] XML_2.5-1 GEOquery_2.8.0 RCurl_0.98-1 bitops_1.0-4.1 > [9] Biostrings_2.12.7 IRanges_1.2.3 biomaRt_2.0.0 Biobase_2.4.1 > [13] JGR_1.6-7 iplots_1.1-3 JavaGD_0.5-2 rJava_0.6-3 > > loaded via a namespace (and not attached): > [1] gtools_2.6.1 > > > > > tutti i telefonini TIM! > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >