hi,
i've tryied to use
readRAST6 instead of readFLOAT6sp
this is the log:
> library(cluster)
> library(cluster)
> x <- readRAST6(c
("er","crosc","longc","slope","profc","minic","maxic"))
.....
.......
........
Percent complete: 100%
r.out.bin complete.
Creating BIL support files ...
Header File = /grassdata/remote/onearth/.tmp/powerbook-g4-12-di-
epifanio.local/maxic.hdr
World File = /grassdata/remote/onearth/.tmp/powerbook-g4-12-di-
epifanio.local/maxic.wld
Exporting Raster as double values(bytes=8)
Using the Current Region settings ...
north=4516560.000000
south=4483080.000000
east=527440.000000
west=485740.000000
r=1674
c=2085
Percent complete: 100%
r.out.bin complete.
> gc()
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 416932 11.2 741108 19.8 692659 18.5
Vcells 23007923 175.6 194536624 1484.2 242896455 1853.2
> morph <- as(x, "data.frame")
R(22751) malloc: *** vm_allocate(size=8421376) failed (error code=3)
R(22751) malloc: *** error: can't allocate region
R(22751) malloc: *** set a breakpoint in szone_error to debug
Errore: memoria 'vector' esaurita (raggiunto il limite?)
R(22751) malloc: *** vm_allocate(size=8421376) failed (error code=3)
R(22751) malloc: *** error: can't allocate region
R(22751) malloc: *** set a breakpoint in szone_error to debug
>
...
R not respond,
i force to quit the shell.
i cant continue to check morph:
str(morph) # look inside morph
summary(morph)
sapply(morph, function(x) any(!is.finite(x)))
# check morph for NAs etc.
Massimo
Il giorno 03/dic/06, alle ore 12:00, r-sig-geo-
[EMAIL PROTECTED] ha scritto:
> On Sat, 2 Dec 2006, Massimo Di Stefano wrote:
>
>> Roger:
>>
>> This is the log,
>>
>>> library(spgrass6)
>> Carico il pacchetto richiesto: sp
>> Carico il pacchetto richiesto: maptools
>> Carico il pacchetto richiesto: foreign
>> Carico il pacchetto richiesto: rgdal
>> Geospatial Data Abstraction Library extensions to R
>> successfully loaded
>>> library(cluster)
>>> sessionInfo()
>> R version 2.4.0 (2006-10-03)
>> powerpc-apple-darwin8.7.0
>>
>> locale:
>> it_IT/it_IT/it_IT/C/it_IT/it_IT
>>
>> attached base packages:
>> [1] "methods" "stats" "graphics" "grDevices"
>> "utils" "datasets"
>> [7] "base"
>>
>> other attached packages:
>> cluster spgrass6 rgdal maptools foreign sp
>> "1.11.2" "0.3-3" "0.5-1" "0.6-3" "0.8-18" "0.9-4"
>>> gc()
>> used (Mb) gc trigger (Mb) max used (Mb)
>> Ncells 408935 11.0 597831 16 531268 14.2
>> Vcells 320324 2.5 786432 6 472905 3.7
>>> gmeta6 <- gmeta6()
>>> x <-
>> readFLOAT6sp(c("er","crosc","longc","slope","profc","minic","maxic"))
>> Warning messages:
>> 1: perl = TRUE ? implementato solo nei locale UTF-8
>> 2: perl = TRUE ? implementato solo nei locale UTF-8
>> 3: perl = TRUE ? implementato solo nei locale UTF-8
>> 4: perl = TRUE ? implementato solo nei locale UTF-8
>> 5: perl = TRUE ? implementato solo nei locale UTF-8
>> 6: perl = TRUE ? implementato solo nei locale UTF-8
>> 7: perl = TRUE ? implementato solo nei locale UTF-8
>
> Nowadays I would suggest readRAST6() instead of readFLOAT6sp(),
> because it
> uses r.out.bin rather than r.out.arc from GRASS. The perl=TRUE
> warnings
> seems to be coming from string comparison somewhere inside a function
> called by readFLOAT6sp(), I don't think they are the problem.
>
>
>
>>> gc()
>> used (Mb) gc trigger (Mb) max used
>> (Mb)
>> Ncells 418204 11.2 741108 19.8 699974
>> 18.7
>> Vcells 22643234 172.8 191414408 1460.4 238993684
>> 1823.4
>>> morph <- data.frame(cbind(x$er, x$crosc, x$longc,
>> x$slope, x$profc, x$minic, x$maxic))
>
> morph <- as(x, "data.frame")
>
> str(morph) # look inside morph
> summary(morph)
>
> sapply(morph, function(x) any(!is.finite(x)))
> # check morph for NAs etc.
>
>
>>> gc()
>> used (Mb) gc trigger (Mb) max used
>> (Mb)
>> Ncells 418451 11.2 741108 19.8 699974
>> 18.7
>> Vcells 46682176 356.2 153131526 1168.4 238993684
>> 1823.4
>> <er, x$crosc, x$longc, x$slope/max(x$slope), x$profc,
>> x$minic, x$maxic))
>>> gc()
>> used (Mb) gc trigger (Mb) max used
>> (Mb)
>> Ncells 418453 11.2 741108 19.8 699974
>> 18.7
>> Vcells 46682176 356.2 137841862 1051.7 238993684
>> 1823.4
>>> names(morph) <-
>> c("er","crosc","longc","slope_n","profc","minic","maxic")
>>> gc()
>> used (Mb) gc trigger (Mb) max used
>> (Mb)
>> Ncells 418456 11.2 741108 19.8 699974
>> 18.7
>> Vcells 46682180 356.2 137841862 1051.7 238993684
>> 1823.4
>>> morph.clara <- clara(morph, k=5, stand=F)
>> Errore in clara(morph, k = 5, stand = F) :
>> Observations
>> 1929241,1931311,1933381,1935451,1937521,1939591,1941661,1943731,19458
>> 01,1947871,1949941,1952011,1954081,1956151,1958221,1960291,1962361,19
>> 64431,1966501,1968571,1970641,1972711,1974781,1976851,1978921,1980991
>> ,
>> 1983061,1985131,1987201,1989271,1991341,1993411,1995481,1997551,19996
>> 21,2001691,2003761,2005831,2007901,2009971,2012041,2014111,2016181,20
>> 18251,2020321,2022391,2024461,2026531,2028601,2030671,2032741,2034811
>> ,
>> 2036881,2038951,2041021,2043091,2045161,2047231,2049301,2051371,20534
>> 41,2055511,2057581,205965
>> 1,2061721,2063791,2065861,2067931,2070001,2072071,2074141,2076211,207
>> 8281,2080351,2082421,2084491,2086561,2088631,2090701,2092771,2094841,
>> 2096911,2098981,2101051,2103121,2105191,2107261,2109331,2111401,21134
>> 71,2115541,2117611,2119681,2121751,2123821,21258
>> 91,2127961,2130031,2132101,2134171,2136241,2138311,2140381,2142451,21
>> 44521,2146591,2148661,2150731,2152801,2154871,2156941,2159011,2161081
>> ,2163151,2165221,2167291,2169361,2171431
>>> traceback()
>> 2: stop(ngettext(length(i), sprintf("Observation %d
>> has", i[1]),
>> sprintf("Observations %s have", paste(i,
>> collapse = ","))),
>> " *only* NAs --> omit for clustering")
>> 1: clara(morph, k = 5, stand = F)
>>
>> is this log usefool ?
>
> Yes, I think the problem is firstly that there are NAs in morph,
> and then
> that the string listing the row numbers of the NAs exceeds 8K
> characters
> (your earlier message had: Errore in sprintf(fmt, ...) : La lunghezza
> della stringa eccede la dimensione del buffer di 8192)
>
>
> So try clara on morph once you have omitted the NAs. If the NAs are
> for
> all variables in a row, coercing from SpatialGridDataFrame to
> SpatialPixelsDataFrame will work, if only some, you need to set the
> whole
> row to NA, coerce, cluster, add the clara results to the
> SpatialPixelsDataFrame, coerce back to SpatialGridDataFrame, then
> back to
> GRASS.
>
> Once this is resolved, please post back to the list as well as to
> me, NAs
> do happen, expecially in geomorphometrics, for example around the
> edges
> where the filter is not fully within the window and/or mask.
>
> Best wishes,
>
> Roger
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