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.
Related
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.
I'm trying to install a package called "DiabetesTxPath-master" from local files.(The file can be downloaded in https://github.com/rohit43/DiabetesTxPath)
I used the code below installing it.
'filename<-"DiabetesTxPath-master.zip"'
install.packages(filename,type="binary",repos=NULL)
but when I try to load the packaged by the code below,
library(DiabetesTxPath)
error comes up.
there is no package called ‘DiabetesTxPath-master'
There is no problem in location.
.libPaths()
[1] "C:/Program Files/R/R-3.4.2/library"'
and this is where I want my package to be installed.
(and I see my packaged installed in the folder with my eyes!)
2.I've also tried to run as an administrator. it didn't work either.
So what could be the probelm, and how could I fix this?
Any comment would be appreciated so much.
I've been trying it so hard for a week.
Try using
library(devtools)
install_github("rohit43/DiabetesTxPath")
the problem arises because the dependencies for this package
ERROR: dependencies 'FeatureExtraction', 'CohortMethod',
'OhdsiSharing' are not available for package 'DiabetesTxPath'
are not available for this package in R 3.5 and above .
Now you need to install older version of R where these dependencies were supported and try using the above method.
I am trying to build my first R package (GitHub link). It is currently passing all local checks with devtools::check(), but failing on Travis:
ERROR: dependency ‘Rmpfr’ is not available for package ‘streamDepletr’
Looking at the Installed package versions section of the travis-ci output, Rmpfr is not listed. However, my DESCRIPTION file includes it as an import:
Imports:
Rmpfr,
dplyr,
magrittr
and Rmpfr is available on CRAN; my question is, how do I get travis-ci to install it?
The solution may be related to this previous question where the author had to include Java in their .travis.yml file. For Rmpfr, it looks like the MPFR C library is necessary. Is there a way to instruct travis to install this library in my .travis.yml file? Or am I barking up the wrong tree?
As you found out, you need the libmpfr-dev package to be installed. You can do this by adding
addons:
apt:
packages:
- libmpfr-dev
to your .travis.yml. See the documentation for reference.
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)
I am creating an R package on GitHub, LW1949, that depends on another R package on GitHub, jvamisc. When I try to install LW1949 using
require(devtools)
devtools::install_github("user/LW1949")
I get the message: Skipping 1 packages not available: jvamisc.
How can I point the import(jvamisc) part of the LW1949 package (in NAMESPACE) to Github instead of CRAN to find this dependency?
Surely this question has been asked and answered before, but I was not successful searching for it (perhaps because the search terms are so common - R, package, GitHub, etc.). I did stumble across Travis CI and Packrat, neither of which I've used. No idea if they would help. I would prefer as simple a fix as possible. (Wouldn't we all?)
I'm using R version 3.1.3 for Windows in R Studio Version 0.98.1103.
This question seems to have been answered quite recently, addressed in this issue of the devtools' github repository.
Package developer POV:
do:
usethis::use_package("jvamisc")
devtools::document()
to add the dependency in the Imports field of your DESCRIPTION file.
manually add a field "Remotes:" in the DESCRIPTION file, specifying where on github R should look for the package:
#in DESCRIPTION
Imports: ...,
jvamisc,
...
Remotes: JVAdams/jvamisc
End-user POV:
the end user has to have the latest development version of devtools (or at least the one corresponding to commit #f21ca3516c). You have to somehow 'force him' to update his devtools version (I guess just put this in the installation instructions... Can't think of a better way)
devtools::install_github(“hadley/devtools”, ref = “f21ca3516c”)
Restart the R Session on unload/reload the devtools package.
do the usual install_github:
require(devtools)
devtools::install_github("user/LW1949")
I guess this functionality will be added sooner or later to the CRAN version of devtools, so there will be no need for the user to fetch the dev version and he would go directly to step 3).
The steps and additional options are detailed in this vignette.
The actual solution seems to add in your DESCRIPTION file the line
Remotes: hadley/testthat
see the documentation of devtools :
# Git
Remotes: git::https://github.com/hadley/ggplot2.git
# Bitbucket
Remotes: bitbucket::sulab/mygene.r#default, dannavarro/lsr-package
# Bioconductor
Remotes: bioc::3.3/SummarizedExperiment#117513, bioc::release/Biobase
# SVN
Remotes: svn::https://github.com/hadley/stringr
# URL
Remotes: url::https://github.com/hadley/stringr/archive/master.zip
# Local
Remotes: local::/pkgs/testthat
# Gitorious
Remotes: gitorious::r-mpc-package/r-mpc-package