To me it seems like writeBin() writes one char/byte more than expected.
> con <- file("testbin", "wb")
> writeBin("ttccggaa", con)
> close(con)
> con <- file("testbin", "rb")
> readBin(con, what="character")
[1] "ttccggaa"
> seek(con, what=NA)
[1] 9
> close(con)
> con <- file("testbin", "rb")
> readBin(con, what="raw", n=20)
[1] 74 74 63 63 67 67 61 61 00
> seek(con, what=NA)
[1] 9
> close(con)
As the numbering starts with 0 the position should be 8 and not 9 after
reading. There were two older threads which look very similar to my problem:
http://tolstoy.newcastle.edu.au/R/e2/devel/06/11/1119.html
http://r.789695.n4.nabble.com/Re-Problem-reading-binaries-created-with-fortran-More-infos-td974396.html
Thanks in advance,
Christian
> sessionInfo()
R version 2.12.0 (2010-10-15)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] Biostrings_2.18.2 IRanges_1.8.8
loaded via a namespace (and not attached):
[1] Biobase_2.10.0
from ?seek
?seek? returns the current position (before any move), as a
(numeric) byte offset from the origin, if relevant, or ?0? if not.
Your string is nul terminated (9 bytes long). That would be the
current offset. If you only read one byte, you'd have to be more than
0 bytes offset.
Jeff
On Fri, Feb 4, 2011 at 4:35 AM, Christian Ruckert
<cruckert at uni-muenster.de> wrote:> To me it seems like writeBin() writes one char/byte more than expected.
>
>> con <- file("testbin", "wb")
>> writeBin("ttccggaa", con)
>> close(con)
>
>> con <- file("testbin", "rb")
>> readBin(con, what="character")
> [1] "ttccggaa"
>> seek(con, what=NA)
> [1] 9
>> close(con)
>
>> con <- file("testbin", "rb")
>> readBin(con, what="raw", n=20)
> [1] 74 74 63 63 67 67 61 61 00
>> seek(con, what=NA)
> [1] 9
>> close(con)
>
> As the numbering starts with 0 the position should be 8 and not 9 after
> reading. There were two older threads which look very similar to my
problem:
>
> http://tolstoy.newcastle.edu.au/R/e2/devel/06/11/1119.html
>
http://r.789695.n4.nabble.com/Re-Problem-reading-binaries-created-with-fortran-More-infos-td974396.html
>
> Thanks in advance,
> Christian
>
>
>
>> sessionInfo()
> R version 2.12.0 (2010-10-15)
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> locale:
> [1] C
>
> attached base packages:
> [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base
>
> other attached packages:
> [1] Biostrings_2.18.2 IRanges_1.8.8
>
> loaded via a namespace (and not attached):
> [1] Biobase_2.10.0
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
--
Jeffrey Ryan
jeffrey.ryan at lemnica.com
www.lemnica.com
On 04/02/2011 5:35 AM, Christian Ruckert wrote:> To me it seems like writeBin() writes one char/byte more than expected.You want writeChar rather than writeBin to avoid the null termination of strings. Duncan Murdoch> > con<- file("testbin", "wb") > > writeBin("ttccggaa", con) > > close(con) > > > con<- file("testbin", "rb") > > readBin(con, what="character") > [1] "ttccggaa" > > seek(con, what=NA) > [1] 9 > > close(con) > > > con<- file("testbin", "rb") > > readBin(con, what="raw", n=20) > [1] 74 74 63 63 67 67 61 61 00 > > seek(con, what=NA) > [1] 9 > > close(con) > > As the numbering starts with 0 the position should be 8 and not 9 after > reading. There were two older threads which look very similar to my problem: > > http://tolstoy.newcastle.edu.au/R/e2/devel/06/11/1119.html > http://r.789695.n4.nabble.com/Re-Problem-reading-binaries-created-with-fortran-More-infos-td974396.html > > Thanks in advance, > Christian > > > > > sessionInfo() > R version 2.12.0 (2010-10-15) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > [1] C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] Biostrings_2.18.2 IRanges_1.8.8 > > loaded via a namespace (and not attached): > [1] Biobase_2.10.0 > > ______________________________________________ > R-devel at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel