I want to use mice function to handle the missing data that I have in (data). I installed the package and I called the library. However, when I am trying to apply the function to my data it gives me error as below:
(Error in mice(data[, 5:9], m = 3, seed = 123) :
could not find function "mice")
I have a normal data frame that includes NAs
install.packages('mice')
library(mice)
library(VIM)
md.pattern(data)
md.pairs(data)
My_New_Data <- mice(data[,5:9], m=3, seed=123)
I am expecting the function to solve the problem and replace the NAs with reasonable values. It did not work at all!
Edit (incorporating comment suggestion)
In the comments the running mice::mice(data[, 5:9], m = 3, seed = 123). I ran this and the following error was returned.
Error in get(Info[i, 1], envir = env):
lazy-load database 'C:/Users/MUSTAFA KAMAL/Documents/R/win-library/3.5/broom/R/broom.rdb' is corrupt
In addition:
Warning message: In get(Info[i, 1], envir = env) : internal error -3 in R_decompress1
In order to incorporate an answer to this question, I will rewrite my comment which resolved the problem, in the form of a short answer.
From the comments executing mice::mice(data[, 5:9], m = 3, seed = 123) resulted in an error message, showing the directory ~/Documents/R/win-library/**3.5**/broom/R/broom.rdb being corrupt.
From the corrupted directory path, one can see that OP was running R-3.5.x, while the newest version is R-3.6.x. Some packages updated since the most recent R-update has experienced similar problems, as such a first step towards solving these types of issues is updating R. The installr contains the function updateR which can help smooth over such updates, while also updating any outdated packages.
As a side note, an update sometimes fails to update the actual packages or results in other packages being corrupted, as such if an error persists one solution is to simply delete and re-install the package (or the entire ~/Documents/R/win-library/3.z/ directory). In the question from OP the corrupt package is the broom package, as such one could re-install this package by running
remove.packages("broom")
install.packages("broom")
which should resolve any leftover issues. Note however multiple packages might be corrupt, and likely only one will be shown every time the function is executed. In such cases a full package clear will do the trick, but requires re-installing all packages. For this one can export all installed packages prior to removing them all, by noting that a full list of installed packages is contained in installed.packages(), which can then be exported to a file with for example write.table or write.csv.
Related
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.
Trying to figure out why I am getting this error (never seen it before, google is no help):
Error in check_dots_used(action = warn) : unused argument (action = warn)
I am getting the error for the very basic trial below, but also for group_by/count, but not filter or select.
x <- c(1, 2, 3, 4, 5)
y <- runif(5)
tibble(x, y)
Error in check_dots_used(action = warn) : unused argument (action = warn)
I had the same problem: urganmax's solution to update to ellipsis-0.3.1 in a comment did it for me. Moving this as an answer so it is easier to find.
I had to update/re-install tidyverse and the ellipsis package explicitly:
install.packages("tidyverse")
install.packages("ellipsis")
Then restart your session and library your packages (or unload and reload your packages).
I'm pretty certain that your version of the ellipsis package (part of the tidyverse) is out of sync with the other tidyverse packages you have. update.packages() should work ... (if you want to live dangerously, update.packages(ask=FALSE) to update all packages without asking for confirmation for each one).
From the tidyverse NEWS file:
All functions that take ... have been instrumented with functions from the ellipsis package to warn if you’ve supplied arguments that are ignored (typically because you’ve misspelled an argument name) (#573).
I've been trying to get bathymetry lines from marmap and recently got the following error message when getNOAA.bathy function is called
Querying NOAA database ...This may take seconds to minutes, depending on grid size
Error in if (ncol(x) == 3 & !exists("bathy", inherits = FALSE)) { : argument is of length zero
This happens even with something as simple as
map <- getNOAA.bathy(lon1=10,lon2=19,lat1=67,lat2=71,resolution=10, keep=TRUE)
I updated the package to the latest version (1.0.4) as I read that there could be issues related to server access. I've also tried running the above script in R rather than RStudio, but the error persists...
The function works fine if I use previously downloaded data, but now I needed use use another set of coordinates for a new map.
Any help is much appreciated!
You need to (re)install both rgdal and raster packages. This is already documented here on the GitHub Issue pages of the marmap package.
For anyone else looking, the reported error can also result from the server being down - R doesn't give any indication of this. You can check https://www.ncei.noaa.gov/alerts for scheduled outages.
For several months now, the same error message seem to have plagued Windows users, event with all packages up to date.
marmap v1.0.9 is now available on GitHub:
remotes::install_github("ericpante/marmap")
This version should solve this infamous Error message:
Error in if (ncol(x) == 3 & !exists("bathy", inherits = FALSE)) { :
argument is of length zero
I have been able to confirm that the error was due to a limitation in the length of urls that the raster package can handle on Windows. The geotif files from NOAA's servers are now downloaded with utils::download.file() in a temporary file on the user's disk and then imported in R using raster::raster().
marmap v1.0.9 will be available on CRAN servers in the next few days.
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 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