I am trying to use Travis CI with an R package (specifically this in-development package here).
When I update a repository, I get the following message (see the logs here):
Error: processing vignette 'comparing-mclust-and-mplus-output.Rmd' failed with diagnostics:
'roxygen2' >= 5.0.0 must be installed for this functionality.
Execution halted
This is consistent across two different packages--although the version of roxygen2 that I have is 6.0.1. I haven't been able to find others with this particular issue on either Stack Overflow or the roxygen2 GitHub page. I used usethis::use_travis() to set up the package for use with Travis (i.e., add travis.yml file.
Any ideas about how to address this?
So I believe the problem you have is with your DESCRIPTION file. Travis will install all package dependencies before trying to build the package / vignettes, so the version you have installed locally is of no consequence.
Rather, you need to be sure that roxygen2 is a dependency of your package (probably only needed in Suggests if it is necessary to build but not use your package). So adding:
Suggests:
roxygen2
To your DESCRIPTION file should fix the issue!
Related
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 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.
The latest version of a package that my package Imports introduced a breaking change (I think it may be a bug and have filed an issue about it). When I specify the specific version of the package needed in my package's DESCRIPTION file, i.e.:
Imports:
packageName (== 0.1)
Then the package builds locally fine and passes all tests. However, the package does not pass the Travis-CI build; the following error is returned:
Package required and available but unsuitable version(packageName)
Does this error suggest that the package will not pass CRAN's checks? How can I address it? The source for the package is here.
I am developing an R package for which I wrote some test files using R package testthatand placed the files under tests folder. I ran R CMD build on a Linux machine with R version 3.0.0. The command failed because testthat package requires R version at least 3.1.0.
Two following things I can do, but I am not sure which is better.
I can remove whole things in tests folder, so that my R package will also work for R version less than 3.1.0. As I notice, test files are not required for building an R package. Those are only useful for the developer.
I can keep all test files, but explicitly mention Depends: R (>= 3.1.0) in the DESCRIPTION file. The downside is that: (1) the package will be available to less users; and (2) more important, it depends on testthat package. Whatever updates there might affect my package potentially.
Which one do you think is better?
[update]
I followed the suggestion from # hrbrmstr, which is, I first built the package using R 3.1.0, and then check it on a Linux machine with R 3.0.0. But I still failed. The log is as follows.
* checking package namespace information ... OK
* checking package dependencies ... ERROR
Package suggested but not available: ‘testthat’
The suggested packages are required for a complete check.
Checking can be attempted without them by setting the environment
variable _R_CHECK_FORCE_SUGGESTS_ to a false value.
Any ideas to fix this issue?Or should I take approach 1 or 2 as stated above?
I was trying to install RTextTools package for R, but failed. Here is the output from the screen
> > install.packages("RTextTools")
Warning in install.packages("RTextTools") :
argument 'lib' is missing: using 'C:\Users\datamining\Documents/R/win-library/2.10'
--- Please select a CRAN mirror for use in this session ---
Warning: unable to access index for repository http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/2.10
Warning message:
In getDependencies(pkgs, dependencies, available, lib) :
package ‘RTextTools’ is not available
What's the reason for this problem, and how to fix it? Thanks.
There are two distinct, but related, issues:
You are running version 2.10 of R which is two years old. CRAN supports only the current version with pre-built binaries. You could try installing from source.
RTextTools, as can be seen on its CRAN page also requires at least R version 2.13.
So in short: you should upgrade.
I have resolved the issue. I have Download RTextTools From Given Link.
https://cran.r-project.org/src/contrib/Archive/RTextTools/
and copy RTextTools_1.4.2.tar.gz file in project root folder then run this command in project folder in terminal
"R CMD INSTALL RTextTools_1.4.2.tar.gz"
After running this command I receive below error
"ERROR: dependencies ‘SparseM’, ‘randomForest’, ‘tree’, ‘e1071’, ‘ipred’, ‘caTools’, ‘maxent’, ‘glmnet’, ‘tau’ are not available for package ‘RTextTools’".
Now install each dependencies from RStudio or RConsole (Any Editor used by you) by simply running this code.
install.packages("caTools").
Install all 9 required packages One By One (In My Case it was 9 Packages Dependencies required by RTextTools) all packages will be installed except 'maxent'.
Now download maxent from the given link.
https://cran.r-project.org/src/contrib/Archive/maxent/.
and copy maxent_1.3.3.1.tar file in project folder then run this command in project folder in terminal.
"R CMD INSTALL maxent_1.3.3.1.tar"
Now For RTextTools Run this command again in Terminal.
"R CMD INSTALL RTextTools_1.4.2.tar.gz"
All is done Now..
But the Last Step is
Load the RTextTools using.
library(RTextTools)
You will see one more Error: Load SparseM Now Loading SparseM use code below.
library(SparseM)
and in the last Load RTextTools
library(RTextTools)
RTextTools is dependent on a number of packages, most of which require R 2.13+. You should always keep R updated to the latest version, since each update contains numerous bug fixes and performance enhancements.
If you can't install packages from repository or the packages are not available anymore, just follow this steps:
Install.packages("devtools")
check -- library("devtools")
install_github("cran/maxent")
install_github("cran/RTextTools")