On Thu, Nov 19, 2009 at 7:16 AM, <mauede@alice.it> wrote: > I could not retrieve the message you indicated. I usually save them in a > dedicated mailbox folder. > Hello, Maura. You'll want to click the link in the email that Tony kindly provided (it is still in this email, below my reply), you'll find Steffen's reply to your last post of this problem. > Anyway, I did browse through the PDF file accessible from BiomaRt page of > Bioconductor documentation (containing also biomaRt installation > instructions). I remember reading those examples last Summer when I started > using Biomart s/w. They are very useful indeed, but I could not find any mention to "batch". I > guess my problem is more general. That is, how shall I run a batch R script > ? > I think I have to read and learn from the documentation of R CMD BATCH > command. I guess the hard part will be to retrieve and extract the data I > am looking for from the batch bulk output file. Outside Bioconductor web site I also found a PDF file entitled "BioMart 0.7 > Documentation" which illustrates the technique to build Marts, > configure Marts, query Marts, and usage of third-party s/w. The query Marts > section includes a paragraph "6.1.3 Batch jobs and scripting" > I see that is refers to a data base language called MQL. > Is this the right document to get a quick hang of it ? > You can certainly spend time doing the things you mention above and you might learn something interesting, but I don't think you'll find them particularly helpful. Sean > -----Messaggio originale----- > Da: tc.fhcrc@gmail.com per conto di Tony Chiang > Inviato: mer 18/11/2009 18.30 > A: mauede@alice.it > Cc: Steffen@stat.berkeley.edu; Bioconductor List; Stefano Rovetta > Oggetto: Re: [BioC] BioMart error occurred again > > I think that you have asked this question (a number of times) before. > Please > see Steffen's answer to you via the link (and please note Sean's requests): > > > http://thread.gmane.org/gmane.science.biology.informatics.conductor/ 25759/focus=25778 > > Within a 7 hour period, there could be a number of things that can occur > between your connection to Biomart. Batch queries would be the way forward > as per Steffen's comments if you are not already doing this. > > > On Wed, Nov 18, 2009 at 8:38 AM, <mauede@alice.it> wrote: > > > This time the following error occurred after roughly 7-hour no- stop > > running. > > > > > > > > OPEN NEW CONNECTION ON FILE: hsa-miR-199a- 5p_V_MirBase_FastaFiles.txt > > > > **** WRITE 3UTR SEQUENCE TO FILE: > > hsa-miR-199a-5p_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() > > Error: could not find function "sessioninfo" > > > infosession() > > Error: could not find function "infosession" > > > 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] JGR_1.6-7 iplots_1.1-3 JavaGD_0.5-2 rJava_0.6-3 > > [5] CORNA_1.2 XML_2.5-1 GEOquery_2.8.0 RCurl_0.98-1 > > [9] bitops_1.0-4.1 biomaRt_2.0.0 Biobase_2.4.1 gdata_2.4.2 > > [13] microRNA_1.2.0 Rlibstree_0.3-2 Biostrings_2.12.7 IRanges_1.2.3 > > > > loaded via a namespace (and not attached): > > [1] gtools_2.6.1 > > > > > > tutti i telefonini TIM! > > > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > > > tutti i telefonini TIM! > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]