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Question: query regarding memory allocation...please help
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5.8 years ago by
Guest User12k
Guest User12k wrote:
> f1=list.celfiles(path="D://urvesh//3",full.names=TRUE) > memory.size() [1] 11.45 > x1=ReadAffy(filenames=f1) Error: cannot allocate vector of size 806.3 Mb In addition: Warning messages: 1: In dimnames(x) <- dn : Reached total allocation of 1535Mb: see help(memory.size) 2: In dimnames(x) <- dn : Reached total allocation of 1535Mb: see help(memory.size) 3: In dimnames(x) <- dn : Reached total allocation of 1535Mb: see help(memory.size) 4: In dimnames(x) <- dn : Reached total allocation of 1535Mb: see help(memory.size) > help(memory.size) starting httpd help server ... done this is the error which i am getting...please try to help me out..and i even tried extending memory size to 4095 using memory.limit(size=4095) ..but still the problem remains..... -- output of sessionInfo(): > f1=list.celfiles(path="D://urvesh//3",full.names=TRUE) > memory.size() [1] 11.45 > x1=ReadAffy(filenames=f1) Error: cannot allocate vector of size 806.3 Mb In addition: Warning messages: 1: In dimnames(x) <- dn : Reached total allocation of 1535Mb: see help(memory.size) 2: In dimnames(x) <- dn : Reached total allocation of 1535Mb: see help(memory.size) 3: In dimnames(x) <- dn : Reached total allocation of 1535Mb: see help(memory.size) 4: In dimnames(x) <- dn : Reached total allocation of 1535Mb: see help(memory.size) > help(memory.size) starting httpd help server ... done this is the error which i am getting...please try to help me out..and i even tried extending memory size to 4095 using memory.limit(size=4095) ..but still the problem remains..... -- Sent via the guest posting facility at bioconductor.org.
ADD COMMENTlink modified 5.8 years ago by James W. MacDonald48k • written 5.8 years ago by Guest User12k
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gravatar for James W. MacDonald
5.8 years ago by
United States
James W. MacDonald48k wrote:
Hi Urvesh, Please don't send the same exact email with slightly different subject line (one minute apart!). I'm not sure what you expect to gain by doing so, but rest assured that you will simply irritate those who might help you. On 2/28/2013 4:11 AM, urvesh patel [guest] wrote: >> f1=list.celfiles(path="D://urvesh//3",full.names=TRUE) >> memory.size() > [1] 11.45 >> x1=ReadAffy(filenames=f1) > Error: cannot allocate vector of size 806.3 Mb > In addition: Warning messages: > 1: In dimnames(x)<- dn : > Reached total allocation of 1535Mb: see help(memory.size) > 2: In dimnames(x)<- dn : > Reached total allocation of 1535Mb: see help(memory.size) > 3: In dimnames(x)<- dn : > Reached total allocation of 1535Mb: see help(memory.size) > 4: In dimnames(x)<- dn : > Reached total allocation of 1535Mb: see help(memory.size) >> help(memory.size) > starting httpd help server ... done > > this is the error which i am getting...please try to help me out..and i even tried extending memory size to 4095 using memory.limit(size=4095) ..but still the problem remains..... The obvious answer here is that you don't have enough memory, and depending on how many celfiles you have, 4 Gb may never be enough. You can try justRMA(), which uses less memory, or you can try the xps package, which will also use less memory, or you can try aroma.affymetrix, which isn't a BioC package, but which uses less memory as well. Best, Jim > > > -- output of sessionInfo(): > >> f1=list.celfiles(path="D://urvesh//3",full.names=TRUE) >> memory.size() > [1] 11.45 >> x1=ReadAffy(filenames=f1) > Error: cannot allocate vector of size 806.3 Mb > In addition: Warning messages: > 1: In dimnames(x)<- dn : > Reached total allocation of 1535Mb: see help(memory.size) > 2: In dimnames(x)<- dn : > Reached total allocation of 1535Mb: see help(memory.size) > 3: In dimnames(x)<- dn : > Reached total allocation of 1535Mb: see help(memory.size) > 4: In dimnames(x)<- dn : > Reached total allocation of 1535Mb: see help(memory.size) >> help(memory.size) > starting httpd help server ... done > > this is the error which i am getting...please try to help me out..and i even tried extending memory size to 4095 using memory.limit(size=4095) ..but still the problem remains..... > > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
ADD COMMENTlink written 5.8 years ago by James W. MacDonald48k
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