Dear R Devs,
I am unsure how to resolve this NOTE in my package build (I am
comfortable with the possibly misspelled words part):
Package has help file(s) containing install/render-stage \Sexpr{}
expressions but no prebuilt PDF manual.
I've dozens of files and no idea which one(s) offend, or if I am missing
some other detail. (Aside: I am using mathjaxr... not sure if that is
the issue.)
Links for winbuilder logs are here for the time being:
https://win-builder.r-project.org/qG7LHs2Yf18p
https://win-builder.r-project.org/BBXdLV7kDOuI
https://win-builder.r-project.org/63RmX21pnrAw ?This check passes
Thank you very much,
Alexis Dinno
PS Am including the log from the R-release winbuilder check in case my
links expire:
* using log directory
'd:/RCompile/CRANguest/R-oldrelease/tost.suite.Rcheck'
* using R version 4.4.3 (2025-02-28 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.3.0
GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'tost.suite/DESCRIPTION' ... OK
* this is package 'tost.suite' version '3.15'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [8s] NOTE
Maintainer: 'Alexis Dinno <alexis.dinno at pdx.edu>'
New submission
Possibly misspelled words in DESCRIPTION:
Kolmogorov (9:402)
McNemar's (9:198)
OLS (9:289)
Smirnov (9:413)
Stata (9:47)
Wilcoxon (9:312, 9:340)
nonparametric (9:546)
rrp (9:842)
rrpi (9:855)
tost (9:18, 9:65, 9:837, 9:850)
Package has help file(s) containing install/render-stage \Sexpr{}
expressions but no prebuilt PDF manual.
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'tost.suite' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [1s] OK
* checking whether the package can be loaded with stated dependencies
... [1s] OK
* checking whether the package can be unloaded cleanly ... [1s] OK
* checking whether the namespace can be loaded with stated dependencies
... [1s] OK
* checking whether the namespace can be unloaded cleanly ... [1s] OK
* checking loading without being on the library search path ... [1s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [16s] OK
* checking Rd files ... [1s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... [0s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... [7s] OK
* checking PDF version of manual ... [12s] OK
* checking HTML version of manual ... [5s] OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 NOTE
[R-pkg-devel] How to resolve help files with \Sexpr{} warning?
4 messages · @di@@o m@iii@g oii pdx@edu, Iris Simmons, Ivan Krylov
I believe R CMD build changed the default from --manual to --no-manual, I'm not sure why. You could add --manual when you build the tarball or you could add BuildManual: TRUE to your DESCRIPTION.
On Mon, Apr 14, 2025, 09:41 <adinno at pdx.edu> wrote:
Dear R Devs,
I am unsure how to resolve this NOTE in my package build (I am
comfortable with the possibly misspelled words part):
Package has help file(s) containing install/render-stage \Sexpr{}
expressions but no prebuilt PDF manual.
I've dozens of files and no idea which one(s) offend, or if I am missing
some other detail. (Aside: I am using mathjaxr... not sure if that is
the issue.)
Links for winbuilder logs are here for the time being:
https://win-builder.r-project.org/qG7LHs2Yf18p
https://win-builder.r-project.org/BBXdLV7kDOuI
https://win-builder.r-project.org/63RmX21pnrAw ?This check passes
Thank you very much,
Alexis Dinno
PS Am including the log from the R-release winbuilder check in case my
links expire:
* using log directory
'd:/RCompile/CRANguest/R-oldrelease/tost.suite.Rcheck'
* using R version 4.4.3 (2025-02-28 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.3.0
GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'tost.suite/DESCRIPTION' ... OK
* this is package 'tost.suite' version '3.15'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [8s] NOTE
Maintainer: 'Alexis Dinno <alexis.dinno at pdx.edu>'
New submission
Possibly misspelled words in DESCRIPTION:
Kolmogorov (9:402)
McNemar's (9:198)
OLS (9:289)
Smirnov (9:413)
Stata (9:47)
Wilcoxon (9:312, 9:340)
nonparametric (9:546)
rrp (9:842)
rrpi (9:855)
tost (9:18, 9:65, 9:837, 9:850)
Package has help file(s) containing install/render-stage \Sexpr{}
expressions but no prebuilt PDF manual.
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'tost.suite' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [1s] OK
* checking whether the package can be loaded with stated dependencies
... [1s] OK
* checking whether the package can be unloaded cleanly ... [1s] OK
* checking whether the namespace can be loaded with stated dependencies
... [1s] OK
* checking whether the namespace can be unloaded cleanly ... [1s] OK
* checking loading without being on the library search path ... [1s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [16s] OK
* checking Rd files ... [1s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... [0s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... [7s] OK
* checking PDF version of manual ... [12s] OK
* checking HTML version of manual ... [5s] OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 NOTE
______________________________________________ R-package-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
? Sun, 13 Apr 2025 21:54:03 -0700 (PDT) adinno at pdx.edu ?????:
Package has help file(s) containing install/render-stage \Sexpr{}
expressions but no prebuilt PDF manual.
This is a relatively recent change (r85348, October 2023). Previously, R CMD build detected non-build-time dynamic content in the package documentation and built the manual automatically. Nowadays I think you have to set BuildManual: yes in your DESCRIPTION before building the package. (There's R CMD build --no-manual, but I'm not seeing a command line option to override it from "no" to "yes".)
(Aside: I am using mathjaxr... not sure if that is the issue.)
Correct, that must be what's producing the render-stage dynamic content: https://github.com/wviechtb/mathjaxr/blob/8900cbbb2eda4dc45b776cc203c2942b6289fac3/man/macros/mathjax.Rd#L4
Best regards, Ivan
Dear Iris and Ivan, Together both your comments were very helpful, and both pointed me at a solution to resolve my issue and to explain why this change in behavior emerged, and how my package was triggering the behavior. Solution that worked: Editing the DESCRIPTION file to add the line BuildManual: TRUE Solution that did *not* work (along with variations): R CMD build --manual ?Resulted in: Warning: unknown option ?--manual? R CMD --manual build R --manual CMD build R CMD check --manual Note: I am using R version 4.4.3 (2025-02-28) -- "Trophy Case" on Ubuntu 24.04 Thank you both very much for this help! Alexis Dinno