One of my R package's dependencies displays startup messages when loaded. I would like to suppress these startup messages.
The only fix I found so far was removing the offending package from the Depends: line in my DESCRIPTION file. Then calling suppressPackageStartupMessages(require("offendingPackage")) in .onLoad of my package.
I would rather keep the offending package as part of my Depends, but it seems that anything specified in depends is automatically loaded and therefore can't be supressed.
The suppressPackageStartupMessages() function works if and only if the startup messages are actually written with packageStartupMessage() -- see the help page.
Many packages just use cat(), which one could consider a buglet. In that case
suppressMessages(library(foo))
works better.
If you work with namespaces, you can specify the package in Imports, and load the necessary functions using import or importFrom. This way, the package is not attached, but the necessary functions can be loaded and used by your package. Without attaching, the startup messages are not given, so this approach assures you won't see any startup messages of packages specified in Imports.
Make sure you check that you imported everything that is of importance. If the package you import is dependent on other packages, I'm not sure everything you need to use those functions is imported. You might have to do a bit of puzzling to get everything you need loaded. On the plus side, using Imports assures that any dependencies check will be carried out correctly.
Another option is to not specify the package in Depends, but in Suggests in the DESCRIPTION file, and use the option #Dirk gave you. This will give a correct dependency check if 'dependencies=TRUE' is set in install.packages(). But personally I think using the namespaces is a lot more clean.
A quick hack to do this inline in a script or environment is to override library()/require() to wrap the suppressPackageStartupMessages() method:
> library(here) # This shows a message
here() starts at /home/z/development/
> require(here) # This shows a message
Loading required package: here
here() starts at /home/y
The workaround:
> flibrary <- library
> library <- function(...) suppressPackageStartupMessages(flibrary(...))
> library(here) # No messages
>
> frequire <- require
> require <- function(...) suppressPackageStartupMessages(frequire(...))
> require(here) # No messages
>
Related
Currently I have in my package DESCRIPTION, a dependency on dbplyr:
Imports:
dbplyr,
dplyr
dbplyr is useful almost solely because of the S3 methods it defines: https://github.com/tidyverse/dbplyr/blob/main/NAMESPACE. The actual functions you call to use dbplyr are almost entirely from dplyr.
By putting dbplyr in my Imports, it should automatically get loaded, but not attached, which should be enough to register its S3 methods: https://r-pkgs.org/dependencies-mindset-background.html#sec-dependencies-attach-vs-load.
This seems to work fine, but whenever I R CMD check, it tells me:
N checking dependencies in R code (10.8s)
Namespace in Imports field not imported from: ‘dbplyr’
All declared Imports should be used.
Firstly, why does R CMD check even check this, considering that it often makes sense to load packages without importing them. Secondly, how am I supposed to satisfy R CMD check without loading things into my namespace that I don't want or need?
I am pretty sure two of your assumptions are false.
First, putting Imports: dbplyr into your DESCRIPTION file won't load it, so its methods won't be loaded from that alone. Basically the Imports field in the DESCRIPTION file just guarantees that dbplyr is available to be loaded when requested. If you import something via the NAMESPACE file, that will cause it to be loaded. If you evaluate dbplyr::something that will cause it to be loaded. Executing loadNamespace("dbplyr") is another way, and there are a few others. You may also load some other package that loads it.
Second, I think you have misinterpreted the error message. It isn't saying that you loaded it without importing it (though it would complain about that too), it is saying that it can't detect any use of it in your package, so maybe it shouldn't be a requirement for installing your package.
Unfortunately, the code to detect uses is fallible, so it sometimes misses uses. Examples I've heard about are:
if the package is only used in the default value for a function argument. This has been fixed in R-devel.
if the package is only used during the build to construct some object, e.g. code like someclass <- R6::R6Class( ... ) needs R6, but the check code won't see it because it looks at someclass, not at the source code that created it.
if the use of the package is hidden by specifying the name of the package in a character variable.
if the need for the package is indirect, e.g. you need to use ggplot2::geom_hex. That needs the hexbin package, but ggplot2 only declares it as "Suggested".
These examples come from this discussion: https://github.com/hadley/r-pkgs/issues/828#issuecomment-1421353457 .
The recommended workaround there is to create an object that refers to the imported package explicitly, e.g. putting the line
dummy_r6 <- function() R6::R6Class
into your package is enough to suppress the note without actually loading R6. (It will be loaded if you ever call this function.)
However, your requirement is stronger: you do need to make sure dbplyr is loaded if you want its methods to be used. I'd put something in your .onLoad() function that triggers the load. For example,
.onLoad <- function(lib, pkg) {
# Make sure the dbplyr methods are loaded
loadNamespace("dbplyr")
}
EDITED TO ADD: As pointed out in the comments, there's a bug in the check code that means it won't detect this as being a use of dbplyr. You really need to do both things, e.g.
.onLoad <- function(lib, pkg) {
# Make sure the dbplyr methods are loaded
loadNamespace("dbplyr")
# Work around bug in code checking in R 4.2.2 for use of packages
dummy <- function() dbplyr::across_apply_fns
}
The function used in the dummy construction is arbitrary; it probably doesn't even need to exist, but I chose one that does.
As my code evolves from version to version, I'm aware that there are some packages for which I've found better/more appropriate packages for the task at hand or whose purpose was limited to a section of code which I've now phased out.
Is there any easy way to tell which of the loaded packages are actually used in a given script? My header is beginning to get cluttered.
Update 2020-04-13
I've now updated the referenced function to use the abstract syntax tree (AST) instead of using regular expressions as before. This is a much more robust way of approaching the problem (it's still not completely ironclad). This is available from version 0.2.0 of funchir, now on CRAN.
I've just got around to writing a quick-and-dirty function to handle this which I call stale_package_check, and I've added it to my package (funchir).
e.g., if we save the following script as test.R:
library(data.table)
library(iotools)
DT = data.table(a = 1:3)
Then (from the directory with that script) run funchir::stale_package_check('test.R'), we'll get:
Functions matched from package data.table: data.table
**No exported functions matched from iotools**
Have you considered using packrat?
packrat::clean() would remove unused packages, for example.
I've written a command-line script to accomplish this task. You can find it in this Github gist. I'm sure there are edge cases that it misses, but it works pretty well, on both R scripts and Rmd files.
My approach always is to close my R script or IDE (i.e. RStudio) and then start it again.
After this I run my function without loading any dependecies/packages beforehand.
This should result in various warning and error messages telling you which functions couldn't be found and executed. This again will give you hints on what packages are necessary to load beforehand and which one you can leave out.
I'm creating an R package and it cannot show any kind of message from imported packages when it loads. I'm having a problem with an specific package, mFilter. If I import it, I always get
‘mFilter’ version: 0.1-3
‘mFilter’ is a package for time
series filtering
See ‘library(help="mFilter")’ for
details
Author: Mehmet Balcilar,
mbalcilar#yahoo.com
when the user loads my package, regardless of adding suppressMessages('mFilter') in the .onLoad file.
I really need to use mFilter. So removing it from Imports list doesn't help. Does anyone know what should I do?
I don't think you can. In the mFilter package, instead of using message() in .onLoad(), the authors have incorrectly used
if(interactive() || getOption("verbose"))
writeLines(strwrap(txt, indent = 4, exdent = 4))
If you are using the package interactively this will always execute and won't be suppressed.
If you can limit your use of mFilter to just a few functions, you could Suggest mFilter rather than Import or Depend on it. Then, in the functions that need it, you could capture.output(require(mFilter, quietly = TRUE)) to load the package (and stop with a message that mFilter needs to be installed if the load is unsuccessful).
Alternately, you could take the same approach, but have the loading of mFilter take place in your package's .onLoad.
You may even be able to do something tricky where mFilter is listed in DESCRIPTION Imports (to guarantee it gets installed) but isn't imported in the NAMESPACE file. It would probably (at least) throw a warning during check, but it would probably work just fine.
I'm developing an R package which needs to use parallelisation as made available by the snowfall package. snowfall doesn't seem to import the same was as other packages like ggplot2, data.table, etc. I've included snowfall, rlecuyer, and snow in the description file, name space file, and as an import argument in the function itself. When I try to access this function, I get the following error:
Error in sfInit() : could not find function "setDefaultClusterOptions"
The sfInit function seems to have a nostart / nostop argument which it says is related to nested usage of sfInit but that doesn't seem to do the trick for me either.
The actual code itself uses an sfInit (which is where I get the error), some sfExports and sfLibrarys, and an sfLapply.
Possible solution:
It seems to work if I move snow from the import section to the depends section in the Desciption file. I don't know why though.
When you include a package in 'Depends' when one attaches your package they also attach the package on which your package Depends to their namespace.
This and other differences between Depends and Imports is explained well in other questions on this site.
If you look at {snowfall}'s DESCRIPTION you'll see that it Depends on {snow}. It is plausible that the authors of snowfall know something we don't and that {snow} has to be attached to the global search path in order to work. In fact that is the top caveat in the top answer to the question I linked above...
... if your package relies on a package A which itself "Depends" on
another package B, your package will likely need to attach A with a
"Depends directive.
This is because the functions in package A were written with the
expectation that package B and its functions would be attached to the
search() path.
So, in your case, it just so happens that all {snowfall} wants is {snow} and you happened to provide it. However, it appears the more correct behavior may be for you to Depend on {snowfall} directly.
setDefaultClusterOptions is a function from the snow package. You need to import that too.
I've hit an issue trying to import a package (namely, 'robfilter') inside one of my own packages. One of its methods that I am trying to use, adore.filter, is failing at this line:
data(critvals)
With error 'data set 'critvals' not found'.
The function works fine if I load the library via require(robfilter). However, this means that in order to use my custom package which calls adore.filter, I will have to load my own package, and then load robfilter. Not a huge problem but slightly annoying.
I'm not sure if the problem is that there is an extra step I need to do in order to make critvals visible within my package, or if perhaps there is something the package author needed to do (and hasn't done) to add critvals to its package namespace; there is no sign of 'critvals' in the robfilter NAMESPACE file. I haven't encountered this issue before and don't really understand how the use of data() inside a package is supposed to work.
There are two solutions as far as I know:
Either ask the robfilter Maintainer to put the data needed by robfiler in the internal data file of robfilter. (R/sysdata.rda)
Or make your package Depends on robfilter
So it works if you put robfilter in the depends section of your description file. But in my case (both are my packages), I was trying to avoid the Depends solution as it loads the imported package and also any other package will need to depend ont its imported package... See my question is quite a duplicate of yours but not in the same context.