Scenario:
Warning: <PACKAGE-A> does not have <PACKAGE-B> in its dependencies:
...
Loading <PACKAGE-B> into <PACKAGE-A> from project dependency, futuree warnings for <PACKAGE-A> are suppressed.
After adding <PACKAGE-B> into dependencies section of Project.toml of <PACKAGE-A>, throws another missing dependency warning and suppresses further missing dependencies.
Please guide me in disabling the suppression of warnings to get fine/granular logs for better debugging.
Related
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")
I have a github clone of the glue R package for reasons. The name of this package is changed into glue.1.3.1 in this repository from its DESCRIPTION file for similar reasons. As a control group, I have an identical repository but this one's name is not changed in any way
If I do
devtools::install_github('oganm/glue.1.3.1')
the installation will fail
Error: package or namespace load failed for ‘glue.1.3.1’ in library.dynam(lib, package, package.lib):
shared object ‘glue.so’ not found
Error: loading failed
Execution halted
If I do
devtools::install_github('oganm/glue)
the installation will be successful.
If I do the same thing to most other packages, there are no problems but it seems like the source code of pacakges that need compilation, the change in the package name causes problems. For instance, you can repeat the issue with dplyr here
The question is, what causes this issue? What do I need to do so that I can reliably change names of packages that require compilation?
This might be a rather general question: How to deal with incompatible packages in meteor?
In my case I'm using the testing suite velocity and jasmine, which is not compatible with the current version of autoform-file package.
My html-reporter would just continue executing the test without actually getting the result due to the following error:
Errors prevented startup:
While selecting package versions:
error: Potentially incompatible change required to top-level dependency: yogiben:autoform-file 0.3.0, was 0.4.2.
Constraints on package "yogiben:autoform-file":
To allow potentially incompatible changes to top-level dependencies, you must pass --allow-incompatible-update on the command line.
Your application has errors. Waiting for file change.
I was thinking of downgrading the autoform-file package to 0.3.0 however, I didn't find any information on how to do it.
I was able to install the package at a specific version using:
meteor add yogiben:autoform-file#=0.3.0
That worked for me.
I try to install scale in R by:
devtools::install_github("scale",username="hadley/scale")
But
Downloading github repo hadley/scale/scale#master
Error in download(dest, src, auth) : client error: (404) Not Found
In addition: Warning message:
Username parameter is deprecated. Please use hadley/scale/scale
The general syntax of install_github function is:
install_github(repo)
where repo is in the format username/repository
The syntax of both username and repository should be checked, to avoid the message
Error in download(dest, src, auth) : client error: (404) Not Found
It is also a good practice to compare versions available on both GitHub and CRAN. In the case of identical versions available, the simplest would be:
install.packages(pkg, dependencies = TRUE)
where dependencies argument ensures the installation of all packages which pkg depends on/links to/imports/suggests.
During installing rJava package, I got the following error messages:
checking JNI data types... configure: error: One or more JNI types differ from the corresponding native type. You may need to use non-standard compiler flags or a different compiler in order to fix this.
ERROR: configuration failed for package ‘rJava’
May I know what is the cause for this failure and how to fix this issue? Thanks.
If it installed but does not work try first : remove.package("rJava") and the install.package("rJava"). Some times helps. If still ahvgin problem post more data. But unless it's not necessary.
EDIT : see also java path if it's correctly set up. Sometimes its messed up.