Error in DoRun

[Daniel Gates]

HI Barb,

That seems to have all the functions loaded. Unfortunately, as I'm
walking through the example script that you gave I'm running into this
error though:


#This is the code:
a<-doRun(
phy = phy,
traits = char,
intrinsicFn=brownianIntrinsic, #name which intrinsic model
extrinsicFn=nullExtrinsic, #name which extrinsic model
startingPriorsFns="uniform", #distribution for starting state prior
startingPriorsValues=matrix(c(min(char[,1]), max(char[,1]))), #prior
values
intrinsicPriorsFns=c("exponential"), #distribution for intrinsic
prior
intrinsicPriorsValues=matrix(c(10, 10), nrow=2, byrow=FALSE),
#intrinsic prior values
extrinsicPriorsFns=c("fixed"), #distribution for extrinsic prior
extrinsicPriorsValues=matrix(c(0, 0), nrow=2, byrow=FALSE), #fixed at
0
TreeYears=1000,
standardDevFactor=0.2,
plot=F,
StartSims=200, #number of initial simulations
epsilonProportion=0.5, #What proportion of initial particles to keep
epsilonMultiplier=0.5, #What proportion of particles to keep for
subsequent generations
nStepsPRC=5, #number of generations
maxTries=1,
numParticles=100, #how many accepted particles to keep for each
generation
debug=F,
whenToKill=20,
jobName=6,
stopRule=F,
multicore=F, #initial sims (ie StartSims) are set up to be
multithreaded if T
coreLimit=1
)


#this is the result
**** TRY 1 of 1 ****

Number of initial simulations set to 200
Using 1 core(s) for initial simulations

Error: could not find function "%dopar%"
>


Seems to be something S4 or parallelization related

[B.Banbury]

Yep, dopar is part of the foreach package for parallelization (which I made a suggested package).  Darn it! Can you see if foreach gives you the same error as doMC did on your machine? 

______________________
Barb Banbury
Postdoctoral Research Associate
Ecology and Evolutionary Biology
University of Tennessee, Knoxville

[dga...@huskers.unl.edu]

Hi Barb,

I'm not exactly sure what you mean, I guess I don't see doMC called anywhere in here. I've loaded foreach and replaced the doRun with the loaded foreach call from the foreach package but it didn't run any simulations (although it didn't raise any errors) is that what you mean?

[B.Banbury]

Ooops, my mistake.  I thought you were having problems with doMC, when you had issues with rgl.  Sorry.  Ok, so lets back up a little bit, because I am also not sure what you mean by this: "...and replaced the doRun with the loaded foreach call...".  If you were able to load the foreach package, then you should be able to run sims from the example file.  Is that not working?  

Barb

PS, we should have a meeting soon.  Derrick, do you have time this week?  Did you get the doodle email?  

______________________
Barb Banbury
Postdoctoral Research Associate
Ecology and Evolutionary Biology
University of Tennessee, Knoxville

[dga...@huskers.unl.edu]

ah yes my mistake there. All it took was loading the package foreach at the start of the file, now it all seems to be running. Thanks!

[B.Banbury]

Whoo hoo!  Great news!  I hope we worked out some of the bugs in the meantime.  

Let me know if anything else happens that shouldn't.  

What does everyone think of meeting on Friday at 12 EST?  

______________________
Barb Banbury
Postdoctoral Research Associate
Ecology and Evolutionary Biology
University of Tennessee, Knoxville

[dga...@huskers.unl.edu]

that works for me I'll mark my calendar for 11 CT

[Hilmar Lapp]

works for me (assuming you mean EDT :-)

On May 9, 2012, at 4:26 PM, dga...@huskers.unl.edu wrote:

ah yes my mistake there. All it took was loading the package foreach at the start of the file, now it all seems to be running. Thanks!

-- 

===========================================================

: Hilmar Lapp  -:- Durham, NC -:- informatics.nescent.org :

===========================================================

[dzwickl]

Hi All,

Sorry, I was out of town the first part of this week and not really
checking email. Unfortunately this Friday at 12 EDT doesn't work for
me as I have a Dr. appt. In general the time would work. The
earliest that I could easily do would probably be 1:30 EDT (we are 3
hr. earlier out here). So, you are welcome to meet without me, or we
could do it later in the day.

Sorry about that.
Derrick

[Hilmar Lapp]

I can't do later that day (nor, actually, earlier). However, being primary mentor already for another project, I wasn't expecting to participate regularly in the weekly calls for this one, but rather to focus on situations or questions where my knowledge of R might come in complementary. So I'll stand back here and let you all go ahead at a time that works for you because otherwise I'll become unhelpful fast simply by virtue of my calendar.

-hilmar

Sent with a tap.

[Derrick Zwickl]

Ok, thanks Hilmar. We don't want to suck up too much of your time
anyway, given that you have another GSoC student and are the tertiary
mentor on this one. Your R expertise will definitely be welcome and
helpful though!

So, for the rest of you, what is your preference? I'd prefer something
1PM EDT or later, with any day of the week being fine. Based on the
doodle it looks like a little later on Friday would work for everyone
besides Hilmar.

Cheers,
Derrick

[B.Banbury]

I am open all afternoon, so whatever works for everyone else will work for me.  

Barb

______________________
Barb Banbury
Postdoctoral Research Associate
Ecology and Evolutionary Biology
University of Tennessee, Knoxville

[Brian O'Meara]

I can do 1:30 on Friday, but like Hilmar, it's not critical that I be able to make meetings.

Brian

_______________________________________
Brian O'Meara
Assistant Professor
Dept. of Ecology & Evolutionary Biology
U. of Tennessee, Knoxville
http://www.brianomeara.info

Students wanted: Applications due Dec. 15, annually
Postdoc collaborators wanted: Check NIMBioS' website
Calendar: http://www.brianomeara.info/calendars/omeara

[dga...@huskers.unl.edu]

I can do 1:30 eastern tomorrow

-Dan

[B.Banbury]

Lets go ahead and plan for 1:30 then tomorrow.  For future weeks lets plan for 12, since it is an open time slot for everyone.  

Barb

______________________
Barb Banbury
Postdoctoral Research Associate
Ecology and Evolutionary Biology
University of Tennessee, Knoxville

[Derrick Zwickl]

Ok, then lets plan on 1:30.  Talk to you then.

Derrick

[dga...@huskers.unl.edu]

sounds good!

---

From: treevo-...@googlegroups.com [treevo-...@googlegroups.com] on behalf of Derrick Zwickl [dzw...@gmail.com]
Sent: Thursday, May 10, 2012 1:27 PM
To: treevo-...@googlegroups.com
Subject: Re: Error in DoRun