I have a utilities package foo, and have developed another package bar which calls functions in foo.
foo is available on a URL (not Github or any such service) as source files. I install/update it using
install.packages("//mywebsite.com/foo",
repos = NULL,
type = "source")
I now want to share bar with others. I've read the devtools page on dependencies and understand I merely have to add a Remotes section to my DESCRIPTION file.
However, the example for a URL-based remote dependency is:
# URL
Remotes: url::https://github.com/hadley/stringr/archive/master.zip
What concerns me here is that the example uses a .zip file, but the package foo is only available as a raw source directory.
Will this work? Can I simply use
Remotes: url:://mywebsite.com/foo
Or does this only work with zipped files?
I notice the following example, for local packages, does not have an extension (Remotes: local::/pkgs/testthat), which makes me hopeful it's representing a source directory and that therefore that'll also work for URLs, but am not sure.
It looks like remotes::install_url requires a .zip, .tar, or .tar.gz, and that's likely what would be called to install the dependency if you specify Remotes: url:://mywebsite.com/foo.
If your code is in a Git repo (even if not on GitHub/GitLab) you can refer directly to the repo. Or if it's on a network drive you can refer to it using local instead of url, since remotes::install_local can handle directories.
Related
I will let an R project run on a data center and the team working there has no access to the Internet, so they will have to download the R libraries from an internal repository (on their Intranet) where all the packages are hosted.
It is possible to change the repository from where the libraries are downloaded?
and how can we point to this repository if I will provide them with my renv.lock file?
Could be solved by doing this? :
repos <- c(CRAN = "https://cloud.r-project.org", WORK = "https://work.example.org")
options(repos = repos)
See here
Thanks a lot
It is possible to change the repository from where the libraries are downloaded?
Yes, and the example code you shared is correct: the active package repositories used in an R session are controlled via the repos option.
and how can we point to this repository if I will provide them with my renv.lock file?
If you're working within an renv project with an auto-loader, then renv will automatically set the repositories from the lockfile when R is started. Otherwise, you can call renv::load("/path/to/project") to explicitly load a project at some location.
I'd recommend reading https://rstudio.github.io/renv/articles/renv.html for more details.
I found myself in the situation where my private repos were set, but whenever I ran renv::init(), it wouldn't point to them. The simplest solution I could come up with from reading the renv docs:
Before calling renv::init(), call the function: Sys.getenv("RENV_CONFIG_REPOS_OVERRIDE").
If it returns anything other than the URL to your private package repository then call the function: Sys.setenv("RENV_CONFIG_REPOS_OVERRIDE" = "your_private_package_repository_url")
Call the function renv::init()
I want to be able to import or using a package that I'm writing in a directory ~/projects/ExamplePkg from my main Julia REPL / from another project or environment.
By ]foo I mean "use the foo command at the Julia Pkg REPL". Type ] at the Julia REPL to enter the Pkg REPL. Use ]help <command name> for more info or check the link below.
Ensure that your package has a Project.toml that gives it a UUID and names it (generate one with ]generate from the Julia REPL or with the PkgTemplates package) and that it is in a git repo with at least one commit including all the relevant files.
Then choose how you would like to use the package.
You probably want to run ]dev ~/projects/ExamplePkg:
If dev is used on a local path, that path to that package is recorded and used when loading that package. The path will be recorded relative to the project file, unless it is given as an absolute path.
If you use dev and you change the dependencies in the dev'd package, then you should probably run ]resolve in all environments that depend on the package.
Or you can run ]add ~/projects/ExamplePkg:
Instead of giving a URL of a git repo to add we could instead have given a local path to a git repo. This works similarly to adding a URL. The local repository will be tracked (at some branch) and updates from that local repo are pulled when packages are updated. Note that changes to files in the local package repository will not immediately be reflected when loading that package. The changes would have to be committed and the packages updated in order to pull in the changes.
In Julia versions <1.4: If you accidentally ]add a package before the git repo is set up correctly then you might get ERROR: GitError(Code:EUNBORNBRANCH, Class:Reference, reference 'refs/heads/master' not found). Unfortunately, Julia will probably have cached the bad repo, and you will need to remove that from ~/.julia/clones/<gibberish>/. You can find the dir to remove with grep: $ grep ExamplePkg ~/.julia/clones/*/config.
Documentation: https://julialang.github.io/Pkg.jl/v1/managing-packages/
you can try
path_to_package = "~/projects/ExamplePkg"
push!(LOAD_PATH,path_to_package)
# then use it, ExamplePkg is the package's name
using ExamplePkg
But you have to run codes above whenever you restart Julia.
reference is Workflow tips-Julia Documentation
My package is hosted in github, and user can install it through devtools::install_github.
Now I'm using pkgdown to generate documentation site, which created a 10M docs folder. Then I found devtools::install_github always download the whole master zip ball which become quite slow.
I tried to exclude the docs folder with these attempts:
.Rbuildignore, turned out it's only about bundled package, while install_github is installing source package so it doesn't work.
put package in pkg folder, put the generated docs folder out of pkg folder. However the whole master zip ball is always downloaded, even with subdir = "pkg" specified.
put development in a branch, and to create a special package branch without docs folder. Merge two branch but let package branch exclude docs folder. I tried make .gitignore to be branch specific but it doesn't seem to work. This seemed to be impossible.
My newest attempt is to create a separate repo solely for the website, just let pkgdown create the website in that folder like build_site(path = "../docsite/docs"). This should solve the problem and is simple and clean. The only imperfection is the website url will not be the usually pattern.
EDIT: with the latest version of pkgdown, there is no path parameter anymore, you need to specify it in the site configuration yaml, which works better (you don't need to specify it in every command).
I have been using git for a while but just recently started using packrat. I would like my repository to be self contained but at the same time I do not want to include CRAN packages as they are available. It seems once R is opened in a project with packrat it will try to use packages from project library; if they are not available then it will try to install from src in the project library; if they are not available it will look at libraries installed in that computer. If a library is not available in the computer; would it look at CRAN next?
What files should I include in my git repo as a minimum (e.g., packrat.lock)?
You can choose to set an external CRAN-like repository with the source tarballs of the packages and their versions that you'd like available for your project. The default behaviour, however, is to look to CRAN next, as you've identified in your question. Check out the packrat.lock file, you will see that for each package you use in packrat, there is an option called source: CRAN (if you've downloaded the file from CRAN, that is).
When you have a locally stored package source file, the contents of the lockout for said package change to the following:
Package: FooPackage
Source: source
Version: 0.4-4
Hash: 44foo4036fb68e9foo9027048d28
SourcePath: /Users/MyName/Documents/code/myrepo/RNetica
I'm a bit unclear on your final question: What files should I include in my git repo as a minimum (e.g., packrat.lock)? But I'm going to take this as a) combination of what files should be present for packrat to run, and b) which of those files should be committed to the git-repo. To answer the first question, I illustrate with initialising packrat on an existing R project.
When you run packrat::init(), two important things happen (among others):
1. All the packrat scaffolding, including source tarballs etc are created under: PackageName/packrat/.
2. packrat/lib*/ is added to your .gitignore file.
So from this, we can see that anything under packrat/lib*/ doesn't need to be committed to your git-repo. This leaves the following 3 files to be committed:
packrat/init.R
packrat/packrat.lock
packrat/packrat.opts
packrat.lock is needed for collaborating with others through a version control system; it helps keep your private libraries in sync. packrat.opts allows you to specify different project specific options for packrat. The file is automatically generated using get_opts and set_opts. Committing this file to the git-repo will ensure that any options you specify are maintained for all collaborators. A final file to be committed to the repo is .Rprofile. This file tells R to use the private package library (when R is started from the project directory).
Depending on your needs, you can choose to commit the source tar balls to the repository, or not. If you don't want them available in your git-repo, you simply add packrat/src/ to the .gitignore. But, this will mean that anyone accessing the git-repo will not have access to the package source code, and the files will be downloaded from CRAN, or from wherever the source line dictates within the packrat.lock file.
From your question, it sounds like committing the packrat/src/ folder contents to your repo might be what you need.
I'm at a loss as to how to install the RBloomberg package. The only source for the files seems to be GitHub. The offered zip file is called blpwrapper-master.zip which embeds an rbloomberg folder. When I try to install the zip file (in RStudio), I get an error message that it cannot open a compressed file. I rezipped just the rbloomberg folder, but that led nowhere either. How does one go about this?
In general things can be installed from Github using the devtools package. For example:
library("devtools")
install_github("username/packagename")
I don't know who authors so Rbloomberg, but you can swap in the appropriate Github username in the above.
Note: Sometimes this won't work because a developer uses a non-traditional .git directory structure, but it should work in most cases. Indeed, that is the case here (as #rawr points out), where you need to use a slightly different path to point to package (which is in a subdirectory of the git repo):
install_github("johnlaing/blpwrapper/rbloomberg")