[R-pkg-devel] Vignette rebuilding failed
Duncan Murdoch
murdoch@dunc@n @end|ng |rom gm@||@com
Sat Apr 1 23:36:50 CEST 2023
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
>
>
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