This issue has been around for a year or more and relates to using seek()
on a gzip connection.  In GEOquery, I use seeks on gzipped files relatively
extensively.  I currently ignore the warnings since they do not seem to be
consequential, but it is an annoyance.  There is a note in the R source, if
I recall, about this issue, so I doubt that the warning will go away
anytime soon.

Sean


On Mon, Aug 27, 2012 at 10:16 AM, Kasper Daniel Hansen <
kasperdanielhansen@gmail.com> wrote:

> (fixing some Rgraphviz stuff).
>
> If I do (in R)
>
> library(graph)
> g1_gz <- gzfile(system.file("GXL/graphExample-01.gxl.gz",package="graph"),
> open="rb")
> readLines(g1_gz)
>
> I get
>
> Warning message:
> In readLines(g1_gz) :
>   seek on a gzfile connection returned an internal error
>
> but it seems to parse fine.  When I look at the file, say doing (in a
> shell)
>   gunzip -t graphExample_01.gxl.gz
> it seems to be in good shape.
>
> Is there anyone who can hint at what is going on here?
>
> [ The warning is in
>   src/main/connections.c
> in the R sources ]
>
> Kasper
>
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