I'm running the following code:
dat1 <- returns
for (j in 1:12) set(dat1, j = j, value = wind(dat1[[j]]))
And getting the following error message:
Error in wind(dat1[[j]]) : could not find function "wind"
My search for a solution mainly involves packages that aren't properly installed. I'm not 100% sure but I think it isn't related to that.
Best
To check if the function is really loaded into the namespace you have to try to
print the function:
print(wind)
Error in print(wind) : object 'wind' not found
You have to look if the package is correctly loaded
library("foo")
Check package dependency in case of error.
I use the findFn-function in sos-package to search for function names. Unfortunately dataset names also appear in the same column:
install.packages("sos")
library(sos)
findFn("wind")
There is a wind function (or dataset name) in packages: gstat, ismev, NPCirc, BAMBI, ggmap, gcookbook, CircOutlier, plotly, and circular.
Related
I'm trying to include a function from the Bioconductor package "simpIntLists" in my own package. "import(simpIntLists)" is added to the Namespace file.
However, the function results in an error
do_xy <- function(organism, IDType){
network <- simpIntLists::findInteractionList(organism, IDType)
}
do_xy("human", "EntrezId")
#Error message
data set ‘HumanBioGRIDInteractionEntrezId’ not foundError in get("HumanBioGRIDInteractionEntrezId") :
object 'HumanBioGRIDInteractionEntrezId' not found
# results in the same error (outside of the function)
simpIntLists::findInteractionList(organism, IDType)
It works fine when simpIntLists is attached
# works
library(simpIntLists)
network <- simpIntLists::findInteractionList(organism, IDType)
I saw the code here (https://bioconductor.org/packages/release/data/experiment/html/simpIntLists.html).
This code does not seem to take into account the situation where the package is used without installation.
For your information, the relevant part to this error is around the line 52.
else if (organism == 'human'){
if (idType == 'EntrezId'){
data(HumanBioGRIDInteractionEntrezId);
interactionList <- get("HumanBioGRIDInteractionEntrezId");
}
It tries to fetch the data to the namespace but it fails to do so if the package is not imported via library yet. This only generates a warning. The error then occurs when it tries to use the data because it does not exist in the namespace.
A workaround is that you import the data in your code explicitly. Then you can use the function as below. Note that the warning remains because of the embedded package code. If the warning is annoying, use suppressWarnings.
data(HumanBioGRIDInteractionEntrezId, package="simpIntLists")
simpIntLists::findInteractionList("human", "EntrezId")
I am trying to use the function accumcomp.long in the Biodiversity.R package in order to adjust my species accumulation curves in ggplot.
However, calling the function accumcomp.long gives me an error, suggesting that this function perhaps does no longer exists.
accum.long1 <- accumcomp.long(Accum.1, ci=NA, label.freq=5)
Error in accumcomp.long(Accum.1, ci = NA, label.freq = 5) :
could not find function "accumcomp.long"
The function BiodiversityR::accumcomp.long
returns
Error: 'accumcomp.long' is not an exported object from 'namespace:BiodiversityR'
I am not certain whether this is an issue with the package, the way the package is loaded into my R space, or perhaps unrelated to the package simply the format of my data.
My community and environment files are of dataframe class. I have tried loading them as .csv files as well as .rda files, but the error remains.
??accumcomp.long
renders "No results found".
I am using R version 3.5.3 (2019-03-11)
Any suggestions as to what else I could try?
Thanks in advance!
I re-installed the package BiodiversityR and included force = T (as per this thread https://community.rstudio.com/t/could-not-find-function-error-even-though-fun-is-in-namespace-and-has-an-rd-file/91243). I then reloaded the package. I am not sure what force = T does, but the accumcomp.long function now works.
Goal: mas5 normalize data.
Problem: when I try the following R code, I get this
error: unable to find an inherited method for function bg.correct for signature ExpressionFeatureSet, character
I have looked on SO, and found the following: What does this mean: unable to find an inherited method for function ‘A’ for signature ‘"B"’, but I am not exactly sure how to fix my specific problem and use the mas5 function properly. I have also looked at this affy manual but still stuck...
installpkg("affy")
library('affy')
setwd("/Users/er/Desktop/DesktopFolders/DataSets/CD8Helios/Microarray/CELfiles/CEL")
cel_Files <- list.celfiles()
affyRaw <- read.celfiles(cel_Files)
eset <- mas5(affyRaw)
If you are sure that the .cel files were created based on experiments performed on the type of array that works with affy package than you should try this workflow using ReadAffy from affy package.
cel_Files <- list.celfiles()
affyRaw <- affy::ReadAffy(filenames=cel_Files)
eset <- mas5(affyRaw)
However, it might be the case that the affy package is not designed for your array type. Then, you should switch to the oligo and oligoClasses packages and normalize with analogous function rma
cel_Files <- oligoClasses::list.celfiles()
affyRaw <- oligo::read.celfiles(cel_Files)
eset <- oligo::rma(affyRaw)
I tried to run the code in Chapter 7 Data mining with R learning with case study book but I got an error in following line:
rankWorkflows(svm, maxs = TRUE)
The error was:
Error in as.character.default(X[[i]], ...) : no method for coercing
this S4 class to a vector
Then I searched on the internet and found following solution:
importMethodsFrom(GenomicRanges, as.data.frame)
and again again I got a new error:
Error: could not find function "importMethodFrom"
I searched a lot but I got nothing :(
You can try using library(sos) to find the packages where your function is located.
library(sos)
findFn("replaceherewithyourfunction")
Based on the answer of #Bea, there does not seem to be a importMethodsFrom anywhere in R. My guess is you found the call in a NAMESPACE file. Those files have different syntax than normal R scripts.
If you want to load a specific function from an R package (rather than all functions from a package), you can use libraryname::functionname instad of functionname in your code. In your case, replace as.data.frame with GenomicRanges::as.data.frame
If this does not work (for example because you don't have as.data.frame anywhere in your code), you can also load the whole GenomicRanges library with library(GenomicRanges)
Need some assistance in R. I ran the lm function and assigned it to variable. Then I used that variable to retrieve summary using pool() function.
Here's the code but getting argument data is missing. I saw same example but didn't get that error.
> modelFit1 <- with(imputed,lm(MPG ~ CYLINDERS+SIZE+HP+WEIGHT+ACCEL+ENG_TYPE))
> summary(pool(modelFit1))
Error in pool(modelFit1) : argument "data" is missing, with no default
Appreciate any help. Thanks.
I also had this error. In my case it was due to conflicting packages. I had loaded packages: "mice" and "mi", and "mitools", among others. There is no 'data' argument necessary for 'pool' in the "mice" package, but mi::pool does require a data argument. If you are using mice and following examples in mice's documentation, Try
pooled <- mice::pool(modelFit1))
summary(pooled)