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Currently the package only instruments functions which are defined at top level of a package namespace. But sometimes additional functions are stored inside environments which then do not get instrume…
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# Background
Currently, the package uses `batchtools::waitForJobs()` every second (`getOption("future.wait.delay", 1.0)`) to poll the scheduler to see when jobs are finished. Polling the scheduler t…
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MWE:
``` r
test_that("capture.output", {
expect_true(length(capture.output(message("foo"), type = "message")) == 1)
})
```
Session info:
```
R version 3.2.4 (2016-03-10)
Platform: x86_64-apple-darw…
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Using TORQUE / PBS as an example, one can use:
```sh
#PBS -N
```
in the template file to make the name of the job to the be the batchtools job hash. This makes the job hash to show up as the nam…
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For instance, a PBS job with `-l vmem=1gb` gave:
```sh
$ tail /home/henrik/projects/tests/.future/20170626_111627-54Dsqf/sample_1_38265500/logs/joba810736cd1202b8e75d829f18ca5d611.log
[...]
Chrom…
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Make `%label%` the job name for schedulers. This is the case with future.BatchJobs.
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How do I make sure that folders in /home/rstudio permit me to add subfolders?
A minimal example:
I run
`docker run --rm -p 8787:8787 rocker/verse:3.4.1`,
go to localhost:8787
and then do what…
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Running `qcmd --exec Rscript 3.pscbs.R` with `chromosomes: c(1:22, "X", "Y", "M")` gave:
```r
[...]
Sample 1 ('Patient300,Z00363_vs_Z00346') of 1 ...
...
Loading required package: methods
Atta…
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@SRHilz wrote:
I have finally gotten the chance to try running the Costello PSCN pipeline on my own (I want to eventually be able to run it for our lab), and have two quick questions I wanted to se…
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how can i set the "init" arg, but avoid that the first object is not joined in again?
more concrete example:
say my jobs results are all lists. from the lists, i only want element "foo".
my …