[R] Memory issue?
I have a script that sometimes produces the following error:
Error in assign(".target", met...@target, envir = envir) :
formal argument "envir" matched by multiple actual arguments
Do you think this is a memory issue? I don't know what else it could be
as it doesn't always occur even if the script is run with exactly the
same data.
Does rm() actually free up memory?
Thanks
Dan
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[R] Memory Issue
Hi, I'm new to R and there is something I'm missing about how it uses memory. I'm doing a simple query (using RODBC package) and immediately set the data.frame to null close the connection/channel and explicitly call to the garbage collector (gc()) however when I look in the task monitor I see both "VM size" and ""Mem Usage" increased every time (for the RGui). I tried this on different configurations: windowxp64 / windowsxp and R version 2.4.1 and 2.5.1. What I'm doing wrong? Thanks, Yoni. __ 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.
Re: [R] Memory issue?
Daniel Brewer wrote:
I have a script that sometimes produces the following error:
Error in assign(".target", met...@target, envir = envir) :
formal argument "envir" matched by multiple actual arguments
Do you think this is a memory issue? I don't know what else it could be
as it doesn't always occur even if the script is run with exactly the
same data.
Does rm() actually free up memory?
Thanks
Dan
Hi,
There are multiple threads on this subject on the R-help list, googling
for "formal argument matched by mutiple actual arguments" lead me to:
http://tolstoy.newcastle.edu.au/R/help/05/08/10698.html
So this is probably not a memory issue. Freeing up memory can be done
using gc().
cheers and hth,
Paul
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P.O. Box 80.115
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Phone: +31302535773
Fax:+31302531145
http://intamap.geo.uu.nl/~paul
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Re: [R] Memory issue?
I had similar issues with memory occupancy. You should explicitly call gc() to call the garbage collector (free memory routine) after you do rm() of the big objects. D. __ 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] R memory issue for writing out the file
Hello, all, First thanks in advance for helping me. I am now handling a data frame, dimension 11095400 rows and 4 columns. It seems work perfect in my MAC R (Mac Pro, Intel Chip with 4G RAM) until I was trying to write this file out using the command: write.table(all,file="~/Desktop/alex.lgen",sep=" ",row.names=F,na="0",quote=F,col.names=F) I got the error message: R(319,0xa000d000) malloc: *** vm_allocate(size=88764416) failed (error code=3) R(319,0xa000d000) malloc: *** error: can't allocate region R(319,0xa000d000) malloc: *** set a breakpoint in szone_error to debug I then confirmed in Windows (Windows XP, 1G RAM) R by trying it again. It seems that it has to do with my R memory limit allocation. I read all the online help and still could not figure out the way to solve the problem. Also I do not understand why the data could be easily handled within R but could not write out due to the insufficient memory. I am not good at both R and computers. Sorry for my naive questions if it sounds bothersome. -- Xiaojing WANG Dept. of Human Genetics Univ. of Pittsburgh, PA 15261 Tel: 412-624-8157 [[alternative HTML version deleted]] __ 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.
Re: [R] R memory issue for writing out the file
Hi Xiaojing, That's a big table! You might try 'write' (you'll have to work harder to get your data into an appropriate format). You might also try the R-2.7 release candidate, which I think is available here http://r.research.att.com/ for the mac. There was a change in R-2.7 that will make writing large tables without row names more efficient; this might well be where you are running in to problems. Best, Martin Xiaojing Wang wrote: > Hello, all, > > First thanks in advance for helping me. > > I am now handling a data frame, dimension 11095400 rows and 4 columns. It > seems work perfect in my MAC R (Mac Pro, Intel Chip with 4G RAM) until I was > trying to write this file out using the command: > > write.table(all,file="~/Desktop/alex.lgen",sep=" > ",row.names=F,na="0",quote=F,col.names=F) > > I got the error message: > > R(319,0xa000d000) malloc: *** vm_allocate(size=88764416) failed (error > code=3) > R(319,0xa000d000) malloc: *** error: can't allocate region > R(319,0xa000d000) malloc: *** set a breakpoint in szone_error to debug > > > I then confirmed in Windows (Windows XP, 1G RAM) R by trying it again. It > seems that it has to do with my R memory limit allocation. > > I read all the online help and still could not figure out the way to solve > the problem. Also I do not understand why the data could be easily handled > within R but could not write out due to the insufficient memory. I am not > good at both R and computers. Sorry for my naive questions if it sounds > bothersome. > > -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M2 B169 Phone: (206) 667-2793 __ 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.
Re: [R] R memory issue for writing out the file
Try to write the data.frame to file in blocks of rows by calling write.table() multiple times - see argument 'append' for write.table(). That will probably require less memory. /Henrik On Tue, Apr 15, 2008 at 6:12 PM, Xiaojing Wang <[EMAIL PROTECTED]> wrote: > Hello, all, > > First thanks in advance for helping me. > > I am now handling a data frame, dimension 11095400 rows and 4 columns. It > seems work perfect in my MAC R (Mac Pro, Intel Chip with 4G RAM) until I was > trying to write this file out using the command: > > write.table(all,file="~/Desktop/alex.lgen",sep=" > ",row.names=F,na="0",quote=F,col.names=F) > > I got the error message: > > R(319,0xa000d000) malloc: *** vm_allocate(size=88764416) failed (error > code=3) > R(319,0xa000d000) malloc: *** error: can't allocate region > R(319,0xa000d000) malloc: *** set a breakpoint in szone_error to debug > > > I then confirmed in Windows (Windows XP, 1G RAM) R by trying it again. It > seems that it has to do with my R memory limit allocation. > > I read all the online help and still could not figure out the way to solve > the problem. Also I do not understand why the data could be easily handled > within R but could not write out due to the insufficient memory. I am not > good at both R and computers. Sorry for my naive questions if it sounds > bothersome. > > > -- > Xiaojing WANG > Dept. of Human Genetics > Univ. of Pittsburgh, PA 15261 > Tel: 412-624-8157 > > [[alternative HTML version deleted]] > > __ > 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.
Re: [R] R memory issue for writing out the file
What are you going to do with the table after you write it out? Are you just going to read it back into R? If so, have you tried using 'save'? On Tue, Apr 15, 2008 at 12:12 PM, Xiaojing Wang <[EMAIL PROTECTED]> wrote: > Hello, all, > > First thanks in advance for helping me. > > I am now handling a data frame, dimension 11095400 rows and 4 columns. It > seems work perfect in my MAC R (Mac Pro, Intel Chip with 4G RAM) until I was > trying to write this file out using the command: > > write.table(all,file="~/Desktop/alex.lgen",sep=" > ",row.names=F,na="0",quote=F,col.names=F) > > I got the error message: > > R(319,0xa000d000) malloc: *** vm_allocate(size=88764416) failed (error > code=3) > R(319,0xa000d000) malloc: *** error: can't allocate region > R(319,0xa000d000) malloc: *** set a breakpoint in szone_error to debug > > > I then confirmed in Windows (Windows XP, 1G RAM) R by trying it again. It > seems that it has to do with my R memory limit allocation. > > I read all the online help and still could not figure out the way to solve > the problem. Also I do not understand why the data could be easily handled > within R but could not write out due to the insufficient memory. I am not > good at both R and computers. Sorry for my naive questions if it sounds > bothersome. > > > -- > Xiaojing WANG > Dept. of Human Genetics > Univ. of Pittsburgh, PA 15261 > Tel: 412-624-8157 > >[[alternative HTML version deleted]] > > __ > 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 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.
