While using the Boot function from the car package I get the error message
Error in get(".y.boot", envir = .carEnv) : object '.carEnv' not found
I suspect I have inadvertently changed/set something in my OS and have no idea what it might be. Running the code below returns an error on my desktop but runs without error on a laptop running the same OS (Yosemite) as well as a desktop running Windows 7 (all using R-3.1.2). The code that triggers the message is
library(car)
swiss.lm <- lm(Fertility ~ Education, data = swiss)
BC <- Boot(swiss.lm, R = 999, method = "case") # No Problems
BR <- Boot(swiss.lm, R = 999, method = "residual") # Problems now
Error in get(".y.boot", envir = .carEnv) : object '.carEnv' not found
I have reinstalled R but the error still appears when running the above code. Any suggestions as to what I have done and how to get the code to run and find the environment would be most appreciated. TIA!
> sessionInfo()
R version 3.1.2 (2014-10-31)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] car_2.0-24
loaded via a namespace (and not attached):
[1] boot_1.3-15 grid_3.1.2 lattice_0.20-29 lme4_1.1-7 MASS_7.3- 37 Matrix_1.1-5
[7] mgcv_1.8-4 minqa_1.2.4 nlme_3.1-119 nloptr_1.0.4 nnet_7.3-9 parallel_3.1.2
[13] pbkrtest_0.4-2 quantreg_5.11 Rcpp_0.11.4 SparseM_1.6 splines_3.1.2 tools_3.1.2
Looks like a reproducible bug in a car package. According to package news the changes in latest version (2.0-24) are related to .carEnv handling.
I tried to get around the issue by simply assigning the .carEnv before call to Boot with
.carEnv <- car:::.carEnv
This makes the Boot function execute without errors, but I am not sure of any other effects.
The package maintainer emailed me and indicated a bug had been introduced in 2.0-24 and that he would attempt to fix the bug.
Related
I'd like to unload a package without having to restart R (mostly because restarting R as I try out different, conflicting packages is getting frustrating, but conceivably this could be used in a program to use one function and then another--although namespace referencing is probably a better idea for that use).
?library doesn't show any options that would unload a package.
There is a suggestion that detach can unload package, but the following both fail:
detach(vegan)
Error in detach(vegan) : invalid name argument
detach("vegan")
Error in detach("vegan") : invalid name argument
So how do I unload a package?
Try this (see ?detach for more details):
detach("package:vegan", unload=TRUE)
It is possible to have multiple versions of a package loaded at once (for example, if you have a development version and a stable version in different libraries). To guarantee that all copies are detached, use this function.
detach_package <- function(pkg, character.only = FALSE)
{
if(!character.only)
{
pkg <- deparse(substitute(pkg))
}
search_item <- paste("package", pkg, sep = ":")
while(search_item %in% search())
{
detach(search_item, unload = TRUE, character.only = TRUE)
}
}
Usage is, for example
detach_package(vegan)
or
detach_package("vegan", TRUE)
You can also use the unloadNamespace command, as in:
unloadNamespace("sqldf")
The function detaches the namespace prior to unloading it.
You can uncheck the checkbox button in RStudio (packages).
I tried what kohske wrote as an answer and I got error again, so I did some search and found this which worked for me (R 3.0.2):
require(splines) # package
detach(package:splines)
or also
library(splines)
pkg <- "package:splines"
detach(pkg, character.only = TRUE)
When you are going back and forth between scripts it may only sometimes be necessary to unload a package. Here's a simple IF statement that will prevent warnings that would appear if you tried to unload a package that was not currently loaded.
if("package:vegan" %in% search()) detach("package:vegan", unload=TRUE)
Including this at the top of a script might be helpful.
I hope that makes your day!
detach(package:PackageName) works and there is no need to use quotes.
Another option is
devtools::unload("your-package")
This apparently also deals with the issue of registered S3 methods that are not removed with unloadNamespace()
You can try all you want to remove a package (and all the dependencies it brought in alongside) using unloadNamespace() but the memory footprint will still persist. And no, detach("package:,packageName", unload=TRUE, force = TRUE) will not work either.
From a fresh new console or Session > Restart R check memory with the pryr package:
pryr::mem_used()
# 40.6 MB ## This will depend on which packages are loaded obviously (can also fluctuate a bit after the decimal)
Check my sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 17763)
Matrix products: default
locale:
[1] LC_COLLATE=English_Canada.1252 LC_CTYPE=English_Canada.1252 LC_MONETARY=English_Canada.1252 LC_NUMERIC=C
[5] LC_TIME=English_Canada.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_3.6.1 pryr_0.1.4 magrittr_1.5 tools_3.6.1 Rcpp_1.0.3 stringi_1.4.3 codetools_0.2-16 stringr_1.4.0
[9] packrat_0.5.0
Let's load the Seurat package and check the new memory footprint:
library(Seurat)
pryr::mem_used()
# 172 MB ## Likely to change in the future but just to give you an idea
Let's use unloadNamespace() to remove everything:
unloadNamespace("Seurat")
unloadNamespace("ape")
unloadNamespace("cluster")
unloadNamespace("cowplot")
unloadNamespace("ROCR")
unloadNamespace("gplots")
unloadNamespace("caTools")
unloadNamespace("bitops")
unloadNamespace("fitdistrplus")
unloadNamespace("RColorBrewer")
unloadNamespace("sctransform")
unloadNamespace("future.apply")
unloadNamespace("future")
unloadNamespace("plotly")
unloadNamespace("ggrepel")
unloadNamespace("ggridges")
unloadNamespace("ggplot2")
unloadNamespace("gridExtra")
unloadNamespace("gtable")
unloadNamespace("uwot")
unloadNamespace("irlba")
unloadNamespace("leiden")
unloadNamespace("reticulate")
unloadNamespace("rsvd")
unloadNamespace("survival")
unloadNamespace("Matrix")
unloadNamespace("nlme")
unloadNamespace("lmtest")
unloadNamespace("zoo")
unloadNamespace("metap")
unloadNamespace("lattice")
unloadNamespace("grid")
unloadNamespace("httr")
unloadNamespace("ica")
unloadNamespace("igraph")
unloadNamespace("irlba")
unloadNamespace("KernSmooth")
unloadNamespace("leiden")
unloadNamespace("MASS")
unloadNamespace("pbapply")
unloadNamespace("plotly")
unloadNamespace("png")
unloadNamespace("RANN")
unloadNamespace("RcppAnnoy")
unloadNamespace("tidyr")
unloadNamespace("dplyr")
unloadNamespace("tibble")
unloadNamespace("RANN")
unloadNamespace("tidyselect")
unloadNamespace("purrr")
unloadNamespace("htmlwidgets")
unloadNamespace("htmltools")
unloadNamespace("lifecycle")
unloadNamespace("pillar")
unloadNamespace("vctrs")
unloadNamespace("rlang")
unloadNamespace("Rtsne")
unloadNamespace("SDMTools")
unloadNamespace("Rdpack")
unloadNamespace("bibtex")
unloadNamespace("tsne")
unloadNamespace("backports")
unloadNamespace("R6")
unloadNamespace("lazyeval")
unloadNamespace("scales")
unloadNamespace("munsell")
unloadNamespace("colorspace")
unloadNamespace("npsurv")
unloadNamespace("compiler")
unloadNamespace("digest")
unloadNamespace("R.utils")
unloadNamespace("pkgconfig")
unloadNamespace("gbRd")
unloadNamespace("parallel")
unloadNamespace("gdata")
unloadNamespace("listenv")
unloadNamespace("crayon")
unloadNamespace("splines")
unloadNamespace("zeallot")
unloadNamespace("reshape")
unloadNamespace("glue")
unloadNamespace("lsei")
unloadNamespace("RcppParallel")
unloadNamespace("data.table")
unloadNamespace("viridisLite")
unloadNamespace("globals")
Now check sessionInfo():
R version 3.6.1 (2019-07-05)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 17763)
Matrix products: default
locale:
[1] LC_COLLATE=English_Canada.1252 LC_CTYPE=English_Canada.1252 LC_MONETARY=English_Canada.1252 LC_NUMERIC=C
[5] LC_TIME=English_Canada.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] tools_3.6.1 stringr_1.4.0 rstudioapi_0.10 pryr_0.1.4 jsonlite_1.6 gtools_3.8.1 R.oo_1.22.0
[8] magrittr_1.5 Rcpp_1.0.3 R.methodsS3_1.7.1 stringi_1.4.3 plyr_1.8.4 reshape2_1.4.3 codetools_0.2-16
[15] packrat_0.5.0 assertthat_0.2.1
Check the memory footprint:
pryr::mem_used()
# 173 MB
Link to screen-cast demonstration
Note also that you can only use unload() once. If you use it a second time without rerunning library(), y'll get the not very informative error message invalid 'name' argument:
library(vegan)
#> Loading required package: permute
#> Loading required package: lattice
#> This is vegan 2.5-6
detach("package:vegan", unload=TRUE)
detach("package:vegan", unload=TRUE)
#> Error in detach("package:vegan", unload = TRUE): invalid 'name' argument
Created on 2020-05-09 by the reprex package (v0.3.0)
I would like to add an alternative solution. This solution does not directly answer your question on unloading a package but, IMHO, provides a cleaner alternative to achieve your desired goal, which I understand, is broadly concerned with avoiding name conflicts and trying different functions, as stated:
mostly because restarting R as I try out different, conflicting packages is getting frustrating, but conceivably this could be used in a program to use one function and then another--although namespace referencing is probably a better idea for that use
Solution
Function with_package offered via the withr package offers the possibility to:
attache a package to the search path, executes the code, then removes the package from the search path. The package namespace is not unloaded, however.
Example
library(withr)
with_package("ggplot2", {
ggplot(mtcars) + geom_point(aes(wt, hp))
})
# Calling geom_point outside withr context
exists("geom_point")
# [1] FALSE
geom_point used in the example is not accessible from the global namespace. I reckon it may be a cleaner way of handling conflicts than loading and unloading packages.
Just go to OUTPUT window, then click on Packages icon (it is located between Plot and Help icons). Remove "tick / check mark" from the package you wanted be unload.
For again using the package just put a "tick or Check mark" in front of package or use :
library (lme4)
Connected with #tjebo answer.
TL;DR
Please use pkgload:::unload instead of devtools::unload as they are the same function (1 to 1) and pkgload is a much lighter package (nr of dependencies). devtools simply reexporting the pkgload:::unload function.
Unfortunately devtools is a huge dependency (as devtools has a lot of own dependencies), which is more development stage targeted. So if you want to use the unload function in your own package or you care about library size please remember to use pkgload:::unload instead of devtools::unload. devtools simply reexporting the pkgload:::unload function.
Please check the footer of the devtools::unload function to quickly confirm the reexport or go to the github repo
> devtools::unload
function (package = pkg_name(), quiet = FALSE)
{
if (package == "compiler") {
oldEnable <- compiler::enableJIT(0)
if (oldEnable != 0) {
warning("JIT automatically disabled when unloading the compiler.")
}
}
if (!package %in% loadedNamespaces()) {
stop("Package ", package, " not found in loaded packages or namespaces")
}
unregister_methods(package)
unloaded <- tryCatch({
unloadNamespace(package)
TRUE
}, error = function(e) FALSE)
if (!unloaded) {
unload_pkg_env(package)
unregister_namespace(package)
}
clear_cache()
unload_dll(package)
}
<bytecode: 0x11a763280>
<environment: namespace:pkgload>
When I run my shiny application, I got an error message saying
Error in prob[tw, uni.c] :
invalid or not-yet-implemented 'Matrix' subsetting
That same code ran without error when it was not on Shiny. Any idea how I can troubleshoot this?
I'm not sure how to reproduce the data here, but prob is of class dgCMatrix from the Matrix package, tw is a single integer, and uni.c is a numeric vector.
EDIT:
sessionInfo() output:
R version 3.1.1 (2014-07-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
locale:
[1] LC_COLLATE=English_Singapore.1252 LC_CTYPE=English_Singapore.1252 LC_MONETARY=English_Singapore.1252
[4] LC_NUMERIC=C LC_TIME=English_Singapore.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] shiny_0.10.1 Matrix_1.1-4
loaded via a namespace (and not attached):
[1] bitops_1.0-6 caTools_1.17.1 digest_0.6.4 grid_3.1.1 htmltools_0.2.6 httpuv_1.3.0 lattice_0.20-29
[8] Rcpp_0.11.3 RJSONIO_1.3-0 tools_3.1.1 xtable_1.7-4
It turned out to be a bug in my code that is exposed by how Shiny works.
Outside Shiny, the function where the code resides worked seamlessly, being fed input from another function in the right format.
In Shiny, I expected the function in server.R to receive the input after the submitButton button is pressed, with sensible input keyed into the field. Apparently, even before the first press of button, the default value in the input field (which was not a sensible one) was passed to my function. That default value is not well-handled by my function and caused the error. Both changing the default value, and building extra error-checking in my function, worked to solve the issue.
Apologies for the confusion; this was a learning experience to be careful with default values and with Shiny processing sequence.
I tried using bfFixefLMER_t.fnc or fitLMER.fnc from the LMERConvenienceFunctions package. In both the cases, I get an error that "the input model is not a mer object".
I tried out the examples from http://artax.karlin.mff.cuni.cz/r-help/library/LMERConvenienceFunctions/html/00Index.html. I get the same errors.
For example when I run from the example
fitLMER.fnc(mB, backfit.on = "t", item = FALSE,
ran.effects = c("(FreqB | Subject)",
"(LengthB | Subject)", "(WMC | Item)"))
this is the result I get.
Warning in fitLMER.fnc(mB, backfit.on = "t", item = FALSE, ran.effects = c("(FreqB | Subject)", :resetting argument "method" to "t"
**backfitting fixed effects**
Warning in bfFixefLMER_t.fnc(model = model, item = item, method = method, :factor variable with more than two levels in model terms, backfitting on t-values is not appropriate, please use function "bfFixefLMER_F.fnc" instead.
Error in bfFixefLMER_t.fnc(model = model, item = item, method = method, : the input model is not a mer object
Has anyone had this experience with these functions?
There are functions that back fit fixed effects and forward fit random effects.
Is there a way to do forward fitting of fixed effects for the glmer models? Or is this statistically meaningless? I am working on ecological modelling, so my understanding of advanced stats is not much, so, please, if someone can explain in layman's terms better
sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_GB.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_GB.UTF-8
[7] LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] LMERConvenienceFunctions_2.0 lme4_0.99999911-8
[3] RcppEigen_0.3.1.2.1 Rcpp_0.10.4
[5] Matrix_1.0-12 lattice_0.20-23
[7] LCFdata_1.0
loaded via a namespace (and not attached):
[1] grid_3.0.1 MASS_7.3-28 minqa_1.2.1 nlme_3.1-111 rpart_4.1-2
[6] splines_3.0.1 tools_3.0.1
You are using an (older) version of the overhauled lme4 package that returns merMod objects instead of mer objects, and hence is not compatible with LMERConvenienceFunctions. I get the same error when using the soon-to-be-released version 1.0-4.
If I install the latest version from CRAN instead (0.999999-2), no errors arise. I suggest removing your current lme4 and installing the latest from CRAN, and checking its version:
> detach("package:lme4",unload=TRUE)
> remove.packages("lme4")
> install.packages("lme4")
> packageVersion("lme4")
[1] ‘0.999999.2’
This should fix your problems. Be aware, however, that you will lose the advantages of the new version.
Also, in the coming days the new lme4 should appear on CRAN, breaking LMERConvenienceFunctions again if you update your packages. I guess, however, that the authors of LMERConvenienceFunctions will update their package soon to be compatible again.
Why do I get R-crashing segfaults when specifying custom linetypes in R? The four linetypes below are effectively identical, in that they cycle through the same size of dashes and spaces in the same order (they just start at different points in the cycle).
plot.new()
abline(0.1,0,lty='28282383') # works
abline(0.2,0,lty='83282823') # works
abline(0.3,0,lty='28238328') # segfault
abline(0.4,0,lty='23832828') # segfault
Here is the full error message for the first of the two deadly lines above:
*** caught segfault ***
address 0xbf981000, cause 'memory not mapped'
Segmentation fault
Looks like a bug in the Cairo graphics device - I get a crash with a default X11() graphics device but not with X11(type="Xlib") or pdf(). RStudio possibly works because it possibly uses its own methods to capture the graphics.
I don't see anything about this in the description of 2.15.1-patched:
http://cran.r-project.org/bin/windows/base/NEWS.R-2.15.1patched.html
so I tried that and have now reported it as a bug:
https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=15055
Seems to work for me via RStudio on a mac. What OS? What version of R?
> plot.new()
> abline(0.1,0,lty='28282383') # works
> abline(0.2,0,lty='83282823') # works
> abline(0.3,0,lty='28238328') # segfault
> abline(0.4,0,lty='23832828') # segfault
> sessionInfo()
R version 2.15.0 (2012-03-30)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
locale:
[1] C/en_US.UTF-8/C/C/C/C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] reshape2_1.2.1
loaded via a namespace (and not attached):
[1] plyr_1.7.1 stringr_0.6.1 tools_2.15.0
I'd like to unload a package without having to restart R (mostly because restarting R as I try out different, conflicting packages is getting frustrating, but conceivably this could be used in a program to use one function and then another--although namespace referencing is probably a better idea for that use).
?library doesn't show any options that would unload a package.
There is a suggestion that detach can unload package, but the following both fail:
detach(vegan)
Error in detach(vegan) : invalid name argument
detach("vegan")
Error in detach("vegan") : invalid name argument
So how do I unload a package?
Try this (see ?detach for more details):
detach("package:vegan", unload=TRUE)
It is possible to have multiple versions of a package loaded at once (for example, if you have a development version and a stable version in different libraries). To guarantee that all copies are detached, use this function.
detach_package <- function(pkg, character.only = FALSE)
{
if(!character.only)
{
pkg <- deparse(substitute(pkg))
}
search_item <- paste("package", pkg, sep = ":")
while(search_item %in% search())
{
detach(search_item, unload = TRUE, character.only = TRUE)
}
}
Usage is, for example
detach_package(vegan)
or
detach_package("vegan", TRUE)
You can also use the unloadNamespace command, as in:
unloadNamespace("sqldf")
The function detaches the namespace prior to unloading it.
You can uncheck the checkbox button in RStudio (packages).
I tried what kohske wrote as an answer and I got error again, so I did some search and found this which worked for me (R 3.0.2):
require(splines) # package
detach(package:splines)
or also
library(splines)
pkg <- "package:splines"
detach(pkg, character.only = TRUE)
When you are going back and forth between scripts it may only sometimes be necessary to unload a package. Here's a simple IF statement that will prevent warnings that would appear if you tried to unload a package that was not currently loaded.
if("package:vegan" %in% search()) detach("package:vegan", unload=TRUE)
Including this at the top of a script might be helpful.
I hope that makes your day!
detach(package:PackageName) works and there is no need to use quotes.
Another option is
devtools::unload("your-package")
This apparently also deals with the issue of registered S3 methods that are not removed with unloadNamespace()
You can try all you want to remove a package (and all the dependencies it brought in alongside) using unloadNamespace() but the memory footprint will still persist. And no, detach("package:,packageName", unload=TRUE, force = TRUE) will not work either.
From a fresh new console or Session > Restart R check memory with the pryr package:
pryr::mem_used()
# 40.6 MB ## This will depend on which packages are loaded obviously (can also fluctuate a bit after the decimal)
Check my sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 17763)
Matrix products: default
locale:
[1] LC_COLLATE=English_Canada.1252 LC_CTYPE=English_Canada.1252 LC_MONETARY=English_Canada.1252 LC_NUMERIC=C
[5] LC_TIME=English_Canada.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_3.6.1 pryr_0.1.4 magrittr_1.5 tools_3.6.1 Rcpp_1.0.3 stringi_1.4.3 codetools_0.2-16 stringr_1.4.0
[9] packrat_0.5.0
Let's load the Seurat package and check the new memory footprint:
library(Seurat)
pryr::mem_used()
# 172 MB ## Likely to change in the future but just to give you an idea
Let's use unloadNamespace() to remove everything:
unloadNamespace("Seurat")
unloadNamespace("ape")
unloadNamespace("cluster")
unloadNamespace("cowplot")
unloadNamespace("ROCR")
unloadNamespace("gplots")
unloadNamespace("caTools")
unloadNamespace("bitops")
unloadNamespace("fitdistrplus")
unloadNamespace("RColorBrewer")
unloadNamespace("sctransform")
unloadNamespace("future.apply")
unloadNamespace("future")
unloadNamespace("plotly")
unloadNamespace("ggrepel")
unloadNamespace("ggridges")
unloadNamespace("ggplot2")
unloadNamespace("gridExtra")
unloadNamespace("gtable")
unloadNamespace("uwot")
unloadNamespace("irlba")
unloadNamespace("leiden")
unloadNamespace("reticulate")
unloadNamespace("rsvd")
unloadNamespace("survival")
unloadNamespace("Matrix")
unloadNamespace("nlme")
unloadNamespace("lmtest")
unloadNamespace("zoo")
unloadNamespace("metap")
unloadNamespace("lattice")
unloadNamespace("grid")
unloadNamespace("httr")
unloadNamespace("ica")
unloadNamespace("igraph")
unloadNamespace("irlba")
unloadNamespace("KernSmooth")
unloadNamespace("leiden")
unloadNamespace("MASS")
unloadNamespace("pbapply")
unloadNamespace("plotly")
unloadNamespace("png")
unloadNamespace("RANN")
unloadNamespace("RcppAnnoy")
unloadNamespace("tidyr")
unloadNamespace("dplyr")
unloadNamespace("tibble")
unloadNamespace("RANN")
unloadNamespace("tidyselect")
unloadNamespace("purrr")
unloadNamespace("htmlwidgets")
unloadNamespace("htmltools")
unloadNamespace("lifecycle")
unloadNamespace("pillar")
unloadNamespace("vctrs")
unloadNamespace("rlang")
unloadNamespace("Rtsne")
unloadNamespace("SDMTools")
unloadNamespace("Rdpack")
unloadNamespace("bibtex")
unloadNamespace("tsne")
unloadNamespace("backports")
unloadNamespace("R6")
unloadNamespace("lazyeval")
unloadNamespace("scales")
unloadNamespace("munsell")
unloadNamespace("colorspace")
unloadNamespace("npsurv")
unloadNamespace("compiler")
unloadNamespace("digest")
unloadNamespace("R.utils")
unloadNamespace("pkgconfig")
unloadNamespace("gbRd")
unloadNamespace("parallel")
unloadNamespace("gdata")
unloadNamespace("listenv")
unloadNamespace("crayon")
unloadNamespace("splines")
unloadNamespace("zeallot")
unloadNamespace("reshape")
unloadNamespace("glue")
unloadNamespace("lsei")
unloadNamespace("RcppParallel")
unloadNamespace("data.table")
unloadNamespace("viridisLite")
unloadNamespace("globals")
Now check sessionInfo():
R version 3.6.1 (2019-07-05)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 17763)
Matrix products: default
locale:
[1] LC_COLLATE=English_Canada.1252 LC_CTYPE=English_Canada.1252 LC_MONETARY=English_Canada.1252 LC_NUMERIC=C
[5] LC_TIME=English_Canada.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] tools_3.6.1 stringr_1.4.0 rstudioapi_0.10 pryr_0.1.4 jsonlite_1.6 gtools_3.8.1 R.oo_1.22.0
[8] magrittr_1.5 Rcpp_1.0.3 R.methodsS3_1.7.1 stringi_1.4.3 plyr_1.8.4 reshape2_1.4.3 codetools_0.2-16
[15] packrat_0.5.0 assertthat_0.2.1
Check the memory footprint:
pryr::mem_used()
# 173 MB
Link to screen-cast demonstration
Note also that you can only use unload() once. If you use it a second time without rerunning library(), y'll get the not very informative error message invalid 'name' argument:
library(vegan)
#> Loading required package: permute
#> Loading required package: lattice
#> This is vegan 2.5-6
detach("package:vegan", unload=TRUE)
detach("package:vegan", unload=TRUE)
#> Error in detach("package:vegan", unload = TRUE): invalid 'name' argument
Created on 2020-05-09 by the reprex package (v0.3.0)
I would like to add an alternative solution. This solution does not directly answer your question on unloading a package but, IMHO, provides a cleaner alternative to achieve your desired goal, which I understand, is broadly concerned with avoiding name conflicts and trying different functions, as stated:
mostly because restarting R as I try out different, conflicting packages is getting frustrating, but conceivably this could be used in a program to use one function and then another--although namespace referencing is probably a better idea for that use
Solution
Function with_package offered via the withr package offers the possibility to:
attache a package to the search path, executes the code, then removes the package from the search path. The package namespace is not unloaded, however.
Example
library(withr)
with_package("ggplot2", {
ggplot(mtcars) + geom_point(aes(wt, hp))
})
# Calling geom_point outside withr context
exists("geom_point")
# [1] FALSE
geom_point used in the example is not accessible from the global namespace. I reckon it may be a cleaner way of handling conflicts than loading and unloading packages.
Just go to OUTPUT window, then click on Packages icon (it is located between Plot and Help icons). Remove "tick / check mark" from the package you wanted be unload.
For again using the package just put a "tick or Check mark" in front of package or use :
library (lme4)
Connected with #tjebo answer.
TL;DR
Please use pkgload:::unload instead of devtools::unload as they are the same function (1 to 1) and pkgload is a much lighter package (nr of dependencies). devtools simply reexporting the pkgload:::unload function.
Unfortunately devtools is a huge dependency (as devtools has a lot of own dependencies), which is more development stage targeted. So if you want to use the unload function in your own package or you care about library size please remember to use pkgload:::unload instead of devtools::unload. devtools simply reexporting the pkgload:::unload function.
Please check the footer of the devtools::unload function to quickly confirm the reexport or go to the github repo
> devtools::unload
function (package = pkg_name(), quiet = FALSE)
{
if (package == "compiler") {
oldEnable <- compiler::enableJIT(0)
if (oldEnable != 0) {
warning("JIT automatically disabled when unloading the compiler.")
}
}
if (!package %in% loadedNamespaces()) {
stop("Package ", package, " not found in loaded packages or namespaces")
}
unregister_methods(package)
unloaded <- tryCatch({
unloadNamespace(package)
TRUE
}, error = function(e) FALSE)
if (!unloaded) {
unload_pkg_env(package)
unregister_namespace(package)
}
clear_cache()
unload_dll(package)
}
<bytecode: 0x11a763280>
<environment: namespace:pkgload>