I am having trouble unloading the namespace for a package I created in R. Every time I try to do so I get the following error:
Error in .mergeMethodsTable(generic, mtable, get(tname, envir = env), :
trying to get slot "defined" from an object of a basic class ("environment") with no
slots
Calls: unloadNamespace ... -> .updateMethodsInTable -> .mergeMethodsTable
Here are the results of a call to traceback() after the above error occurs.
>4: .mergeMethodsTable(generic, mtable, get(tname, envir = env), attach)
3: .updateMethodsInTable(fdef, where, attach)
2: methods:::cacheMetaData(ns, FALSE, ns)
1: unloadNamespace("coleXcms")
I honestly have tried everything I can think of, but to no avail. I'm pretty new to R so I was hoping someone might be able to help me.
Also, don't know if this will be useful, but here is my package's unloading hook. (The name of my package is coleXcms)
.onUnload <- function(libpath) {
mzR:::rampCloseAll()
library.dynam.unload("coleXcms", libpath)
}
The function I have used with success is unloadNamespace. It appears that library.dynam.unload is designed to remove the DLLs but it's not clear to me that it will remove the rest of a package.
Related
I'm trying to include a function from the Bioconductor package "simpIntLists" in my own package. "import(simpIntLists)" is added to the Namespace file.
However, the function results in an error
do_xy <- function(organism, IDType){
network <- simpIntLists::findInteractionList(organism, IDType)
}
do_xy("human", "EntrezId")
#Error message
data set ‘HumanBioGRIDInteractionEntrezId’ not foundError in get("HumanBioGRIDInteractionEntrezId") :
object 'HumanBioGRIDInteractionEntrezId' not found
# results in the same error (outside of the function)
simpIntLists::findInteractionList(organism, IDType)
It works fine when simpIntLists is attached
# works
library(simpIntLists)
network <- simpIntLists::findInteractionList(organism, IDType)
I saw the code here (https://bioconductor.org/packages/release/data/experiment/html/simpIntLists.html).
This code does not seem to take into account the situation where the package is used without installation.
For your information, the relevant part to this error is around the line 52.
else if (organism == 'human'){
if (idType == 'EntrezId'){
data(HumanBioGRIDInteractionEntrezId);
interactionList <- get("HumanBioGRIDInteractionEntrezId");
}
It tries to fetch the data to the namespace but it fails to do so if the package is not imported via library yet. This only generates a warning. The error then occurs when it tries to use the data because it does not exist in the namespace.
A workaround is that you import the data in your code explicitly. Then you can use the function as below. Note that the warning remains because of the embedded package code. If the warning is annoying, use suppressWarnings.
data(HumanBioGRIDInteractionEntrezId, package="simpIntLists")
simpIntLists::findInteractionList("human", "EntrezId")
I'm in the process of writing an R package. One of my functions takes another function and some other data-related arguments and runs a %dopar% loop using the foreach package. This foreach-using function is used inside the one of the main functions of my package.
When I call the main function from another file, after having loaded my package, I get the message
Error in { : task 1 failed - "could not find function "some_function"
where some_function is some function from my package. I get this message, with varying missing function, when I set the .export argument in the call to foreach to any of the following:
ls(as.environment("package:mypackagename"))
ls(.GlobalEnv)
ls(environment())
ls(parent.env(environment()))
ls(parent.env(parent.env(environment()))
And even concatenations of the above. I also tried passing my package name to the .package argument, which only yields the error message
Error in e$fun(obj, substitute(ex), parent.frame(), e$data) : worker initialization failed: there is no package called ‘mypackagename’
I feel like I have tried just about everything, and I really need this piece of code to work. I should note that it does work if I use %do% instead of %dopar%. What am I doing wrong?
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
I'm working on an R package where one of the functions contains a match.fun call to a function in a package that's imported to the package namespace. But on loading the package, the match.fun call can't find the function name. From Hadley Wickham's description I think I'm doing everything right, but this is clearly not the case.
Example:
# in the package file header, for creation of the NAMESPACE via roxygen2:
##` #import topicmodels
# The function declaration in the package
ModelTopics <- function(doc.term.mat, num.topics, topic.method="LDA"){
topic.fun <- match.fun(topic.method)
output <- topic.fun(doc.term.mat, k=num.topics)
return(output)
}
And then in R:
> library(mypackage)
> sample.output <- ModelTopics(my.dtm, topic.method="LDA", num.topics=5)
Error in get(as.character(FUN), mode = "function", envir = envir) :
object 'LDA' of mode 'function' was not found
From my understanding of namespaces, the match.fun call should have access to the package namespace, which should include the topicmodels functions. But that doesn't appear to be the case here. If I import topicmodels directly to the global namespace for the R session, then this works.
Any help is much appreciated. This is R64 2.14.1 running on OSX.
UPDATE:
The package is here
Re the DESCRIPTION file, perhaps that's the problem: roxygen2 doesn't update the DESCRIPTION file with Imports: statements. But none of the other packages are listed there, either; only the match.fun calls appear to be affected.
Re the NAMESPACE extract, here's the import section:
import(catspec)
import(foreach)
import(gdata)
import(Hmisc)
import(igraph)
import(lsa)
import(Matrix)
import(plyr)
import(RecordLinkage)
import(reshape)
import(RWeka)
import(stringr)
import(tm)
import(topicmodels)
I believe this an issue of scope. Although you have imported topicmodels and thus LDA, you haven't exported these functions, so they aren't available in the search path.
From ?match.fun:
match.fun is not intended to be used at the top level since it will
perform matching in the parent of the caller.
Thus, since you are using ModelTopics in the global environment, and LDA isn't available in the global environment, the match.fun call fails.
It seems to me you have two options:
Option 1: use get
An alternative would be to use get where you can specify the environment. Consider this: try to use match.fun to find print.ggplot in the package ggplot2:
match.fun("print.ggplot")
Error in get(as.character(FUN), mode = "function", envir = envir) :
object 'print.ggplot' of mode 'function' was not found
Since print.ggplot isn't exported, match.fun can't find it.
However, get does find it:
get("print.ggplot", envir=environment(ggplot))
function (x, newpage = is.null(vp), vp = NULL, ...)
{
set_last_plot(x)
if (newpage)
grid.newpage()
data <- ggplot_build(x)
gtable <- ggplot_gtable(data)
if (is.null(vp)) {
grid.draw(gtable)
}
else {
if (is.character(vp))
seekViewport(vp)
else pushViewport(vp)
grid.draw(gtable)
upViewport()
}
invisible(data)
}
<environment: namespace:ggplot2>
Option 2: Export the functions from topicmodels that you need
If you make the necessary functions from topicmodels available in your NAMESPACE, your code should also work.
Do this by either:
Selective exporting LDA and other functions to the namespace using #export
Declare a dependency, using Depends: topicmodels - this is the same as calling library(topicmodels) in the global environment. This will work, but is possibly a bit of a brute force approach. It also means that any subsequent library call can mask your LDA function, thus leading to unexpected results.
Answering my own question: the DESCRIPTION file wasn't updating the Imports: and Depends: fields after re-roxygenizing the updated code. Hence the match.fun issues. Out of curiousity, why does this affect match.fun but not a range of other function calls made elsewhere to imported package functions?
I would like to create a function within a package with a NAMESPACE that will save some variables. The problem is that when load is called on the .Rdata file it
tries to load the namespace of the package that contained the function that created the .Rdata file, but this package need not be loaded.
This example function is in a package in a namespace :
create.global.function <- function(x, FUN, ...) {
environment(FUN) <- .GlobalEnv
assign(".GLOBAL.FUN", function(x) { FUN(x, ...) }, env=.GlobalEnv)
environment(.GLOBAL.FUN) <- .GlobalEnv
save(list = ls(envir = .GlobalEnv, all.names = TRUE),
file = "/tmp/.Rdata",
envir = .GlobalEnv)
}
The environment(.GLOBAL.FUN) <- .GlobalEnv calls are not sufficient and attaching gdb to the R process confirms it is serializing a NAMESPACESXP here with the name of the package namespace and the load fails because it is unable to load this.
Is it possible to fully strip the namespace out of the .GLOBAL.FUN before I save it such that it can be loaded into other R instances without trying to load the namespace?
#JorisMeys snowfall and the others do not offer exactly this functionality.
snowfall uses sfExport ( from clusterFunctions.R in snowfall) to export local and global objects to the slave nodes, and this in turn uses sfClusterCall which is a wrapper around the clusterCall function from snow.
res <- sfClusterCall( assign, name, val, env = globalenv(),
stopOnError = FALSE )
And the snow library is loaded on the clients getting around any namespace issues as I mentioned in the last sentence of my question I would like to not load the namespace there.
Furthermore, it seems to make simplified assumptions such as that the nodes will share an NFS mount point for shared data (e.g. sfSource function in clusterFunctions.R).
I am more interested in something like a case where a node saves an .Rdata file then scp's it to another node that need not have the package namespace loaded.
It seems I can for now solve my original problem by using eval.parent and substitute:
assign(".GLOBAL.FUN",
eval.parent(substitute(function(y) { FUN(y, ...) })),
env=.GlobalEnv)
I apologize for the posting snafu, but I do not have an edit link although I posted this question, nor is there any place for me to leave a "comment" in the same way that I have this big text field for an answer. I've flagged this for moderation so I can get some help with that and have referenced the FAQ which talks about buttons that do not appear for me for leaving comments. there is some problem with this new account.