Hi r-help-boun...@r-project.org napsal dne 08.01.2009 14:26:32:
> Dear Jim and Henrik, > > > What exactly is the problem you are trying to solve. > > Is it going to be read by some other program? > > I simply want to print the data out. Surely, this data > will be manipulated (with Excel or other > programming languages) by other people suit to their purpose. > > Typically the print out from the loop looks like this: > > ATCGATCGATCGGGGGGGGGGGGGGGTTTGCGGG 10 11.992 > CCCCCCCCGGGCCATCGGTCAGGGAATTGACGGAA 2 0.222 > ..... > up to ~16 million lines. Just curious. Can Excel manipulate 16 mil lines? > > > How much physical memory do you have on your machine? > 6GB > > > Is there paging occuring due to the size of the objects? > Don't quite understand what do you mean by that > So sorry for my lack of knowledge in R. > > > Have you consider creating a structure with 10,000 of the variables > > each time through the loop and then writing them out? > > Never thought about that. Can you be specific how can this be achieved? declare an object make a loop fill an object inside loop output this object into a file e.g. by write.table start again with new part of your data Regards Petr > > - Gundala Viswanath > Jakarta - Indonesia > > > > On Thu, Jan 8, 2009 at 10:10 PM, jim holtman <jholt...@gmail.com> wrote: > > What exactly is the problem you are trying to solve. What is going to > > be done with the data? Is it going to be read by some other program? > > How much physical memory do you have on your machine? Is there paging > > occuring due to the size of the objects? Have you consider creating a > > structure with 10,000 of the variables each time through the loop and > > then writing them out? A lot will depend on how much free memory you > > have. I will also ask one of my favorite questions; "tell me what you > > want to do, not how you want to do it". > > > > On Thu, Jan 8, 2009 at 6:12 AM, Gundala Viswanath <gunda...@gmail.com> wrote: > >> Dear all, > >> > >> I found that printing with 'cat' is very slow. > >> > >> For example in my machine this snippet > >> > >> __BEGIN__ > >> > >> # I need to resolve to use this type of loop. > >> # because using write(), I need to create a matrix which > >> # consumes so much memory. Note that "foo, bar, qux" object > >> # is already very large (>2Gb) > >> > >> for ( s in 1:length(x) ) { > >> cat(as.character(foo[s]),"\t",bar[s],"\t", qux[s],"\n") > >> } > >> __END__ > >> > >> for "x" of size ~1.5million, takes more than 10 hours to print. > >> On my Linux 1994.MHz AMD processor. > >> > >> Is there any faster alternatives to "cat" ? > >> > >> > >> - Gundala Viswanath > >> Jakarta - Indonesia > >> > >> ______________________________________________ > >> R-help@r-project.org mailing list > >> https://stat.ethz.ch/mailman/listinfo/r-help > >> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > >> and provide commented, minimal, self-contained, reproducible code. > >> > > > > > > > > -- > > Jim Holtman > > Cincinnati, OH > > +1 513 646 9390 > > > > What is the problem that you are trying to solve? > > > > ______________________________________________ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.