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

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

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

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

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

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

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

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

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

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