Re: [Bioc-devel] namespace question

2016-04-05 Thread Michael Lawrence
You need R 3.4 for right now. On Tue, Apr 5, 2016 at 1:16 PM, Karim Mezhoud wrote: > ==> R CMD INSTALL --no-multiarch --with-keep.source bioCancer > > * installing to library > ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library’ > * installing *source* package ‘bioCancer’ ... > ** R

Re: [Bioc-devel] namespace question

2016-04-05 Thread Karim Mezhoud
==> R CMD INSTALL --no-multiarch --with-keep.source bioCancer * installing to library ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library’ * installing *source* package ‘bioCancer’ ... ** R ** inst ** preparing package for lazy loading Error in loadNamespace(i, c(lib.loc, .libPaths()),

Re: [Bioc-devel] namespace question

2016-04-05 Thread Michael Lawrence
Yea, with the closing ) On Tue, Apr 5, 2016 at 12:37 PM, Karim Mezhoud wrote: > If I include manually the exception, I hve to write this? > > import(shiny, except=c('dataTableOutput','renderDataTable') > Thanks > Karim > > On Tue, Apr 5, 2016 at 7:28 PM, Michael Lawrence > wrote: >> >> Roxygen d

Re: [Bioc-devel] namespace question

2016-04-05 Thread Karim Mezhoud
If I include manually the exception, I hve to write this? import(shiny, except=c('dataTableOutput','renderDataTable') Thanks Karim On Tue, Apr 5, 2016 at 7:28 PM, Michael Lawrence wrote: > Roxygen does not yet support the feature. For now you'll have to live > with the warning or just importFro

Re: [Bioc-devel] namespace question

2016-04-05 Thread Michael Lawrence
Roxygen does not yet support the feature. For now you'll have to live with the warning or just importFrom(shiny, ...). Maybe there is some way to manually patch the NAMESPACE with Roxygen? Honestly, I would recommend against using Roxygen to manage your NAMESPACE. Just write the thing... On Tue

Re: [Bioc-devel] namespace question

2016-04-05 Thread Karim Mezhoud
Hi, Actually I have conflict between DT and shiny Warning: replacing previous import ‘shiny::dataTableOutput’ by ‘DT::dataTableOutput’ when loading ‘bioCancer’ Warning: replacing previous import ‘shiny::renderDataTable’ by ‘DT::renderDataTable’ when loading ‘bioCancer’ I would like to import sh

Re: [Bioc-devel] namespace question

2016-04-05 Thread Michael Lawrence
I will try to sneak that in since it seems to work and it would be nice to use it before this Fall. On Tue, Apr 5, 2016 at 10:32 AM, Dan Tenenbaum wrote: > Michael, do you know if this change will be (or has already been) backported > into R-3.3.0? > > Thanks. > Dan > > > - Original Message

Re: [Bioc-devel] namespace question

2016-04-05 Thread Dan Tenenbaum
Michael, do you know if this change will be (or has already been) backported into R-3.3.0? Thanks. Dan - Original Message - > From: "Lihua Zhu" > To: "Dan Tenenbaum" , "Michael Lawrence" > > Cc: "bioc-devel" > Sent: Tuesday, April 5, 2016 9:49:26 AM > Subject: Re: [Bioc-devel] names

Re: [Bioc-devel] namespace question

2016-04-05 Thread Zhu, Lihua (Julie)
Dan, That is great! Thanks for letting us know! Michael, thank for making it happen so quickly! It works like a charm! Best, Julie On 4/2/16 1:58 PM, "Bioc-devel on behalf of Dan Tenenbaum" wrote: >BTW, looks like the change has been made to R-devel: > > CHANGES IN R-devel NEW FEATURES >

Re: [Bioc-devel] big file ReactomeFI --> bioC annotate package

2016-04-05 Thread Obenchain, Valerie
Hi Karim, I can help you put together an annotation package. Here are the general guidelines: http://www.bioconductor.org/developers/package-guidelines/ We ask that annotations packages implement the select() interface from AnnotationDbi (eg, keys(), columns(), keytypes(), etc.). You can see ho

[Bioc-devel] big file ReactomeFI --> bioC annotate package

2016-04-05 Thread Karim Mezhoud
Dear bioC developer, I included in my bioCancer/inst/extdata a Reactome FI database (/ http://reactomews.oicr.on.ca:8080/caBigR3WebApp2015/FIsInGene_031516_with_annotations.txt.zip ) Gene1Gene2AnnotationDirectionScore 16-5-5CDC42predicted-0.82 16-5-5RHOJpred