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.
Related
I've built an R package and it's available on CRAN. I am updating one of the vignettes and I would like to install a package from GitHub in the vignette. The R CMD Checks ran smoothly on my machine, but after submission to CRAN I received a message indicating that I need to install the package to a temporary library.
I used this code to attempt to install the package to a temporary directory. The code works on my local machine and the R CMD Checks pass locally (devtools::check() and devtools::check(remote = TRUE)). But the checks fail when run on the CRAN machine (rhub::check_for_cran()).
# adding temp_path to .libPaths
temp_path <- file.path(tempdir(), "gt_folder"); dir.create(temp_path)
lib_path <-.libPaths()
.libPaths(c(lib_path, temp_path))
remotes::install_github("rstudio/gt", lib = temp_path)
gt::gt(mtcars)
This is the error I see from rhub::check_for_cran(). It seems the dependencies are not being handled correctly.
ERROR: dependencies 'lazyeval', 'reshape2', 'scales', 'tibble' are not available for package 'ggplot2'
- removing 'C:/Users/USERVzKWFkopnQ/AppData/Local/Temp/RtmpIjoZQH/working_dir/RtmpiwGvJu/gt_folder/ggplot2'
ERROR: dependencies 'fansi', 'utf8', 'vctrs' are not available for package 'pillar'
- removing 'C:/Users/USERVzKWFkopnQ/AppData/Local/Temp/RtmpIjoZQH/working_dir/RtmpiwGvJu/gt_folder/pillar'
The downloaded source packages are in
'C:\Users\USERVzKWFkopnQ\AppData\Local\Temp\RtmpIjoZQH\working_dir\RtmpiwGvJu\downloaded_packages'
ERROR: dependencies 'checkmate', 'commonmark', 'dplyr', 'fs', 'ggplot2', 'sass', 'scales', 'tibble', 'tidyselect' are not available for package 'gt'
- removing 'C:/Users/USERVzKWFkopnQ/AppData/Local/Temp/RtmpIjoZQH/working_dir/RtmpiwGvJu/gt_folder/gt'
Quitting from lines 18-45 (install_from_github.Rmd)
Error: processing vignette 'install_from_github.Rmd' failed with diagnostics:
there is no package called 'gt'
--- failed re-building 'install_from_github.Rmd'
SUMMARY: processing the following file failed:
'install_from_github.Rmd'
Error: Vignette re-building failed.
Execution halted
Here's a light-weight package with only one function and a vignette illustrating the problem https://github.com/ddsjoberg/pkginstallgh
Here is the note I received from CRAN
Dear maintainer,
Pls see
<https://cran.r-project.org/web/checks/check_results_gtsummary.html>.
The check problems on the Debian systems are caused by attempts to write
to the user library to which all packages get installed before checking
(and which now is remounted read-only for checking).
Having package code which is run as part of the checks and attempts to
write to the user library violates the CRAN Policy's
Packages should not write in the user’s home filespace (including
clipboards), nor anywhere else on the file system apart from the R
session’s temporary directory (or during installation in the location
pointed to by TMPDIR: and such usage should be cleaned up).
In your case, you need to teach remotes::install_github("rstudio/gt") to
install to a temporary library and use it from there.
Complete newbie here, so there is probably something glaringly bad here. I created a Project following Hadley Wickham's book on R packages, and now I am trying add it to github for remote install (repository for reference).
Running devtools::install_github("alutterb/abcmlr") generated the following output:
Downloading GitHub repo alutterb/abcmlr#master
√ checking for file 'C:\Users\amlut\AppData\Local\Temp\RtmpMpn5uJ\remotes7146c405dd7\alutterb-abcmlr-918bf05/DESCRIPTION' ...
- preparing 'abcmlr':
√ checking DESCRIPTION meta-information ...
- checking for LF line-endings in source and make files and shell scripts
- checking for empty or unneeded directories
- building 'abcmlr_0.1.0.tar.gz'
Installing package into ‘C:/Users/amlut/Documents/R/win-library/3.5’
(as ‘lib’ is unspecified)
* installing *binary* package 'abcmlr' ...
cp: unknown option -- )
Try '/Rtools/bin/cp --help' for more information.
ERROR: installing binary package failed
* removing 'C:/Users/amlut/Documents/R/win-library/3.5/abcmlr'
In R CMD INSTALL
Error in i.p(...) :
(converted from warning) installation of package ‘C:/Users/amlut/AppData/Local/Temp/RtmpMpn5uJ/file71463953e7b/abcmlr_0.1.0.tar.gz’ had non-zero exit status
In my repository, I have a Linux executable that is to be used with wsl as well as an .exe file that is called in my R code. These may be the culprits, but I am not entirely sure. The error states that it failed to install the binary package, but install_github() takes a source package, so I am not sure what is going on. Any help is appreciated.
Thank you.
EDIT: This problem is solved. It was because of a line in my DESCRIPTION file that had to do with Built.
Check your %PATH% and type: where cp.
Another cp (like one from the Git for Windows distribution) might overshadow the RTools cp, which might explain the error message.
As commented by the OP hkj447, the error was trigger by a line in the DESCRIPTION file:
Built: R 3.5.3; ; 2019-06-14 21:17:43 UTC; windows
As seen in this thread:
You have a field called 'Built:' in your package's DESCRIPTION file;
R normally tries to inject that field itself when it builds your package from sources.
I deleted "Built"'s line in DESCRIPTION and then installed again.
This time, no error appeared.
I wish to include a static PDF file in vignette of my R package biglasso. I followed the instruction here and here. However when I run R CMD check, there is always a NOTE saying:
Vignette sources in 'inst/doc' with no 'vignettes' directory:
'biglasso.pdf.asis'
A 'vignettes' directory is required as from R 3.1.0
and
* checking for old-style vignette sources ... NOTE
Vignette sources only in 'inst/doc':
'biglasso.pdf.asis'
A 'vignettes' directory is required as from R 3.1.0
and these will not be indexed nor checked
Here is the complete package check information.
Could anyone explain to me what this note means and how to fix it?
In a package I'm developing with R Studio, I create vignettes via devtools::use_vignette("mydoc.Rnw"), which gives a standard vignette header like
---
title: "Title"
author: "Michael Friendly"
date: "`r Sys.Date()`"
output: rmarkdown::html_vignette
vignette: >
%\VignetteIndexEntry{Title}
%\VignetteEngine{knitr::rmarkdown}
%\VignetteEncoding{UTF-8}
---
I have followed all the instructions in http://yihui.name/knitr/demo/vignette/ and http://r-pkgs.had.co.nz/vignettes.html. The vignettes are listed on the CRAN page for the package, yet they seem inaccessible in an R session with the package loaded.
> browseVignettes("matlib")
No vignettes found by browseVignettes("matlib")
> library(tools)
> names(vignetteEngine(package = 'matlib'))
Error in getEngine(name, package) :
None of packages ‘matlib’ have registered vignette engines
I know that other packages with knitr-processed .Rmd vignettes are accessible from the package, but can't figure out why mine are not.
What is missing?
My vignettes/ directory contains only the .Rmd files (no PDFs), but that seems the same as, e.g., https://github.com/yihui/knitr/tree/master/vignettes.
Note devtools does not build vignettes by default when you devtools::install() (same thing for some install_* functions like install_github()) a package from a directory. You have to specify the argument build_vignettes = TRUE when you install the package. Currently there is no way to build vignettes using devtools if you just use the RStudio button Build & Reload. You have to Build Source Package, and run R CMD INSTALL on the tarball. Or run devtools::install(build_vignettes = TRUE) in the R console.
Well, I find a dark magic which can work around this situation.
From Configure Build Tools..., RStudio allows us to custom options for R CMD INSTALL when you click the Build & Reload button. In current implementation, it behaves like running R CMD INSTALL [options] pkg at the parent directory of the package directory.
It turns out that these options can be arbitrary strings, even including ;, thus enable us to run bash commands.
For example, we can specify -v; cd pkg; cp vignettes/*html inst/doc; R CMD INSTALL --no-multiarch --with-keep.source .; echo
In this way, -v nullify RStudio's R CMD INSTALL. Then we can copy built html files in vignette/ to inst/doc/ before we install the package using our own R CMD INSTALL. (cd pkg; frees us from type package name multiple times in subsequent commands. echo nullify the package name appended by RStudio.
I know there are many drawbacks in this trick, such as hard-coding package name which is error prone if the package name is changed latter.
Use it at your own risk.
Hope RStudio will comes out a elegant solution soon.
On my end, using devtools::install(build_vignettes = TRUE) would solve the vignettes problem: browseVignettes("mypackage") would work normally. But every time I tried to open a help file ?myfunction, there would be an error message:
Error in fetch(key) : lazy-load database
'/Library/Frameworks/R.framework/Versions/3.6/Resources/library/mypackage/help/mypackage.rdb' is corrupt
The safest way to solve both issues, in my opinion, is to do R CMD build mypackage and R CMD INSTALL mypackage.1.0.tar.gz.
My previously-functioning R package lllcrc recently broke, so I tweaked it, and now I'm having trouble building it again because it acts like it can't see my documentation files:
R CMD INSTALL lllcrc
* installing to library ‘/home/[...]/3.1’
* installing *source* package ‘lllcrc’ ...
** R
** preparing package for lazy loading
** help
No man pages found in package ‘lllcrc’
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (lllcrc)
This is totally weird because I definitely have a complete set of .Rd files in the man folder; in fact, I generated all of these using roxygen2, and all of this worked previously. The R CMD INSTALL even works enough so that the package actually installs and all of its examples run. But documentation is missing. Running ?foo just gives a "no documentation" message.
Another thing: R CMD Rd2pdf lllcrc generates the .pdf documentation as I would expect.
Any ideas?
I just had the same error message ... if you are using roxygen and RStudio then your problem might be the same. The reason became apparent when looking at "Configure build tools" in the "Build" drop-down menu: you need to tick the checkbox "Generate documentation with Roxygen". After that, everything worked.