[Bioc-devel] Controlling vignette compilation order

Aaron Lun infinite@monkey@@with@keybo@rd@ @ending from gm@il@com
Mon Dec 24 09:02:35 CET 2018 

A working example of knitr caching across workflows is now available at https://github.com/LTLA/BiocWorkCache <https://github.com/LTLA/BiocWorkCache>. 

It uses “~/chipseq.log” as a log to demonstrate that the code in the most-upstream workflow (“test1.Rmd”) is indeed only executed once during the BUILD.

Note that the compilation of upstream vignettes involves a system call out to a separate R session. This avoids some difficult issues with caching when a Rmd file is compiled from within another Rmd file - trying to use rmarkdown::render() on the upstream vignette within a downstream vignette does not generate a cache that is recognized when BUILD goes onto compile the upstream vignette.

-A

> On 23 Dec 2018, at 01:24, Aaron Lun <infinite.monkeys.with.keyboards using gmail.com> wrote:
> 
> Yes, I had noticed the vignettes.rds as well, and I figured that would be a problem.
> 
> I just tried setting set cache=TRUE in my vignettes, implemented such that BUILDing each downstream vignette will also run all upstream vignettes on which it depends (that haven’t already been compiled). If an upstream vignette is run in this manner, it caches the results of each code chunk to avoid repeated work when it gets compiled “for real” by R CMD BUILD.
> 
> This seems to work on initial inspection (the caches are produced for the upstream vignettes upon running one downstream vignette). I’ll have to check whether this plays nice with R CMD BUILD. I will probably have to write a function to isolate the scope of the execution of each upstream vignette, to avoid polluting the namespace and cache of each downstream vignette.
> 
> -A
> 
>> On 22 Dec 2018, at 19:22, Henrik Bengtsson <henrik.bengtsson using gmail.com <mailto:henrik.bengtsson using gmail.com>> wrote:
>> 
>> On Sat, Dec 22, 2018 at 10:56 AM Michael Lawrence
>> <lawrence.michael using gene.com <mailto:lawrence.michael using gene.com>> wrote:
>>> 
>>> Anything that eventually lands in inst/doc is a vignette, I think, so
>>> there might be a hack around that.
>> 
>> Just so this is not misread - it's *not* possible to just hack your
>> vignette "product" files (PDF or HTML) into inst/doc and thinking
>> you're good.  R keeps track of package vignettes in a "vignette
>> index", e.g.
>> 
>>> readRDS(system.file(package = "utils", "Meta", "vignette.rds"))
>>        File              Title        PDF        R Depends Keywords
>> 1 Sweave.Rnw Sweave User Manual Sweave.pdf Sweave.R   tools
>> 
>> which is created during 'R CMD build' by parsing and compiling the
>> vignettes (https://github.com/wch/r-source/blob/tags/R-3-5-2/src/library/tools/R/build.R#L283-L393 <https://github.com/wch/r-source/blob/tags/R-3-5-2/src/library/tools/R/build.R#L283-L393>).
>> This vignette index is used to find package vignettes (e.g.
>> utils::vignette()) and build the HTML vignette index.
>> 
>> Also, one vignette source (e.g. Rnw, Rmd, ...) can only produce one
>> vignette product (PDF or HTML) in the vignette index.  You can output
>> other files (e.g. image files) in a relative folder that the vignette
>> references, which is why for instance non-self-contained HTML files
>> work.  Thus, one ad-hoc, not-so-nice hack that OP could do is to have
>> a single main vignette that produces and links to all child vignettes.
>> However, personally, I'd aim for using memoization/caching (to file)
>> such that each vignette can be compiled independently of the others
>> (and in any order), while still reusing intermediate
>> results/calculations produced by earlier vignettes.
>> 
>> /Henrik
>> 
>>> 
>>> On Fri, Dec 21, 2018 at 11:26 PM Aaron Lun
>>> <infinite.monkeys.with.keyboards using gmail.com <mailto:infinite.monkeys.with.keyboards using gmail.com>> wrote:
>>>> 
>>>> I gave it a shot:
>>>> 
>>>> https://github.com/LTLA/DrakeTest <https://github.com/LTLA/DrakeTest> <https://github.com/LTLA/DrakeTest <https://github.com/LTLA/DrakeTest>>
>>>> 
>>>> This uses a single “controller” Rmd file to trigger Drake::make. Running this file will instruct Drake to compile all of the other vignettes following the desired dependency structure.
>>>> 
>>>> The current sticking point is that I need to move the Drake-controlled Rmd files out of “vignettes/“, otherwise they’ll just be compiled as usual without consideration of their dependencies. This causes problems as R CMD BUILD only recognizes the controller Rmd file as the sole vignette, and doesn’t retain or index the HTML files produced from the other Rmd files as side-effects of running the controller.
>>>> 
>>>> Are there any better ways to subvert the vignette building procedure to get the desired effect of running drake::make() and recognition of the resulting HTMLs as vignettes?
>>>> 
>>>> -A
>>>> 
>>>>> On 18 Dec 2018, at 17:41, Michael Lawrence <lawrence.michael using gene.com <mailto:lawrence.michael using gene.com>> wrote:
>>>>> 
>>>>> Sounds like a use case for drake...
>>>>> 
>>>>> On Tue, Dec 18, 2018 at 6:58 AM Aaron Lun <infinite.monkeys.with.keyboards using gmail.com <mailto:infinite.monkeys.with.keyboards using gmail.com> <mailto:infinite.monkeys.with.keyboards using gmail.com <mailto:infinite.monkeys.with.keyboards using gmail.com>>> wrote:
>>>>> @Michael In this case, the resource produced by vignette X is a SingleCellExperiment object containing the results of various processing steps (normalization, clustering, etc.) described in that vignette.
>>>>> 
>>>>> I can imagine a lazy evaluation model for this, but it wouldn’t be pretty. If I had another vignette Y that depended on the SCE produced by vignette X, I would need Y to execute all of the steps in X if X hadn’t already been run before Y. This gets us into the territory of Makefile-like dependencies, which seems even more complicated than simply specifying a compilation order.
>>>>> 
>>>>> You might ask why X and Y are split into two separate vignettes. The use of different vignettes is motivated by the complexity of the workflows:
>>>>> 
>>>>> - Vignette 1 demonstrates core processing steps for one read-based single-cell RNAseq dataset.
>>>>> - Vignette 2 demonstrates (slightly different) core steps for a UMI-based dataset.
>>>>> - … so on for a bunch of other core steps for different types of data.
>>>>> - Vignette 6 demonstrates extra optional steps for the two SCEs produced by vignettes 1 & 3.
>>>>> - … and so on for a bunch of other optional steps.
>>>>> 
>>>>> The separation between core and optional steps into separate documents is desirable. From a pedagogical perspective, I would very much like to get the reader through all the core steps before even considering the extra steps, which would just be confusing if presented so early on. Previously, everything was in a single document, which was difficult to read (for users) and to debug (for me), especially because I had to use contrived variable names to avoid clashes between different sections of the workflow that did similar things.
>>>>> 
>>>>> @Martin I’ve been using BiocFileCache for all of the online resources that are used in the workflow. However, this is only for my (and the reader’s) convenience. I use a local cache rather than the system default, to ensure that the downloaded files are removed after package build. This is intentional as it forces the package builder to try to re-download resources when compiling the vignette, thus ensuring the validity of the URLs. For a similar reason, I would prefer not to cache the result objects for use in different R sessions. I could imagine caching the result objects for use by a different vignette in the same build session, but this gets back to the problem of ensuring that the result object is generated by one vignette before it is needed by another vignette.
>>>>> 
>>>>> -A
>>>>> 
>>>>>> On 18 Dec 2018, at 14:14, Martin Morgan <mtmorgan.bioc using gmail.com <mailto:mtmorgan.bioc using gmail.com> <mailto:mtmorgan.bioc using gmail.com <mailto:mtmorgan.bioc using gmail.com>>> wrote:
>>>>>> 
>>>>>> Also perhaps using BiocFileCache so that the result object is only generated once, then cached for future (different session) use.
>>>>>> 
>>>>>> On 12/18/18, 8:35 AM, "Bioc-devel on behalf of Michael Lawrence" <bioc-devel-bounces using r-project.org <mailto:bioc-devel-bounces using r-project.org> <mailto:bioc-devel-bounces using r-project.org <mailto:bioc-devel-bounces using r-project.org>> on behalf of lawrence.michael using gene.com <mailto:lawrence.michael using gene.com> <mailto:lawrence.michael using gene.com <mailto:lawrence.michael using gene.com>>> wrote:
>>>>>> 
>>>>>>   I would recommend against dependencies across vignettes. Ideally someone
>>>>>>   can pick up a vignette and execute the code independently of any other
>>>>>>   documentation. Perhaps you could move the code generating those shared
>>>>>>   resources to the package. They could behave lazily, only generating the
>>>>>>   resource if necessary, otherwise reusing it. That would also make it easy
>>>>>>   for people to write their own documents using those resources.
>>>>>> 
>>>>>>   Michael
>>>>>> 
>>>>>>   On Tue, Dec 18, 2018 at 5:22 AM Aaron Lun <
>>>>>>   infinite.monkeys.with.keyboards using gmail.com <mailto:infinite.monkeys.with.keyboards using gmail.com> <mailto:infinite.monkeys.with.keyboards using gmail.com <mailto:infinite.monkeys.with.keyboards using gmail.com>>> wrote:
>>>>>> 
>>>>>>> In a number of my workflow packages (e.g., simpleSingleCell), I rely on a
>>>>>>> specific compilation order for my vignettes. This is because some vignettes
>>>>>>> set up resources or objects that are to be used by later vignettes.
>>>>>>> 
>>>>>>> From what I understand, vignettes are compiled in alphanumeric ordering of
>>>>>>> their file names. As such, I give my vignettes fairly structured names,
>>>>>>> e.g., “work-1-reads.Rmd”, “work-2-umi.Rmd” and so on.
>>>>>>> 
>>>>>>> However, it becomes rather annoying when I want to add a new vignette in
>>>>>>> the middle somewhere. This results in some unnatural numberings, e.g.,
>>>>>>> “work-0”, “3b”, which are ugly and unintuitive. This is relevant as
>>>>>>> BiocStyle::Biocpkg() links between vignettes require you to use the
>>>>>>> destination vignette’s file name; so difficult names complicate linking,
>>>>>>> especially if the names continually change to reflect new orderings.
>>>>>>> 
>>>>>>> Is there an easier way to control vignette compilation order? WRE provides
>>>>>>> no (obvious) guidance, so I would like to know what non-standard hacks are
>>>>>>> known to work on the build machines. I can imagine something dirty whereby
>>>>>>> one ”reference” vignette contains code to “rmarkdown::render" all other
>>>>>>> vignettes in the specified order… ugh.
>>>>>>> 
>>>>>>> -A
>>>>>>> 
>>>>>>> _______________________________________________
>>>>>>> Bioc-devel using r-project.org <mailto:Bioc-devel using r-project.org> <mailto:Bioc-devel using r-project.org <mailto:Bioc-devel using r-project.org>> mailing list
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>>>>>>> 
>>>>>>> 
>>>>>> 
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>>>>>> 
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>>>>>> 
>>>>> 
>>>>> _______________________________________________
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