[R-SIG-Mac] source() hangs on import
Don McKenzie
dmck at u.washington.edu
Sat May 18 20:12:21 CEST 2013
On 18-May-13, at 8:14 AM, Robert J Goedman wrote:
> Don,
>
> Slightly modified, your example:
>
> N <- 5e4
>
> cat('Create myfile\n')
> system.time(myfile <- data.frame(x1=runif(N),x2=runif(N),x3=runif(N)))
> head(myfile)
>
> cat('\nSave myfile\n')
> system.time(save("myfile",file="./R/R_projects/R Support/Debug/
> myfile.RData"))
> remove(myfile)
>
> cat('Load myfile\n')
> system.time(load("./R/R_projects/R Support/Debug/myfile.RData"))
> head(myfile)
>
> cat('\nDump myfile\n')
> system.time(dump("myfile",file="./R/R_projects/R Support/Debug/
> myfile.R"))
> remove(myfile)
>
> cat('Source myfile\n')
> system.time(source("./R/R_projects/R Support/Debug/myfile.R"))
> head(myfile)
>
> produces:
>
>> source('/Users/rob/Projects/R/R_projects/R support/Debug/
>> DumpAndSave_test.r', print.eval=TRUE)
> Create myfile
> user system elapsed
> 0.005 0.001 0.006
> x1 x2 x3
> 1 0.611084090 0.4841179 0.47273937
> 2 0.596409008 0.2234015 0.19283019
> 3 0.273999461 0.7524927 0.02346372
> 4 0.691567956 0.4921780 0.48312317
> 5 0.001781206 0.1211497 0.12041949
> 6 0.002494183 0.6935539 0.23262610
>
> Save myfile
> user system elapsed
> 0.161 0.001 0.162
> Load myfile
> user system elapsed
> 0.007 0.001 0.008
> x1 x2 x3
> 1 0.611084090 0.4841179 0.47273937
> 2 0.596409008 0.2234015 0.19283019
> 3 0.273999461 0.7524927 0.02346372
> 4 0.691567956 0.4921780 0.48312317
> 5 0.001781206 0.1211497 0.12041949
> 6 0.002494183 0.6935539 0.23262610
>
> Dump myfile
> user system elapsed
> 0.335 0.005 0.338
> Source myfile
> user system elapsed
> 22.252 0.238 22.440
> x1 x2 x3
> 1 0.611084090 0.4841179 0.47273937
> 2 0.596409008 0.2234015 0.19283019
> 3 0.273999461 0.7524927 0.02346372
> 4 0.691567956 0.4921780 0.48312317
> 5 0.001781206 0.1211497 0.12041949
> 6 0.002494183 0.6935539 0.23262610
>
> For N=1e5, the elapsed time for source() is ~100seconds. It is
> slow, but eventually will return on my machine .
>
> Regards,
> Rob J. Goedman
> goedman at icloud.com
Rob -- thanks for taking the time to try that out. Simon's
suggestion to switch to save() and load() seems better all around, so
I'll move to that usage. I should get out more -- that seems to
have been the standard for a while.
Don
>
>
>
>
> On May 17, 2013, at 7:16 PM, Don McKenzie <dmck at u.washington.edu>
> wrote:
>
>> Yes. Duh. Overthinking the "reproducible" part and responding too
>> quickly. Here's one that produces the behavior.
>>
>> myfile <- data.frame(x1=runif(100000),x2=runif(100000),x3=runif
>> (100000))
>> dump("myfile",file="myfileR")
>> source("myfileR")
>>
>> The source() part takes ~10 sec. in R 2.9.2 on my old powermac,
>> but hangs in 3.0.0.
>>
>> Don
>>
>>
>> On 17-May-13, at 6:51 PM, Simon Urbanek wrote:
>>
>>>
>>> On May 17, 2013, at 9:41 PM, Donald McKenzie wrote:
>>>
>>>> Simon -- I can't reproduce it for the list because the window
>>>> it's running in always hangs and R freezes. I tried. But it
>>>> basically looks like
>>>>
>>>>> dump("my.file",file="myfileR")
>>>>> source("myfileR")
>>>> HANG..... (yellow colored ball)
>>>>
>>>
>>> Well, you can simply provide the myfileR that hangs for you ...
>>>
>>> Cheers,
>>> Simon
>>>
>>>
>>>> I will go with your suggestions below and report back if need
>>>> be. Thanks for the help.
>>>>
>>>> Don
>>>>
>>>> On Fri, 17 May 2013, Simon Urbanek wrote:
>>>>
>>>>>
>>>>> On May 17, 2013, at 7:20 PM, Don McKenzie wrote:
>>>>>
>>>>>> I checked the archives since the release of R 3.0.0 and didn't
>>>>>> see anything on this.
>>>>>>
>>>>>> Trying to import data previously exported with dump(), source
>>>>>> () hangs and I have to force quit R. This happens with data
>>>>>> objects
>>>>>> as small as 5 kb.
>>>>>
>>>>> Do you have a reproducible example?
>>>>>
>>>>>
>>>>>> Has anyone encountered this and found a workaround? Is there
>>>>>> now a preferred method to export R objects?
>>>>>>
>>>>>
>>>>> The preferred method has always been to use serialization (save/
>>>>> load or saveRDS/readRDS).
>>>>>
>>>>> Cheers,
>>>>> Simon
>>>>>
>>>>>
>>>>>> Thanks for any suggestions.
>>>>>>
>>>>>> on a macbook pro with 4 gb RAM.
>>>>>>
>>>>>>> R.version
>>>>>> _
>>>>>> platform x86_64-apple-darwin10.8.0
>>>>>> arch x86_64
>>>>>> os darwin10.8.0
>>>>>> system x86_64, darwin10.8.0
>>>>>> status
>>>>>> major 3
>>>>>> minor 0.0
>>>>>> year 2013
>>>>>> month 04
>>>>>> day 03
>>>>>> svn rev 62481
>>>>>> language R
>>>>>> version.string R version 3.0.0 (2013-04-03)
>>>>>> nickname Masked Marvel
>>>>>>
>>>>>>
>>>>>>
>>>>>> Don McKenzie
>>>>>> Research Ecologist
>>>>>> Pacific Wildland Fire Sciences Lab
>>>>>> US Forest Service
>>>>>>
>>>>>> Affiliate Professor
>>>>>> School of Environmental and Forest Sciences
>>>>>> University of Washington
>>>>>>
>>>>>> phone: 206-732-7824
>>>>>> dmck at uw.edu
>>>>>>
>>>>>> _______________________________________________
>>>>>> R-SIG-Mac mailing list
>>>>>> R-SIG-Mac at r-project.org
>>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>>>>>
>>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> R-SIG-Mac mailing list
>>>>> R-SIG-Mac at r-project.org
>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>>>>
>>>>
>>>>
>>>
>>
>>
>>
>>
>>
>> Don McKenzie, Research Ecologist
>> Pacific Wildland Fire Sciences Lab
>> US Forest Service
>> phone: 206-732-7824
>>
>> Affiliate Professor
>> School of Environmental and Forest Sciences
>> University of Washington
>>
>> _______________________________________________
>> R-SIG-Mac mailing list
>> R-SIG-Mac at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>
Don McKenzie, Research Ecologist
Pacific Wildland Fire Sciences Lab
US Forest Service
phone: 206-732-7824
Affiliate Professor
School of Environmental and Forest Sciences
University of Washington
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