Context
I've been developing a proprietary package (call it "my_pkg") with vignettes, in RStudio with the latest version (4.1.1) of R. I'm working on a Lenovo ThinkPad with the following software
sysname release version machine
"Windows" "10 x64" "build 19043" "x86-64"
as provided by Sys.info().
Until recently, my devtools workflow has been reasonably smooth (with one occasional exception). However, I've begun to encounter a very puzzling error, which occurs under conditions virtually identical to those beforehand, when the workflow proceeded without issue.
Despite the fact that my vignettes always built successfully before, and I have not edited them in the meantime, the build now fails for architecturally specific reasons...
Error : package 'my_pkg' is not installed for 'arch = x64'
...when and only when I include the vignettes in the build.
I have reinstalled R (and Rtools and RStudio) from scratch, reinstalled devtools (and its dependencies), and "rewound" my project to the last Git commit at which devtools::check() succeeded. I have also walked through extensive troubleshooting with responders like @SteffenMoritz and @Alexis, for whom I have appended further information in the section Info by Request.
Unfortunately, nothing has worked.
Failure With devtools::check()
When I run devtools::check(), everything starts promisingly...
i Updating my_pkg documentation
i Loading my_pkg
Writing NAMESPACE
Writing NAMESPACE
-- Building --------------------------------------------------------------------------------- my_pkg --
Setting env vars:
* CFLAGS : -Wall -pedantic
* CXXFLAGS : -Wall -pedantic
* CXX11FLAGS: -Wall -pedantic
-------------------------------------------------------------------------------------------------------
√ checking for file 'C:\Users\greg\Workspace\R\Packages\my_pkg/DESCRIPTION' ...
- preparing 'my_pkg': (733ms)
√ checking DESCRIPTION meta-information ...
- installing the package to build vignettes
-----------------------------------
- installing *source* package 'my_pkg' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'my_pkg'
finding HTML links ... done
foo html
my_pkg-package html
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
...until the step testing if installed package can be loaded from temporary location. Here an error occurs:
Error : package 'my_pkg' is not installed for 'arch = x64'
Error: loading failed
Execution halted
ERROR: loading failed
- removing 'C:/Users/greg/AppData/Local/Temp/RtmpSaabgx/Rinst332419517258/my_pkg'
-----------------------------------
ERROR: package installation failed
Error in (function (command = NULL, args = character(), error_on_status = TRUE, :
System command 'Rcmd.exe' failed, exit status: 1, stdout + stderr (last 10 lines):
E> ** building package indices
E> ** installing vignettes
E> ** testing if installed package can be loaded from temporary location
E> Error : package 'my_pkg' is not installed for 'arch = x64'
E> Error: loading failed
E> Execution halted
E> ERROR: loading failed
E> * removing 'C:/Users/greg/AppData/Local/Temp/RtmpSaabgx/Rinst332419517258/my_pkg'
E> -----------------------------------
E> ERROR: package installation failed
Type .Last.error.trace to see where the error occurred
The .Last.error.trace suggests an issue with pkgbuild specifically:
> .Last.error.trace
Stack trace:
1. devtools::check()
2. withr::with_envvar(pkgbuild::compiler_flags(FALSE), action = "prefix", ...
3. base:::force(code)
4. pkgbuild::build(pkg$path, tempdir(), args = build_args, quiet = quiet, ...
5. withr::with_temp_libpaths(rcmd_build_tools(options$cmd, c(options$path, ...
6. base:::force(code)
7. pkgbuild:::rcmd_build_tools(options$cmd, c(options$path, options$args), ...
8. pkgbuild:::with_build_tools(callr::rcmd_safe(..., env = env, ...
9. withr::with_path(rtools_path(), code)
10. base:::force(code)
11. callr::rcmd_safe(..., env = env, spinner = FALSE, show = FALSE, ...
12. callr:::run_r(options)
13. base:::with(options, with_envvar(env, do.call(processx::run, ...
14. base:::with.default(options, with_envvar(env, do.call(processx::run, ...
15. base:::eval(substitute(expr), data, enclos = parent.frame())
16. base:::eval(substitute(expr), data, enclos = parent.frame())
17. callr:::with_envvar(env, do.call(processx::run, c(list(bin, args = real_cmdargs, ...
18. base:::force(code)
19. base:::do.call(processx::run, c(list(bin, args = real_cmdargs, ...
20. (function (command = NULL, args = character(), error_on_status = TRUE, ...
21. throw(new_process_error(res, call = sys.call(), echo = echo, ...
I have no clue as to why the architecture
Error : package 'my_pkg' is not installed for 'arch = x64'
should be an issue only now. There have been no substantive changes to my computer.
Despite the message package installation failed, and despite the fact that I've run devtools::check() rather than devtools::install(), the package acts as if it were "halfway" installed! I can type my_p in the console, and RStudio will autocomplete my_pkg; and I can then type my_pkg:: and RStudio will supply the standard autocompletion list of the functions in my_pkg, which are all available.
However, typing my_pkg:: not only summons the @exported functions but also exposes my internal functions and data, as if I had typed my_pkg:::!
Success With devtools::install() or devtools::build(vignettes = FALSE)
Oddly, when I actually run devtools::install(), or comparably devtools::build_vignettes(vignettes = FALSE), the process completes without a hitch!
√ checking for file 'C:\Users\greg\Workspace\R\Packages\my_pkg/DESCRIPTION' ...
- preparing 'my_pkg': (640ms)
√ checking DESCRIPTION meta-information ...
- checking for LF line-endings in source and make files and shell scripts (384ms)
- checking for empty or unneeded directories
Removed empty directory 'my_pkg/inst/libs'
Omitted 'LazyData' from DESCRIPTION
- building 'my_pkg_0.0.0.9000.tar.gz'
Running "C:/Users/greg/R/bin/x64/Rcmd.exe" INSTALL \
"C:\Users\greg\AppData\Local\Temp\Rtmpozvh26/my_pkg_0.0.0.9000.tar.gz" --install-tests
* installing to library 'C:/Users/greg/R/library'
* installing *source* package 'my_pkg' ...
** using staged installation
** R
** inst
** tests
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'my_pkg'
finding HTML links ... done
foo html
my_pkg-package html
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
*** arch - i386
*** arch - x64
** testing if installed package can be loaded from final location
*** arch - i386
*** arch - x64
** testing if installed package keeps a record of temporary installation path
* DONE (my_pkg)
Making 'packages.html' ... done
Now, the autocompletion works entirely as expected, and only the appropriate functions are exposed by my_pkg:: and my_pkg::: respectively.
Failure With devtools::install(build_vignettes = TRUE) or devtools::build()
Yet there is one further plot twist. When I use devtools::install(build_vignettes = TRUE), or comparably devtools::build(), I get a similar error to that with devtools::check():
√ checking for file 'C:\Users\greg\Workspace\R\Packages\my_pkg/DESCRIPTION' ...
- preparing 'my_pkg': (672ms)
√ checking DESCRIPTION meta-information ...
- installing the package to build vignettes
-----------------------------------
- installing *source* package 'my_pkg' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'my_pkg'
finding HTML links ... done
foo html
my_pkg-package html
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Error : package 'my_pkg' is not installed for 'arch = x64'
Error: loading failed
Execution halted
ERROR: loading failed
- removing 'C:/Users/greg/AppData/Local/Temp/RtmpM7RbHr/Rinst504119422cd/my_pkg'
-----------------------------------
ERROR: package installation failed
Error in (function (command = NULL, args = character(), error_on_status = TRUE, :
System command 'Rcmd.exe' failed, exit status: 1, stdout + stderr (last 10 lines):
E> ** building package indices
E> ** installing vignettes
E> ** testing if installed package can be loaded from temporary location
E> Error : package 'my_pkg' is not installed for 'arch = x64'
E> Error: loading failed
E> Execution halted
E> ERROR: loading failed
E> * removing 'C:/Users/greg/AppData/Local/Temp/RtmpM7RbHr/Rinst504119422cd/my_pkg'
E> -----------------------------------
E> ERROR: package installation failed
Type .Last.error.trace to see where the error occurred
Success With devtools::build_vignettes()
Bizarrely, despite the issues above with building vignettes, everything somehow runs smoothly when I call devtools::build_vignettes() sans arguments or with dependencies = TRUE:
i Building my_pkg vignettes
√ Creating 'doc/'
√ Adding '^doc$' to '.Rbuildignore'
√ Setting active project to '<no active project>'
√ Adding '/doc/' to '.gitignore'
√ Setting active project to '<no active project>'
i Moving backstory.html, intro.html, library.html, template.html, usage.html, backstory.R, intro.R, library.R, template.R, and usage.R to doc/
i Copying backstory.Rmd, intro.Rmd, library.Rmd, template.Rmd, and usage.Rmd to doc/
√ Creating 'Meta/'
√ Adding '^Meta$' to '.Rbuildignore'
√ Setting active project to '<no active project>'
√ Adding '/Meta/' to '.gitignore'
√ Setting active project to '<no active project>'
i Building vignette index
Note
Assuming that the fault was mine, and that I had unwittingly introduced an issue somewhere within my R project, I switched to an entirely different Git branch. The most recent commit to this branch had passed devtools::check() with flying colors. However, even after switching over to this "safe" branch, those same issues continued!
Between that last successful check and when the issues began, I made no updates to:
- R itself
- RStudio
- Any R packages
- My computer's software (with the exception of a minor anti-malware update from Microsoft).
- My computer's hardware
Likewise, the vignettes have been present since far earlier in the project.
Conclusion
I'm hoping to roll out a proof of concept for my_pkg in the rather near future, and the vignettes are quite essential to its usability.
Info by Request
Since "my_pkg" is proprietary, I here anonymize my personal and organizational information (names, filepaths, etc.) as above.
For @SteffenMoritz
Would you mind sharing your DESCRIPTION file and the vignette header/meta information?
The DESCRIPTION file:
Package: my_pkg
Title: Proprietary Package for My Org
Version: 0.0.0.9000
Authors@R:
person(given = "Greg",
family = "Lastname",
role = c("aut", "cre"),
email = c("glastname@myorg.com"))
Description: The `my_pkg` package is a proprietary project for My Org,
and as such I have changed the names to project the innocent.
License: file LICENSE
Encoding: UTF-8
LazyData: true
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.1.2
URL: https://github.com/myorg/my_pkg
BugReports: https://github.com/my_org/my_pkg/issues
Suggests:
knitr,
rmarkdown,
testthat (>= 3.0.0)
Config/testthat/edition: 3
VignetteBuilder: knitr
Depends:
R (>= 2.10)
The vignette headers:
intro.Rmd:
---
title: "A Catchphrase!"
author: "Gregory Lastname"
date: "`r Sys.Date()`"
output: rmarkdown::html_vignette
vignette: >
%\VignetteIndexEntry{A Catchphrase!}
%\VignetteEngine{knitr::rmarkdown}
%\VignetteEncoding{UTF-8}
---
```{r, include = FALSE}
knitr::opts_chunk$set(
# Show no output.
eval = FALSE, results = "hide",
# Show no dialog.
message = FALSE, warning = FALSE,
# Show no errors.
error = TRUE, purl = FALSE,
# Default format.
collapse = TRUE, comment = "#>"
)
```
backstory.Rmd:
---
title: "A Reference, to Science Fiction"
author: "Gregory Lastname"
date: "`r Sys.Date()`"
output: rmarkdown::html_vignette
vignette: >
%\VignetteIndexEntry{A Reference, to Science Fiction}
%\VignetteEngine{knitr::rmarkdown}
%\VignetteEncoding{UTF-8}
---
```{r, include = FALSE}
knitr::opts_chunk$set(
# Show no output.
eval = FALSE, results = "hide",
# Show no dialog.
message = FALSE, warning = FALSE,
# Show no errors.
error = TRUE, purl = FALSE,
# Default format.
collapse = TRUE, comment = "#>"
)
```
library.Rmd
---
title: "A Generic One-Liner"
author: "Gregory Lastname"
date: "`r Sys.Date()`"
output: rmarkdown::html_vignette
vignette: >
%\VignetteIndexEntry{A Generic One-Liner}
%\VignetteEngine{knitr::rmarkdown}
%\VignetteEncoding{UTF-8}
---
```{r, include = FALSE}
knitr::opts_chunk$set(
# Show no output.
eval = FALSE, results = "hide",
# Show no dialog.
message = FALSE, warning = FALSE,
# Show no errors.
error = TRUE, purl = FALSE,
# Default format.
collapse = TRUE, comment = "#>"
)
```
template.Rmd
---
title: "A Well-Written Description"
author: "Gregory Lastname"
date: "`r Sys.Date()`"
output: rmarkdown::html_vignette
vignette: >
%\VignetteIndexEntry{A Well-Written Description}
%\VignetteEngine{knitr::rmarkdown}
%\VignetteEncoding{UTF-8}
---
```{r, include = FALSE}
knitr::opts_chunk$set(
# Show no output.
eval = FALSE, results = "hide",
# Show no dialog.
message = FALSE, warning = FALSE,
# Show no errors.
error = TRUE, purl = FALSE,
# Default format.
collapse = TRUE, comment = "#>"
)
```
usage.Rmd
---
title: "An Exhortation!"
author: "Gregory Lastname"
date: "`r Sys.Date()`"
output: rmarkdown::html_vignette
vignette: >
%\VignetteIndexEntry{An Exhortation!}
%\VignetteEngine{knitr::rmarkdown}
%\VignetteEncoding{UTF-8}
---
```{r, include = FALSE}
knitr::opts_chunk$set(
# Show no output.
eval = FALSE, results = "hide",
# Show no dialog.
message = FALSE, warning = FALSE,
# Show no errors.
error = TRUE, purl = FALSE,
# Default format.
collapse = TRUE, comment = "#>"
)
```
For @Alexis
What do you see if you open the
.Rprojfile with a text editor?
The my_pkg.Rproj file, as opened in MS Notepad. NOTE: This file has not been modified since the very initial commit.
Version: 1.0
RestoreWorkspace: No
SaveWorkspace: No
AlwaysSaveHistory: Default
EnableCodeIndexing: Yes
UseSpacesForTab: Yes
NumSpacesForTab: 2
Encoding: UTF-8
RnwWeave: Sweave
LaTeX: pdfLaTeX
AutoAppendNewline: Yes
StripTrailingWhitespace: Yes
LineEndingConversion: Posix
BuildType: Package
PackageUseDevtools: Yes
PackageInstallArgs: --no-multiarch --with-keep.source
PackageRoxygenize: rd,collate,namespace
By request
Does it work if you run
R CMD build/INSTALL ...from the command line?
I also built from the command line
greg@CO-GLASTNAME MINGW64 ~/Workspace/R
$ R CMD build C:/Users/greg/Workspace/R/Packages/my_pkg
but I got the same output echoed above:
* checking for file 'C:/Users/greg/Workspace/R/Packages/my_pkg/DESCRIPTION' ... OK
* preparing 'my_pkg':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
-----------------------------------
* installing *source* package 'my_pkg' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'my_pkg'
finding HTML links ... done
foo html
my_pkg-package html
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Error : package 'my_pkg' is not installed for 'arch = x64'
Error: loading failed
Execution halted
ERROR: loading failed
* removing 'C:/Users/greg/AppData/Local/Temp/RtmpgFIc2r/Rinst1cc0231a6b37/my_pkg'
-----------------------------------
ERROR: package installation failed