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Cannot run simple SGE example #48
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Hey!
So far, I've been using a pretty simple template file:
It would be great if you could help me with that! And thanks for maintaining this pretty awesome package. Best, |
Could you post the output of: library(BatchJobs)
setConfig(debug = TRUE)
reg = makeRegistry("debug")
findRunning(reg) |
How much do you use the package at your facility? Would you be willing to test for us if we ever do interface changes for the backends BEFORE the release? |
Thanks for the fast answer! Good to read it's just a tiny fix. Thanks! |
I pushed the mini fix. Can you pls test and report? Also, for later would you send me your mail address and name? So I might ask you again about an SGE test? I am here: It is also good to hear that people use BatchExperiments we mainly get feedback for BatchJobs. |
Installed it, and it works as a treat. Thanks for fixing so quickly! All the best, |
Thx for the test. I will try to get this on CRAN soon, I can drop you a message. Or keep this open till it has happened. |
I see we had the last CRAN release 5 weeks ago, so they should allow a new one without special asking. I will check whether we have a "round" release now. |
Thanks, everyone, for solving this bug so fast I missed the entire process! Will test when pushed out to CRAN. On Aug 14, 2014, at 9:59 AM, berndbischl <notifications@github.commailto:notifications@github.com> wrote: I see we had the last CRAN release 5 weeks ago, so they should allow a new one without special asking. I will check whether we have a "round" release now. —
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Will release today. Closing. |
I am trying to get a simple example working on my SGE cluster. Session info below. I'd greatly appreciate any ideas for figuring this out. BiocParallel is not available for R 3.1.1.
Maybe my SGE template is not correct? I expect not because this code seems to fail on a simple qstat.
I am using the following configuration:
cluster.functions = makeClusterFunctionsSGE("/home/poirierj/R_libs/BatchJobs/etc/simple.tmpl", list.jobs.cmd = c("qstat", "-u poirierj"))
mail.start = "none"
mail.done = "none"
mail.error = "none"
db.driver = "SQLite"
db.options = list()
debug = TRUE
$output
character(0)
Error: $ operator is invalid for atomic vectors
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_0.4.1 BatchJobs_1.3 BBmisc_1.7
loaded via a namespace (and not attached):
[1] brew_1.0-6 checkmate_1.2 codetools_0.2-8 DBI_0.2-7
[5] digest_0.6.4 fail_1.2 foreach_1.4.2 iterators_1.0.7
[9] parallel_3.0.2 RSQLite_0.11.4 sendmailR_1.1-2 stringr_0.6.2
[13] tools_3.0.2
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