I am trying to publish a shiny app, but getting the following error. My code is working fine in Rstudio though. Only get this error when I try to publish it.
install.packages("BiocManager")
BiocManager::install("Rgraphviz")
Error: Unhandled Exception: Child Task 1195199124 failed: Error parsing manifest: Unable to determine package source for Bioconductor package BiocGenerics: Repository must be specified
Execution halted
How can I solve this problem? How to specify a repository? TIA
Before publishing your app, run options(repos = BiocManager::repositories()) on your console. Do NOT copy this code to your app scripts. Then, publish your app. No need of install.packages("BiocManager") or BiocManager::install("Rgraphviz")
Related
I've been trying to install the Sleuth package in R all morning and it keeps giving me errors. This is how I tried to install it:
if(!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("DESeq2")
BiocManager::install ("rhdf5")
install.packages("devtools")
devtools:: install_github("pachterlab/sleuth")
I did use the library() command.
I get the following error messages:
Error: object 'h5write.default' is not exported by 'namespace:rhdf5'
Execution halted
ERROR: lazy loading failed for package 'sleuth'
removing 'C:/Users/31625/OneDrive/Documents/R/win-library/4.1/sleuth'
I was having the same issue and found that there's current an open issue on Github discussing this problem.
Currently there is a workaround which was shared in the same issue on Github:
Run git clone https://github.com/pachterlab/sleuth
Remove the last line in ./sleuth/NAMESPACE which is the h5write.default that raises the error during installation - ignore the warning in the first line
Then in R: devtools::install('./sleuth/')
It worked for me while using Linux - ZorinOS and R 4.1.2 but it should work on Windows as well.
Someone also opened a PR to fix the whole issue but it seems they are not updating the package anymore (unfortunately).
I used shiny output in rmarkdown to create an interactive document and was able to see local html file but when trying to publish it to shinyapps.io, I get an error message:
Error: An error has occurred. Check your logs or contact the app author for clarification.
I checked the logs in the shinyapps.io, I see the following error:
Warning: there is no package called "tidyverse"
Please help me with resolving this issue so that I can create an interactive document with shiny+rmarkdown
Thanks,
Venkat
I am trying to deploy a shiny app onto shinyapps.io but I get the following output in Deploy tab:
Error: package or namespace load failed for �shiny�:
.onLoad failed in loadNamespace() for 'shiny', details:
call: .Call("_httpuv_getRNGState", PACKAGE = "httpuv")
error: "_httpuv_getRNGState" not available for .Call() for package "httpuv"
Error: loading failed
Execution halted
The app I am trying to deploy is the template/draft app you get when you start a new shiny web app file from RStudio. At first I thought the cause of the error might be something in my original apps that I tried to upload.
Would anyone be able to assist in fixing or at least explaining what might be causing the error.
I don't have enough reputation points to just leave a comment, but if you search Google for your error lots of information comes up (i.e. here or here). It appears to be either an error with the install of httpuv or one of the packages it is linked to (such as Rcpp or later), so update those packages and see if that works.
I am not able to install packages in R console in dashDB from IBM Bluemix. I am executing the below line:
install.packages('tm')
I am getting this error:
Installing package into ‘/usr/lib64/R/library’ (as ‘lib’ is unspecified)
Warning in install.packages("tm") :
'lib = "/usr/lib64/R/library"' is not writable
Error in install.packages("tm") : unable to install packages
Execution halted
mv: cannot stat `/mnt/blumeta0/home/<userID>//<...>/<...>/output/*': No such file or directory
I have also tried giving the library parameters like this:
install.packages('tm', lib='/mnt/blumeta0/home/<userID>/R/x86_64-redhat-linux-gnu-library/3.2/lib')
I get this error:
Warning in install.packages("tm", lib = "/mnt/blumeta0/home/<userID>/R/x86_64-redhat-linux-gnu-library/3.2/lib/"):
'lib = "/mnt/blumeta0/home/<userID>/R/x86_64-redhat-linux-gnu-library/3.2/lib/"' is not writable.
Execution halted
mv: cannot stat `/mnt/blumeta0/home/dash107933//.3hwv1S2IEeq813rI935Gurz/1467874427867/output/*': No such file or directory
What could be the issue here? Do I have to do any other configuration changes before I try to install the packages? I have also tried to use .libPaths() function to set the library to above mentioned path.
The packages are getting installed properly in RStudio interface though.
Could you please help? Thanks!
PS: The keyinfo and UserIDs are removed in above statements.
I have installed packages using the 'Install Packages' menu item from the Tools Menu. Did you try that ?
See this picture for the menu location. Bluemix R Studio Web Interface
I'm trying to deploy an application on shinyapps.io using rattle for decision tree visualisation. Deploying on shinyapps server fails showing this:
Error: Unhandled Exception: Child Task ######### failed: Error building image: Error building RGtk2 (2.20.31). Build exited with non-zero status: 1
Does anyone have a solution for installing RGtk2 on shinyapps?
Well, it seems to be impossible.
The only solution i found was to use prp library which seems to be a good alternative.