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Peter

2010-Mar-06 03:08 UTC

[R] memory error in for loop

hi,

I have been attempting to run this script and am getting some strange 
results. The script connects to a database and retrieves a series of 
tables, using sequential sql statements. I have tested all of the sql 
statements in the PostGreSQL terminal and they all return the desired 
results. I place each table into a list and run a FOR loop for 'i' in 
the list. The script generates the first map perfectly and begins to 
draw the second and then crashes in the middle of creating the second 
plot. I am suspicious that somehow i have a problem in my for loop that 
results in memory overload but I have been struggling to figure it out 
all day with no success. I have included below the for loop in the code 
and the beginning of the error message that is produced in the terminal. 
Any suggestions would be most welcome.

thanks in advance,

peter

script:

#create a list of results tables
matrixlist <- list(r_baseline, r_badlce, r_cblend, r_fedforest, r_ffv, 
r_hiencrop, r_loencrop, r_maxfeed) 
#par(mfcol= c(5,5))
for (i in matrixlist){
                                        
  ptable<-i[,-1]#create plot matrix w/o price point column

  ptable [is.na(ptable)] <- 0 #convert NA values to 0
                                
  maxval<-max(ptable) #create volume axis
  interval<-ceiling(maxval)/27
  mgy<- seq(0,ceiling(maxval), 
by=interval)                                     
  fprice <- c(i$price_point)#create price point axis
  #pdf(paste(i,"fuel_pw.pdf", sep=""), bg="white")
  matplot(ptable, fprice, type="l", col= rainbow(length(names(i))))
  #rm(i,ptable, fprice, maxval, interval, mgy)
  dev.off()
}

and the resulting error:

+   fprice <- c(i$price_point)#create price point axis
+   #pdf(paste(i,"fuel_pw.pdf", sep=""),
bg="white")
+   matplot(ptable, fprice, type="l", col= rainbow(length(names(i))))
+   rm(i,ptable, fprice, maxval, interval, mgy)
+   dev.off()
+ }
matplot: doing 17 plots with  col= ("#FF0000FF" "#FF5500FF"
"#FFAA00FF" "#FFFF00FF" "#AAFF00FF"
"#55FF00FF" "#00FF00FF"
"#00FF55FF" "#00FFAAFF" "#00FFFFFF"
"#00AAFFFF" "#0055FFFF"
"#0000FFFF" "#5500FFFF" "#AA00FFFF"
"#FF00FFFF" "#FF00AAFF"
"#FF0055FF") pch= ("1" "2" "3"
"4" "5" "6" "7" "8"
"9" "0" "a" "b" "c"
"d" "e" "f" "g" "h"
"i" "j" "k" "l" "m"
"n" "o" "p" "q" "r"
"s" "t"
"u" "v" "w" "x" "y"
"z" "A" "B" "C" "D"
"E" "F" "G" "H" "I"
"J" "K"
"L" "M" "N" "O" "P"
"Q" "R" "S" "T" "U"
"V" "W" "X" "Y" "Z") ...

matplot: doing 23 plots with  col= ("#FF0000FF" "#FF4000FF"
"#FF8000FF" "#FFBF00FF" "#FFFF00FF"
"#BFFF00FF" "#80FF00FF"
"#40FF00FF" "#00FF00FF" "#00FF40FF"
"#00FF80FF" "#00FFBFFF"
"#00FFFFFF" "#00BFFFFF" "#0080FFFF"
"#0040FFFF" "#0000FFFF"
"#4000FFFF" "#8000FFFF" "#BF00FFFF"
"#FF00FFFF" "#FF00BFFF"
"#FF0080FF" "#FF0040FF") pch= ("1" "2"
"3" "4" "5" "6" "7"
"8" "9" "0"
"a" "b" "c" "d" "e"
"f" "g" "h" "i" "j"
"k" "l" "m" "n" "o"
"p" "q"
"r" "s" "t" "u" "v"
"w" "x" "y" "z" "A"
"B" "C" "D" "E" "F"
"G" "H"
"I" "J" "K" "L" "M"
"N" "O" "P" "Q" "R"
"S" "T" "U" "V" "W"
"X" "Y"
"Z") ...

Garbage collection 3 = 2+0+1 (level 0) ...
3.6 Mbytes of cons cells used (38%)
0.8 Mbytes of vectors used (13%)
*** glibc detected *** /usr/lib/R/bin/exec/R: double free or
corruption (!prev): 0x094f8c38 ***
======= Backtrace: ========/lib/i686/cmov/libc.so.6[0xb7486824]
/lib/i686/cmov/libc.so.6[0xb74880b3]
/lib/i686/cmov/libc.so.6(cfree+0x6d)[0xb748b0dd]
/usr/lib/libpq.so.5(PQclear+0xf6)[0xb6e53976]
/home/ptittmann/R/i486-pc-linux-gnu-library/2.10/RdbiPgSQL/libs/RdbiPgSQL.so(PgSQLclearResult+0x25)[0xb6fc2665]
/usr/lib/R/lib/libR.so(R_RunWeakRefFinalizer+0x161)[0xb76721f1]
/usr/lib/R/lib/libR.so[0xb7672357]
/usr/lib/R/lib/libR.so[0xb76743fe]
/usr/lib/R/lib/libR.so(Rf_allocVector+0xb8)[0xb7675628]
/usr/lib/R/lib/libR.so(Rf_usemethod+0x41d)[0xb768306d]

Uwe Ligges

2010-Mar-07 17:04 UTC

head link

[R] memory error in for loop

Probably a bug in the RdbiPgSQL package you are using. Please ciontact 
its maintainer and send a reproducible example.

Best,
Uwe Ligges


On 06.03.2010 04:08, Peter wrote:> hi,
>
> I have been attempting to run this script and am getting some strange
> results. The script connects to a database and retrieves a series of
> tables, using sequential sql statements. I have tested all of the sql
> statements in the PostGreSQL terminal and they all return the desired
> results. I place each table into a list and run a FOR loop for 'i'
in
> the list. The script generates the first map perfectly and begins to
> draw the second and then crashes in the middle of creating the second
> plot. I am suspicious that somehow i have a problem in my for loop that
> results in memory overload but I have been struggling to figure it out
> all day with no success. I have included below the for loop in the code
> and the beginning of the error message that is produced in the terminal.
> Any suggestions would be most welcome.
>
> thanks in advance,
>
> peter
>
> script:
>
> #create a list of results tables
> matrixlist <- list(r_baseline, r_badlce, r_cblend, r_fedforest, r_ffv,
> r_hiencrop, r_loencrop, r_maxfeed) #par(mfcol= c(5,5))
> for (i in matrixlist){
> ptable<-i[,-1]#create plot matrix w/o price point column
>
> ptable [is.na(ptable)] <- 0 #convert NA values to 0
> maxval<-max(ptable) #create volume axis
> interval<-ceiling(maxval)/27
> mgy<- seq(0,ceiling(maxval), by=interval) fprice <-
> c(i$price_point)#create price point axis
> #pdf(paste(i,"fuel_pw.pdf", sep=""),
bg="white")
> matplot(ptable, fprice, type="l", col= rainbow(length(names(i))))
> #rm(i,ptable, fprice, maxval, interval, mgy)
> dev.off()
> }
>
> and the resulting error:
>
> + fprice <- c(i$price_point)#create price point axis
> + #pdf(paste(i,"fuel_pw.pdf", sep=""),
bg="white")
> + matplot(ptable, fprice, type="l", col=
rainbow(length(names(i))))
> + rm(i,ptable, fprice, maxval, interval, mgy)
> + dev.off()
> + }
> matplot: doing 17 plots with col= ("#FF0000FF"
"#FF5500FF"
> "#FFAA00FF" "#FFFF00FF" "#AAFF00FF"
"#55FF00FF" "#00FF00FF"
> "#00FF55FF" "#00FFAAFF" "#00FFFFFF"
"#00AAFFFF" "#0055FFFF"
> "#0000FFFF" "#5500FFFF" "#AA00FFFF"
"#FF00FFFF" "#FF00AAFF"
> "#FF0055FF") pch= ("1" "2" "3"
"4" "5" "6" "7" "8"
"9" "0" "a" "b" "c"
> "d" "e" "f" "g" "h"
"i" "j" "k" "l" "m"
"n" "o" "p" "q" "r"
"s" "t"
> "u" "v" "w" "x" "y"
"z" "A" "B" "C" "D"
"E" "F" "G" "H" "I"
"J" "K"
> "L" "M" "N" "O" "P"
"Q" "R" "S" "T" "U"
"V" "W" "X" "Y" "Z") ...
>
> matplot: doing 23 plots with col= ("#FF0000FF"
"#FF4000FF"
> "#FF8000FF" "#FFBF00FF" "#FFFF00FF"
"#BFFF00FF" "#80FF00FF"
> "#40FF00FF" "#00FF00FF" "#00FF40FF"
"#00FF80FF" "#00FFBFFF"
> "#00FFFFFF" "#00BFFFFF" "#0080FFFF"
"#0040FFFF" "#0000FFFF"
> "#4000FFFF" "#8000FFFF" "#BF00FFFF"
"#FF00FFFF" "#FF00BFFF"
> "#FF0080FF" "#FF0040FF") pch= ("1"
"2" "3" "4" "5" "6"
"7" "8" "9" "0"
> "a" "b" "c" "d" "e"
"f" "g" "h" "i" "j"
"k" "l" "m" "n" "o"
"p" "q"
> "r" "s" "t" "u" "v"
"w" "x" "y" "z" "A"
"B" "C" "D" "E" "F"
"G" "H"
> "I" "J" "K" "L" "M"
"N" "O" "P" "Q" "R"
"S" "T" "U" "V" "W"
"X" "Y"
> "Z") ...
>
> Garbage collection 3 = 2+0+1 (level 0) ...
> 3.6 Mbytes of cons cells used (38%)
> 0.8 Mbytes of vectors used (13%)
> *** glibc detected *** /usr/lib/R/bin/exec/R: double free or
> corruption (!prev): 0x094f8c38 ***
> ======= Backtrace: ========> /lib/i686/cmov/libc.so.6[0xb7486824]
> /lib/i686/cmov/libc.so.6[0xb74880b3]
> /lib/i686/cmov/libc.so.6(cfree+0x6d)[0xb748b0dd]
> /usr/lib/libpq.so.5(PQclear+0xf6)[0xb6e53976]
>
/home/ptittmann/R/i486-pc-linux-gnu-library/2.10/RdbiPgSQL/libs/RdbiPgSQL.so(PgSQLclearResult+0x25)[0xb6fc2665]
>
> /usr/lib/R/lib/libR.so(R_RunWeakRefFinalizer+0x161)[0xb76721f1]
> /usr/lib/R/lib/libR.so[0xb7672357]
> /usr/lib/R/lib/libR.so[0xb76743fe]
> /usr/lib/R/lib/libR.so(Rf_allocVector+0xb8)[0xb7675628]
> /usr/lib/R/lib/libR.so(Rf_usemethod+0x41d)[0xb768306d]
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

Gabor Grothendieck

2010-Mar-07 17:08 UTC

head link

[R] memory error in for loop

Try the RpgSQL package and see if you get the same problem.

On Fri, Mar 5, 2010 at 10:08 PM, Peter <ptittmann at gmail.com>
wrote:> hi,
>
> I have been attempting to run this script and am getting some strange
> results. The script connects to a database and retrieves a series of
tables,
> using sequential sql statements. I have tested all of the sql statements in
> the PostGreSQL terminal and they all return the desired results. I place
> each table into a list and run a FOR loop for 'i' in the list. The
script
> generates the first map perfectly and begins to draw the second and then
> crashes in the middle of creating the second plot. I am suspicious that
> somehow i have a problem in my for loop that results in memory overload but
> I have been struggling to figure it out all day with no success. I have
> included below the for loop in the code and the beginning of the error
> message that is produced in the terminal. Any suggestions would be most
> welcome.
>
> thanks in advance,
>
> peter
>
> script:
>
> #create a list of results tables
> matrixlist <- list(r_baseline, r_badlce, r_cblend, r_fedforest, r_ffv,
> r_hiencrop, r_loencrop, r_maxfeed) #par(mfcol= c(5,5))
> for (i in matrixlist){
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?ptable<-i[,-1]#create plot matrix
w/o
> price point column
>
> ?ptable [is.na(ptable)] <- 0 #convert NA values to 0
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?maxval<-max(ptable) #create volume axis
> ?interval<-ceiling(maxval)/27
> ?mgy<- seq(0,ceiling(maxval), by=interval)
> ? ?fprice <- c(i$price_point)#create price point axis
> ?#pdf(paste(i,"fuel_pw.pdf", sep=""),
bg="white")
> ?matplot(ptable, fprice, type="l", col=
rainbow(length(names(i))))
> ?#rm(i,ptable, fprice, maxval, interval, mgy)
> ?dev.off()
> }
>
> and the resulting error:
>
> + ? fprice <- c(i$price_point)#create price point axis
> + ? #pdf(paste(i,"fuel_pw.pdf", sep=""),
bg="white")
> + ? matplot(ptable, fprice, type="l", col=
rainbow(length(names(i))))
> + ? rm(i,ptable, fprice, maxval, interval, mgy)
> + ? dev.off()
> + }
> matplot: doing 17 plots with ?col= ("#FF0000FF"
"#FF5500FF"
> "#FFAA00FF" "#FFFF00FF" "#AAFF00FF"
"#55FF00FF" "#00FF00FF"
> "#00FF55FF" "#00FFAAFF" "#00FFFFFF"
"#00AAFFFF" "#0055FFFF"
> "#0000FFFF" "#5500FFFF" "#AA00FFFF"
"#FF00FFFF" "#FF00AAFF"
> "#FF0055FF") pch= ("1" "2" "3"
"4" "5" "6" "7" "8"
"9" "0" "a" "b" "c"
> "d" "e" "f" "g" "h"
"i" "j" "k" "l" "m"
"n" "o" "p" "q" "r"
"s" "t"
> "u" "v" "w" "x" "y"
"z" "A" "B" "C" "D"
"E" "F" "G" "H" "I"
"J" "K"
> "L" "M" "N" "O" "P"
"Q" "R" "S" "T" "U"
"V" "W" "X" "Y" "Z") ...
>
> matplot: doing 23 plots with ?col= ("#FF0000FF"
"#FF4000FF"
> "#FF8000FF" "#FFBF00FF" "#FFFF00FF"
"#BFFF00FF" "#80FF00FF"
> "#40FF00FF" "#00FF00FF" "#00FF40FF"
"#00FF80FF" "#00FFBFFF"
> "#00FFFFFF" "#00BFFFFF" "#0080FFFF"
"#0040FFFF" "#0000FFFF"
> "#4000FFFF" "#8000FFFF" "#BF00FFFF"
"#FF00FFFF" "#FF00BFFF"
> "#FF0080FF" "#FF0040FF") pch= ("1"
"2" "3" "4" "5" "6"
"7" "8" "9" "0"
> "a" "b" "c" "d" "e"
"f" "g" "h" "i" "j"
"k" "l" "m" "n" "o"
"p" "q"
> "r" "s" "t" "u" "v"
"w" "x" "y" "z" "A"
"B" "C" "D" "E" "F"
"G" "H"
> "I" "J" "K" "L" "M"
"N" "O" "P" "Q" "R"
"S" "T" "U" "V" "W"
"X" "Y"
> "Z") ...
>
> Garbage collection 3 = 2+0+1 (level 0) ...
> 3.6 Mbytes of cons cells used (38%)
> 0.8 Mbytes of vectors used (13%)
> *** glibc detected *** /usr/lib/R/bin/exec/R: double free or
> corruption (!prev): 0x094f8c38 ***
> ======= Backtrace: ========> /lib/i686/cmov/libc.so.6[0xb7486824]
> /lib/i686/cmov/libc.so.6[0xb74880b3]
> /lib/i686/cmov/libc.so.6(cfree+0x6d)[0xb748b0dd]
> /usr/lib/libpq.so.5(PQclear+0xf6)[0xb6e53976]
>
/home/ptittmann/R/i486-pc-linux-gnu-library/2.10/RdbiPgSQL/libs/RdbiPgSQL.so(PgSQLclearResult+0x25)[0xb6fc2665]
> /usr/lib/R/lib/libR.so(R_RunWeakRefFinalizer+0x161)[0xb76721f1]
> /usr/lib/R/lib/libR.so[0xb7672357]
> /usr/lib/R/lib/libR.so[0xb76743fe]
> /usr/lib/R/lib/libR.so(Rf_allocVector+0xb8)[0xb7675628]
> /usr/lib/R/lib/libR.so(Rf_usemethod+0x41d)[0xb768306d]
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

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