When I run my shiny application, I got an error message saying
Error in prob[tw, uni.c] :
invalid or not-yet-implemented 'Matrix' subsetting
That same code ran without error when it was not on Shiny. Any idea how I can troubleshoot this?
I'm not sure how to reproduce the data here, but prob is of class dgCMatrix from the Matrix package, tw is a single integer, and uni.c is a numeric vector.
EDIT:
sessionInfo() output:
R version 3.1.1 (2014-07-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
locale:
[1] LC_COLLATE=English_Singapore.1252 LC_CTYPE=English_Singapore.1252 LC_MONETARY=English_Singapore.1252
[4] LC_NUMERIC=C LC_TIME=English_Singapore.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] shiny_0.10.1 Matrix_1.1-4
loaded via a namespace (and not attached):
[1] bitops_1.0-6 caTools_1.17.1 digest_0.6.4 grid_3.1.1 htmltools_0.2.6 httpuv_1.3.0 lattice_0.20-29
[8] Rcpp_0.11.3 RJSONIO_1.3-0 tools_3.1.1 xtable_1.7-4
It turned out to be a bug in my code that is exposed by how Shiny works.
Outside Shiny, the function where the code resides worked seamlessly, being fed input from another function in the right format.
In Shiny, I expected the function in server.R to receive the input after the submitButton button is pressed, with sensible input keyed into the field. Apparently, even before the first press of button, the default value in the input field (which was not a sensible one) was passed to my function. That default value is not well-handled by my function and caused the error. Both changing the default value, and building extra error-checking in my function, worked to solve the issue.
Apologies for the confusion; this was a learning experience to be careful with default values and with Shiny processing sequence.
Related
While using the Boot function from the car package I get the error message
Error in get(".y.boot", envir = .carEnv) : object '.carEnv' not found
I suspect I have inadvertently changed/set something in my OS and have no idea what it might be. Running the code below returns an error on my desktop but runs without error on a laptop running the same OS (Yosemite) as well as a desktop running Windows 7 (all using R-3.1.2). The code that triggers the message is
library(car)
swiss.lm <- lm(Fertility ~ Education, data = swiss)
BC <- Boot(swiss.lm, R = 999, method = "case") # No Problems
BR <- Boot(swiss.lm, R = 999, method = "residual") # Problems now
Error in get(".y.boot", envir = .carEnv) : object '.carEnv' not found
I have reinstalled R but the error still appears when running the above code. Any suggestions as to what I have done and how to get the code to run and find the environment would be most appreciated. TIA!
> sessionInfo()
R version 3.1.2 (2014-10-31)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] car_2.0-24
loaded via a namespace (and not attached):
[1] boot_1.3-15 grid_3.1.2 lattice_0.20-29 lme4_1.1-7 MASS_7.3- 37 Matrix_1.1-5
[7] mgcv_1.8-4 minqa_1.2.4 nlme_3.1-119 nloptr_1.0.4 nnet_7.3-9 parallel_3.1.2
[13] pbkrtest_0.4-2 quantreg_5.11 Rcpp_0.11.4 SparseM_1.6 splines_3.1.2 tools_3.1.2
Looks like a reproducible bug in a car package. According to package news the changes in latest version (2.0-24) are related to .carEnv handling.
I tried to get around the issue by simply assigning the .carEnv before call to Boot with
.carEnv <- car:::.carEnv
This makes the Boot function execute without errors, but I am not sure of any other effects.
The package maintainer emailed me and indicated a bug had been introduced in 2.0-24 and that he would attempt to fix the bug.
For some reason, a code I usually run in Rstudios is no longer working. I'm hoping that someone has had a similar experience and understands what's going on.
getReturns(c('C','BAC'), start='2004-01-01', end='2008-12-31')
This results in:
Error in unclass(e1) + unclass(e2) :
non-numeric argument to binary operator
I can't find anything online nor on stackoverflow that addresses this issue. Also, I saw that the most recent documentation, from July 2014 doesn't mention anything either:
http://cran.r-project.org/web/packages/stockPortfolio/stockPortfolio.pdf
Does anyone have any idea what's going on here?
It's probably a function name clash issue. Running
timeSeries::getReturns(c('C','BAC'), start='2004-01-01', end='2008-12-31')
gives me the error, but running
stockPortfolio::getReturns(c('C','BAC'), start='2004-01-01', end='2008-12-31')
works fine.
How did this happen?
You must have loaded the stockPortfolio package, and then loaded either timeSeries or another package that depends upon timeSeries. Have a look through your console for a message that looks like
The following object is masked from ‘package:stockPortfolio’:
getReturns
Use the double colon operator (as shown above) to explicitly tell R which package to look in.
I have a similar problem using stockPortfolio in a R Markdown program.
Code that works in a R file does not work in the rmd file.
```{r p3}
recordState()
ff <- allFunds1$Fund
returns <-stockPortfolio::getReturns(ff,freq="month")
save(allFunds1,file='allFunds1.rda')
```
gives the error message and traceback
Error in unclass(e1) + unclass(e2) : non-numeric argument to binary operator
5. structure(unclass(e1) + unclass(e2), class = "Date")
4.`+.Date`(as.Date(origin, ...), x)
3. as.Date.numeric(uDates, origin = minDate)
2. as.Date(uDates, origin = minDate
1. stockPortfolio::getReturns(ff, freq = "month")
My recordState function saves the results of search() and sessionInfo() in the chunk:
[1] "search:"
[1] ".GlobalEnv" "tools:rstudio" "package:stats"
[4] "package:graphics" "package:grDevices" "package:utils"
[7] "package:datasets" "package:methods" "Autoloads"
[10] "package:base"
[1] "sessionInfo():"
R version 3.3.2 (2016-10-31)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X Yosemite 10.10.5
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] Rcpp_0.12.9 digest_0.6.11 dplyr_0.5.0
[4] rprojroot_1.2 assertthat_0.1 R6_2.2.0
[7] xtable_1.8-2 DBI_0.5-1 backports_1.0.5
[10] magrittr_1.5 evaluate_0.10 stringi_1.1.2
[13] stockPortfolio_1.2 rmarkdown_1.3 tools_3.3.2
[16] stringr_1.1.0 readr_1.0.0 yaml_2.1.14
[19] htmltools_0.3.5 knitr_1.15.1 tibble_1.2
The original posting suggests that this error can result from confusing stockPortfolio::getReturns with the function in timeSeries but I have used the full name and do not have either of the libraries loaded.
If I include \usepackage{Sweavel} in my .rnw file, I get an X11 popup error "It seems you are using the Sweave-specific syntax; you may need Sweave2knitr("IPT-baseline-test.rnw") to convert it to knitr" when I compile in RStudio (Version 0.98.484). The document compiles, but I have to dismiss the error.
(1) Any ideas why \usepackage{Sweavel} triggers the error?
(2) Is there a way to turn off the popup since the document compiles anyway?
> sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-apple-darwin10.8.0 (64-bit)
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] knitr_1.5
loaded via a namespace (and not attached):
[1] colorspace_1.2-4 dichromat_2.0-0 digest_0.6.3 evaluate_0.5.1
[5] formatR_0.10 ggplot2_0.9.3.1 grid_3.0.2 gtable_0.1.2
[9] labeling_0.2 MASS_7.3-29 munsell_0.4.2 plyr_1.8
[13] proto_0.3-10 RColorBrewer_1.0-5 reshape2_1.2.2 scales_0.2.3
[17] stringr_0.6.2 tools_3.0.2
You shouldn't need to \usepackage{Sweavel} explicitly, I think -- knitr should handle that automatically. If you really want to suppress this false positive , you can rename Sweavel.sty to a file name that doesn't start with Sweave ... the which_sweave() function at https://github.com/yihui/knitr/blob/de7c65c58acfb1f3f5c0ac2f00b92cd2546be943/R/utils-sweave.R shows you what patterns knitr is looking for to detect "old Sweave syntax", specifically in this case the regular expression
regexp <-
'^\\s*\\\\(usepackage(\\[.*\\])?\\{Sweave|SweaveInput\\{|SweaveOpts\\{)'
So changing to mySweavel.sty should work ...
grepl(regexp,"\\usepackage{Sweave}") ## TRUE
grepl(regexp,"\\usepackage{Sweavel}") ## TRUE
grepl(regexp,"\\usepackage{mySweavel}") ## FALSE
My guess is that you have a newer version of knitr on your new than on your old machine, and it's trying harder to detect old Sweave syntax.
Removing the Sweave tag in the latex document prevented the warnings. It did not prevent the rendering of the file. Thus, the suggestion made in one of the comments above worked... knit2pdf (in my case) figures it out. - E
I have been going through the demos in quantstrat. I have a problem running faber_rebal.r. It fails with the following error:
> out<-applyStrategy.rebalancing(strategy='faber' , portfolios='faber')
Error in `colnames<-`(`*tmp*`, value = c("MaxPos", "LongLevels", "MinPos", :
length of 'dimnames' [2] not equal to array extent
Here is the output of sessionInfo():
R version 3.0.1 (2013-05-16)
Platform: x86_64-w64-mingw32/x64 (64-bit)
locale:
[1] LC_COLLATE=English_South Africa.1252 LC_CTYPE=English_South Africa.1252
[3] LC_MONETARY=English_South Africa.1252 LC_NUMERIC=C
[5] LC_TIME=English_South Africa.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] quantstrat_0.7.8 foreach_1.4.1 blotter_0.8.15
[4] PerformanceAnalytics_1.1.0 FinancialInstrument_1.1 quantmod_0.4-0
[7] Defaults_1.1-1 TTR_0.22-0 xts_0.9-5
[10] zoo_1.7-10 lattice_0.20-23
loaded via a namespace (and not attached):
[1] codetools_0.2-8 grid_3.0.1 iterators_1.0.6 tools_3.0.1
The problem occurs within the function applyStrategy.rebalancing when it calls the private function ruleProc.
I also get the same error on my Ubuntu 12.04 Machine with R 3.0.1.
Any help to get it working would be appreciated.
Thanks
Charles
I had some problems getting the faber_rebal.R demo to work as well.
First, you have to set the timezone:
ttz<-Sys.getenv('TZ')
Sys.setenv(TZ='UTC')
Second, I could get the following line in the add.rule rebalance to work:
refprice=quote(last(getPrice(mktdata)[paste('::',timestamp,sep='')][,1])),
so I changed it to:
refprice=quote(last(getPrice(mktdata)[paste('::','20140119',sep='')][,1])),
I hope that helps.
Best,
Peter
It looks like demo was fixed in the latest update to the package. Try updating to Rev.: 1595 or later
I'm trying to use the R caret module for model generation and I want to use some cross-validation function. I found out that the only cross validation function which works together with rpart is LOOCV (leave one out cross validation).
The following code throws the error:
library(cart)
data(trees)
formula=Volume~Girth+Height
train(formula, data=trees, method='rpart')
Warning message: In nominalTrainWorkflow(dat = trainData, info =
trainInfo, method = method, : There were missing values in
resampled performance measures.
What does this error mean and how do I make it go away? I searched on the internet, not a single hit for this error-message. I traced the error down to the rpart model generation. It somehow outputs this error message, all other mode-generation-methods work fine!
Everything works fine if I use LOOCV.
I traced the warning down to the workflows.R file, but I do not understand why this warning gets thrown.
> sessionInfo()
R version 2.15.0 (2012-03-30)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8
[5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8
[7] LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] earth_3.2-3 plotrix_3.4 plotmo_1.3-1
[4] leaps_2.9 doMC_1.2.5 multicore_0.1-7
[7] iterators_1.0.6 forecast_3.20 RcppArmadillo_0.3.0.2
[10] Rcpp_0.9.10 fracdiff_1.4-1 tseries_0.10-28
[13] zoo_1.7-7 quadprog_1.5-4 caret_5.15-023
[16] foreach_1.4.0 cluster_1.14.2 reshape_0.8.4
[19] plyr_1.7.1 lattice_0.20-6 mda_0.4-2
[22] class_7.3-3 rpart_3.1-52 data.table_1.8.0
loaded via a namespace (and not attached):
[1] codetools_0.2-8 compiler_2.15.0 grid_2.15.0
Using the R Mailinglist and the help of the caret author I found out the following solution:
If for some reason the model which is generated is constant the error occurs. Constant means in this case that for all input values the model always yields the same value. In this case, the calculation of R^2 fails. R^2 is calculated per default by caret. As caret does not use the R^2 value for model selection, you can skip this error.
Two questions remain:
It is not clear to me why the R^2 calculation fails if the model is constant. The code in caret explicitely fails if there are not at least two different values in the model prediction. I replaced the R^2 calculation with a selfwritten one which does not have these limits.
The question why rpart sometimes generates a constant model is still open. Especially why it only generates constant models for other cross validations than LOOCV.
In short: You can ignore the warning and if you need, write your own R^2 to fix the warning.