Hello,
I'm trying to track down the cause of some extreme memory usage and I've been using Dirk Eddelbuettel's lsos() function he posted on stack overflow. There is a large difference between R's RAM usage :
PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND
6637 darstr 20 0 30.0g 29g 4712 S 0 63.2 10:34.43 R
and what objects I have loaded in memory :
lsos()
Type Size PrettySize Rows Columns
A list 552387720 526.8 Mb 2 NA
B GRangesList 552376408 526.8 Mb 4 NA
C SimpleRleList 353421896 337 Mb 24 NA
D GRanges 236410608 225.5 Mb 15272853 NA
E data.frame 6981952 6.7 Mb 24966 14
F data.frame 6782136 6.5 Mb 24966 13
G list 4393704 4.2 Mb 24964 NA
H matrix 3195760 3 Mb 24964 16
I list 1798752 1.7 Mb 24964 NA
J GRanges 312656 305.3 Kb 24964 NA
(The total looks like about 1.5 GB)
I haven't got any calls to external C code in my R script, although the Bioconductor packages I am using do. How can I regain those missing Gigabytes ?
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Dario Strbenac
Research Assistant
Cancer Epigenetics
Garvan Institute of Medical Research
Darlinghurst NSW 2010
Australia