Re: [Rd] socketSelect(..., timeout): non-integer timeouts in (0, 2) (?) equal infinite timeout on Linux - weird

2017-10-04 Thread Henrik Bengtsson
I'd like to follow up/bump the attention to this bug causing the timeout to fail for socketSelect() on Unix. It is still there in R 3.4.2 and R-devel. I've identified the bug in the R source code - the bug is due to floating-point precisions and comparison using >=. See PR17203

Re: [Bioc-devel] library() calls removed in simpleSingleCell workflow

2017-10-04 Thread Aaron Lun
Here's another two cents from me: The explicit library() calls allow for easy copy-pasting if people only want to use/adapt a section of the workflow. In such cases, calling "library(simpleSingleCell)" could drag in a lot of unnecessary packages (e.g., which could hit the DLL limit). Reading

Re: [Bioc-devel] library() calls removed in simpleSingleCell workflow

2017-10-04 Thread Wolfgang Huber
I find `eval=FALSE` chunks not a good idea, since - they confuse users who only see the rendered HTML/PDF (where this flag is not shown) - they are not tested, so more prone to code rot. I'd also like to object to the idea that proximity of a `library` call to code that uses a package is

Re: [Bioc-devel] library() calls removed in simpleSingleCell workflow

2017-10-04 Thread Turaga, Nitesh
Hi Aaron, A work around solution maybe to, put all libraries in a “eval=FALSE” block in the r code chunk ```{r, eval=FALSE} library(scran) library(scater) ``` etc. This way the users can see the library() calls in the vignette. Best, Nitesh > On Oct 4, 2017, at 4:14 PM, Obenchain,

Re: [Bioc-devel] library() calls removed in simpleSingleCell workflow

2017-10-04 Thread Obenchain, Valerie
Hi guys, A little background on this vignette -> package conversion. The workflows were converted to package form because we want to integrate them into the nightly build system instead of supporting separate machines as we're now doing. As part of this conversion, packages loaded in workflow

Re: [Bioc-devel] library() calls removed in simpleSingleCell workflow

2017-10-04 Thread Kasper Daniel Hansen
yeah, that is super super useful to people. In my vignettes (granted, not workflows) I have a separate "Dependencies" section which is basically a series of library() calls. On Wed, Oct 4, 2017 at 3:18 PM, Aaron Lun wrote: > Dear Nitesh, list; > > > The library() calls in the

Re: [Bioc-devel] library() calls removed in simpleSingleCell workflow

2017-10-04 Thread Aaron Lun
Dear Nitesh, list; The library() calls in the simpleSingleCell workflow have been removed. Why is this? I find explicit library() calls to be quite useful for readers of the compiled vignette, because it makes it easier for them to determine the packages that are required to adapt parts of

[Rd] packages: Examples with CPU or elapsed time > 10s

2017-10-04 Thread Michael Friendly
I am perplexed about NOTEs I get from Win Builder on my genridge package, https://github.com/friendly/genridge. It shows, e.g., Examples with CPU or elapsed time > 10s user system elapsed plot3d.ridge 12.4 0.05 12.45 However, if I run *exactly the same code* in my console

Re: [Bioc-devel] Duplicate commit error on and off

2017-10-04 Thread Turaga, Nitesh
Where is your primary development repo on Github? Please send me link. Best, Nitesh > On Oct 4, 2017, at 10:14 AM, Turaga, Nitesh > wrote: > > Hi Thomas, > > The following issue occurred because there was a commit on Aug 17th with all > the duplicates.

Re: [Bioc-devel] Duplicate commit error on and off

2017-10-04 Thread Turaga, Nitesh
Hi Thomas, The following issue occurred because there was a commit on Aug 17th with all the duplicates. Unfortunately, your upstream repository has been contaminated with duplicate commits. Till I figure out a solution on how to fix this, please hold off any further commits. I’ll keep you

Re: [Rd] R CMD Rd2pdf and macros

2017-10-04 Thread Kasper Daniel Hansen
No, I do not get the same as you. I have tested with R-devel and R-patched compiled today. When I do R CMD Rd2pdf mpra I get (as reported a few days ago) Hmm ... looks like a package Converting Rd files to LaTeX Error : mpra/man/mpra-package.Rd:6: file './DESCRIPTION' does not exist

Re: [Rd] R CMD Rd2pdf and macros

2017-10-04 Thread Kurt Hornik
> Kasper Daniel Hansen writes: Interesting. When I take e.g. zTree as the last CRAN package using the \packageTitle macro, R CMD Rd2pdf zTree seems to work fine, but R CMD Rd2pdf zTree/man gives Converting Rd files to LaTeX Warning in parse_Rd("zTree/man/zTree-package.Rd",