[R-pkg-devel] Vignette rebuilding failed
Shota Ochi
@hot@och|1990 @end|ng |rom gm@||@com
Sun Apr 2 00:42:38 CEST 2023
> Error(s) in re-building vignettes:
> ...
> --- re-building ‘lvpp.Rmd’ using rmarkdown
> Quitting from lines 11-15 (lvpp.Rmd)
> Error: processing vignette 'lvpp.Rmd' failed with diagnostics:
> The function xfun::isFALSE() will be deprecated in the future. Please
>consider using base::isFALSE(x) or identical(x, FALSE) instead.
> --- failed re-building ‘lvpp.Rmd’
The error message means a function (knitr::opts_chunk$set) called
xfun::isFALSE() in lines 11-15 (lvpp.Rmd).
However, knitr::opts_chunk$set stopped using xfun::isFALSE().
See the commit shown below.
https://github.com/yihui/knitr/commit/ccb07c4c2266666f7375e5df242103672bd629ac
Updating knitr package should fix the error.
I tested your package on my Ubuntu machine and
got no error even after removing vignettes from .Rbuildignore.
I believe the cause of the error is not your package but your environment.
Best,
Shota Ochi
2023年4月2日(日) 6:44 Duncan Murdoch <murdoch.duncan using gmail.com>:
> The error message seems pretty clear: "The function xfun::isFALSE()
> will be deprecated in the future. Please consider using base::isFALSE(x)
> or identical(x, FALSE) instead".
>
> So don't use xfun::isFALSE().
>
> Duncan Murdoch
>
>
>
> On 31/03/2023 5:01 p.m., Deepankar Basu wrote:
> > Hello All,
> >
> > I am in the process of developing an R package (
> > https://github.com/dbasu-umass/clptheory) and have encountered problems
> > with the vignette.
> >
> > I had initially been able to build the vignette but *after *I added a new
> > function to my package, I have been getting the error message that
> > "Vignette rebuilding failed" when I use devtools:check().
> >
> > If I use devtools:check(vignette=FALSE), there are no error messages. I
> can
> > also compile the vignette with knitr.
> >
> > Below is the output from devtools:check(vignette=FALSE)
> >> devtools::check(vignettes = FALSE)
> > ══ Documenting
> >
> ═════════════════════════════════════════════════════════════════════════════════════════════
> > ℹ Updating clptheory documentation
> > ℹ Loading clptheory
> >
> > ══ Building
> >
> ════════════════════════════════════════════════════════════════════════════════════════════════
> > Setting env vars:
> > • CFLAGS : -Wall -pedantic -fdiagnostics-color=always
> > • CXXFLAGS : -Wall -pedantic -fdiagnostics-color=always
> > • CXX11FLAGS: -Wall -pedantic -fdiagnostics-color=always
> > • CXX14FLAGS: -Wall -pedantic -fdiagnostics-color=always
> > • CXX17FLAGS: -Wall -pedantic -fdiagnostics-color=always
> > • CXX20FLAGS: -Wall -pedantic -fdiagnostics-color=always
> > ── R CMD build
> >
> ─────────────────────────────────────────────────────────────────────────────────────────────
> > ✔ checking for file ‘/home/basu15/MyRProjects/clptheory/DESCRIPTION’ ...
> > ─ preparing ‘clptheory’:
> > ✔ checking DESCRIPTION meta-information ...
> > ─ checking for LF line-endings in source and make files and shell
> scripts
> > ─ checking for empty or unneeded directories
> > ─ building ‘clptheory_0.0.0.9000.tar.gz’
> >
> > ══ Checking
> >
> ════════════════════════════════════════════════════════════════════════════════════════════════
> > Setting env vars:
> > • _R_CHECK_CRAN_INCOMING_USE_ASPELL_ : TRUE
> > • _R_CHECK_CRAN_INCOMING_REMOTE_ : FALSE
> > • _R_CHECK_CRAN_INCOMING_ : FALSE
> > • _R_CHECK_FORCE_SUGGESTS_ : FALSE
> > • _R_CHECK_PACKAGES_USED_IGNORE_UNUSED_IMPORTS_: FALSE
> > • NOT_CRAN : true
> > ── R CMD check
> >
> ─────────────────────────────────────────────────────────────────────────────────────────────
> > ─ using log directory
> ‘/tmp/RtmpCSbZbZ/file3f721a56f9d0/clptheory.Rcheck’
> > ─ using R version 4.2.3 (2023-03-15)
> > ─ using platform: x86_64-pc-linux-gnu (64-bit)
> > ─ using session charset: UTF-8
> > ─ using options ‘--no-manual --ignore-vignettes --as-cran’
> > ✔ checking for file ‘clptheory/DESCRIPTION’
> > ─ this is package ‘clptheory’ version ‘0.0.0.9000’
> > ─ package encoding: UTF-8
> > ✔ checking package namespace information
> > ✔ checking package dependencies (2.5s)
> > ✔ checking if this is a source package ...
> > ✔ checking if there is a namespace
> > ✔ checking for executable files ...
> > ✔ checking for hidden files and directories ...
> > ✔ checking for portable file names
> > ✔ checking for sufficient/correct file permissions
> > ✔ checking serialization versions ...
> > ✔ checking whether package ‘clptheory’ can be installed (7.1s)
> > ✔ checking installed package size
> > ✔ checking package directory ...
> > ✔ checking for future file timestamps ...
> > ✔ checking DESCRIPTION meta-information ...
> > ✔ checking top-level files ...
> > ✔ checking for left-over files
> > ✔ checking index information
> > ✔ checking package subdirectories ...
> > ✔ checking R files for non-ASCII characters ...
> > ✔ checking R files for syntax errors ...
> > ✔ checking whether the package can be loaded (1.8s)
> > ✔ checking whether the package can be loaded with stated dependencies
> > (1.6s)
> > ✔ checking whether the package can be unloaded cleanly (1.6s)
> > ✔ checking whether the namespace can be loaded with stated dependencies
> > (1.6s)
> > ✔ checking whether the namespace can be unloaded cleanly (1.8s)
> > ✔ checking loading without being on the library search path (1.8s)
> > ✔ checking dependencies in R code (1.7s)
> > ✔ checking S3 generic/method consistency (2.4s)
> > ✔ checking replacement functions (1.7s)
> > ✔ checking foreign function calls (1.7s)
> > ✔ checking R code for possible problems (9.5s)
> > ✔ checking Rd files ...
> > ✔ checking Rd metadata ...
> > ✔ checking Rd line widths ...
> > ✔ checking Rd cross-references ...
> > ✔ checking for missing documentation entries (1.7s)
> > ✔ checking for code/documentation mismatches (5.1s)
> > ✔ checking Rd \usage sections (2.5s)
> > ✔ checking Rd contents ...
> > ✔ checking for unstated dependencies in examples ...
> > ✔ checking contents of ‘data’ directory ...
> > ✔ checking data for non-ASCII characters (413ms)
> > ✔ checking LazyData
> > ✔ checking data for ASCII and uncompressed saves ...
> > ─ checking files in ‘vignettes’ ... SKIPPED
> > ✔ checking examples (4.9s)
> > ✔ checking for non-standard things in the check directory
> > ✔ checking for detritus in the temp directory
> >
> >
> > ── R CMD check results
> > ─────────────────────────────────────────────────────────── clptheory
> > 0.0.0.9000 ────
> > Duration: 55.1s
> >
> > 0 errors ✔ | 0 warnings ✔ | 0 notes ✔
> >
> > Below is the output form devtools:check()
> >
> >> devtools::check()
> > ══ Documenting
> >
> ═════════════════════════════════════════════════════════════════════════════════════════════
> > ℹ Updating clptheory documentation
> > ℹ Loading clptheory
> >
> > ══ Building
> >
> ════════════════════════════════════════════════════════════════════════════════════════════════
> > Setting env vars:
> > • CFLAGS : -Wall -pedantic -fdiagnostics-color=always
> > • CXXFLAGS : -Wall -pedantic -fdiagnostics-color=always
> > • CXX11FLAGS: -Wall -pedantic -fdiagnostics-color=always
> > • CXX14FLAGS: -Wall -pedantic -fdiagnostics-color=always
> > • CXX17FLAGS: -Wall -pedantic -fdiagnostics-color=always
> > • CXX20FLAGS: -Wall -pedantic -fdiagnostics-color=always
> > ── R CMD build
> >
> ─────────────────────────────────────────────────────────────────────────────────────────────
> > ✔ checking for file ‘/home/basu15/MyRProjects/clptheory/DESCRIPTION’ ...
> > ─ preparing ‘clptheory’:
> > ✔ checking DESCRIPTION meta-information ...
> > ─ installing the package to build vignettes
> > ✔ creating vignettes (9.9s)
> > ─ checking for LF line-endings in source and make files and shell
> scripts
> > ─ checking for empty or unneeded directories
> > ─ building ‘clptheory_0.0.0.9000.tar.gz’
> >
> > ══ Checking
> >
> ════════════════════════════════════════════════════════════════════════════════════════════════
> > Setting env vars:
> > • _R_CHECK_CRAN_INCOMING_USE_ASPELL_ : TRUE
> > • _R_CHECK_CRAN_INCOMING_REMOTE_ : FALSE
> > • _R_CHECK_CRAN_INCOMING_ : FALSE
> > • _R_CHECK_FORCE_SUGGESTS_ : FALSE
> > • _R_CHECK_PACKAGES_USED_IGNORE_UNUSED_IMPORTS_: FALSE
> > • NOT_CRAN : true
> > ── R CMD check
> >
> ─────────────────────────────────────────────────────────────────────────────────────────────
> > ─ using log directory
> ‘/tmp/RtmpCSbZbZ/file3f72577bb739/clptheory.Rcheck’
> > ─ using R version 4.2.3 (2023-03-15)
> > ─ using platform: x86_64-pc-linux-gnu (64-bit)
> > ─ using session charset: UTF-8
> > ─ using options ‘--no-manual --as-cran’
> > ✔ checking for file ‘clptheory/DESCRIPTION’
> > ─ this is package ‘clptheory’ version ‘0.0.0.9000’
> > ─ package encoding: UTF-8
> > ✔ checking package namespace information
> > ✔ checking package dependencies (2.9s)
> > ✔ checking if this is a source package ...
> > ✔ checking if there is a namespace
> > ✔ checking for executable files ...
> > ✔ checking for hidden files and directories ...
> > ✔ checking for portable file names
> > ✔ checking for sufficient/correct file permissions
> > ✔ checking serialization versions ...
> > ✔ checking whether package ‘clptheory’ can be installed (7.6s)
> > ✔ checking installed package size ...
> > ✔ checking package directory
> > ✔ checking for future file timestamps ...
> > ✔ checking ‘build’ directory ...
> > ✔ checking DESCRIPTION meta-information ...
> > ✔ checking top-level files ...
> > ✔ checking for left-over files
> > ✔ checking index information ...
> > ✔ checking package subdirectories ...
> > ✔ checking R files for non-ASCII characters ...
> > ✔ checking R files for syntax errors ...
> > ✔ checking whether the package can be loaded (2s)
> > ✔ checking whether the package can be loaded with stated dependencies
> > (1.8s)
> > ✔ checking whether the package can be unloaded cleanly (1.7s)
> > ✔ checking whether the namespace can be loaded with stated dependencies
> > (1.8s)
> > ✔ checking whether the namespace can be unloaded cleanly (1.8s)
> > ✔ checking loading without being on the library search path (1.8s)
> > ✔ checking dependencies in R code (1.7s)
> > ✔ checking S3 generic/method consistency (2.3s)
> > ✔ checking replacement functions (1.6s)
> > ✔ checking foreign function calls (1.7s)
> > ✔ checking R code for possible problems (10s)
> > ✔ checking Rd files (367ms)
> > ✔ checking Rd metadata ...
> > ✔ checking Rd line widths ...
> > ✔ checking Rd cross-references ...
> > ✔ checking for missing documentation entries (2.1s)
> > ✔ checking for code/documentation mismatches (8.9s)
> > ✔ checking Rd \usage sections (3.3s)
> > ✔ checking Rd contents ...
> > ✔ checking for unstated dependencies in examples ...
> > ✔ checking contents of ‘data’ directory (335ms)
> > ✔ checking data for non-ASCII characters (584ms)
> > ✔ checking LazyData
> > ✔ checking data for ASCII and uncompressed saves (535ms)
> > ✔ checking installed files from ‘inst/doc’
> > ✔ checking files in ‘vignettes’
> > ✔ checking examples (6.9s)
> > ✔ checking for unstated dependencies in vignettes ...
> > ✔ checking package vignettes in ‘inst/doc’
> > E checking re-building of vignette outputs (594ms)
> > Error(s) in re-building vignettes:
> > ...
> > --- re-building ‘lvpp.Rmd’ using rmarkdown
> > Quitting from lines 11-15 (lvpp.Rmd)
> > Error: processing vignette 'lvpp.Rmd' failed with diagnostics:
> > The function xfun::isFALSE() will be deprecated in the future. Please
> > consider using base::isFALSE(x) or identical(x, FALSE) instead.
> > --- failed re-building ‘lvpp.Rmd’
> >
> > SUMMARY: processing the following file failed:
> > ‘lvpp.Rmd’
> >
> > Error: Vignette re-building failed.
> > Execution halted
> >
> > ✔ checking for non-standard things in the check directory
> > ✔ checking for detritus in the temp directory
> >
> > See
> > ‘/tmp/RtmpCSbZbZ/file3f72577bb739/clptheory.Rcheck/00check.log’
> > for details.
> >
> >
> > ── R CMD check results
> > ─────────────────────────────────────────────────────────── clptheory
> > 0.0.0.9000 ────
> > Duration: 1m 6.2s
> >
> > ❯ checking re-building of vignette outputs ... ERROR
> > Error(s) in re-building vignettes:
> > ...
> > --- re-building ‘lvpp.Rmd’ using rmarkdown
> > Quitting from lines 11-15 (lvpp.Rmd)
> > Error: processing vignette 'lvpp.Rmd' failed with diagnostics:
> > The function xfun::isFALSE() will be deprecated in the future. Please
> > consider using base::isFALSE(x) or identical(x, FALSE) instead.
> > --- failed re-building ‘lvpp.Rmd’
> >
> > SUMMARY: processing the following file failed:
> > ‘lvpp.Rmd’
> >
> > Error: Vignette re-building failed.
> > Execution halted
> >
> > 1 error ✖ | 0 warnings ✔ | 0 notes ✔
> >
> > My package is available here: https://github.com/dbasu-umass/clptheory
> >
> > Any help will be appreciated. (I found a few pages like this
> > <https://github.com/r-lib/devtools/issues/2140> on this problem but the
> > issue does not seem to have been resolved).
> >
> > Thank you.
> > DB
> >
> >
>
> ______________________________________________
> R-package-devel using r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>
[[alternative HTML version deleted]]
More information about the R-package-devel
mailing list