search

vastgroup / vast-tools

A toolset for profiling alternative splicing events in RNA-Seq data.
MIT License
78 stars 29 forks source link

Error in vast-tools diff #33

Closed mirimia closed 9 years ago

mirimia commented 9 years ago

Hi Tim,

I'm getting this error in diff:

Trying to load required package: optparse Trying to load required package: RColorBrewer Trying to load required package: reshape2 Trying to load required package: ggplot2 Trying to load required package: grid Trying to load required package: parallel Error in loadNamespace(name) : there is no package called ‘labeling’ Calls: plotPrint ... tryCatch -> tryCatchList -> tryCatchOne -> Execution halted

It happens sometime after it analyzes (and detects as differentially included) quite a few AS events already, so I'm not sure why it happens.

Thanks, Manu

UBrau commented 9 years ago

Hi,

This may or may not be related, but I've been having a similar experience on the cluster with identical jobs that UAE the package GenomicRanges either running or dying. In this case it could be happening when diff spawns the parallel processes.

Ulrich

On Jan 9, 2015 9:50 AM, Manuel Irimia notifications@github.com wrote:

Hi Tim,

I'm getting this error in diff:

Trying to load required package: optparse Trying to load required package: RColorBrewer Trying to load required package: reshape2 Trying to load required package: ggplot2 Trying to load required package: grid Trying to load required package: parallel Error in loadNamespace(name) : there is no package called ‘labeling’ Calls: plotPrint ... tryCatch -> tryCatchList -> tryCatchOne -> Execution halted

It happens sometime after it analyzes (and detects as differentially included) quite a few AS events already, so I'm not sure why it happens.

Thanks, Manu

— Reply to this email directly or view it on GitHubhttps://github.com/vastgroup/vast-tools/issues/33.

mirimia commented 9 years ago

I'm running this on the CRG cluster (I'm not sure I've ever tried diff here, but I think I did). R version is 3.1.1 (2014-07-10).

I'll try on the bc cluster now to see if I get the same error.

Thx

mirimia commented 9 years ago

It works well in the BC cluster, with R version 3.0.1. So it might be that? (it's weird as the one that didn't work is a newer version).

UBrau commented 9 years ago

Could it be a problem that the package in question is only available in your local install but is not compatible with the newer R version that is running on some nodes?

_u

On 09/01/15 15:05, Tim Sterne-Weiler wrote:

Is the R you are using at CRG a global install or is it your local user install? I wouldn't think the newer R version would be a problem...

Sent from my iPhone

On Jan 9, 2015, at 1:21 PM, Manuel Irimia notifications@github.com<mailto:notifications@github.com> wrote:

It works well in the BC cluster, with R version 3.0.1. So it might be that? (it's weird as the one that didn't work is a newer version).

— Reply to this email directly or view it on GitHubhttps://github.com/vastgroup/vast-tools/issues/33#issuecomment-69384342.

— Reply to this email directly or view it on GitHub https://github.com/vastgroup/vast-tools/issues/33#issuecomment-69390743.

timbitz commented 9 years ago

OK. The problem looks to be dependencies: 'labeling' is a dependent package that is installed by default when you install ggplot2 if you require dependencies. I thought the loadPackages function required dependencies but it looks like maybe not. So I have added that now.

mirimia commented 9 years ago

Thanks. I've pulled the last change but it still gives the error. Should I do something else? (like, re-install any bit?).

M

timbitz commented 9 years ago

Yes. You can probably just open R and install.packages('labeling'). Or delete ggplot2 and re-install with the script which should now also install that dependency. =