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?)
Related
I've deployed a Shiny app on shinyapps.io that executes code that is inserted within the app. For example, if you insert the following code within the app:
1 + 2
The Shiny app returns:
3
This works fine as long as all the packages used in the inserted code have been specified already during the deployment process of the app.
However, if an unknown package is used within the inserted code, the Shiny app doesn't work anymore. For example, the following input returns an error message:
install.packages("Hmisc")
1 + 2
Output:
'lib = ".../lib/R/library"' is not writable
Warning in install.packages("Hmisc") :
Warning: Error in install.packages: unable to install packages
This could be solved by specifying all required packages (i.e. "Hmisc") during the deployment of the app. However, since I don't know all the required packages before the deployment of the app, I need to find a way to install and load packages AFTER the deployment. How could I do that?
As per my above comment: we need to add a writable libPath on app or session start.
This can be done by placing the following line of code in the global (app start) or server part (session start) of the app:
.libPaths(c(tempdir(), .libPaths()))
PS: tempdir() can be replaced with any other writable directory and a repository should be provided to install.packages' repos parameter as the R session isn't interactive().
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.
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'm using Resharper inspect CLI tool for static code analysis(JetBrains.ReSharper.CommandLineTools.2018.3.1\InspectCode.exe) on a dotnet core 2.1 console application I've created. Within the solution, there is a separate project which is just a package used in the console app.
Layout is as follows:
When I run the inspectCode.exe as follows:
JetBrains.ReSharper.CommandLineTools.2018.3.1\InspectCode.exe "AI.DL.Backup\AI.DL.Backup.csproj" /o:"CodeInspection_20222.xml" /profile:"AI.DL.Backup.sln.DotSettings"
I get the following issue:
Output xml report has the following:
<IssueType WikiUrl="https://www.jetbrains.com/resharperplatform/help?Keyword=RedundantNameQualifier" Severity="WARNING" Description="Redundant name qualifier" CategoryId="CodeRedundancy" Category="Redundancies in Code" Id="RedundantNameQualifier"/>
<Issue Message="Qualifier is redundant" Line="5" Offset="146-154" File="AI.DL.Backup\src\AI.DL.Backup\Startup.cs" TypeId="RedundantNameQualifier"/>
The problem seems to be that it cannot find the dll project referenced and is throwing code analysis error (code HAS been built already, so bin/obj folders exist with relevant dlls/packages required).
Ling 5 (as specified) is just the using statement for the separate package, which it cannot resolve and is deeming to be redundant.
using AI.DL.DocumentManagement;
using AI.DL.DocumentManagement.Stores;
Going by the generated XML report, I can see that it can't find the namespace within the separate package. Why would this be? Anyone seen this before?
I was able to work around this issue when I repointed the "inspect.exe" to my solution file instead of individual project!
Hi I'm having a million problems trying to publish my app to shiny.io.
Firstly, I have Rtools 3.2 installed in my computer and set to the Path, but it is not recognized in the registry. Nevermind, this code should fix it:
install.packages("installr")
library(installr)
install.Rtools(choose_version = FALSE, check = TRUE, use_GUI = TRUE,
page_with_download_url = "http://cran.r-project.org/bin/windows/Rtools/, keep_install_file=TRUE")
install.packages("devtools")
library(devtools)
devtools::install_github('rstudio/shinyapps')
Next, to deploy my app to my shiny.io account:
library(shinyapps)
shinyapps::setAccountInfo(name='xxxx', token='xxxxxxxxxx', secret='xxxxxxxx')
Then my app starts running in a browser, and I click publish to my shiny account. However, when the app is being deployed, it shows the following error:
Preparing to deploy application...Error: /v1/applications/ 400 - Validation Error
Execution halted
Any ideas what the problems may be? Thank you.
I had the same error returned. In my case the problem was the name of the app itself. Deployed apps must have names at least 4 characters long with no spaces.
Setting an application name solved this problem for me. My application directory contained a space.
deployApp(appName = "myapp")
I had the same problem, however, my app name was fine and even adding 'appName =' did not help. Just a side note that this issue came up because I changed the name of my folder in effort to change the name of my app in shinyapp.io
The only thing that worked for me is publishing through the "Publish" button of Rstudio on upper right. I would recommend publishing using that instead of command. You can select files you do not want to publish within the App folder and you can publish the app under a different name then your local name.
I also had similar errors and the issue was resolved after I changed the name of the directory that holds the "app.R" file from only 3 characters to more than 4 characters.