[BioC] lumiHumanIDMapping package does not exist for windows?

[Dan Tenenbaum]

On Thu, May 3, 2012 at 9:59 PM, Ekta Jain <Ekta_Jain at jubilantbiosys.com> wrote:
> Hi Dan,
> The tar.gz works on linux and a separate .gz file must be there for it to work on window. Correct me if i am wrong

You are wrong. ;)
tar.gz is the source package type, and the appropriate type for linux,
but will install on any platform if you specify type="source" in your
biocLite() command.
.tgz is the extension for native Mac packages and .zip is the
extension for native windows packages.

Dan


>here but as far as i have seen most packages have both tar.gz and .gz files the former for linux based systems and the latter for windows machines.
>
> Ekta
>
> -----Original Message-----
> From: Dan Tenenbaum [mailto:dtenenba at fhcrc.org]
> Sent: 04 May 2012 10:17
> To: Ekta Jain
> Cc: bioconductor at r-project.org
> Subject: Re: [BioC] lumiHumanIDMapping package does not exist for windows?
>
> On Thu, May 3, 2012 at 9:42 PM, Ekta Jain <Ekta_Jain at jubilantbiosys.com> wrote:
>> Hi Dan,
>> Found the windows package at http://bioc.ism.ac.jp/2.8/data/annotation/html/lumiHumanIDMapping.html
>>
>> I am going to download and use this as a locally downloaded package. It is version 1.10 which I think is the latest version?
>
>
> The type="source" flag to biocLite() installs the .tar.gz (source)
> package, or at least it is supposed to. I'm not sure why it isn't
> working for you.
>
> The link you sent above says the version is 1.10.0.
>
> Dan
>
>
>
>
>>
>> Regards,
>> Ekta
>>
>> -----Original Message-----
>> From: Dan Tenenbaum [mailto:dtenenba at fhcrc.org]
>> Sent: 04 May 2012 09:25
>> To: Ekta Jain
>> Cc: bioconductor at r-project.org
>> Subject: Re: [BioC] lumiHumanIDMapping package does not exist for windows?
>>
>> On Thu, May 3, 2012 at 8:35 PM, Ekta Jain <Ekta_Jain at jubilantbiosys.com> wrote:
>>> Dear Dan,
>>> That wouldn't work as well. If we don't have the package available on Bioconductor.org then biocLite will not be able to download it.
>>>
>>
>> What is the exact error message, and the output of sessionInfo()?
>>
>> Also what is the output of
>>  getOption("BioC_mirror")
>> ?
>>
>>> I did originally start with the way you suggested. When it didn't work thought of downloading the relevant .gz file from Bioconductor, which is not available.
>>>
>>
>>
>> The .gz file is available, see the you emailed. However, biocLite() is
>> the preferred way to install it, so let's figure out why that is not
>> working.
>> Dan
>>
>>
>>> Any help would be great !!!
>>>
>>> Thanks,
>>> Ekta
>>>
>>> -----Original Message-----
>>> From: Dan Tenenbaum [mailto:dtenenba at fhcrc.org]
>>> Sent: 03 May 2012 23:22
>>> To: Ekta Jain
>>> Cc: bioconductor at r-project.org
>>> Subject: Re: [BioC] lumiHumanIDMapping package does not exist for windows?
>>>
>>> On Thu, May 3, 2012 at 4:39 AM, Ekta Jain <Ekta_Jain at jubilantbiosys.com> wrote:
>>>> Dear All,
>>>> The lumiHumanIDMapping package does not seem to have the windows binary files available on the Bioconductor website - http://www.bioconductor.org/packages/release/data/annotation/html/lumiHumanIDMapping.html
>>>>
>>>> Can anyone please tell me where i can get the same .gz package from?
>>>
>>> I'll look into why this is not available for windows, but in the
>>> meantime you can install it as follows:
>>>
>>> source("http://bioconductor.org/biocLite.R")
>>> biocLite("lumiHumanIDMapping", type="source")
>>>
>>> Dan
>>>
>>>>
>>>> Many Thanks,
>>>> Ekta
>>>> Senior Research Associate
>>>> Bioinformatics Department
>>>> Jubilant Biosys Pvt Ltd,
>>>> #96, Industrial Suburb, 2nd Stage
>>>> Yeshwantpur, Bangalore 560 022
>>>> Ph No : +91-80-66628346
>>
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