Hi,
I am trying to use "read.pnm" from the package "pixmap" to
read more
than 10 thousand image files in "mydir".
> file.list <- dir( "mydir", full=T)
> for( i in 1:length(file.list) ) {
print(i)
x <- read.pnm(file.list[i])
}
In the beginning it was fine. But after reading 1020 images or so, the
read.pnm function
seems to crash on me:
[1] 1017
[1] 1018
[1] 1019
[1] 1020
Error in open.connection(con, open = "rb") :
unable to open connection
In addition: Warning message:
cannot open file `/mydir/myfile1020.ppm'
Then the R environment seems to crash too because I can't read any other
files anymore. Neither can I use function "dir".
dir("mydir")
character(0)
Warning message:
list.files: "mydir" is not a readable directory
I quit R and close all other applications and come back. The problem is
easily repeated.
THe following is my system information. The linux version is Redhat 8.0.
> R.version
_
platform i686-pc-linux-gnu
arch i686
os linux-gnu
system i686, linux-gnu
status
major 1
minor 6.1
year 2002
month 11
day 01
language R
Your help is highly appreciated!
Best Regards,
Jonathan
Reconformed on R v1.6.2 (no patch) on WinXP Pro. Here is my
troubleshooting. Using the following files
-rwx------+ 1 hb None 29943 Jun 30 2002 hb.ppm
-rwx------+ 1 hb None 2049 Jul 20 2002 logosm-gray.pgm
-rwx------+ 1 hb None 379 Jul 20 2002 logosm-mono.pbm
-rwx------+ 1 hb None 3682 Feb 2 1998 logosm.jpg
-rwx------+ 1 hb None 5924 Jun 29 2002 logosm.ppm
# R --vanilla
library(pixmap)
# The following fails to read the file at try 509:
for( i in 1:2000 ) { print(i); x <- read.pnm("logosm.ppm"); }
# The following fails to read the file at try 509:
for( i in 1:2000 ) { print(i); x <- read.pnm("logosm-mono.pbm"); }
# The following fails to read the file at try 509:
for( i in 1:2000 ) { print(i); x <- read.pnm("logosm-gray.pgm"); }
# The following fails to read the file at try 509:
for( i in 1:2000 ) { print(i); x <- read.pnm("hb.ppm"); }
Note that I have to restart R between each file; the problem is not just
locking one file, but it messes up the I/O for all files. I get the same
result over and over again after restarting R and it does not seem like
the filesize matters. Most I/O seems to fails. My dir() and file.show()
still works though. Can not save workspace when quiting R etc. Trying to
delete "logosm.ppm" using WinXP Explorer won't work - the file is
locked.
> R.version
_
platform i386-pc-mingw32
arch i386
os mingw32
system i386, mingw32
status
major 1
minor 6.2
year 2003
month 01
day 10
language R
Cheers
Henrik Bengtsson
> -----Original Message-----
> From: r-help-admin at stat.math.ethz.ch
> [mailto:r-help-admin at stat.math.ethz.ch] On Behalf Of Jonathan Q. Li
> Sent: den 28 februari 2003 10:55
> To: r-help at stat.math.ethz.ch
> Subject: [R] File opening error after 1020 files opened
>
>
> Hi,
>
> I am trying to use "read.pnm" from the package "pixmap"
to read more
> than 10 thousand image files in "mydir".
>
> > file.list <- dir( "mydir", full=T)
> > for( i in 1:length(file.list) ) {
> print(i)
> x <- read.pnm(file.list[i])
> }
>
> In the beginning it was fine. But after reading 1020 images
> or so, the
> read.pnm function
> seems to crash on me:
>
> [1] 1017
> [1] 1018
> [1] 1019
> [1] 1020
> Error in open.connection(con, open = "rb") :
> unable to open connection
> In addition: Warning message:
> cannot open file `/mydir/myfile1020.ppm'
>
> Then the R environment seems to crash too because I can't
> read any other
> files anymore. Neither can I use function "dir".
>
> dir("mydir")
> character(0)
> Warning message:
> list.files: "mydir" is not a readable directory
>
> I quit R and close all other applications and come back. The
> problem is
> easily repeated.
> THe following is my system information. The linux version is
> Redhat 8.0.
>
> > R.version
> _
> platform i686-pc-linux-gnu
> arch i686
> os linux-gnu
> system i686, linux-gnu
> status
> major 1
> minor 6.1
> year 2002
> month 11
> day 01
> language R
>
>
> Your help is highly appreciated!
> Best Regards,
> Jonathan
>
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> http://www.stat.math.ethz.ch/mailman/listinfo/> r-help
jonathan_li@agilent.com
2003-Feb-28 05:10 UTC
[R] File opening error after 1020 files opened
I experimented with openning just one file repeatedly.
# R
library(pixmap)
filename <- dir("mydir", full=T)[1]
for(i in 2000){ print(i); tmp <- read.pnm(filename); }
The file open failed at when i=1021. So the difference in when file openning
fails is due to the difference in system, not to the fact that I am openning
different files each time.
Thanks,
Jonathan
-----Original Message-----
From: Henrik Bengtsson [mailto:hb at maths.lth.se]
Sent: Thursday, February 27, 2003 4:53 PM
To: 'Jonathan Q. Li'; r-help at stat.math.ethz.ch
Subject: RE: [R] File opening error after 1020 files opened
Reconformed on R v1.6.2 (no patch) on WinXP Pro. Here is my
troubleshooting. Using the following files
-rwx------+ 1 hb None 29943 Jun 30 2002 hb.ppm
-rwx------+ 1 hb None 2049 Jul 20 2002 logosm-gray.pgm
-rwx------+ 1 hb None 379 Jul 20 2002 logosm-mono.pbm
-rwx------+ 1 hb None 3682 Feb 2 1998 logosm.jpg
-rwx------+ 1 hb None 5924 Jun 29 2002 logosm.ppm
# R --vanilla
library(pixmap)
# The following fails to read the file at try 509:
for( i in 1:2000 ) { print(i); x <- read.pnm("logosm.ppm"); }
# The following fails to read the file at try 509:
for( i in 1:2000 ) { print(i); x <- read.pnm("logosm-mono.pbm"); }
# The following fails to read the file at try 509:
for( i in 1:2000 ) { print(i); x <- read.pnm("logosm-gray.pgm"); }
# The following fails to read the file at try 509:
for( i in 1:2000 ) { print(i); x <- read.pnm("hb.ppm"); }
Note that I have to restart R between each file; the problem is not just
locking one file, but it messes up the I/O for all files. I get the same
result over and over again after restarting R and it does not seem like
the filesize matters. Most I/O seems to fails. My dir() and file.show()
still works though. Can not save workspace when quiting R etc. Trying to
delete "logosm.ppm" using WinXP Explorer won't work - the file is
locked.
> R.version
_
platform i386-pc-mingw32
arch i386
os mingw32
system i386, mingw32
status
major 1
minor 6.2
year 2003
month 01
day 10
language R
Cheers
Henrik Bengtsson
> -----Original Message-----
> From: r-help-admin at stat.math.ethz.ch
> [mailto:r-help-admin at stat.math.ethz.ch] On Behalf Of Jonathan Q. Li
> Sent: den 28 februari 2003 10:55
> To: r-help at stat.math.ethz.ch
> Subject: [R] File opening error after 1020 files opened
>
>
> Hi,
>
> I am trying to use "read.pnm" from the package "pixmap"
to read more
> than 10 thousand image files in "mydir".
>
> > file.list <- dir( "mydir", full=T)
> > for( i in 1:length(file.list) ) {
> print(i)
> x <- read.pnm(file.list[i])
> }
>
> In the beginning it was fine. But after reading 1020 images
> or so, the
> read.pnm function
> seems to crash on me:
>
> [1] 1017
> [1] 1018
> [1] 1019
> [1] 1020
> Error in open.connection(con, open = "rb") :
> unable to open connection
> In addition: Warning message:
> cannot open file `/mydir/myfile1020.ppm'
>
> Then the R environment seems to crash too because I can't
> read any other
> files anymore. Neither can I use function "dir".
>
> dir("mydir")
> character(0)
> Warning message:
> list.files: "mydir" is not a readable directory
>
> I quit R and close all other applications and come back. The
> problem is
> easily repeated.
> THe following is my system information. The linux version is
> Redhat 8.0.
>
> > R.version
> _
> platform i686-pc-linux-gnu
> arch i686
> os linux-gnu
> system i686, linux-gnu
> status
> major 1
> minor 6.1
> year 2002
> month 11
> day 01
> language R
>
>
> Your help is highly appreciated!
> Best Regards,
> Jonathan
>
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> http://www.stat.math.ethz.ch/mailman/listinfo/> r-help