[Bioc-devel] rtracklayer: BigWigFIle on Windows

Kasper Daniel Hansen kasperdanielhansen at gmail.com
Fri Sep 18 05:16:11 CEST 2015


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.


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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