[Bioc-devel] rtracklayer: BigWigFIle on Windows

[Michael Lawrence]

I've never tested it, and reports up until now have been negative. It would
help to know the error message (if any) and characteristics of the systems
that work or don't work. Given that it works in some circumstances, it
sounds like we could make it work more reliably.

Michael

On Thu, Sep 17, 2015 at 8:16 PM, Kasper Daniel Hansen <
kasperdanielhansen at gmail.com> wrote:

> Thanks.
>
> While fetching data over the internet is pretty nice, for me there is a
> big difference between being able to read local BigWig files and not being
> able to read anything at all.  Wrt. your answer I am a bit unclear whether
> you expect it to work on a machine local file on Windows.
>
> Best,
> Kasper
>
> On Thu, Sep 17, 2015 at 6:14 PM, Michael Lawrence <
> lawrence.michael at gene.com> wrote:
>
>> I would say that it's unsupported, and surprising that it actually worked
>> for you. It would require some non-trivial engineering to get it fully
>> working on Windows. For example, to access data via HTTP, one would need to
>> implement or integrate an HTTP client based on Windows sockets, as well as
>> abstract Jim Kent's code, which is based on POSIX-specific things like
>> integer file descriptors.
>>
>>
>> On Thu, Sep 17, 2015 at 1:09 PM, Kasper Daniel Hansen <
>> kasperdanielhansen at gmail.com> wrote:
>>
>>> In the man page for trackLayer::BigWigFile it says "These functions do
>>> not work on Windows".  Despite this statement, which seems to have been
>>> around for a while, I and several of my students seems to be able to
>>> execute something like
>>>   import(bwFile, which = my.gr, as = "Rle")
>>> on Windows on a BigWig file.  In my case the OS is Windows 7 run under a
>>> virtual machine on a Mac.  In the virtual machine I don't have full
>>> support.  For example, the code above works when bwFile is a BigWigFile
>>> pointing to a BigWig file stored on my local hard drive, but does not work
>>> when I query a url; in that case I get a weird error message.  However, I
>>> have at least one student for which this does not seem to work on Windows.
>>>
>>> I was unaware of this when I designed a quiz problem involving importing
>>> a BigWigFile.  I am surprised that it works at all.  What is the current
>>> state of BigWig file support on Windows? Clearly some of it works on some
>>> systems.
>>>
>>> Best,
>>> Kasper
>>>
>>>
>>
>

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