[BioC] Package qvalue - can it be installed without TCL-TK support?

[Giuseppe Gallone]

Dear Bernd

thanks, I will definitely test it.

Best wishes,
Giuseppe

On 05/23/14 17:32, Bernd Klaus wrote:
> Hi Guiseppe,
>
> If I may shamelessly promote a package from my former group,
>
> fdrtool (CRAN)
>
> http://strimmerlab.org/software/fdrtool/
>
> essentially uses the qvalue algorithm if you give it p-values,
> so the results should be the same.
>
> Best wishes,
>
> Bernd
>
>
> On Fri, 23 May 2014 09:05:15 -0700
> Peter Langfelder <peter.langfelder at gmail.com> wrote:
>
>> Another solution is to find an old version of qvalue, e.g., here:
>>
>> http://cran.r-project.org/src/contrib/Archive/qvalue/
>>
>> The version 1.1.1 is, to the best of my knowledge, the last that did
>> not use the graphical interface and the Tcl/Tk that comes with it.
>>
>> Peter
>>
>>
>> On Fri, May 23, 2014 at 8:51 AM, Giuseppe Gallone
>> <giuseppe.gallone at dpag.ox.ac.uk> wrote:
>>> John
>>>
>>> thanks, I will try what you suggested.
>>>
>>> Best wishes
>>> Giuseppe
>>>
>>>
>>> On 05/23/14 15:31, John Blischak wrote:
>>>>
>>>> A short-term solution would be to download the source code and just
>>>> directly use the qvalue function.
>>>>
>>>>    wget
>>>>
>>>> http://bioconductor.org/packages/release/bioc/src/contrib/qvalue_1.38.0.tar.gz
>>>>    tar xzf qvalue_1.38.0.tar.gz
>>>>
>>>> Then source the code in R:
>>>> source("qvalue/R/qvalue.R")
>>>>
>>>> If you wanted to install, you could edit the source code. I'd imagine
>>>> deleting the function qvalue.gui and removing the references to tcltk in
>>>> the package DESCRIPTION and NAMESPACE would allow you to install it from
>>>> source.
>>>>
>>>> John
>>>>
>>>>
>>>> On Fri, May 23, 2014 at 7:44 AM, Giuseppe Gallone
>>>> <giuseppe.gallone at dpag.ox.ac.uk <mailto:giuseppe.gallone at dpag.ox.ac.uk>>
>>>>
>>>> wrote:
>>>>
>>>>      Hi
>>>>
>>>>      I need the qvalue package however I don't need the TCL-TK interface.
>>>>
>>>>      My R installation was compiled without native TCL-TK support and it
>>>>      is inconvenient for me atm to reinstall/replace etc to add support.
>>>>
>>>>      As a consequence, as it stands it seems I cannot get qvalue to work
>>>>      on my system.
>>>>
>>>>      Does anybody know of a way to install and run qvalue excluding the
>>>>      TCL-TK bindings?
>>>>
>>>>      Best regards
>>>>      Giuseppe
>>>>
>>>>      _________________________________________________
>>>>      Bioconductor mailing list
>>>>      Bioconductor at r-project.org <mailto:Bioconductor at r-project.org>
>>>>      https://stat.ethz.ch/mailman/__listinfo/bioconductor
>>>>
>>>>      <https://stat.ethz.ch/mailman/listinfo/bioconductor>
>>>>      Search the archives:
>>>>      http://news.gmane.org/gmane.__science.biology.informatics.__conductor
>>>> <http://news.gmane.org/gmane.science.biology.informatics.conductor>
>>>>
>>>>
>>>
>>> _______________________________________________
>>> Bioconductor mailing list
>>> Bioconductor at r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>> Search the archives:
>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor