Sounds like a use case for drake...
On Tue, Dec 18, 2018 at 6:58 AM Aaron Lun <
infinite.monkeys.with.keyboa...@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, cl
Hi Aaron,
Right now 'R CMD build' evaluates all vignettes in the same R session.
Personally I see this as an undesirable feature and hope that it will
change in the future. Problem with this is that when a vignette hits the
max DLL limit, breaking it down into smaller vignettes doesn't help.
A
The devel build report hasn't posted yet but I took a look at the new
compiler flag output Herve implemented. The results show tokay2 is
indeed using
CXX11FLAGS: -O3 -march=native -mtune=native
This is inconsistent with what we have in the R/etc//Makeconf for
both architectures on both tokay1
Codetools should probably be ignoring those. Will have a look
Sent from my iPhone
> On Dec 18, 2018, at 6:54 AM, Shepherd, Lori
> wrote:
>
> Can you please open an issue for this so we don't lose track of it -
>
> https://github.com/Bioconductor/BiocCheck/issues
>
>
>
> Lori Shepherd
>
>
Hi Anand,
The issue is the way you have updated your version numbers.
Note that the last commit on upstream/master was the release version bump where
your package has a version “1.9.0”. Please update the version to “1.9.1” and
try pushing after the merge. I’ve outlined the steps you should ta
Hi Nitesh,
I have checked my remotes, they are fine.
$ git remote -v
origin https://github.com/PoisonAlien/maftools.git (fetch)
origin https://github.com/PoisonAlien/maftools.git (push)
upstreamg...@git.bioconductor.org:packages/maftools.git (fetch)
upstreamg...@git.bioconducto
@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 anoth
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"
wrote:
I would recommend against dependencies across vignettes. Ideally someone
can pick
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
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
Can you please open an issue for this so we don't lose track of it -
https://github.com/Bioconductor/BiocCheck/issues
Lori Shepherd
Bioconductor Core Team
Roswell Park Cancer Institute
Department of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263
_
Dear Valerie,
thanks for the heads-up on this.
Best,
Christian
Am 12/17/2018 um 6:52 PM schrieb Obenchain, Valerie:
> Hi Christian,
>
> This is a known - there are no Mac binaries for El Capitan for R 3.6 at
> this point. We don't build Cairo from source on the Mac builder, we use
> the binary
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