[R] bug in closing gzfile-opened connections?

Duncan Murdoch murdoch at stats.uwo.ca
Wed Jul 4 01:10:35 CEST 2007

On 03/07/2007 1:37 PM, David Reiss wrote:
> Hi,
> I am making multiple calls to gzfile() via read.table(), e.g.
>> x <- read.table( gzfile( "xxx.gz" ) )
> After i do this many times (I haven't counted, but probably between 50 and
> 100 times) I get the error message:
> Error in open.connection(file, "r") : unable to open connection
> In addition: Warning message:
> cannot open compressed file 'xxx.gz'
> however, I also find that:
>> showConnections()
>      description class mode text isopen can read can write
> so there are no (apparently) open connections. Calling closeAllConnections()
> does not fix the problem. I have to quit and re-start R.
> I am using R 2.5.0 on a Mac (OSX 10.4.9).
> Anyone know if this is a bug or a 'feature'? I see from the gzfile help
> that:
>  In general functions using connections
>      will open them if they are not open, but then close them again, so
>      to leave a connection open call 'open' explicitly.

You didn't give a reproducible example, so I couldn't say.  When I 
create a gzipped version of a write.table output and run

for(i in 1:1000) read.table(gzfile(f))

in R 2.5.0 I don't see a problem.  This is on Windows, but I doubt that 
makes a difference.

Duncan Murdoch

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