Dear Kasper yes. Probably better even would be to wrap the initial 'actual' attempt to connect to the server in a tryCatch. If successful, execute the rest of the vignette, if not, replace it with a cached one, and eventually, if that happens repeatedly, send someone (e.g. the maintainer) a warning. It is a pity that the Sweave syntax does not make it easier to do computations on the document. Best wishes Wolfgang Mar/13/12 10:29 PM, Kasper Daniel Hansen scripsit:: > Writing a command that pings the biomaRt server on is trying to > connect to and returns TRUE if the pinging works (assuming that the > server accepts pings) is probably a very good way to start. > > Kasper > > On Tue, Mar 13, 2012 at 5:19 PM, Wolfgang Huber<whuber at="" embl.de=""> wrote: >> Dear Steffen >> >> thank you. I understand your argument: in some cases, the code in the >> vignette may fail due to transient network or server problems (I wonder how >> often this is nowadays still the case?). Unfortunately, it can also fail due >> to persistent changes in the content of the queried BioMart databases. I >> think an automated way of catching the latter is important - rather than >> putting this burden on users, who may be unexperienced and might get quite >> frustrated. >> >> Does anyone have a clever idea on how to solve this dilemma? >> >> Best wishes >> Wolfgang >> >> >> Mar/12/12 4:46 PM, Steffen Durinck scripsit:: >>> >>> Hi Wolfgang, Heidi, >>> >>> I'll give the biomaRt vignette an update later this week. All examples >>> in the vignette used to be run during the package building process but >>> often the build would fail due to internet connection problems or slow >>> server responses, issues unrelated to the biomaRt package itself. This >>> is the main reason why I deactivated running them as there was often >>> nothing wrong with the examples but the package build would fail and I >>> wanted to keep many examples in the vignette so users can understand the >>> wide variety of different queries available to them through biomaRt. >>> >>> Cheers, >>> Steffeb >>> >>> On Thu, Mar 8, 2012 at 7:06 AM, Wolfgang Huber<whuber at="" embl.de="">>> <mailto:whuber at="" embl.de="">> wrote: >>> >>> Dear Heidi, >>> thanks! >>> >>> Dear Steffen, >>> it seems that the code example in the biomaRt vignette where Rong >>> got this from would benefit from being updated. >>> >>> Best wishes >>> Wolfgang >>> >>> >>> >>> >>> >>> Heidi Dvinge scripsit 03/07/2012 10:49 PM: >>> >>> Hi Rong> >>> >>> Hello, >>> when I use the biomaRt package from R/bioconductor, >>> there appears a problem: >>> library("biomaRt") >>> ensembl=useMart("ensembl",__dataset="hsapiens_gene___ensembl") >>> refseqinds=c("NM_005359","NM___000546") >>> >>> ipro=getBM(attributes=c("__refseq_dna","interpro","__interpro_de scription"),__filters="refseq_dna",values=__refseqinds,mart=ensembl) >>> >>> >>> it looks like you're using RefSeq *mRNA* IDs, not *DNA* IDs. The >>> following >>> works: >>> >>> >>> ipro=getBM(attributes=c("__refseq_mrna","interpro","__interpro_d escription"),__filters="refseq_mrna",values=__refseqinds,mart=ensembl) >>> ipro >>> >>> refseq_mrna interpro interpro_description >>> 1 NM_000546 IPR011615 p53, DNA-binding domain >>> 2 NM_000546 IPR010991 p53, tetramerisation domain >>> 3 NM_000546 IPR013872 p53 transactivation domain >>> 4 NM_000546 IPR002117 p53 tumour suppressor family >>> 5 NM_005359 IPR001132 SMAD domain, Dwarfin-type >>> 6 NM_005359 IPR003619 MAD homology 1, Dwarfin-type >>> 7 NM_005359 IPR013019 MAD homology, MH1 >>> >>> HTH >>> \Heidi >>> >>> >>> ipro >>> [1] refseq_dna interpro interpro_description<0 rows> (or >>> 0-length >>> row.names) >>> >>> Can anyone tell me what's the problem? Are there any other >>> way to retrieve >>> the gene name from refseq gene ID? >>> >>> -- output of sessionInfo(): >>> >>> sessionInfo() >>> >>> R version 2.14.1 (2011-12-22) >>> Platform: x86_64-apple-darwin9.8.0/x86___64 (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_2.10.0 >>> >>> loaded via a namespace (and not attached): >>> [1] RCurl_1.91-1 tools_2.14.1 XML_3.9-4 >>> >>> >>> >>> -- >>> Best wishes >>> Wolfgang >>> >>> Wolfgang Huber >>> EMBL >>> http://www.embl.de/research/__units/genome_biology/huber >>> <http: www.embl.de="" research="" units="" genome_biology="" huber=""> >>> >>> >>> _________________________________________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org<mailto:bioconductor at="" r-project.org=""> >>> https://stat.ethz.ch/mailman/__listinfo/bioconductor >>> <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor=""> >>> Search the archives: >>> http://news.gmane.org/gmane.__science.biology.informatics.__conductor >>> <http: news.gmane.org="" gmane.science.biology.informatics.conductor=""> >>> >>> >> >> >> -- >> Best wishes >> Wolfgang >> >> Wolfgang Huber >> EMBL >> http://www.embl.de/research/units/genome_biology/huber >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor -- Best wishes Wolfgang Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber