In my code, I get the error message saying that there is an unexpected "=". I have tried running the line without certain "=", but that only causes other error messages, like "unused arguments". This is supposed to help, along with the rest of the code, with making a plot easier to read.
Here is the line of code:
Tricep.peaks <- data.frame (findpeaks(Tricep_falt, npeaks=8, minpeaksheight=.01, minpeaksdistance=freq=5))
Here is the error message:
Error: unexpected '=' in "Tricep.peaks <- data.frame (findpeaks(Tricep_falt, npeaks=8, minpeaksheight=.01, minpeaksdistance=freq="
Packages running are, signal, zoo, matlab, ggplot2, pracma, purrr, dplyr
As the error message shows, the error is caused by minpeaksdistance=freq=5 which looks like a typo to me.
According to https://www.rdocumentation.org/packages/pracma/versions/1.9.9/topics/findpeaks, the parameter is called minpeakdistance but not minpeaksdistance.
The OP probably meant minpeakdistance=5 or minpeakdistance=freq.
Related
I am running a simulation study in R. Occassionally, my simulation study produces an error message. As I implemented my simulation study in a function, the simulation stops when this error message occurs. I know that it is bad practice to suppress errors, but at this moment to me there is no other option than to suppress the error and then go on with the next simulation until the total number of simulations I like to run. To do this, I have to suppress the error message R produces.
To do this, I tried different things:
library(base64)
suppressWarnings
suppressMessages
options(error = expression(NULL))
In the first two options, only warnings and message are suprressed, so that's no help. If I understand it correctly, in the last case, all error messages should be avoided. However, that does not help, the function still stops with an error message.
Has someone any idea why this does not work the way I expect it to work? I searched the internet for solutions, but could only find the above mentioned ways.
In the function I am running my simulation, a part of the code is analysed by the external program JAGS (Gibbs sampler) and the error message is produced by this analysis. Might this be where it goes wrong?
Note that I do not have to supress a certain/specific error message, as there are no other error messages produced, it is 'good enough' to have an option that supresses just all error messages.
Thanks for your time and help!
As suggested by the previous solution, you can use try or tryCatch functions, which will encapsulate the error (more info in Advanced R). However, they will not suppress the error reporting message to stderr by default.
This can be achieved by setting their parameters. For try, set silent=TRUE. For tryCatch set error=function(e){}.
Examples:
o <- try(1 + "a")
> Error in 1 + "a" : non-numeric argument to binary operator
o <- try(1 + "a", silent=TRUE) # no error printed
o <- tryCatch(1 + "a")
> Error in 1 + "a" : non-numeric argument to binary operator
o <- tryCatch(1 + "a", error=function(e){})
There is a big difference between suppressing a message and suppressing the response to an error. If a function cannot complete its task, it will of necessity return an error (although some functions have a command-line argument to take some other action in case of error). What you need, as Zoonekynd suggested, is to use try or trycatch to "encapsulate" the error so that your main program flow can continue even when the function fails.
I'm trying to run this code to stretch the axes after creating a matrix based on calculated Euclidean distances:
ds_newA <- sqrt((new[1] -A[1]ˆ2 + (3*(new[2]-A[2]))ˆ2)
However, I'm getting an input error in the R console:
Error: unexpected input in "ds_newA <- sqrt((new[1] -A[1])ˆ"
Error: unexpected input in "ds_newB <- sqrt((new[1] -B[1])ˆ"
How should the code for formatted?
As noticed in the SO thread Error: unexpected symbol/input/string constant/numeric constant/SPECIAL in my code :
These errors mean that the R code you are trying to run or source is not syntactically correct. That is, you have a typo.
To fix the problem, read the error message carefully. The code provided in the error message shows where R thinks that the problem is. Find that line in your original code, and look for the typo.
Most probably, here this is due to the symbol ˆ you are using, which is not the appropriate one for an exponent ^:
# correct symbol ^:
> 2^2
[1] 4
# wrong symbol you seem to use ˆ :
> 2ˆ2
Error: unexpected input in "2ˆ"
Change it to the correct one ^ and you will be fine.
I am using the function FixedPoint() from the package FixedPoint for some computations in R. Even if a fixed point of some function cannot be found, FixedPoint() still returns output (indicating the error) and, in addition, returns an error message. I want to suppress any such additional error messages from being printed. Neither try(), nor suppressWarnings(), nor suppressMessages() seem to work. Please find an example below that produces such an additional error message.
library(FixedPoint)
ell=0.95
delta=0.1
r=0.1
lambda=1
tH=1
tL=0.5
etaL=1
etaH=1
sys1=function(y){
A=y[1]
B=y[2]
TA=(etaM*(1-exp(-(lambda*A+lambda*(A+B)+2*delta)*tL))-2*lambda*A^2-lambda*A*B)/2/delta
TB=(etaM*exp(-(lambda*A+lambda*(A+B)+2*delta)*tL)*(1-exp(-(lambda*(A+B)+2*delta)*(tH-tL)))-lambda*B^2-lambda*A*B)/2/delta
return(c(TA,TB))
}
FixedPoint(sys1,c(1.90,0.04))
This seems to work:
cc <- capture.output(ff <- FixedPoint(sys1,c(1.90,0.04)),type="message")
where ff now holds the output you want. (Alternately, you could wrap capture.output(...) in invisible() rather than assigning its return value to a variable.)
The problem seems to be that the error message emanates from an un-silence-d try() clause within the package code.
The knitr would always evaluate the R code before formatting the output, so just wondering how can I know whether the R code evaluation has error. Thanks
Basically it boils down to three lines of code in the evaluate package. The key is withCallingHandlers(), which can be used to capture errors, messages, and warnings, etc. A minimal example:
withCallingHandlers(1 + 'a', error = function(e) {
cat('An error occurred! The error object is:\n')
str(e)
})
If you don't want the error to halt R, you can wrap the code in try().
Trying to use the latest version of methylSig package (0.3.2), and getting an error when using the methylSigCalc function.
I get a cryptic error message after it figures out the number of loci:
Total number of bases: 2.59m
Error in result[, 3] : subscript out of bounds”
I tried running the code of the methylSigCalc function line by line, and the first error I encounter is when it gets to the methylSig_dataProcess function (below is the error after specifying just one core to try to get a useful error message):
Error in do.call(rbind, lapply(which(validLoci),
methylSig_dataProcess, : error in evaluating the argument 'args' in
selecting a method for function 'do.call': Error in match.fun(FUN) :
object 'methylSig_dataProcess' not found
It does seem that methylSig_dataProcess is now missing from the package.
Any suggestions on where I might be going wrong?
Many thanks,
gogatea