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

collection of analyses stemming from other packages, but that wasn't enough apparently. Laurent -Aaron From: Bioc-devel <bioc-devel-boun...@r-project.org <mailto:bioc-devel-boun...@r-project.org>> on behalf of Wolfgang Huber <wolfgang.hu...@embl.de &

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

the simpleSingleCell > >> package is simply a vehicle for the compiled > >> workflow, it shouldn't be > >> involved in analyses of other data. > >> > >> > >> > &

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

revious >> objects, etc. make it >> difficult to break up the workflow. If multiple files >> are present in >> vignettes/, can they be directed to execute in a >> specific order, and would >

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

behalf of Wolfgang Huber <wolfgang.hu...@embl.de <mailto:wolfgang.hu...@embl.de>> Sent: Thursday, 5 October 2017 8:26 AM To: bioc-devel@r-project.org <mailto:bioc-devel@r-proje

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

here dependencies on previous objects, etc. make it >>>> difficult to break up the workflow. If multiple files are present in >>>> vignettes/, can they be directed to execute in a specific order, and >>>> would >>>> output files from one vignette

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

t during the execution of another? -Aaron *From:* Wolfgang Huber <wolfgang.hu...@embl.de> *Sent:* Thursday, 5 October 2017 6:23:47 PM *To:* Laurent Gatto; Aaron Lun *Cc:* bioc-devel@r-project.org *Subject:* Re: [Bioc-devel] library() calls removed in simpleSingleCell workflow I agree it is

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

<valerie.obench...@roswellpark.org> Sent: Friday, 6 October 2017 6:36:44 AM To: Aaron Lun; Wolfgang Huber; bioc-devel@r-project.org Subject: Re: [Bioc-devel] library() calls removed in simpleSingleCell workflow Glad this sparked some interesting dialogue! Regardless of what's decided, this change

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

of another? >> >> >> -Aaron >> >> ---------------- >> *From:* Wolfgang Huber <wolfgang.hu...@embl.de> >> *Sent:* Thursday, 5 October 2017 6:23:47 PM >> *To:* Laurent Gatto; Aaron

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

@embl.de><mailto:wolfgang.hu...@embl.de> Sent: Thursday, 5 October 2017 8:26 AM To: bioc-devel@r-project.org<mailto:bioc-devel@r-project.org> Subject: Re: [Bioc-devel] library() calls removed in simpleSingleCell workflow I find `eval=FALSE` chunks not a good idea, since - they confu

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

nt:* Thursday, 5 October 2017 6:23:47 PM > *To:* Laurent Gatto; Aaron Lun > *Cc:* bioc-devel@r-project.org > *Subject:* Re: [Bioc-devel] library() calls removed in simpleSingleCell > workflow > > I agree it is nice to be able to only load the packages needed for a > certai

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

of Wolfgang Huber <wolfgang.hu...@embl.de> Sent: Thursday, 5 October 2017 8:26 AM To: bioc-devel@r-project.org Subject: 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 HT

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

: bioc-devel@r-project.org Subject: Re: [Bioc-devel] library() calls removed in simpleSingleCell workflow I agree it is nice to be able to only load the packages needed for a certain section of a vignette and not the whole thing. And that too many `::` can make code look unwieldy (though some may ac

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

er <wolfgang.hu...@embl.de> Sent: Thursday, 5 October 2017 8:26 AM To: bioc-devel@r-project.org Subject: 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 th

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

; From: Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Wolfgang > Huber <wolfgang.hu...@embl.de> > Sent: Thursday, 5 October 2017 8:26 AM > To: bioc-devel@r-project.org > Subject: Re: [Bioc-devel] library() calls removed in simpleSingleCell workflow > >

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

;bioc-devel-boun...@r-project.org> on behalf of Wolfgang Huber <wolfgang.hu...@embl.de> Sent: Thursday, 5 October 2017 8:26 AM To: bioc-devel@r-project.org Subject: Re: [Bioc-devel] library() calls removed in simpleSingleCell workflow I find `eval=FALSE` chunks not a good idea, since - they confus

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