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

[Giuseppe Gallone]

Excellent, thanks a lot for your help

Best
Giuseppe

On 05/26/14 04:19, Pengcheng Yang wrote:
> As John suggested, the solution is:
>
> downloaded the package from:
> http://www.bioconductor.org/packages/release/bioc/src/contrib/qvalue_1.38.0.tar.gz
>
>
> untar and modify the file qvalue/NAMESPACE:
>
> delete the following lines:
>
> importFrom(tcltk, tclvalue, "tclvalue<-", tclVar, tkbutton,
>             tkcheckbutton, tkconfigure, tkdestroy, tkentry, tkframe,
>             tkgetOpenFile, tkgetSaveFile, tkgrid, tkinsert, tklabel,
>             tkpack, tkradiobutton, tkscrollbar, tkset, tktext,
>             tktoplevel, tkwm.focusmodel, tkwm.title, tkyview)
>
> and delete the word "qvalue.gui," from the line:
> export(plot.qvalue, qplot, qsummary, qvalue, qvalue.gui, qwrite,
> summary.qvalue)
>
> then re compressed the qvalue directory into qvalue_1.38.0.tar.gz and
> install it using install.packages().
>
> done.
>
> Best,
> pengcheng
>
> On 2014/5/24 0:32, 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
>>>>>
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>>>>>
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