[Bioc-devel] graph file
Thanks both of you. I thought it was crazy that I got a warning form using readLines on a gzfile connection, so I did some testing. If I open the connection with gzfile(FILE) (default is open = ""), I do not get a warning If I open it with gzfile(FILE, open = "rb") I do get the warning.
From ?gzfile
The mode of a connection is determined when actually opened, which
is deferred if ?open = ""? is given (the default for all but
socket connections). An explicit call to ?open? can specify the
mode, but otherwise the mode will be ?"r"?. (?gzfile?, ?bzfile?
and ?xzfile? connections are exceptions, as the compressed file
always has to be opened in binary mode and no conversion of
line-endings is done even on Windows, so the default mode is
interpreted as ?"rb"?.) Most operations that need write access or
text-only or binary-only mode will override the default mode of a
non-yet-open connection.
This seems to indicate that open="" should do the same as open="rb",
but my testing seems to indicate that one gives the warning, the other
one doesn't.
Kasper
On Mon, Aug 27, 2012 at 10:34 AM, Vincent Carey
<stvjc at channing.harvard.edu> wrote:
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 at 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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