I am trying to deploy an app to Shiny.io with a new package via rsconnect::deployApp() that I have developed locally and not hosted on CRAN. My question is similar to this one but I cannot solve using the same recommendation.
My package is installed on a private github repository and my shinyapps.io account settings have access to this private repo. My app depends on packages both on CRAN and now also this new one I have developed.
Could use a bit of direction on how to solve this.
Thanks
Uploading bundle for application: 5447651...Warning:
* May be unable to deploy package dependency 'Mycpp'; could not determine a repository URL for the source 'CRAN'.
* Unable to determine the source location for some packages. Packages should be installed from a package repository like CRAN
or a version control system. Check that options('repos') refers to a package repository containing the needed package
versions.
DONE
Deploying bundle: 6849209 for application: 5447651 ...
Waiting for task: 1273530594
building: Processing bundle: 6849209
building: Parsing manifest
building: Building image: 8100493
building: Fetching packages
building: Building package: Mycpp
################################ Begin Task Log ################################
################################# End Task Log #################################
Error: Unhandled Exception: Child Task 1273530595 failed: Error building image: Error fetching Mycpp (1.0) source. <CRANPackageSource repo='http://cran.rstudio.org'> unable to satisfy package: Mycpp (1.0)
In addition: Warning message:
In FUN(X[[i]], ...) :
Package 'Mycpp 1.0' was installed from sources; Packrat will assume this package is available from a CRAN-like repository during future restores
Related
Hi I'm trying to deploy an app on the server, however, I get the following errors
* May be unable to deploy package dependency "rClr" could not
determine a repository URL for the source CRAN.
* May be unable to deploy package dependency "tlf" could not determine
a repository URL for the source CRAN.
Unable to determine the source location for some packages. Packages
should be installed from a package repository like CRAN or a version
control system. Check that options(repos) refers to a package
repository containing the needed package versions.
The backbone packages can not be installed from Cran and have to be done manually, hence the errors. How can this be fixed in order to deploy the app on the server?
Thanks for all help
I am trying to publish shiny app. It keeps giving me this output:
Preparing to deploy application...DONE
Uploading bundle for application: 5894015...Warning:
* May be unable to deploy package dependency 'AnnotationDbi'; could
not determine a repository URL for the source 'Bioconductor'.
* May be unable to deploy package dependency 'AnnotationFilter'; could
not determine a repository URL for the source 'Bioconductor'.
* May be unable to deploy package dependency 'AnnotationHub'; could
not determine a repository URL for the source 'Bioconductor'.
* May be unable to deploy package dependency 'Biobase'; could not
determine a repository URL for the source 'Bioconductor'.
* May be unable to deploy package dependency 'BiocFileCache'; could
not determine a repository URL for the source 'Bioconductor'.
* May be unable to deploy package dependency 'BiocGenerics'; could not
determine a repository URL for the source 'Bioconductor'.
* May be unable to deploy package dependency 'BiocIO'; could not
determine a repository URL for the source 'Bioconductor'.
* May be unable to deploy package dependency 'BiocParallel'; could not
[... truncated]
Error:
* Application depends on package "rlang" but it is not installed.
Please resolve before continuing.
Execution halted
rlang is installed and I did library(rlang) but that didn't help. rlang version is 1.0.2, is it a version issue? everything is working fine, but it's not deploying for some reason.
The packages I am loading at the start of the shiny app are:
library(rlang)
library(data.table)
library(dplyr)
library(shiny)
library(shinythemes)
library(compGenomRData)
library(BiocManager)
library(DESeq2)
library(org.Hs.eg.db)
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
library(EnsDb.Hsapiens.v86)
library(AnnotationHub)
library(AnnotationDbi)
library(pheatmap)
library(EnhancedVolcano)
library(ggplot2)
library(devtools)
library(clusterProfiler)
library(enrichplot)
library(msigdbr)
library(readxl)
library(annotate)
I need all of them for my server function.
what is the problem here ?
EDIT-
I tried uninstallng rlang library with remove.packages('rlang'), gave me this output:
Error in remove.packages : there is no package called 'rlang'
How is this even possible ?
So here is the error i am getting from the console. I understand that hydromad package is not on cran but I have added it as secondary repos in packages(Tools options in R studio) and in .R profile file. Still I am getting this error
****Preparing to deploy application...DONE
Uploading bundle for application: 2120925...DONE
Deploying bundle: 3058356 for application: 2120925 ...
Waiting for task: 720810692
building: Parsing manifest
building: Building image: 3408182
building: Installing system dependencies
building: Fetching packages
error: Building package: hydromad
########################## Begin Task Log ################################
[2020-04-24T06:51:09.225825780+0000] Execute script: packages/build/sys.sh
+ set -e
+ apt-get update -qq
+ apt-get install -y libapparmor-dev
Reading package lists...
Building dependency tree...
Reading state information...
The following NEW packages will be installed:
libapparmor-dev
0 upgraded, 1 newly installed, 0 to remove and 114 not upgraded.
Need to get 67.8 kB of archives.
After this operation, 229 kB of additional disk space will be used.
Get:1 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libapparmor-dev amd64 2.10.95-0ubuntu2.11 [67.8 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 67.8 kB in 0s (0 B/s)
Selecting previously unselected package libapparmor-dev:amd64.
(Reading database ... 119718 files and directories currently installed.)
Preparing to unpack .../libapparmor-dev_2.10.95-0ubuntu2.11_amd64.deb ...
Unpacking libapparmor-dev:amd64 (2.10.95-0ubuntu2.11) ...
Processing triggers for man-db (2.7.5-1) ...
Setting up libapparmor-dev:amd64 (2.10.95-0ubuntu2.11) ...
########################### End Task Log #################################
Error: Unhandled Exception: Child Task 720810693 failed: Error building image: Error fetching hydromad (0.9-26) source. <CRANPackageSource repo='http://cran.rstudio.org'> unable to satisfy package: hydromad (0.9-26)
In addition: Warning message:
In FUN(X[[i]], ...) :
Package 'hydromad 0.9-26' was installed from sources; Packrat will assume this package is available from a CRAN-like repository during future restores
Execution halted****
Can anyone help me resolve this error? Will be grateful
Welcome to StackOverflow! Your question is quite specific, so I would recommend to use a more specialized resource. The good news is that package hydromad has its own forum
I was playing with dotnet cli to create f# project. I ran the following command to install NewtonSoft.Json NuGet Package.
$>dotnet add src/Library/Library.fsproj package Newtonsoft.Json
the output is
Writing C:\Users\MyUserName\AppData\Local\Temp\tmp440E.tmp
info : Adding PackageReference for package 'Newtonsoft.Json' into project 'src/Library/Library.fsproj'.
info : Restoring packages for c:\Learning\Projects\FSNetCore\FSNetCore\src\Library\Library.fsproj...
info : GET https://api.nuget.org/v3-flatcontainer/newtonsoft.json/index.json
info : OK https://api.nuget.org/v3-flatcontainer/newtonsoft.json/index.json 288ms
error: Unable to load the service index for source https://MyEmployer.pkgs.visualstudio.com/_packaging/NuGetServerName/nuget/v3/index.json.
error: Response status code does not indicate success: 401 (Unauthorized).
I am wondering why this operation has failed due to 401 response from a irrelevant package source which is a private azure artifacts pointed by user-level scoped Nuget.Config file.
$>dotnet nuget --version
NuGet Command Line
5.2.0.3
Package can be installed successfully to projecy by specifying Source and version explicitly
$> dotnet add src/Library/Library.fsproj package Newtonsoft.Json --source https://api.nuget.org/v3-flatcontainer/newtonsoft.json/index.json --version 12.0.2
Writing C:\Users\MyUserName\AppData\Local\Temp\tmp8A3B.tmp
info : Adding PackageReference for package 'Newtonsoft.Json' into project 'src/Library/Library.fsproj'.
info : Restoring packages for c:\Learning\Projects\FSNetCore\FSNetCore\src\Library\Library.fsproj...
info : Package 'Newtonsoft.Json' is compatible with all the specified frameworks in project 'src/Library/Library.fsproj'.
info : PackageReference for package 'Newtonsoft.Json' version '12.0.2' added to file 'c:\Learning\Projects\FSNetCore\FSNetCore\src\Library\Library.fsproj'.
info : Committing restore...
info : Writing assets file to disk. Path: c:\Learning\Projects\FSNetCore\FSNetCore\src\Library\obj\project.assets.json
log : Restore completed in 193.98 ms for c:\Learning\Projects\FSNetCore\FSNetCore\src\Library\Library.fsproj.
Why dotnet cli tried to load the service index from irrelevant package source ?
I want to deploy an application on R shiny on the web, but I get this error
Preparing to deploy application...DONE
Uploading bundle for application: 63131...Error:
* Unable to deploy package dependency 'CellMix'
The package was installed locally from source. Only packages
installed from CRAN, BioConductor and GitHub are supported. Execution
halted
Is there a work around to run the application and deploy on the web.