[Bioc-devel] R CMD check error on shinytest package

Hi For the Prostar package, I began to use the funtionnalities of shinytest wich is a package that provides utilities to automatically test shiny apps. Unfortunately, this package is not available neither on CRAN or Bioconductor (it is available on github

Re: [Bioc-devel] Iterating over BSgenomeViews returns DNAString instead of BSgenomeViews

On Fri, Apr 7, 2017 at 1:13 AM, Hervé Pagès wrote: > > This is the expected behavior. > > Some background: BSgenomeViews are list-like objects where the *list > elements* (i.e. the elements one extracts with [[) are the DNA > sequences from the views --snip-- > The important

Re: [Bioc-devel] R CMD check without WARNING: g++ and STL issue for xcms and mzR

On 04/12/2017 11:31 AM, Neumann, Steffen wrote: Hi, certainly these are good suggestions, but I would tend to simply add some whitelisting functionality if the cause is beyond the package's control. In this case I doubt it is a handler for SIGABRT, since that would not go away with -O2, or

Re: [Bioc-devel] R CMD check without WARNING: g++ and STL issue for xcms and mzR

Hi Steffen, On 04/12/2017 04:22 AM, Neumann, Steffen wrote: Hi Martin and malbec2 admin(s): Some more digging revealed that malbec2

Re: [Bioc-devel] disable windows build for EiR development

Hi Kevin, Just did that. For the record, it's easy to do this yourself: simply add a .BBSoptions file in the top-level folder of the package with the following line in it: UnsupportedPlatforms: win If you change your mind, just remove that file. Cheers, H. On 04/12/2017 01:30 PM, Kevin Horan

[Bioc-devel] disable windows build for EiR development

Can you please disable the windows build for eiR in the development branch? Thanks. Kevin Horan ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Rd] "table(droplevels(aq)$Month)" in manual page of droplevels

Hello, Inline. Em 12-04-2017 16:40, Henric Winell escreveu: (Let's keep the discussion on-list -- I've added back R-devel.) On 2017-04-12 16:39, Ulrich Windl wrote: Henric Winell schrieb am 12.04.2017 um 15:35 in Nachricht

Re: [Rd] "table(droplevels(aq)$Month)" in manual page of droplevels

(Let's keep the discussion on-list -- I've added back R-devel.) On 2017-04-12 16:39, Ulrich Windl wrote: Henric Winell schrieb am 12.04.2017 um 15:35 in Nachricht : On 2017-04-12 14:40, Ulrich Windl wrote: The last

Re: [Bioc-devel] R CMD check without WARNING: g++ and STL issue for xcms and mzR

Hi, certainly these are good suggestions, but I would tend  to simply add some whitelisting functionality if the  cause is beyond the package's control.  In this case I doubt it is a handler for SIGABRT,  since that would not go away with -O2, or would it ? For now, just adding -O2 on Linux

Re: [Bioc-devel] R CMD check without WARNING: g++ and STL issue for xcms and mzR

Suppose you had a handler for SIGABRT in your code. Could CMD check check for that and, if found, refrain from warning? That is somewhat involved and goes beyond Bioc but it seems a principled way of dealing with operations in binary infrastructure whose behavior we cannot control. The problem

Re: [Rd] "table(droplevels(aq)$Month)" in manual page of droplevels

On 2017-04-12 14:40, Ulrich Windl wrote: The last line of the example in droplevels' manual page seems to be incorrect to me. I think it should read: "table(droplevels(aq$Month))". Amazingly (I don't understand) both variants seem to produce the same result (R 3.3.3): --- The manual says that

Re: [Bioc-devel] R CMD check without WARNING: g++ and STL issue for xcms and mzR

I think "we" have to appreciate that the warning about abort/etc and others is really hard to deal with when you're including (large) external source as you do in mzR and for example affxparser / Rgraphviz. Generally fixing those in external code requires a lot of effort, and the further effort

[Rd] "table(droplevels(aq)$Month)" in manual page of droplevels

The last line of the example in droplevels' manual page seems to be incorrect to me. I think it should read: "table(droplevels(aq$Month))". Amazingly (I don't understand) both variants seem to produce the same result (R 3.3.3): --- > aq <- transform(airquality, Month = factor(Month, labels =

Re: [Bioc-devel] R CMD check without WARNING: g++ and STL issue for xcms and mzR

Hi Martin and malbec2 admin(s): Some more digging revealed that malbec2  http://bioconductor.org/checkResults/devel/bioc-LATEST/malbec2-NodeInfo.html is using "CFLAGS=-g -O2 -Wall" but only "CXXFLAGS=-Wall" while e.g. tokay2 uses "CXXFLAGS=-O2 -Wall -mtune=core2" The -O2 optimisation is getting