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[R-pkg-devel] Vignette rebuilding failed

Deepankar Basu 
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)
?? Documenting
?????????????????????????????????????????????????????????????????????????????????????????????
? Updating clptheory documentation
? 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()
?? Documenting
?????????????????????????????????????????????????????????????????????????????????????????????
? Updating clptheory documentation
? 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