devtools package introduces a nice concept of adding dependancies not available in CRAN, into DESCRIPTION file (described in the vignette). However, I have not been able to figure out how to get it to install the dependancies automatically. The vignette linked above certainly hints that is possible and the install command certainly parses for the "remote" (got an error when they were not specified correctly), however, it only installed dependancies from CRAN. Anybody has ideas if there are some parameters I should specify to make the installation automatic?
Thusfar, I have tried install, install_bitbucket and install_local. install managed to download all the dependancies available in CRAN. install_bitbucket did the same and install_local just did not work at all.
The Remotes: field is used to tell devtools where to look for the packages that are listed in the standard Depends:, Imports: and Suggests:.
So make sure that you have the package listed in the appropriate standard field, and its source listed in Remotes. Then running the following should install these packages from the Remotes source:
devtools::install_deps()
Related
I want to use the R package BOLTSSIRR available on GitHub in my R package, which I want to upload to CRAN.
I listed BOLTSSIRR under Suggests: in the DESCRIPTION file and made the link to GitHub available using Additional_repositories: https://github.com/daviddaigithub/BOLTSSIRR.
However, running R CMD check --as-cran I get:
Suggests or Enhances not in mainstream repositories:
BOLTSSIRR
Availability using Additional_repositories specification:
BOLTSSIRR no ?
? ? https://github.com/daviddaigithub/BOLTSSIRR
Additional repositories with no packages:
https://github.com/daviddaigithub/BOLTSSIRR
So the GitHub link does not seem to get recognized in the check. Might I have to change something here?
As you found, you can't use Remotes in a CRAN package. What you need to do is to make sure the .tar.gz file for the package you are depending on is available somewhere. Github doesn't do that automatically, because https://github.com/daviddaigithub/BOLTSSIRR isn't set up as a package repository.
The solution is to create your own small repository, and keep copies of non-CRAN packages there. The drat package (available here: https://github.com/eddelbuettel/drat) makes this easy as long as you have a Github account: follow the instructions here: https://github.com/drat-base/drat. In summary:
Fork https://github.com/drat-base/drat into your account, and clone it to your own computer.
Enable Github Pages with the docs/ folder in the main branch.
Install the drat package into R using remotes::install_github("eddelbuettel/drat"). (I assume this version will make it to CRAN eventually; if you use the current CRAN version instructions are slightly more complicated.)
Build the package you want to insert. You need the source version; you might want binaries too, if those are hard for your users to build.
Run options(dratBranch="docs"); drat::insertPackage(...) to insert those files into your repository.
Commit the changes, and push them to Github.
In the package that needs to use this non-CRAN package, add
Additional_repositories: https://yourname.github.io/drat
to the DESCRIPTION.
You will be responsible for updating your repository if BOLTSSIRR is updated. This is good because the updates might break yours: after all, it's still in development mode. It's also bad because your users won't automatically get bug fixes.
That's it, if I haven't missed anything!
I'm developing an R package in Github (ConceptionTools) that depends on another R package (CreateFlowChart), also in Github. I have followed the instructions for defining remote dependencies. My DESCRIPTION file includes:
Imports: CreateFlowChart
Remotes: github::IMI-ConcePTION/CreateFlowChart
However, when I install my package, with the command:
devtools::install_github("IMI-ConcePTION/ConceptionTools")
This dependency is not installed. I simply get "skipping 1 packages not available: CreateFlowChart". It doesn't appear to be trying to use the Remote, since there is no error related to Github.
When I install the dependency directly, that works:
devtools::install_github("IMI-ConcePTION/CreateFlowChart")
Does anybody have any idea of what could be going on here? I'm racking my brain, as it seems to be a quite straightforward case of what the documentation shows. I'm using R 4.0.3 (on Windows 10) and devtools 2.3.2.
There was a typo in the name of the dependency package in its DESCRIPTION file.
This does not make the package fail when installing it directly, but it leads devtools not to find it as a dependency.
I am creating my first package, which shall be installed through Github. I thought that Rtools was needed only for the person creating it. However, people that tried to install it using Github were asked to update Rtools. Is this really necessary?
Doing some research, I found this: https://community.rstudio.com/t/missing-rtools-should-i-be-worried/27817
One of the answers says the following:
"This means that if you are going to install packages that need
compilation, you also have to install Rtools in your system. "
This is the repo with the package: https://github.com/datazoompuc/PNAD_Covid/tree/master/R/datazoom_pnad_covid
What does this actually mean? How do I know that my package needs compilation?
I thought that Rtools was needed only for the person creating it.
Yes, if and only if you distribute it as a binary. Then the creator uses Rtools to compile and link, and the user just installs, and enjoys.
That is how CRAN works as CRAN compiles for Windows users.
GitHub, however, is foremost a source repository so the installation from GitHub is using a source mode ... and every user will need to compile, and hence have Rtools. (Unless the package and all its depedencies are R-code only.)
You can also have a package repository on GitHub using e.g. the drat package to create it, but that is getting us a little further from the original question.
Your package "needs compilation" — i.e. needs Rtools to install from source (on Windows) — if it contains C or Fortran components, i.e. if you have anything in the src/ directory of your package ...
If you, the package author, don't know if you have C or Fortran code as part of your package, then you almost certainly don't.
It's quite possible that devtools is being overzealous, i.e. detecting that users have a not-most-current Rtools and suggesting (requiring??) that they update it, even though it's not needed for this installation.
I was trying to use actions in a package I wrote. The issue is that the package actions uses remotes in its setup to install CRAN only packages.
Since the package I am working on depends on a non CRAN package that is present on GitHub, both coverage and R CMD checks fail. I tried to avoid this by naively downgrading to an earlier version of the package in depends but some functions are not exported. I am wondering if someone knows a workaround that might help(I cannot open an issue at actions since their support.md file discourages this).
If your package depends on a non-CRAN package, you must include under Remotes: rather than just Imports: in your DESCRIPTION file. Here you would have:
Imports:
actions
Remotes:
r-lib/actions
This will pass checks, but there is no work around for publishing to CRAN if any of your dependencies are not on CRAN, thus you'll get a warning if any packages are present in the Remotes field.
The alternative using Travis is adding r_github_packages: r-lib/actions to your .travis.yml.
After some time, I have found a workaround that for now is good enough if you want to test for the development version(like I wanted). You should include an install_github command in the check.yaml file. Here's an example:
- name: Install dependencies
run: |
install.packages(c("remotes","testthat"),dependencies=TRUE)
remotes::install_github("tidyverse/dplyr")
remotes::install_cran("covr")
shell: Rscript {0}
The above snippet fixed my issue because I wanted to depend on a future dplyr version. You can view the full yaml file here.
EDIT: see edit in end.
I have a R package in github and I'm using devtools::install_github to install it, which also install dependency packages.
Recently this process will install httpuv as source package, but compiling it in Mac meet errors with automake (something like this). I installed automake, then there was error with clang: error: unsupported option '-fopenmp'.
The issue and the possible solutions 1 2 seemed to be quite complicated. I think the CRAN version of httpuv probably will work for me, and I don't want my users to go through so many errors and fixing compiler errors.
I'd like to just install all dependency packages from CRAN in binary. For some packages that do need the more up to date version, I have specified it in my package description with remote section.
I checked install_github, then install, then install.packages. It seemed that the default behavior for binary vs source package is
An alternative (and the current default) is "both" which means ‘use
binary if available and current, otherwise try source’. The action if
there are source packages which are preferred but may contain code
which needs to be compiled is controlled by
getOption("install.packages.compile.from.source").
My getOption("install.packages.compile.from.source") is interactive. This is actually a preferred behavior for me. However I never see the interactive prompt.
I tried to give a type = "binary" parameter in install_github, but it doesn't seem to work, maybe it's not passed to every dependency package install?
EDIT:
I found the situation is a little bit more complex:
my app specified to install shiny github version via remote in description. shiny specified to install httpuv github version in remote section too. So this is actually the intended behavior.
I'm not sure if there is a solution available, other than require CRAN version of shiny in my package.
EDIT 2: It's more complex than my previous findings.
I removed remote section in my package description, supposedly only CRAN version is needed. However install_github still install most dependencies from github.
I finally found out that I have these dependencies github version installed, so their description in my local disk have the github remote information, and install_github found this information and "upgrade" them again, even when some of them have no change.
So I need to uninstall them first, only use CRAN version.
The really problem here is that if a dependency package is already new, it should not be installed. It could be a bug of devtools.
install_github passes arguments to devtools::install, and there upgrade_dependencies= FALSE and maybe even dependencies = FALSE might be what you're after:
install_github("you/urPackage", upgrade_dependencies = FALSE)