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
--
The purpose of studying economics is not to acquire a set of ready-made
answers to economic questions, but to learn how to avoid being deceived by
economists.
~ Joan Robinson
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