I'm using knitr to build an R package vignette. This process worked before R 3.0, but I haven't been able to rebuild the package under R 3.1.1.
When I try R CMD build I get an error message:
R CMD build Causata
* checking for file ‘Causata/DESCRIPTION’ ... OK
* preparing ‘Causata’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ...
ERROR Error in loadVignetteBuilder(vigns$pkgdir) :
vignette builder 'knitr' not found Calls: <Anonymous> -> loadVignetteBuilder
In addition:
Warning message: In tools::buildVignettes(dir = ".", tangle = TRUE) :
Files named as vignettes but with no recognized vignette engine:
‘vignettes/Causata-vignette.rnw’ (Is a VignetteBuilder field missing?)
Execution halted
My vignette file has a VignetteEngine call -- here are the first three lines:
% !Rnw weave = knitr
%\VignetteEngine{knitr::knitr}
%\VignetteIndexEntry{Model training and export}
My package description file includes a VignetteBuilder field:
VignetteBuilder: knitr
I think I'm following the instructions for Rnw vignettes, so I'm baffled by the error message I'm seeing.
Incidentally, if I try to build the vignette directly then everything seems to work perfectly. This command generates the vignette PDF:
tools::buildVignettes(dir=".", tangle=TRUE)
My trouble seems to be only with R CMD build. Why won't the build work?
Here's my complete package DESCRIPTION file for reference:
Package: Causata
Type: Package
Title: Analysis utilities for binary classification and Causata users.
Version: 5.0-1
Date: 2014-10-09
Author: Justin Hemann, David Barker, Suzanne Weller, Jason McFall
Maintainer: Justin Hemann <justin.hemann#nice.com>
Description: The Causata package provides utilities for
extracting data from the Causata application, training regression / classification
models, and exporting models as PMML for scoring.
Depends: R (>= 2.15.1)
Imports: XML, R.utils, rjson, RCurl, stringr, yaml, boot, foreach, data.table, glmnet, ggplot2, methods
Suggests: knitr, doMC, testthat, pROC, RODBC, RMySQL
VignetteBuilder: knitr
License: GPL
LazyLoad: yes
URL: www.nice.com
According to the feedback of Josh O'Brien, I guess you might have the same issue as him. If you want to add some custom library paths, I'd recommend you to do it in ~/.Renviron using the environment variable R_LIBS_USER, instead of defining the library paths in ~/.Rprofile or Rprofile.site. The latter seems to be ignored by R CMD build and R CMD check.
Or you can add Sys.setenv(R_LIBS_USER="/my/r-package/dir/") to ~/.Rprofile.
Related
I coded an R package that is hosted on my GitHub. I included a vignette, and I can install the package and load the vignette without any issue from R and RStudio by doing:
devtools::install_github("rosalieb/serac", build_vignettes = TRUE)
library(serac)
vignette("serac")
However, I have a few colleagues who cannot install the vignette (the only way they can download the package is by doing devtools::install_github("rosalieb/serac") (default of build_vignettes is FALSE).
It works if they use RStudio, but not in 'regular' R.
I encourage people to use RStudio, but I cannot force them, and eventually, I do not understand why it would work in 'regular' R for me but not for them.
They tried to install pandoc, knitr, Rtools - none of these worked.
Here is the error message when my colleague tries to install the package with the vignette:
v checking for file 'C:\Temp\RtmpO8YwVb\remotesf9842f1431\rosalieb-serac-46a3587/DESCRIPTION'
- preparing 'serac':
checking DESCRIPTION meta-information ...
checking DESCRIPTION meta-information ...
v checking DESCRIPTION meta-information
- installing the package to build vignettes
creating vignettes ...
creating vignettes ...
E creating vignettes (4.9s)
--- re-building 'serac.Rmd' using rmarkdown
Error: processing vignette 'serac.Rmd' failed with diagnostics:
Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed.
--- failed re-building 'serac.Rmd'
RESUME : le traitement du fichier suivant a échoué :
'serac.Rmd'
Erreur : Vignette re-building failed.
Exécution arrêtée
Erreur : Failed to install 'serac' from GitHub:
System command 'Rcmd.exe' failed, exit status: 1, stdout & stderr were printed
Thanks in advance for your help!
The message indicates that rmarkdown::render can't find Pandoc.
It looks for it in three places: in the directory specified by the RSTUDIO_PANDOC environment variable, in directories on the PATH, in the directory opt/pandoc in the user's home directory. So your colleagues who have installed it should make sure it is available in one of those locations. They can see the current values of the environment variables by running
Sys.getenv("PATH")
and
Sys.getenv("RSTUDIO_PANDOC")
Temporary changes can be made using
Sys.setenv(RSTUDIO_PANDOC="/path/to/pandoc/directory")
This needs to happen in the session that is trying to install the package and build the vignette, not in the vignette itself.
How to make permanent changes to those values depends on the details of what system they are running.
I have created an R package (not yet on CRAN) and sent it to a colleague (as a .zip file).
Unfortunately, they were unable to properly build/install it without R throwing an error.
The error received was:
Error: Command failed (1)
In addition: Warning message:
The following packages are referenced using Rcpp::depends attributes however are not listed in the Depends, Imports or LinkingTo fields of the package DESCRIPTION file: RcppProgress
To create the package, I used the RcppArmadillo.package.skeleton() function in R v. 3.4.3.
I works for me, but not for my colleague.
My method in building/installing is:
build("package name") # creates a .tar.gz file
install("package name")
Would simply sending the .tar.gz file to my colleague and simply running install() work?
Here is the DESCRIPTION file:
Package: HACSim
Type: Package
Title: Iterative simulation of species haplotype accumulation curves
Version: 1.0
Date: 2018-04-06
Author: Jarrett Phillips
Maintainer: Jarrett Phillips
Description: Iterative simulation of species haplotype accumulation curves for assessment of sampling completeness
License: GPL (>= 3)
NeedsCompilation: Yes
Imports: ape (>= 5.0),
boot (>= 1.3-20),
investr (>= 1.4.0),
mgcv (>= 1.8-23),
pegas (>= 0.10),
Rcpp (>= 0.12.16),
scam (>= 1.2-2)
LinkingTo: Rcpp,
RcppArmadillo
and NAMESPACE
useDynLib(HACSim, .registration=TRUE)
importFrom(Rcpp, evalCpp)
importFrom(ape, base.freq)
importFrom(ape, read.dna)
importFrom(boot, boot)
importFrom(boot, boot.ci)
importFrom(investr, predFit)
importFrom(MASS, mvrnorm)
importFrom(mgcv, gam)
importFrom(mgcv, gam.check)
importFrom(mgcv, predict.gam)
importFrom(pegas, haplotype)
importFrom(rootSolve, uniroot.all)
importFrom(rootSolve, multiroot)
importFrom(scam, scam)
importFrom(scam, scam.check)
importFrom(scam, predict.scam)
exportPattern("^[[:alpha:]]+")
The error is
The following packages are referenced using Rcpp::depends attributes \
however are not listed in the Depends, Imports or LinkingTo fields of\
the package DESCRIPTION file: RcppProgress
which seems plausible given what you now posted for DESCRIPTION and NAMESPACE.
So here is what I would do:
Create the package using the skeleton generator as you have. Extend as neeed as you have. Then ...
Run R CMD build mypackage then
Run R CME check mypackage_1.2.3.tar.gz
This should give you a clear idea as to whether your sources are in good shape. After that, you can create a binary or zip or ... which your colleague should be able to utilise.
Edit: And you should of course grep for RcppProgress upon which you may indeed have an undeclared dependency.
I am currently building an R package, call it mypackage. I generated a package vignette using devtools::use_vignette("my-vignette"), and filled in my-vignette with content. Of course, because it is a package vignette, I need to demonstrate the use of the functions and data contained in this package itself. However, I'm having issues loading the package and its contents when knitting the vignette.
All of the code chunks in the vignette run without error on my local computer, even after restarting R and clearing the workspace. However, when I attempt to build the package using devtools::build(), the build fails with:
Error in library(mypackage): there is no package called `mypackage` Calls: <Anonymous> ... withCallingHandlers -> withVisible -> eval -> eval -> library Execution halted
The full output in the Console from devtools::build() is:
* checking for file ‘/path/to/mypackage/DESCRIPTION’ ... OK
* preparing ‘mypackage’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
Quitting from lines 39-44 (my-vignette.Rmd)
Error: processing vignette 'my-vignette.Rmd' failed with diagnostics:
'my_function' is not an exported object from 'namespace:mypackage'
Execution halted
devtools::document() runs without error, but devtools::build_vignettes() aparently reaches a different error where it cannot use a specific function (but seems to be able to load the package itself):
> devtools::build_vignettes()
Building mypackage vignettes
Moving basic-mypackage-vignette.html, basic-mypackage-vignette.R to inst/doc/
Copying basic-mypackage-vignette.Rmd to inst/doc/
> devtools::build()
'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet CMD build \
'/path/to/mypackage' --no-resave-data --no-manual
* checking for file ‘/path/to/mypackage/DESCRIPTION’ ... OK
* preparing ‘auctestr’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
Quitting from lines 39-44 (my-vignette.Rmd)
Error: processing vignette 'my-vignette.Rmd' failed with
diagnostics:
could not find function "my_function"
Execution halted
Error: Command failed (1)
> devtools::document()
Updating mypackage documentation
Loading mypackage
I assume this is because the package itself does not exist in my R library; I am just loading that package using devtools::load_all() when doing development. How can I get around this and load my package in order to use its functions and data in the package vignette? Specifically, how can I make the package in its functions available to whatever environment knitr is using to knit the vignette?
I have seen other package vignettes load the package directly using library() without issue; for example, in the stringr vignette.
I hope readers can evaluate this without a fully reproducible example; reproducing the entire example is difficult because it requires a full R package directory structure that is difficult to replicate or share here.
I do load directly my package in my vignettes (library(my_package)).
But considering your error, it might not be the problem...
Can you make sure that my_function is indeed exported. You should add the following code ate the end of the documentation of your function.
#' #export
I added a chunk
```{r, include=FALSE}
devtools::load_all(".")
```
at the beginning of the vignette to work around the problem.
However, this doesn't fix the actual problem, as this should not be necessary.
Alternatively you could use the ::: notation, especially if you are not exporting that function, e.g.
mypackage:::my_function()
I've been using travis-ci successfully so far but I'm having trouble when using travis-ci with R 3.4.0 at the vignette building step with the following error in the "building package" section:
* installing the package to build vignettes
* creating vignettes ... ERROR
Error in loadVignetteBuilder(vigns$pkgdir) :
vignette builder 'knitr' not found
Calls: <Anonymous> -> loadVignetteBuilder
Execution halted
When I run R-CMD-check locally it passes and I don't get any errors
Here's the current .travis.yml
language: R
sudo: false
install:
- R -e "0" --args --bootstrap-packrat
cache:
directories:
- $TRAVIS_BUILD_DIR/packrat/src
- $TRAVIS_BUILD_DIR/packrat/lib
packages: true
r_packages:
- covr
after_success:
- Rscript -e 'library(covr); codecov()'
DESCRIPTION has the vignette line in it:
VignetteBuilder: knitr
knitr is also in my packrat.lock file and packrat is used for the build in .travis.yml.
I've tried the following to no avail:
added knitr to the r_packages in .travis.yml
added knitr to the Imports in DESCRIPTION
added r_check_args: "--no-vignettes" to travis.yml in the hopes of skipping the vignette building step.
added packrat call in travis.yml from install to before_install
I'm pretty knew to building R packages, never mind travis-ci so I'm not sure if I understand why the vignette builder would not have access to the knitr package.
Repo: https://github.com/cormac85/datakindr
Travis: https://travis-ci.org/cormac85/datakindr
One potential problem involves the 'Imports' and/or 'Suggests' sections in your description file.
dplyr needs to be in your suggests, if not imports.
See Hadley's 2015 O'Reilly book, R Packages:
Common problems:
The vignette builds interactively, but when checking, it fails with an error about a missing package that you know is installed. This means that you’ve forgotten to declare that dependency in the DESCRIPTION (usually it should go in Suggests).
So in the end I got the build to pass by just removing packrat config from .travis.yml and replacing it with the normal package building config: cache: packages.
The packrat config I used was suggested in the Travis R Documentation and worked well for the rest of the items in the package but it did not work for the loadVignetteBuilder() step during the build.
I am attempting to prepare a package for submission to the CRAN. In my DESCRIPTION file I include non-CRAN packages in the Depends and Suggests arguments. To tell R where to find the non-CRAN packages, I include the Additional_repositories argument; and I include an .onLoad function at the top of my program (i.e., in 'zzz.R'). I am able to build and check (--as-cran) in RStudio with zero warnings, notes or errors so long as all the Depends and Suggests packages are present. I then use devtools::build() to create a .tar.gz file locally.
To test for a successful local install, I remove the non-CRAN packages from my computer and attempt to install the .tar.gz file that I created. I then get the message:
ERROR: dependency 'smwrQW' is not available for package 'baytrends'
I've read through the
R package dependencies not installed from Additional_repositories
Include non-CRAN package in CRAN package
http://thecoatlessprofessor.com/programming/r-data-packages-in-external-data-repositories-using-the-additional_repositories-field/
How should I deal with "package 'xxx' is not available (for R version x.y.z)" warning?
Unfortunately, the above error continues. I'm confident of the url I'm using since the below install.package line works when run independently
install.packages('smwrQW',repos=c("http://owi.usgs.gov/R"),dependencies = TRUE)
The applicable bits of the DESCRIPTION and zzz.R file are below:
DESCRIPTION:
Date: 2017-03-15
Depends:
R (>= 3.2.0),
lubridate,
mgcv,
smwrQW
License: GPL-3
LazyData: TRUE
RoxygenNote: 6.0.1
Suggests:
dataRetrieval,
devtools,
fitdistrplus,
knitr,
nlme,
pander,
plyr,
rmarkdown,
smwrBase,
smwrGraphs,
smwrStats,
testthat
Additional_repositories: http://owi.usgs.gov/R
VignetteBuilder: knitr
zzz.R:
.onLoad <- function(libname = find.package("baytrends"), pkgname = "baytrends"){
repos = getOption("repos")
repos["USGS"] = "http://owi.usgs.gov/R"
options(repos = repos)
invisible(repos)
# declaration of global variables (https://stackoverflow.com/questions/9439256)
if(getRversion() >= "2.15.1")
utils::globalVariables(c("begin", "methodsList"))
invisible()
}
.onAttach <- function(libname = find.package("baytrends"), pkgname = "baytrends"){
packageStartupMessage("This software program is preliminary or provisional and is subject to revision. ")
}
You cannot have packages from non-standard repos in Depends: or Imports:.
You can have them in Suggests:
Several packages do this; one you could look at is hurricaneexposure which uses this to make a 'too-large-for-CRAN' data package hurricanexposuredata available from a repository created via drat.
So you must move the smwrQR package to Suggests: and then test for it.
Brooke and I have a draft paper (under review) on this which we could send you if you drop us line -- it details all this more than the short answer could.