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 through the text to figure out the
requirements for each code chunk seems like a pain, and lots of "::" are
unwieldy.
More generally, the removal of individual library() calls seems to encourage
the use of a single "library(simpleSingleCell)" call at the top of any
user-developed custom analysis scripts based on the workflow. This seems
conceptually odd to me - the simpleSingleCell package is simply a vehicle for
the compiled workflow, it shouldn't be involved in analyses of other data.
-Aaron
________________________________
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
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 somehow didactic. It's actually a bad
habit: the R interpreter does not care. The relevant package
- can be mentioned in the narrative,
- stated in the code with the pkgname:: prefix.
The latter is good didactics to get people used to the idea of
namespaces, especially since there is an increasing frequency of name
clashes in CRAN, tidyverse, BioC (e.g. consider the various functions
named 'filter' and the obscure malbehaviors that can result from these).
Best wishes
Wolfgang
On 04/10/2017 22:20, Turaga, Nitesh wrote:
> 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, Valerie
>> <valerie.obench...@roswellpark.org> wrote:
>>
>> 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 vignettes were moved
>> to Depends in DESCRIPTION. This enables the user to load a single package
>> instead of many. Packages were moved to Depends instead of Suggests (as is
>> usually done with software packages) because these vignette is the only
>> thing these workflow packages have going - no defined classes or methods.
>> This seemed a more tidy approach and the dependencies are listed in Depends
>> for the user to see. This was my (maybe bad?) idea and Nitesh was the
>> messenger. If you feel the individual loading of packages in the vignette is
>> a key part of the instruction/learning we can leave them as is and list the
>> packages in Suggests.
>>
>> I should also mention that incorporating the workflows into the build system
>> won't happen until after the release. At that time we'll move the
>> repositories from svn to git and it's likely we'll have to ask maintainers
>> to abide by some time/space guidelines. At that point the build machines
>> will be building software, experimental data and workflows and resources
>> aren't unlimited. When that time comes we'll update the workflow guidelines
>> and contact maintainers.
>>
>> Thanks.
>> Valerie
>>
>>
>>
>> On 10/04/2017 12:27 PM, Kasper Daniel Hansen wrote:
>>
>> 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
>> <a...@wehi.edu.au><mailto:a...@wehi.edu.au> wrote:
>>
>>
>>
>> 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 the workflow for their own
>> analyses. If it doesn't hurt the build system, I would prefer to have these
>> library() calls in the vignette.
>>
>>
>> Cheers,
>>
>>
>> Aaron
>>
>> [[alternative HTML version deleted]]
>>
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--
With thanks in advance-
Wolfgang
-------
Wolfgang Huber
Principal Investigator, EMBL Senior Scientist
European Molecular Biology Laboratory (EMBL)
Heidelberg, Germany
wolfgang.hu...@embl.de
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[http://www.huber.embl.de/wordpress/wp-content/uploads/2014/12/helix.jpg]<http://www.huber.embl.de/>
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inter-individual differences by large-scale statistical modelling and
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