I have been using the combcoint library for quite some time. Today I installed some new packages in R for my work and since then I have been getting an error, when I try to run the function bayerhanck. The error itself:
Error in p_value_Fisher_bc ~ poly(stat_Fisher_all_bc, 12) * k_dummy :
object 'rlang_tilde_eval' not found
I assume this there is a technical solution to this, but I have not been able to find it.
Related
I am brand new to this so please forgive my inexperience...I'm trying to learn.
I'm attempting to install an R package called "Doublet Finder" using the specified code given on the Github site.
When I do this, I get this error immediately:
Error in rbind(info, getNamespaceInfo(env, "S3methods")) :
number of columns of matrices must match (see arg 2)
Being new to R, I'm not sure what this error means and when I google this something similar comes up and the individual removed and re-installed ALL of their libraries...that seems crazy. Does anyone have advice on what this could be, how to fix it, or why the package won't install?
Your problem seems to be fairly similar to this one. It might be the case that the dependencies (packages that Doublet Finder relies on) are outdated. What you can try is to follow these steps to uninstall and reinstall all packages with the hope that by updating packages there isn't a version mismatch.
This code is copied from the website above:
ip <- as.data.frame(installed.packages(lib.loc = .libPaths()[1]),
stringsAsFactors = FALSE)
head(ip)
str(ip)
path.lib <- unique(ip$LibPath)
# create a vector with all the names of the packages you want to remove
pkgs.to.remove <- ip[,1]
head(pkgs.to.remove)
str(pkgs.to.remove)
sapply(pkgs.to.remove, remove.packages, lib = path.lib)
sapply(pkgs.to.remove, install.packages, lib = path.lib)
I'm quite new to R and I got an assignment that includes a sourcecode.
Part of the source code includes the following line:
library(preprocessCore)
Then I have in my source code a definition of the following function:
quantile.normalize.raw.gtex <- function(edata.mat)
{
norm_edata = normalize.quantiles(as.matrix(edata.mat))
rownames(norm_edata) = rownames(edata.mat)
colnames(norm_edata) = colnames(edata.mat)
return(norm_edata)
}
Finally, I have an object being initialized to the output of this function, after sending a predefined parameter:
tissue.edata.qn = quantile.normalize.raw.gtex(tissue.edata)
From what I understand, the library function is supposed to include the function normalize.quantiles, which is called in the function that is defined in my source code.
However, when I run the line library(preprocessCore) I get the following error:
Error in library(preprocessCore) :
there is no package called ‘preprocessCore’
I also tried to run the rest of the code and got the error:
Error in normalize.quantiles(as.matrix(edata.mat)) :
could not find function "normalize.quantiles"
I looked for the preprocessCore online and eventually I tried to write install.packages("preprocessCore"), but I got a warning message that this package is only available in version 3.6.0 of R, even though I checked and this is the version that I have.
If somebody has any idea what the problem is, I will appreciate your help.
Thanks in advance
The preprocessCore package is available in Bioconductor. So, to install it, you need the following lines:
source("http://bioconductor.org/biocLite.R")
biocLite("preprocessCore")
After that, you can load the package using library(preprocessCore)
Hope it helps.
I have the package mi installed.
But when I try to run mp.plot (as Thomas Leeper does in this tutorial:) I get the following error message:
mp.plot(mydf)
Error in mp.plot(mydf) : could not find function "mp.plot"
On one website this is called missing.pattern.plot, but that also does not work:
missing.pattern.plot(mydf)
Error in missing.pattern.plot(mydf) :
could not find function "missing.pattern.plot"
Any idea what the issue might be?
I do not really care much if I cannot use this function, but I'm curious as to what is going on in case I later need to use a graph that I really need.
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)
I have written the Boggler package which includes a Play.Boggle() function that calls, on line 87, a progress bar script using shell:
shell(cmd = sprintf('Rscript.exe R/progress_bar.R "%i"', time.limit + 1), wait=FALSE)
Everything works fine when sourcing the files individually and then calling the main Play.Boggle() function, but when I try to check/build the package (under Win7-64 using RStudio), I get a failure message -- here's what the 00install.out reports:
** preparing package for lazy loading
Warning in eval(expr, envir, enclos) : NAs introduced by coercion
Error in time.limit:0 : NA/NaN argument
To make sure the argument "%i" (time.limit + 1) was correctly passed to the progress_bar.R, I added a cat(time.limit) to the script (commenting the rest out to make sure the package would build without any errors) and directed its output to a log file like this:
'Rscript.exe R/progress_bar.R "%i" > out.log'
Conclusion: the time limit is indeed passed along as expected. So I can't figure out why I get this "NA/NaN argument" error message. It must have something to do with lazy loading, concept that I haven't fully got my head around yet.
So my question is: what can I do to successfully check/build this package with full functionality (including progress_bar.R)?
Note: On github, the progress_bar.R script is there but all its content is commented out so that the package can successfully be installed. The shell(...) function call is still active, doing nothing but executing an empty script.
So the problem arises when trying to build or check, in which case all R scripts are executed, as pointed out by Roland. A simple workaround allows the package to check/build without any problems. The fix is just to add to the progress_bar.R the following lines after it tries to recuperate the commandargs (lines 10-11):
if(time.limit %in% c(NA, NaN))
time.limit <- 10 # or any minimal number
There's surely other ways to go about this. But this being a game programmed for fun, I'll happily go with that patch. Hopefully this can be of help to someone down the road and I won't have wasted 50 precious rep points in vain for that bounty! :D