Michael Schubert

Byte-compile modules

2

Does it make sense to byte-compile modules, either upon loading or (ideally) cached? Of course, this would [not be as fast](http://dirk.eddelbuettel.com/blog/2011/04/12/) as using `Rcpp`, but is a speed increase that...

Are retraction notices sufficient?

2

I stumbled across [this paper](https://joss.theoj.org/papers/23161710ad8996910f329efc48c2f1a1), which has a big red RETRACTED notice. I think it's good that JOSS labels papers it retracts clearly while still acessible. However: * If I'm...

Missing gene annotations for exons

2

Hi, When I download legacy exon quantification from *TCGAbiolinks*, the resulting `SummarizedExperiment` I get has the `@rowRanges` contain `start`, `end`, and `chromosome`. It would be great if it also contained...

lfs server usage

19

Hi, I'm playing around with the lfs server a bit, and I can't seem to make it work as I would expect: my lfs files are commited to the git...

E.g. requesting 10 jobs with 4 GB each, if machine has only 8 GB then max request 2

should check this and error out before jobs are started

Add resubmission function

2

*originally posted in #153 by @nick-youngblut* I'm a big fan of snakemake, which allows for automatic resubmission of failed jobs with increased resources (eg., `mem = lambda wildcards, threads, attempt:...

SSH transfer scales badly for large data

7

```r clustermq::Q(object.size, x=list(rnorm(1e8)), n_jobs=1) ``` ``` Connecting USER@HOST via SSH ... Sending common data ... Running 1 calculations (0 objs/0 Mb common; 1 calls/chunk) ... Master: [30.5s 9.3% CPU]; Worker:...

One of the ideas of the option-based configuration of `clustermq` is that code should be portable between compute environments, e.g. when moving to a different HPC scheduler. If moving from...

Support heterogeneous workers

1

Allow concatenation of different workers to a "pool." Workflow logic is basically unchanged, because it does not matter where the workers are as long as they connect to the same...