[BioC] Error: cannot allocate vector of size 618.0 Mb
Henrik Bengtsson
hb at biostat.ucsf.edu
Sat Dec 1 21:24:57 CET 2012
Just to close this thread here. Problem was solved, cf. aroma thread
'[aroma.affymetrix] Error: cannot allocate vector of size 618.0 Mb'
[http://goo.gl/amnbC].
/Henrik
On Mon, Nov 26, 2012 at 10:16 AM, Wong, Chao-Jen <cwon2 at fhcrc.org> wrote:
> Have you tried the command gc(reset=TRUE)? It seems you have enough RAM but too segment. You can first try gc(reset=TRUE) to reset the maximum space. If it still doesn't work, restart your computer.
>
> Cheers,
> Chao-Jen
>
> ----- Original Message -----
> From: "周在威" <zhouzaiwei at 163.com>
> To: bioconductor at r-project.org
> Sent: Monday, November 26, 2012 5:39:10 AM
> Subject: [BioC] Error: cannot allocate vector of size 618.0 Mb
>
> Hello,
> I am currently trying to analyze data from affymetrix human promoter tiling array with the following code :
>> library(aroma.affymetrix)
>
>
>> verbose <- Arguments$getVerbose(-8, timestamp=TRUE)
>> chipType <- "Hs_PromPR_v02"
>> cdf <- AffymetrixCdfFile$byChipType(chipType)
>> print(cdf)
> AffymetrixCdfFile:
> Path: annotationData/chipTypes/Hs_PromPR_v02
> Filename: Hs_PromPR_v02.cdf
> Filesize: 61.95MB
> Chip type: Hs_PromPR_v02
> RAM: 0.00MB
> File format: v4 (binary; XDA)
> Dimension: 2166x2166
> Number of cells: 4691556
> Number of units: 23155
> Cells per unit: 202.62
> Number of QC units: 0
>> s <- AffymetrixCelSet$byName("DS", cdf=cdf)
>> mn <- MatNormalization(s)
>
>
>> csN <- process(mn, verbose=verbose)
> 20121126 20:48:51|Normalization data set for probe-sequence effects...
> 20121126 20:48:51| Locating probe-sequence annotation data...
> 20121126 20:48:51| Getting AromaCellSequenceFile...
> 20121126 20:48:51| Locating...
> 20121126 20:48:51| Chip type: Hs_PromPR_v02
> 20121126 20:48:51| Number of cells: 4691556
> 20121126 20:48:51| Locating AromaCellSequenceFile...
> 20121126 20:48:51| Located file: annotationData/chipTypes/Hs_PromPR_v02/Hs_PromPR_v02.acs
> 20121126 20:48:51| Locating AromaCellSequenceFile...done
> 20121126 20:48:51| Locating...done
> AromaCellSequenceFile:
> Name: Hs_PromPR_v02
> Tags:
> Full name: Hs_PromPR_v02
> Pathname: annotationData/chipTypes/Hs_PromPR_v02/Hs_PromPR_v02.acs
> File size: 116.33 MB (121980713 bytes)
> RAM: 0.00 MB
> Number of data rows: 4691556
> File format: v1
> Dimensions: 4691556x26
> Column classes: raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw
> Number of bytes per column: 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1
> Footer: <createdOn>20081204 16:42:56 EST</createdOn><platform>Affymetrix</platform><chipType>Hs_PromPR_v02</chipType>
> Chip type: Hs_PromPR_v02
> Platform: Affymetrix
> 20121126 20:48:51| Getting AromaCellSequenceFile...done
> 20121126 20:48:51| Locating probe-sequence annotation data...done
> 20121126 20:48:51| Locating match scores annotation data...
> 20121126 20:48:51| Locating AromaCellMatchScoreFile...
> 20121126 20:48:51| Located file: annotationData/chipTypes/Hs_PromPR_v02/Hs_PromPR_v02.acm
> AromaCellMatchScoreFile:
> Name: Hs_PromPR_v02
> Tags:
> Full name: Hs_PromPR_v02
> Pathname: annotationData/chipTypes/Hs_PromPR_v02/Hs_PromPR_v02.acm
> File size: 4.47 MB (4691738 bytes)
> RAM: 0.00 MB
> Number of data rows: 4691556
> File format: v1
> Dimensions: 4691556x1
> Column classes: integer
> Number of bytes per column: 1
> Footer: <createdOn>20081204 16:55:16 EST</createdOn><platform>Affymetrix</platform><chipType>Hs_PromPR_v02</chipType>
> Chip type: Hs_PromPR_v02
> Platform: Affymetrix
> 20121126 20:48:52| Locating AromaCellMatchScoreFile...done
> 20121126 20:48:52| Locating match scores annotation data...done
> 20121126 20:48:52| Reading 'non-missing' cells to fit...
> 20121126 20:48:54| Cells to fit:
> int [1:4200512] 2172 2174 2175 2176 2177 2178 2179 2180 2181 2182 ...
> 20121126 20:48:54| Reading 'non-missing' cells to fit...done
> 20121126 20:48:54| Normalizing 1 arrays...
> 20121126 20:48:54| Path: probeData/DS,MN,lm/Hs_PromPR_v02...
> 20121126 20:48:55| Number cells per chunk: 1000001
> 20121126 20:48:55| Fitting chunk #1 of 5...
> 20121126 20:48:55| Cells:
> int [1:1000001] 2172 2174 2175 2176 2177 2178 2179 2180 2181 2182 ...
> 20121126 20:48:55| Reading design matrix...
> 20121126 20:48:55| Retrieving design matrix...
> 20121126 20:48:55| Cells:
> int [1:1000001] 2172 2174 2175 2176 2177 2178 2179 2180 2181 2182 ...
> 20121126 20:48:55| Locating probe-sequence annotation data...
> 20121126 20:48:55| Getting AromaCellSequenceFile...
> AromaCellSequenceFile:
> Name: Hs_PromPR_v02
> Tags:
> Full name: Hs_PromPR_v02
> Pathname: annotationData/chipTypes/Hs_PromPR_v02/Hs_PromPR_v02.acs
> File size: 116.33 MB (121980713 bytes)
> RAM: 0.00 MB
> Number of data rows: 4691556
> File format: v1
> Dimensions: 4691556x26
> Column classes: raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw
> Number of bytes per column: 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1
> Footer: <createdOn>20081204 16:42:56 EST</createdOn><platform>Affymetrix</platform><chipType>Hs_PromPR_v02</chipType>
> Chip type: Hs_PromPR_v02
> Platform: Affymetrix
> 20121126 20:48:55| Getting AromaCellSequenceFile...done
> 20121126 20:48:55| Locating probe-sequence annotation data...done
> 20121126 20:48:55| Locating match scores annotation data...
> 20121126 20:48:55| Locating match scores annotation data...done
> 20121126 20:48:55| Reading sequence matrix...
> 20121126 20:48:55| Reading sequence matrix...
> 20121126 20:48:55| Reading data frame...
> 20121126 20:48:55| Allocating data object...
> 20121126 20:48:55| Number of rows: 1000001
> 20121126 20:48:55| Column classes: raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw
> 'data.frame': 1000001 obs. of 25 variables:
> $ : raw 00 00 00 00 ...
> $ : raw 00 00 00 00 ...
> $ : raw 00 00 00 00 ...
> $ : raw 00 00 00 00 ...
> $ : raw 00 00 00 00 ...
> $ : raw 00 00 00 00 ...
> $ : raw 00 00 00 00 ...
> $ : raw 00 00 00 00 ...
> $ : raw 00 00 00 00 ...
> $ : raw 00 00 00 00 ...
> $ : raw 00 00 00 00 ...
> $ : raw 00 00 00 00 ...
> $ : raw 00 00 00 00 ...
> $ : raw 00 00 00 00 ...
> $ : raw 00 00 00 00 ...
> $ : raw 00 00 00 00 ...
> $ : raw 00 00 00 00 ...
> $ : raw 00 00 00 00 ...
> $ : raw 00 00 00 00 ...
> $ : raw 00 00 00 00 ...
> $ : raw 00 00 00 00 ...
> $ : raw 00 00 00 00 ...
> $ : raw 00 00 00 00 ...
> $ : raw 00 00 00 00 ...
> $ : raw 00 00 00 00 ...
> 20121126 20:48:55| Allocating data object...done
> 20121126 20:48:55| Reading data...
> 20121126 20:48:59| Reading data...done
> 20121126 20:48:59| Reading data frame...done
> 20121126 20:48:59| Coerce to a character matrix...
> 20121126 20:49:00| Coerce to a character matrix...done
> 20121126 20:49:00| Reading sequence matrix...done
> 20121126 20:49:00| Reading sequence matrix...done
> 20121126 20:49:00| Reading match scores...
> 20121126 20:49:01| Allocating data object...
> 20121126 20:49:01| Number of rows: 1000001
> 20121126 20:49:01| Column classes: integer
> 'data.frame': 1000001 obs. of 1 variable:
> $ : int 0 0 0 0 0 0 0 0 0 0 ...
> 20121126 20:49:01| Allocating data object...done
> 20121126 20:49:01| Reading data...
> 20121126 20:49:01| Reading data...done
> 20121126 20:49:01| Reading match scores...done
> 20121126 20:49:01| Constructing design matrix...
> Error: cannot allocate vector of size 618.0 Mb
> In addition: There were 17 warnings (use warnings() to see them)
> 20121126 20:49:08| Constructing design matrix...done
> 20121126 20:49:08| Retrieving design matrix...done
> 20121126 20:49:08| Reading design matrix...done
> 20121126 20:49:08| Fitting chunk #1 of 5...done
> 20121126 20:49:08| Path: probeData/DS,MN,lm/Hs_PromPR_v02...done
> 20121126 20:49:08| Normalizing 1 arrays...done
> 20121126 20:49:08|Normalization data set for probe-sequence effects...done
>> sessionInfo()
> R version 2.15.2 (2012-10-26)
> Platform: i386-w64-mingw32/i386 (32-bit)
>
>
> locale:
> [1] LC_COLLATE=Chinese_People's Republic of China.936 LC_CTYPE=Chinese_People's Republic of China.936
> [3] LC_MONETARY=Chinese_People's Republic of China.936 LC_NUMERIC=C
> [5] LC_TIME=Chinese_People's Republic of China.936
>
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
>
> other attached packages:
> [1] aroma.affymetrix_2.6.0 affxparser_1.28.1 aroma.apd_0.2.3 R.huge_0.4.1 aroma.light_1.28.0
> [6] aroma.core_2.6.0 matrixStats_0.6.2 R.rsp_0.8.2 R.cache_0.6.5 R.devices_2.1.3
> [11] R.filesets_1.6.0 digest_0.5.2 R.utils_1.18.0 R.oo_1.10.2 R.methodsS3_1.4.2
>
>
>> memory.limit()
> [1] 1535
>> memory.limit(T)
> [1] 1077
> anyone can help me?should i upgrade my pc hardware? Thanks!!
> [[alternative HTML version deleted]]
>
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> --
> Chao-Jen Wong
> Grady Lab / Clinical Research
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Avenue N., M1-B514
> PO Box 19024
> Seattle, WA 98109
> 206.667.4485
> cwon2 at fhcrc.org
>
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