I am running a script that extracts many long strings from remote data bases. Every now and then the remote data base gets out of sync and closes the connection. I have been adviced to implement an R script that queries the data base in batch modality. I never ran an R script in batch modality. I think I have to use R CMD BATCH or something similar Given the amount of data I am extracting, I am concerned about having to parse a huge data file looking for the informattion I need. The less painful modification would consist in running the R script as is but through a cron job. So that the script should be set to sleep on an established frequency and when awakened it should resume from where it was interrupted. Is such a scheme doable in R ? If it is then what are the most important commands to make a script sleep and wake up on a regular basis ? Thank you in advance, Maura tutti i telefonini TIM! [[alternative HTML version deleted]]

Maura Unfortunately you never showed us your code, despite repeated requests to do so. That makes it hard to help (and frankly, ignoring requests for information from people trying to help you is extremely counterproductive). Your comments in your last email in the last thread indicates that you have code that essentially do this for(i in 1:100) getBM(...) If this is true (which we would know if we can see the code), this is why your script fail. There are two problems with this (1) you are not using the vectorized capabilities of R, but more important is (2) you are sending many requests to Biomart and typically such behaviour might mean your IP address will be banned temporarily. They don't like people hammering their services with repeated requests. Instead you should create a query that essentially asks for all your return objects in one request. That should be easy to write, and will be much faster. You might think that processing the output is slightly harder, but that is the thing to do (and with more R experience, processing a big output is actually easier). Regarding your actual question in this email, you seem to be very confused regarding the meaning of a batch job. This word has many different interpretations (not related to R), so it is hard to google for. What you are specifically asking for has everything to do with what operating system you are using (Windows, Linux, OS X) and nothing to do with R. Kasper On Nov 19, 2009, at 18:24 , <mauede at="" alice.it=""> <mauede at="" alice.it=""> wrote: > I am running a script that extracts many long strings from remote > data bases. > Every now and then the remote data base gets out of sync and closes > the connection. > I have been adviced to implement an R script that queries the data > base in batch modality. > I never ran an R script in batch modality. I think I have to use R > CMD BATCH or something similar > Given the amount of data I am extracting, I am concerned about > having to parse a huge data file looking for the > informattion I need. > The less painful modification would consist in running the R script > as is but through a cron job. So that the script > should be set to sleep on an established frequency and when > awakened it should resume from where it was interrupted. > Is such a scheme doable in R ? If it is then what are the most > important commands to make a script sleep and wake up > on a regular basis ? > > Thank you in advance, > Maura > > > > > 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