I'm running a function called mixedpower() that lets you simulate power at different sample sizes. However I get the following error and don't know how to handle it!
Error in makePSOCKcluster(names = spec, ...) :
Cluster setup failed. 11 of 11 workers failed to connect.
Here is a reproducible example. (Just to head off any comments, I know that gear shouldn't be a random variable here, but I'm just using it for the purpose of this example.)
#You can download the mixedpower package like this.
if (!require("devtools")) {
install.packages("devtools", dependencies = TRUE)}
devtools::install_github("DejanDraschkow/mixedpower")
library(mixedpower)
library(lme4)
m <- lmer(mpg ~ cyl + disp + hp + drat + (1|gear), data = mtcars)
mtcars$gear_num <- as.numeric(mtcars$gear)
power <- mixedpower(model = m, data = mtcars, fixed_effects = c("cyl", "disp", "hp", "drat"), simvar = "gear_num", steps = c(3, 4, 5), critical_value = 2)
And if it is helpful I am running RStudio version 1.1.453 on MacOS Mojave version 10.14.6.
I can't test but strongly suspect that your problem is related to a bug in recent versions of R (now patched in more recent versions). This issue describes a workaround of adding the following to your .Rprofile file (it's also possible that updating to the latest patched version of R would do it).
## WORKAROUND: https://github.com/rstudio/rstudio/issues/6692
## Revert to 'sequential' setup of PSOCK cluster in RStudio Console on macOS and R 4.0.0
if (Sys.getenv("RSTUDIO") == "1" && !nzchar(Sys.getenv("RSTUDIO_TERM")) &&
Sys.info()["sysname"] == "Darwin" && getRversion() >= "4.0.0") {
parallel:::setDefaultClusterOptions(setup_strategy = "sequential")
}
Related
I am trying to get H2O working with Sparklyr on my spark cluster (yarn)
spark_version(sc) = 2.4.4
My spark cluster is running V2.4.4
According to this page the compatible version with my spark is 2.4.5 for Sparkling Water and the H2O release is rel-xu patch version 3. However when I install this version I am prompted to update my H2O install to the next release (REL-ZORN). Between the H2O guides and the sparklyr guides it's very confusing and contradictory at times.
Since this is a yarn deployment and not local, unfortunately I can't provide a repex to help with trobleshooting.
url <- "http://h2o-release.s3.amazonaws.com/sparkling-water/rel-2.4/5/sparkling-water-2.4.5.zip"
download.file(url = url,"sparkling-water-2.4.5.zip")
unzip("sparkling-water-2.4.5.zip")
# RUN THESE CMDs FROM THE TERMINAL
cd sparkling-water-2.4.5
bin/sparkling-shell --conf "spark.executor.memory=1g"
# RUN THESE FROM WITHIN RSTUDIO
install.packages("sparklyr")
library(sparklyr)
# REMOVE PRIOR INSTALLS OF H2O
detach("package:rsparkling", unload = TRUE)
if ("package:h2o" %in% search()) { detach("package:h2o", unload = TRUE) }
if (isNamespaceLoaded("h2o")){ unloadNamespace("h2o") }
remove.packages("h2o")
# INSTALLING REL-ZORN (3.36.0.3) WHICH IS REQUIRED FOR SPARKLING WATER 3.36.0.3
install.packages("h2o", type = "source", repos = "https://h2o-release.s3.amazonaws.com/h2o/rel-zorn/3/R")
# INSTALLING FROM S3 SINCE CRAN NO LONGER SUPPORTED
install.packages("rsparkling", type = "source", repos = "http://h2o-release.s3.amazonaws.com/sparkling-water/spark-2.4/3.36.0.3-1-2.4/R")
# AS PER THE GUIDE
options(rsparkling.sparklingwater.version = "2.4.5")
library(rsparkling)
# SPECIFY THE CONFIGURATION
config <- sparklyr::spark_config()
config[["spark.yarn.queue"]] <- "my_data_science_queue"
config[["sparklyr.backend.timeout"]] <- 36000
config[["spark.executor.cores"]] <- 32
config[["spark.driver.cores"]] <- 32
config[["spark.executor.memory"]] <- "40g"
config[["spark.executor.instances"]] <- 8
config[["sparklyr.shell.driver-memory"]] <- "16g"
config[["spark.default.parallelism"]] <- "8"
config[["spark.rpc.message.maxSize"]] <- "256"
# MAKE A SPARK CONNECTION
sc <- sparklyr::spark_connect(
master = "yarn",
spark_home = "/opt/mapr/spark/spark",
config = config,
log = "console",
version = "2.4.4"
)
When I try to establish a H2O context using the next chunk I get the following error
h2o_context(sc)
Error in h2o_context(sc) : could not find function "h2o_context"
Any pointers as to where I'm going wrong would be greatly appreciated.
See this tutorial please. The newer versions of Rsparkling use {H2OContext.getOrCreate(h2oConf)} instead of {h2o_context(sc)}.
I am getting error could not find function "knnImputation"
Rstudio version :- Version 1.2.1335
loaded packages :- c("ggplot2", "corrgram", "DMwR", "usdm", "caret", "randomForest", "e1071",
"DataCombine", "doSNOW", "inTrees", "rpart.plot", "rpart",'MASS','xgboost','stats')
I recommend using the VIM::kNN() imputation as the package DMwR has been removed from CRAN:
https://cran.r-project.org/web/packages/DMwR/index.html
# using DMwR::knnImputation
df_mod <- DMwR::knnImputation(df, k = 7)
# VIM approximate equivalent to DMwR
# Note, for numFun you can substitute stats::weighted.mean, they perform similarly, though some differences on the margins I am not sure of
df_mod <- VIM::kNN(df, k = 7, numFun = laeken::weightedMean, weightDist = TRUE)
I have had some challenges in some circumstances using DMwR::knnImputation, this appears to work well.
I'm using Rcpp to convert a bunch of functions written in C++ into a R package and I've managed to get past all the bugs in the code, but when I run the check, all the code checks out, but when it loads my package "PHit" it gives me that error and halts Execution
This is Windows 10 and I'm using R 3.6 in R Studio. I'm building my package in my works Share drive so others have access if that makes a difference. I've tried reinstalling the package, I've checked the .libpaths() and every solution offered for every similar question. The packages in those questions were external such as dplyr
> pkgname <- "PHit"
> source(file.path(R.home("share"), "R", "examples-header.R"))
> options(warn = 1)
> options(pager = "console")
> base::assign(".ExTimings", "PHit-Ex.timings", pos = 'CheckExEnv')
> base::cat("name\tuser\tsystem\telapsed\n", file=base::get(".ExTimings", pos = 'CheckExEnv'))
> base::assign(".format_ptime",
+ function(x) {
+ if(!is.na(x[4L])) x[1L] <- x[1L] + x[4L]
+ if(!is.na(x[5L])) x[2L] <- x[2L] + x[5L]
+ options(OutDec = '.')
+ format(x[1L:3L], digits = 7L)
+ },
+ pos = 'CheckExEnv')
>
> ### * </HEADER>
> library('PHit')
Error in library("PHit") : there is no package called 'PHit'
Execution halted
I expect it to recognize the package because I can load it in the console just fine although it only contains one out of the several functions that should be available, if it completely compiled as it should
I am having difficulty with creating multiple heatmaps with the ComplexHeatmap package. When I run a script that contains code exactly lifted from the documentation (https://bioconductor.org/packages/release/bioc/vignettes/ComplexHeatmap/inst/doc/s3.a_list_of_heatmaps.html)...
library(ComplexHeatmap)
mat1 = matrix(rnorm(80, 2), 8, 10)
mat1 = rbind(mat1, matrix(rnorm(40, -2), 4, 10))
rownames(mat1) = paste0("R", 1:12)
colnames(mat1) = paste0("C", 1:10)
mat2 = matrix(rnorm(60, 2), 6, 10)
mat2 = rbind(mat2, matrix(rnorm(60, -2), 6, 10))
rownames(mat2) = paste0("R", 1:12)
colnames(mat2) = paste0("C", 1:10)
ht1 = Heatmap(mat1, name = "ht1")
ht2 = Heatmap(mat2, name = "ht2")
class(ht1)
class(ht2)
ht1 + ht2
... I get the error message:
Error in ht1 + ht2 : non-numeric argument to binary operator
Execution halted
I am running R version 3.3.2 (2016-10-31) -- "Sincere Pumpkin Patch" on Mac OS X 10.12.2 with ComplexHeatmap version 1.12.0. Thank you for any help!
I figured it out. The problem was that the "methods" package needs to be attached. If you run the above code directly in R (which I was NOT doing), it works as-is (becuase R apparently loads the methods package by default), but if you have the script in a file and run it via Rscript (which is what I WAS doing), you get the indicated error. However, If you add
library(methods)
to the top of the script, it works via Rscript.
I was working with baby names data set and encountered below error while using transform function. Any guidance/suggestion would be highly appreciated. I did reinstalled the packages but of no avail.
Mac OS X (Mountain Lion)
R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
library(stringr)
require(stringr)
bnames1 <- transform(bnames1,
first = tolower(str_sub(name,1,1)),
last = tolower(str_sub(name,-1,1)),
vowels = vowels(name),
length= nchar(name),
per1000 = 10000 * prop,
one_par = 1/prop
)
Error in tolower(str_sub(name, 1, 1)) :
lazy-load database '/Library/Frameworks/R.framework/Versions/3.1/Resources/library/stringr/R/stringr.rdb' is corrupt
In addition: Warning messages:
1: In tolower(str_sub(name, 1, 1)) :
restarting interrupted promise evaluation
2: In tolower(str_sub(name, 1, 1)) : internal error -3 in R_decompress1
internal error -3 is often a functioning of installing on top of a loaded package. Restart R and restart your application. There may be other issues, but until you do this you won't be going much further.
Try
remove.packages("stringr")
install.packages("stringr")