dear all:
i am shan gao from cornell university. i reported
a bug, and Hervé Pagès said it will be fixed
in solveUserSEW(width(x), start = start, end = end, width = width) :
solving row 686: 'allow.nonnarrowing' is FALSE and the supplied
start (0)
is < 1
This bug should be fixed in Biostrings release (2.20.4) and devel
(2.21.10).
but now when i run the function
clippedReads <- narrow(trimmedReads, start=start(clippedCoords),
end=end(clippedCoords))
the same error reported
Error in solveUserSEW(width(x), start = start, end = end, width =
width) :
solving row 1: 'allow.nonnarrowing' is FALSE and the supplied start
(2) is
> refwidth + 1
i already updated the bioconductor, can you tell me how to fix it
thx
shangao
[[alternative HTML version deleted]]
On Thu, Oct 6, 2011 at 9:45 AM, wang peter <wng.peter at="" gmail.com="">
wrote:
> dear all:
> ? ? ? ? i am shan gao from cornell university. i reported
> a bug, and Hervé Pagès said it will be fixed
>
> ?in solveUserSEW(width(x), start = start, end = end, width = width)
:
> ?solving row 686: 'allow.nonnarrowing' is FALSE and the supplied
start (0)
> is < 1
> This bug should be fixed in Biostrings release (2.20.4) and devel
> (2.21.10).
>
> but now when i run the function
> ?clippedReads <- narrow(trimmedReads, start=start(clippedCoords),
> end=end(clippedCoords))
>
> the same error reported
>
>
> Error in solveUserSEW(width(x), start = start, end = end, width =
width) :
> ?solving row 1: 'allow.nonnarrowing' is FALSE and the supplied start
(2) is
>> refwidth + 1
> i already updated the bioconductor, can you tell me how to fix it
> thx
For ALL bug reports and most other emails, it is necessary to include
the output of sessionInfo(). Without that valuable information, no
one can begin to help you.
Sean
On Thu, Oct 6, 2011 at 10:32 AM, wang peter <wng.peter at="" gmail.com="">
wrote:
>
> sorry, i forgot giving the session informaiton
> ?in solveUserSEW(width(x), start = start, end = end, width = width)
:
> ? solving row 686: 'allow.nonnarrowing' is FALSE and the supplied
start (0)
> is < 1
> This bug should be fixed in Biostrings release (2.20.4) and devel
> (2.21.10).
>
>
> i think the problem because
> some trimmed reads have 0 length, but still exists. so the start >
> width(reads)+1
>
>> sessionInfo()
> R version 2.11.1 (2010-05-31)
> x86_64-unknown-linux-gnu
>
> locale:
> ?[1] LC_CTYPE=en_US.UTF-8?????? LC_NUMERIC=C
> ?[3] LC_TIME=en_US.UTF-8??????? LC_COLLATE=en_US.UTF-8
> ?[5] LC_MONETARY=C????????????? LC_MESSAGES=en_US.UTF-8
> ?[7] LC_PAPER=en_US.UTF-8?????? LC_NAME=C
> ?[9] LC_ADDRESS=C?????????????? LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats???? graphics? grDevices utils???? datasets? methods?? base
Please include the Bioconductor email list when replying to emails.
That way, everyone benefits from answers and you have a better chance
of getting a meaningful answer.
The reason to include the output of sessionInfo() is to see what
version of packages you are using. If you have not loaded the package
generating the error, it will not show up in sessionInfo(), so Martin
and others will not be able to determine with any certainty what
version of various packages you are using.
So, do the following:
1) start a new R session
2) load the relevant libraries
3) include in the email to the list the code in as reproducible form
as possible
4) If you are asking about an error:
a) Provide the output of traceback()
b) Provide the output of sessionInfo()
In most cases, 4a is not necessary, but it never hurts to have it.
Step 4B is always necessary, so please always include it when asking
questions about code, packages, or errors. If you do not know what
either traceback() or sessionInfo() do, check out the help pages.
Sean
