[R] identify object that causes "Error in loadNamespace(name) : there is no package called ‘R.utils’"

[Martin Morgan]

On 04/24/2013 06:03 AM, Duncan Murdoch wrote:
> On 13-04-24 5:46 AM, Liviu Andronic wrote:
>> Dear all,
>> I've bumped into the: "Error in loadNamespace(name) : there is no
>> package called ‘R.utils’" error. I've already read a bit on this (
>> http://www.cybaea.net/Blogs/Data/A-warning-on-the-R-save-format.html )
>> but I have a follow-up question.
>>
>> Given a workspace that automatically loads a package that I don't
>> really need/want (e.g. ‘R.utils’), how do I identify which object
>> requires this package to load? I would like to avoid loading ‘R.utils’
>> every time I open an R session.
>
> That's not easy, because the code in R that triggers that error has no idea of
> the name of the object it is loading.

Maybe traceback() can provide some hints? I did, more or less arbitrarily

library(rms)
a = list(fun=ie.setup)
save(a, file="/tmp/a.rda")
remove.packages("rms")

and then in a new session

 > load("/tmp/a.rda")
Error in loadNamespace(name) : there is no package called 'rms'
 > traceback()
7: stop(e)
6: value[[3L]](cond)
5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
4: tryCatchList(expr, classes, parentenv, handlers)
3: tryCatch(loadNamespace(name), error = function(e) stop(e))
2: getNamespace(c("rms", "3.6-3"))
1: load("/tmp/a.rda")

with the line numbered 2 giving me the necessary hint.

Martin


>
> You could try a binary search to find out, but it will be tedious:
> 1. Install R.utils.
> 2. Load the workspace successfully.
> 3. Delete half the objects, and save it.
> 4. Uninstall R.utils, and see if you can load the workspace.
>
> At this point you'll know if there's an object needing R.utils still left or
> not, and you can repeat the steps until you find a single object that causes the
> problem.  (But it might not be the only one, so deleting it from the original
> workspace might not solve your problem.)
>
> A better approach is to *never* save and load workspaces unless you know exactly
> what is in them.  Always reply "no" to the question about saving your workspace
> (or set that as the default).  If you accidentally end up with a workspace being
> loaded, delete it.
>
> Duncan Murdoch
>
>>
>> Regards,
>> Liviu
>>
>>
>>> sessionInfo()
>> R version 2.15.3 (2013-03-01)
>> Platform: i686-pc-linux-gnu (32-bit)
>>
>> locale:
>>   [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>> LC_TIME=en_US.UTF-8
>>   [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8
>> LC_MESSAGES=en_US.UTF-8
>>   [7] LC_PAPER=C                 LC_NAME=C
>> LC_ADDRESS=C
>> [10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8
>> LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] datasets  grDevices splines   graphics  utils     stats
>> methods   base
>>
>> other attached packages:
>>   [1] R.utils_1.23.2    R.oo_1.13.0       R.methodsS3_1.4.2
>> tables_0.7.57     reshape2_1.2.2
>>   [6] car_2.0-15        nnet_7.3-6        MASS_7.3-23
>> Hmisc_3.10-1      survival_2.37-2
>> [11] foreign_0.8-53
>>
>> loaded via a namespace (and not attached):
>> [1] cluster_1.14.3   grid_2.15.3      lattice_0.20-13  plyr_1.8
>>   rstudio_0.97.312
>> [6] stringr_0.6.2    tools_2.15.3
>>
>>
>
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