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 It might be the case that the dependencies (packages that Doublet Finder relies on) are outdated.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$LibPath)
# create a vector with all the names of the packages you want to remove
pkgs.to.remove <- ip[,1]
head(pkgs.to.remove)
str(pkgs.to.remove)
sapply(pkgs.to.remove, remove.packages, lib = path.lib)
sapply(pkgs.to.remove, install.packages, lib = path.lib)
Related
I'm doing an R project on RStudio (RStudio 2021.09.1+372 "Ghost Orchid" Release for Windows), (R version 4.1.2).
I'm working on Windows 10 x64.
I want to create an Undirected Graph from a dataset:
library(gRbase)
library(gRim)
library(gRain)
data(BodyFat)
BodyFat <- BodyFat[-c(31,42,48,76,86,96,159,169,175,182,206),]
BodyFat$Age <- sqrt(BodyFat$Age)
BodyFat$Weight <- sqrt(BodyFat$Weight)
names(BodyFat)[names(BodyFat) == 'BodyFat'] <- 'BodyFatPerc'
gRbodyfat <- BodyFat[,2:15]
graph.MyGraph <- cmod(~.^., data = gRbodyfat)
AIC.MyGraph <- gRbase::stepwise(graph.MyGraph)
I'm still exploring RStudio and graphical models, so I run these lines from the console, one by one.
When I run the last line of code, R session aborts and I get the following pop-up message:
I've also tried the following lines of code (I changed the last line):
library(gRbase)
library(gRim)
library(gRain)
data(BodyFat)
BodyFat <- BodyFat[-c(31,42,48,76,86,96,159,169,175,182,206),]
BodyFat$Age <- sqrt(BodyFat$Age)
BodyFat$Weight <- sqrt(BodyFat$Weight)
names(BodyFat)[names(BodyFat) == 'BodyFat'] <- 'BodyFatPerc'
gRbodyfat <- BodyFat[,2:15]
graph.MyGraph <- cmod(~.^., data = gRbodyfat)
AIC.MyGraph <- stepwise(graph.MyGraph)
but I get the same problem. I tried three or four times running those lines of code, R aborted everytime.
My gRbase, gRim, gRain, Rgraphviz and RBGL libraries are in the home folder:
C:/Users/MyUser/Documents/R/win-library/4.1
Any advice?
EDIT:
I've tried uninstalling/reinstalling R, Rtools, RStudio, reinstalling libraries, updating them, I've tried launching RStudio as Administrator, I've tried changing computer.
The last thing I tried is this:
uninstalling R, Rtools and RStudio
deleting .RData and .Renviron files in the Documents folder
deleting all libraries
downloading R (latest version) from CRAN webpage and installing it as Administrator
downloading Rtools (latest version from webpage) and installing it as Administrator
creating the .Renviron file as described here
downloading RStudio (latest version from webpage) and installing it as Administrator
installing BiocManager as described here (when asked to update Matrix library I said NO, I thought it could be the problem)
installing gRbase, gRim, gRain libraries as described here (when asked to update fansi library I said NO because it said "There are binary versions available but the source versions are later", I thought it could be the problem)
Tried again the lines of code
Still got the problem, R session aborted again.
A friend of mine doing a similar project used gRbase::stepwise function, so I inserted his code in the console and the function worked. So I think the problem might be the object of the function, graph.MyGraph. The cmod function works fine, so maybe there's a problem with gRbodyfat, which is used to build graph.MyGraph.
If I run these lines (I tried changing the dataset, I used BodyFat instead of gRbodyfat):
graph.MyGraph <- cmod(~.^., data = BodyFat)
AIC.MyGraph <- gRbase::stepwise(graph.MyGraph)
I get the following error:
Error in dim(res) <- c(NSEL, NSET) :
dims [product 210] do not match the length of object [14]
Don't know what to do.
EDIT:
I've tried debugging gRbase::stepwise function and I get this:
The problem appears to be the iModel function.
EDIT:
I've discovered that if I use graph.MyGraph <- cmod(~.^1, data = gRbodyfat) the gRbase::stepwise function works fine.
I recently updated my MacBook air (2017) to the Mojave OS and proceeded to update my version of R and Rstudio. Unfortunately, ever since the 'plotTangentSpace' command no longer functions appropriately even when attempting to run the example 'plethodon' code from the Geomorph vingette, I always receive the following error in the output (bolded below):
data(plethodon)
Y.gpa<-gpagen(plethodon$land) #GPA-alignment
|====================================================================================| 100%
gp <- interaction(plethodon$species, plethodon$site)
plotTangentSpace(Y.gpa$coords, groups = gp)
Error in plotTangentSpace(Y.gpa$coords, groups = gp) :
unused arguments (Y.gpa$coords, groups = gp)
I have tried uninstalling and reinstalling R for a MacOS many times including versions 4.0.2, 3.6.3, 3.6.1, and 3.2.1. I have also uninstalled and reinstalled XQuartz several times.
If anyone has encountered a similar issue or has any other ideas I can try I would really appreciate the help. Thank you!
If you execute:
?plotTangentSpace
You should see that this is a deprecated function. That means you should not be using it. It says:
Notes for geomorph 3.3.0 and subsequent versions
I suspect you have not updated your copy of the vignette. There are instructions on the help page for an alternate approach. The example in the help page for the suggested function is:
data(plethspecies)
Y.gpa <- gpagen(plethspecies$land) #GPA-alignment
### Traditional PCA
PCA <- gm.prcomp(Y.gpa$coords)
summary(PCA)
plot(PCA, main = "PCA")
For the plethodon data they suggest:
PCA.w.phylo <- gm.prcomp(Y.gpa$coords, phy = plethspecies$phy)
summary(PCA.w.phylo)
plot(PCA.w.phylo, phylo = TRUE, main = "PCA.w.phylo")
So start a new session (to unload the currently loaded geomorph namespace, and execute this at the r session command line:
install.packages("geomorph")
You should be getting version 3.3.1 of the geomorph package.
I think I found the problem! In my case, the error was due to a old version of the package RRPP, which is required by Geomorph. After updating it, Geomorph is working perfectly! Hope this can be useful for you too.
I came across the same error but after updating the RRPP and rgl packages required for geomorph, the gm.prcomp() function worked for me. I hope this helps if you haven't figured it out already.
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 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.
I am trying to find out time series anomaly detection in which i need to install new R packages. In this i m following https://github.com/business-science/anomalize site. In this i needed to install 2 packages: tidyverse and anomalize.
can anyone help me on installing package mentioned above as I am getting
error "package or namespace load failed for tidyverse"
Also while adding zip of tidyverse and anomalize do I need to add any other packages and dependencies in that as I am adding only those 2 packages thinking there r no other dependencies I needed for those 2?
you can see in code that I created R_Package.zip and put tidyverse.zip and anomalize.zip in that that
dataset1 <- maml.mapInputPort(1)
data.set <- data.frame(installed.packages())
#install.packages(“src/R_Package/tidyverse_1.2.1.zip”, lib = “.”,
repos = NULL, verbose = TRUE);
#library(tidyverse, lib.loc=”.”, verbose=TRUE);
install.packages("src/tidyverse.zip",lib=".",repos=NULL,verbose=TRUE)
library(R_package, lib.loc = ".", verbose=TRUE);
install.packages("src/anomalize.zip",lib=".",repos=NULL,verbose=TRUE)
library(R_package, lib.loc = ".", verbose=TRUE);
#success <- library("tidyverse", lib.loc = ".",
logical.return = TRUE, verbose = TRUE)
#library(tidyverse)
maml.mapOutputPort("dataset1");
Regarding the error message, notice that it may take some time for the installed packages to become actually available; quoting from Adding R Packages In Azure ML blog post:
Note: In one instance, we ran into an issue where the package was not
loaded into the workspace immediately. We had to wait about half an
hour before we could use the package. You may be running into this
issue as well if you see a message that looks something like this
and you’ve used the above method to check which packages are in your
workspace and the package in question appears on that list. If this is
the case, we suggest waiting a bit before running your experiment
again.
AFAIK yes, you also need to add the package dependencies; the SO thread Install R Packages in Azure ML contains some useful hints.