confirmed at sessionInfo given below and on a similar mac devel build

r-devel has some stuff on inherent bugginess of zlib, e.g,

http://r.789695.n4.nabble.com/Issue-with-seek-on-gzipped-connections-in-R-devel-td3836934.html

if this is a problem getting through check we could likely store the gxl
stuff uncompressed



> sessionInfo()
R Under development (unstable) (2012-07-20 r59915)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.ISO8859-1      LC_NUMERIC=C
 [3] LC_TIME=en_US.ISO8859-1       LC_COLLATE=en_US.ISO8859-1
 [5] LC_MONETARY=en_US.ISO8859-1   LC_MESSAGES=C
 [7] LC_PAPER=C                    LC_NAME=C
 [9] LC_ADDRESS=C                  LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.iso88591 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices datasets  tools     utils     methods
[8] base

other attached packages:
[1] graph_1.35.1         weaver_1.23.0        codetools_0.2-8
[4] digest_0.5.2         BiocInstaller_1.5.12

loaded via a namespace (and not attached):
[1] BiocGenerics_0.3.0


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
>
> _______________________________________________
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

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