i have program loads large spatialpolygonsdataframe object (1.4gb) memory performs analysis, attempts remove object. however, @ system memory using system command free shows object remains until r session reset. can reproduce memory leak using rworldmap , rworlxtra packages make large list of world maps, each spatialpolygonsdataframe, trying remove them:
install.packages("sp") install.packages("rworldmap") install.packages("rworldxtra") library(sp) library(rworldmap) library(rworldxtra) these.maps.large <- lapply(1:100, function(x) assign(paste0("a_", x), getmap(resolution = "high"))) these.maps.smaller <- lapply(1:20, function(x) assign(paste0("a_", x), getmap(resolution = "high"))) # frees memory rm(list="these.maps.smaller") gc(reset=t) # fails free memory rm(list="these.maps.large") gc(reset=t) edit here output calling system2("free") after each stage.
restarting r session... > library(sp) > library(rworldmap) ### welcome rworldmap ### short introduction type : vignette('rworldmap') > library(rworldxtra) > system2("free") total used free shared buff/cache available mem: 131987656 1386468 118712292 540008 11888896 129731040 swap: 4194300 3505464 688836 > these.maps.large <- lapply(1:100, function(x) assign(paste0("a_", x), getmap(resolution = "high"))) > system2("free") total used free shared buff/cache available mem: 131987656 2708040 117390660 540008 11888956 128409404 swap: 4194300 3505464 688836 > rm(list="these.maps.large") > gc(reset=t) used (mb) gc trigger (mb) max used (mb) ncells 585803 31.3 9601876 512.8 585803 31.3 vcells 711198 5.5 96623732 737.2 711198 5.5 > system2("free") total used free shared buff/cache available mem: 131987656 2708428 117390424 540008 11888804 128409168 swap: 4194300 3505464 688836 restarting r session... > library(sp) > library(rworldmap) ### welcome rworldmap ### short introduction type : vignette('rworldmap') > library(rworldxtra) > system2("free") total used free shared buff/cache available mem: 131987656 1386696 118711988 540008 11888972 129730744 swap: 4194300 3505464 688836 > these.maps.smaller <- lapply(1:20, function(x) assign(paste0("a_", x), getmap(resolution = "high"))) > system2("free") total used free shared buff/cache available mem: 131987656 1699628 118399100 540008 11888928 129417836 swap: 4194300 3505464 688836 > rm(list="these.maps.smaller") > gc(reset=t) used (mb) gc trigger (mb) max used (mb) ncells 702817 37.6 2564361 137.0 702817 37.6 vcells 966452 7.4 21638748 165.1 966452 7.4 > system2("free") total used free shared buff/cache available mem: 131987656 1699612 118399116 540008 11888928 129417852 swap: 4194300 3505464 688836 has got idea why case , way might possible remove 1 of these large sp objects without having reset session?
r version 3.2.3 (2015-12-10) platform: x86_64-redhat-linux-gnu (64-bit) running under: scientific linux 7.2 (nitrogen)
you don't show output. see:
> rm(list="these.maps.smaller") > gc(reset=t) used (mb) gc trigger (mb) max used (mb) ncells 7782803 415.7 14442815 771.4 7782803 415.7 vcells 113371012 865.0 184235296 1405.7 113371012 865.0 > # fails free memory > rm(list="these.maps.large") > gc(reset=t) used (mb) gc trigger (mb) max used (mb) ncells 524121 28 11554252 617.1 524121 28 vcells 649283 5 147388236 1124.5 649283 5 which suggest removing these large maps releases memory; value equal obtained in fresh session after loading packages.
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