[BioC] Affy. memory allocation trouble!
Jens Vilstrup Johansen
jvj@nordicbioscience.com
Thu, 21 Nov 2002 10:10:23 +0100
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Hi
I get this error message. How do I solve this?
>library(affy)
> Data <- ReadAffy ()
reading CDF file
processing information
reading 2 CEL files..
preparing probe level object
Error: cannot allocate vector of size 3874 Kb
In addition: Warning message:=20
Reached total allocation of 127Mb: see help(memory.size)=20
I don't know if this is helpfull:
> gc()
used (Mb) gc trigger (Mb)
Ncells 301800 8.1 1068187 28.6
Vcells 66248 0.6 8156627 62.3
> memory.size()
[1] 102909640
> memory.limit()
[1] 133619712
Thanks!
regards,
Jens Johansen
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<P><FONT SIZE=3D2 FACE=3D"Courier New">Hi</FONT>
</P>
<P><FONT SIZE=3D2 FACE=3D"Courier New">I get this error message. How do =
I solve this?</FONT>
</P>
<P><FONT SIZE=3D2 FACE=3D"Courier New">>library(affy)</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Courier New">> Data <- ReadAffy =
()</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Courier New">reading CDF file</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Courier New">processing information</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Courier New">reading 2 CEL files..</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Courier New">preparing probe level =
object</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Courier New">Error: cannot allocate vector of =
size 3874 Kb</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Courier New">In addition: Warning message: =
</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Courier New">Reached total allocation of =
127Mb: see help(memory.size) </FONT>
</P>
<P><FONT SIZE=3D2 FACE=3D"Courier New">I don't know if this is =
helpfull:</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Courier New">> gc()</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Courier =
New"> used (Mb) gc =
trigger (Mb)</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Courier New">Ncells 301800 =
8.1 1068187 28.6</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Courier New">Vcells 66248 =
0.6 8156627 62.3</FONT>
</P>
<P><FONT SIZE=3D2 FACE=3D"Courier New">> memory.size()</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Courier New">[1] 102909640</FONT>
</P>
<P><FONT SIZE=3D2 FACE=3D"Courier New">> memory.limit()</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Courier New">[1] 133619712</FONT>
</P>
<P><FONT SIZE=3D2 FACE=3D"Courier New">Thanks!</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Courier New">regards,</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Courier New"> Jens Johansen</FONT>
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