[BioC] lumiHumanIDMapping package does not exist for windows?

[Ekta Jain]

Hi Dan,
Thanks for that info :) I am clueless as to why it wouldn't then install it from biocLite. I've got it working in R anyway so will proceed using what I have from the previous link.

Thank you for your time here.

Regards,
-E

-----Original Message-----
From: Dan Tenenbaum [mailto:dtenenba at fhcrc.org] 
Sent: 04 May 2012 10:40
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 9:59 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
>>
> The information contained in this electronic message and in any attachments to this message is confidential, legally privileged and intended only for use by the person or entity to which this electronic message is addressed. If you are not the intended recipient, and have received this message in error, please notify the sender and system manager by return email and delete the message and its attachments and also you are hereby notified that any distribution, copying, review, retransmission, dissemination or other use of this electronic transmission or the information contained in it is strictly prohibited. Please note that any views or opinions presented in this email are solely those of the author and may not represent those of the Company or bind the Company. Any commitments made over e-mail are not financially binding on the company unless accompanied or followed by a valid purchase order. This message has been scanned for viruses and dangerous content by Mail Scanner, and is believed to be clean. The Company accepts no liability for any damage caused by any virus transmitted by this email.
> www.jubl.com
>
The information contained in this electronic message and in any attachments to this message is confidential, legally privileged and intended only for use by the person or entity to which this electronic message is addressed. If you are not the intended recipient, and have received this message in error, please notify the sender and system manager by return email and delete the message and its attachments and also you are hereby notified that any distribution, copying, review, retransmission, dissemination or other use of this electronic transmission or the information contained in it is strictly prohibited. Please note that any views or opinions presented in this email are solely those of the author and may not represent those of the Company or bind the Company. Any commitments made over e-mail are not financially binding on the company unless accompanied or followed by a valid purchase order. This message has been scanned for viruses and dangerous content by Mail Scanner, and is believed to be clean. The Company accepts no liability for any damage caused by any virus transmitted by this email.
www.jubl.com