Help with AMI hosted on bioconductor page, ami-a3d126c8
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@niteshturaga-8667
Last seen 8 months ago
United States

Hi,

I'm trying to use BiocParallel on the AWS EC2 service using the AMI provided on this page http://www.bioconductor.org/help/bioconductor-cloud-ami/#custom (AMI ID: ami-a3d126c8)

When I try to reproduce the vignette, I get the error that not all parallel infrastructures are recognized in this build of the image. Can someone help me run through the vignette as given without producing errors? Is it possible on the AMI's given by bioconductor. 

> library(BiocParallel)
'BiocParallel' did not register default BiocParallelParams:
  invalid class “SnowParam” object: 'workers' must be integer(1) and >= 0

> sessionInfo()
R version 3.2.1 (2015-06-18)
Platform: x86_64-unknown-linux-gnu (64-bit)
Running under: Ubuntu 14.04.2 LTS

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] BiocParallel_1.3.31  BiocInstaller_1.19.6

loaded via a namespace (and not attached):
[1] parallel_3.2.1       futile.logger_1.4.1  lambda.r_1.1.7
[4] futile.options_1.0.0

 

 

Thanks.

 

BiocParallel amazon • 1.0k views
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Entering edit mode

It looks like you posted a follow up and then retracted it. Just to clarify -

The AMI comes pre-loaded with a snapshot of the current packages at the time and is not updated regularly. Because the devel branch is under constant development it would not be surprising that one of these packages has a bug. (Things are much more stable in the release branch.) I asked you to update so we would be working with the same versions when troubleshooting. It's not the case that 1.3.51 is the only version that works with the AMI, it is just the most recent devel version.

I'm sorry if it took a lot of time to update all packages. I should have mentioned that you can update a single package with biocLite("BiocParallel").

Valerie

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Entering edit mode
@valerie-obenchain-4275
Last seen 8 months ago
United States

Hi,

Yes, BiocParallel works on the AMI and I can help walk you through the vignette.

First you need to update your version of BiocParallel and other packages. Run

biocLite()

Check to make sure BiocParallel 1.3.51 was installed. Then try the vignette again.

Valerie

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