[Bioc-devel] library() calls removed in simpleSingleCell workflow
About the DLL limit: Just wanna make sure you're aware of "new" environment variable R_MAX_NUM_DLLS available in R (>= 3.4.0). It allows you to push the current default limit of 100 open DLLs a bit higher. It can be set in .Renviron or before, e.g. $ R_MAX_NUM_DLLS=500 R This, of course, assumes that you can set it, which you might not be able to do on build servers. Also, there is an upper limit min(0.6*fd_limit,1000) that depends on the number of files you can have open at the same time (fd_limit), e.g. on my Ubuntu 16.04 I've got: $ ulimit -Sn 1024 so R_MAX_NUM_DLLS=614 is the maximum for me. /Henrik
On Thu, Oct 5, 2017 at 11:22 AM, Wolfgang Huber <wolfgang.huber at embl.de> wrote:
Breaking up long workflows into several smaller "modules" each with a clearly defined input and output is a good idea, certainly for didactic & maintenance reasons. It doesn't "solve" the DLL issue though, it only avoids it (for now)... I believe you can use a Makefile for your vignettes (https://cran.r-project.org/doc/manuals/R-exts.html#Writing-package-vignettes), and this might be a good way of managing which depends on which. For passing along output/input, perhaps local .RData files are good enough, perhaps some wheel-reinventing can also be avoided by using https://bioconductor.org/packages/release/bioc/html/BiocFileCache.html (haven't actually used it yet, though). Wolfgang 5.10.17 20:02, Aaron Lun scripsit:
This may relate to what I was thinking with respect to solving the DLL
problem, by breaking up large workflows into modules that can be executed in
separate R sessions. The same approach would also make it easier to
associate package dependencies with specific parts of the workflow.
In my particular situation, it is easy to break up the workflow into
sections that can be executed completely independently. However, I can also
imagine situations where 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 persist during the execution of another?
-Aaron
------------------------------------------------------------------------
*From:* Wolfgang Huber <wolfgang.huber at embl.de>
*Sent:* Thursday, 5 October 2017 6:23:47 PM
*To:* Laurent Gatto; Aaron Lun
*Cc:* bioc-devel at 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 actually increase
readability).
But relying on manually sprinkled in `library` calls seems like a hack
prone to error. And there are always bound to be dependencies that are
non-local, e.g. on general infrastructure like SummarizedExperiment,
ggplot2, dplyr.
So: do we need a way to computationally determine the dependencies of a
vignette section, including highlighting/eliminating potential name
clashes (b/c the warnings about masking emitted at package loading are
easily ignored)? This seems like a straightforward engineering task.
Eventually with such code analysis we could get rid of explicit
`library` calls altogether :)
Wolfgang
5.10.17 08:53, Laurent Gatto scripsit:
On 5 October 2017 00:11, Aaron Lun wrote:
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.
I can confirm that this is a possibility. Before workflows became available, I created the RforProteomics package that essentially provided one relatively large vignette to demonstrate a variety of applications of R/Bioconductor for mass spectrometry and proteomics. I think this has been a useful way to disseminate R and Bioconductor in these respective communities, but also lead to the confusion that it was that package that "did all the stuff", i.e. people saying that they were using RforProteomics to do a task that was described in the vignette. The RforProteomics vignette does explicitly call library at the beginning of each section and explained that the package was only a collection of analyses stemming from other packages, but that wasn't enough apparently. Laurent
-Aaron
________________________________
From: Bioc-devel <bioc-devel-bounces at r-project.org> on behalf of
Wolfgang Huber <wolfgang.huber at embl.de>
Sent: Thursday, 5 October 2017 8:26 AM
To: bioc-devel at 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.Obenchain at 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
<alun at wehi.edu.au><mailto:alun at 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
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-- With thanks in advance- Wolfgang ------- Wolfgang Huber Principal Investigator, EMBL Senior Scientist European Molecular Biology Laboratory (EMBL) Heidelberg, Germany wolfgang.huber at embl.de http://www.huber.embl.de
-- With thanks in advance- Wolfgang ------- Wolfgang Huber Principal Investigator, EMBL Senior Scientist European Molecular Biology Laboratory (EMBL) Heidelberg, Germany wolfgang.huber at embl.de http://www.huber.embl.de
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