Typically, when starting up an renv project, one gets a message that looks something like this:
* Project '~/path/to/project' loaded. [renv 0.10.0]
I am trying to suppress this message, particularly when non-interactively running a script from this project.
Checking the package help, I noted ?config i.e. User-Level Configuration of renv. Specifically, I found synchronized.check, of which the document states is for controlling how renv lockfile synchronization is checked (this is also outputted to the console). However, I couldn't find how to control the main startup message. I also checked the ?settings but found nothing relevant either.
I've tried fiddling with options and Sys.setenv without luck so far.
So, is it possible to suppress the message, seeing that the renv script activate.R controls how the package itself is loaded?
You are correct that there isn't a specific documented way to configure this in renv. For now, you can set:
options(renv.verbose = FALSE)
before renv is loaded. (You may want to turn it back to TRUE if you want renv to display other messages as part of its normal work.)
You can suppress library startup messages with suppressPackageStartupMessages, e.g.
suppressPackageStartupMessages(library(igraph))
There is also suppressMessages for arbitrary function calls.
Related
This bounty has ended. Answers to this question are eligible for a +100 reputation bounty. Bounty grace period ends in 4 hours.
antonio wants to draw more attention to this question:
Explain what is the proper workflow when you are building two packages, where one depends on the other. What is the correct way to run devtools::check() on the depending-on package?
I want to add a local package dependency using R devtools.
The suggested way to add packages to the package DESCRIPTION file is one of the two functions use_package() and use_dev_package(), from the usethis package. The latter adds a dependency on an in-development package. The function help shows the following prototype:
use_dev_package(package, type = "Imports", remote = NULL)
where remote is
a character string to specify the remote, e.g. ‘"gitlab::jimhester/covr"’, using any syntax supported by the remotes package.
The remotes vignette shows the following
# Local
Remotes: local::/pkgs/testthat
So the command should be along these lines:
use_dev_package(foopack, type = "Imports", remote = "local::<foopack>")
However, what should be the path to the foopack. An absolute one or relative to project dir? The root package directory or the R directory with the code, or perhaps the foopack.tar.gz build?
All attempts failed for me.
Needless to say that, beyond having the local dependency properly listed in the DESCRIPTION file, I need it to be seen by the devtools build & check functions.
Edit
As regards use_dev_package(), I found a solution:
if I use devtools::check(), then the dependency appears in the search path, and use_dev_package() does not complain any more (see answer below).
However, it is still unclear to me what arguments should I use to make a development check() for the main package, in particular when the package has a vignette.
Ideally, I should be able to pass the check with local dependencies by passing cran = FALSE, but this still gives
"Package required but not available".
It seems that I have to check the local dependencies before adding them to the description file.
devtools::check("path/to/foopack")
usethis::use_dev_package("foopack", remote ="local::path/to/foopack")
The paths can be relative or absolute, and even a single colon works.
It might be worth noting that, when I build the main package, I can use the ordinary:
devtools::build()
but, for a successful check, I need to use the remote argument:
devtools::check(remote = TRUE)
I can't see a rationale for restating what is in the DESCRIPTION file, but I do not have enough expertise to say it's a bug.
Let's see what the others say in this regard.
Edit
Unfortunately, it seems that the remote argument above does not apply to vignettes. So, if I add a vignette to the package, checks fail with local packages
Until an actual solution is found, all I can do is (sadly) to ignore vignette checks:
devtools::check(remote = TRUE, vignettes = FALSE)
I wanted to make internally sharing/locally launching a shiny app developed with the {golem} framework a little more robust.
Hence, I used the renv package and installed the shiny app as a local package into a project folder.
I proceeded as follows (thanks #Kat for the suggestion):
initialize renv using renv::init(bare = TRUE)
renv::install("my_local_package")
renv::snapshot(type = "all")
renv::isolate()
Writing a launch file consisting of:
library(golempackage)
renv::restore()
golempackage::run_app(options = list(launch.browser = TRUE))
Share folder.
However, when launching the shiny app on a different computer (or a docker testing environment), I get the following error caused by the package bslib. Same happens when I delete my cache:
An error has occurred!
File attachments must exist: 'C:/Users/XYZ/AppData/Local/R/cache/R/renv/cache/v5/.../bslib/lib/bs3/assets/fonts'
Note: this error even occurs if I set the cache to be project-local and share it inside the project folder.
However, now the error message does not reference the global but the project-local cache. Unfortunately still as an absolute path which throws an error for other users.
This is all super weird and I have not the slightest idea why this occurs.
I would like to avoid removing bslib.
As far as I can see, the error is coming from the sass package, e.g.
https://github.com/rstudio/sass/blob/f7a954027447dd0b9826ec01c7084c89a6e64fcc/R/layers.R#L442-L443
While I don't know exactly know what's going on, you could probably use the R debugger to check why that's failing. (Does the referenced folder exist in both cases? Are you expecting renv to be using the cache in the second case?)
When running R CMD check I get the following note:
checking for future file timestamps ... NOTE
unable to verify current time
I have seen this discussed here, but I am not sure which files it is checking for timestamps, so I'm not sure which files I should look at. This happens locally on my windows and remotely on different systems (using github actions).
Take a look at https://svn.r-project.org/R/trunk/src/library/tools/R/check.R
The check command relies on an external web resource:
now <- tryCatch({
foo <- suppressWarnings(readLines("http://worldclockapi.com/api/json/utc/now",
warn = FALSE))
This resource http://worldclockapi.com/ is currently not available.
Hence the following happens (see same package source):
if (is.na(now)) {
any <- TRUE
noteLog(Log, "unable to verify current time")
See also references:
https://community.rstudio.com/t/r-devel-r-cmd-check-failing-because-of-time-unable-to-verify-current-time/25589
So, unfortunately this requires a fix in the check function by the R development team ... or the web-resource coming online again.
To add to qasta's answer, you can silence this check by setting the _R_CHECK_SYSTEM_CLOCK_ environment variable to zero e.g Sys.setenv('_R_CHECK_SYSTEM_CLOCK_' = 0)
To silence this in a persistent manner, you can set this environment variable on R startup. One way to do so is through the .Renviron file, in the following manner:
install.packages("usethis") (If not installed already)
usethis::edit_r_environ()
Add _R_CHECK_SYSTEM_CLOCK_=0 to the file
Save, close file, restart R
I don't know what is going on, everything was working great but suddenly I started to have this error message on the documentation:
Error in fetch(key) : lazy-load database '......descopl.rdb' is
corrupt
I removed almost all my code and build again then publish to Github, but when I use the other laptop to download the package, the package is being downloaded and loaded but I can't call any of the functions, and the documentation states that error.
I don't know what caused the problem, I am using roxygen to generate the documentation.
https://github.com/WilliamKinaan/descopl
It seems that the error arises when the package cannot be decompressed by R (as #rawr established, it is corrupt). This solutions have worked for me:
1) Check for possible errors in the creation of the .Rdb files
2) Try restarting your R session (e.g. .rs.restartR() if in RStudio)
3) The package might have been installed in your computer (even though it does not work). Remove it using ?remove.packages()
I have had this problem with roxygen2 as well. Couldn't see any problem with any of my functions. In the end deleting the .rdb file and then getting roxygen2 to rebuild it seemed to solve the problem.
I think the explanation for what is causing this is here.
It's related to devtools.
Per #Zfunk
cd ~/Rlibs/descopl/help
rm *.rdb
Restart R. Look at the help for the package again. Fixed!
I received this error after re-installing a library whilst another R session was running.
Simply restarting the existing R session(s) solved for me (i.e. running .rs.restartR() to restart the sessions)
If you are using R-studio:
1) ctrl+shift+f10 to restart r session
2) tools -> Check for package updates -> update all packages
3) library(ggmap)
Problem is solved.
Basically all answers require restarting R to resolve the issue, but I found myself in an environment where I really didn't want to restart R.
I am posting here a somewhat hack-ish solution suggested by Jim Hester in a bug report about the lazy-load corruption issue.
The gist of it is that the package may have some vestigial S3 methods listed in session's .__S3MethodsTable__. environment. I don't have a very systematic way of identifying which S3 methods in that environment come from where, but I think a good place to start is the print methods, and looking for S3method registrations in the package's NAMESPACE.
You can then remove those S3 methods from the .__S3MethodsTable__. environment and try again, e.g.
rm(list="print.object", envir = get(".__S3MethodsTable__.", envir = baseenv()))
You may also need to unload some DLLs if some new messages come up like
no such symbol glue_ in package /usr/local/lib/R/site-library/glue/libs/glue.so
You can check getLoadedDLLs() to see which such files are loaded in your session. In the case of glue here, the following resolved the issue:
library.dynam.unload('glue', '/usr/local/lib/R/site-library/glue')
I got this error on RStudio on mac OS - updating all the packages and restarting r session did the trick.
I'm trying to get R (running on Windows) to download some packages from the Internet, but the download fails because I can't get it to correctly use the necessary proxy server. The output text when I try the Windows menu option Packages > Install package(s)... and select a CRAN mirror is:
> utils:::menuInstallPkgs()
--- Please select a CRAN mirror for use in this session ---
Warning: unable to access index for repository http://cran.opensourceresources.org/bin/windows/contrib/2.12
Warning: unable to access index for repository http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/2.12
Error in install.packages(NULL, .libPaths()[1L], dependencies = NA, type = type) :
no packages were specified
In addition: Warning message:
In open.connection(con, "r") :
cannot open: HTTP status was '407 Proxy Authentication Required'
I know the address and port of the proxy, and I also know the address of the automatic configuration script. I don't know what the authentication is called, but when using the proxy (in a browser and some other applications), I enter a username and password in a dialog window that pops up.
To set the proxy, I tried each of the following:
Sys.setenv(http_proxy="http://proxy.example.com:8080")
Sys.setenv("http_proxy"="http://proxy.example.com:8080")
Sys.setenv(HTTP_PROXY="http://proxy.example.com:8080")
Sys.setenv("HTTP_PROXY"="http://proxy.example.com:8080")
For authentication, I similarly tried setting the http_proxy_user environment variable to:
ask
user:passwd
Leaving it untouched
Am I using the right commands in the right way?
You have two options:
Use --internet2 or setInternet2(TRUE) and set the proxy details in the control panel, in Internet Options
Do not use either --internet2 or setInternet2(FALSE), but specify the environment variables
EDIT: One trick is, you cannot change your mind between 1 and 2, after you have tried it in a session, i.e. if you run the command setInternet2(TRUE) and try to use it e.g. install.packages('reshape2'), should this fail, you cannot then call setInternet2(FALSE). You have to restart the R session.
As of R version 3.2.0, the setInternet2 function can set internet connection settings and change them within the same R session. No need to restart.
When using option 2, one way (which is nice and compact) to specify the username and password is http_proxy="http://user:password#proxy.example.com:8080/"
In the past, I have had most luck with option 2
If you want internet2 to be used everytime you use R you could add the following line to the Rprofile.site file which is located in R.x.x\etc\Rprofile.site
utils::setInternet2(TRUE)
I've solved my trouble editing the file .Renviron as documented in Proxy setting for R.
EDITED
The solutions based on the setInternet2 statement do not work with the recent R versions because setInternet2 is declared defunct.
I'm using the 4.2.1 (on Win 11Pro) while I never had any problems in previous versions .
So to solve the problem need to modify some config files in order to fix the proxy issue not only for packages installation but, in general, also to acced to a remote resource (ie. boundary maps in my case).
The question "Proxy setting for R" collect a lot of solutions. I've found that this one has solved both my problems (packages installation and remote resources) explaining step-by-step how to edit the file .Renviron
Other solutions based on the customization of the file Renviron.site for me doesn't work
install.packages("RCurl")
that will solve your problem.