> Here is my namespace. It says not to edit, but I had been told to add > the importFrom. So I didn't use > devtools::document() for fear roxygen2 would get rid of it.
`devtools::check()` calls `document()` automatically so your changes to the NAMESPACE file get overwritten. You can see this in the output. To solve this, add the appropriate roxygen2 tag somewhere in your package e.g. ``` #' @importFrom stats var sd etc NULL ``` Best, Lionel On 4/4/23, Lionel Henry <lio...@posit.co> wrote: >> Here is my namespace. It says not to edit, but I had been told to add >> the importFrom. So I didn't use >> devtools::document() for fear roxygen2 would get rid of it. > > `devtools::check()` calls `document()` automatically so your changes to > the NAMESPACE file get overwritten. You can see this in the output. > > To solve this, add the appropriate roxygen2 tag somewhere in your package > e.g. > > ``` > #' @importFrom stats var sd etc > NULL > ``` > > Best, > Lionel > > On 4/4/23, Dennis Boos <b...@ncsu.edu> wrote: >> Thanks so much to all of you. If you have time, I'm getting really >> contradictory results. >> >> 1. It first seemed to have passed the check in Rstudio (I used >> device::build() in the R window and then clicked on check in the drop >> down >> menu under build). >> >> ==> devtools::check(document = FALSE, args = c('--as-cran')) >> ── R CMD check results Monte.Carlo.se 0.1.1 ──── >> Duration: 56.6s >> 0 errors ✔ | 0 warnings ✔ | 0 notes ✔ >> >> R CMD check succeeded >> >> However, I then couldn't find the tar.gz where it was supposed to be. It >> was just gone. >> >> >> Here is my namespace. It says not to edit, but I had been told to add >> the importFrom. So I didn't use >> devtools::document() for fear roxygen2 would get rid of it. >> >> # Generated by roxygen2: do not edit by hand >> importFrom("stats", "cor", "sd", "var") >> export(boot.se) >> export(jack.se) >> export(mc.se.matrix) >> export(mc.se.vector) >> export(pairwise.se) >> export(sim.samp) >> >> 4. Here is my DESCRIPTION file >> >> Package: Monte.Carlo.se >> Type: Package >> Title: Monte Carlo Standard Errors >> Version: 0.1.1 >> Author: Dennis Boos, Kevin Matthew, Jason Osborne >> Maintainer: Dennis Boos <b...@ncsu.edu> >> Description: Computes Monte Carlo standard errors for summaries of >> Monte Carlo output. Summaries and their standard errors are based on >> columns of Monte Carlo simulation output. Dennis D. Boos and Jason A. >> Osborne (2015) <doi:10.1111/insr.12087>. >> License: GPL-3 >> Encoding: UTF-8 >> RoxygenNote: 7.2.3 >> Suggests: knitr, rmarkdown >> Imports: stats >> VignetteBuilder: knitr >> >> 5. And because of your advice: " It sounds as though you're using >> Roxygen2 to generate your NAMESPACE file. >> ff so, you need @imports directives in the comments >> (conventionally before the function that uses the import, but I think it >> doesn't really matter where)." >> >> So I put "@imports" in the function that had trouble >> >> #' @examples >> #' \donttest{ >> #' # Using the output data matrix hold generated in vignette Example3, >> #' # calculate jackknife and bootstrap standard errors >> #' # for the differences and ratios of the CV estimates. >> #' # First get the components of hold needed. >> #' >> #' @imports >> #' >> #' trim20 <- function(x){mean(x,.2)} # 20% trimmed mean function >> >> Was that the correct thing to do? >> >> 6. And here are the failed check results. I'm clueless at this point. >> >> ==> devtools::check(document = FALSE, args = c('--as-cran')) >> ══ 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 'C:\Users\boos\Dropbox\My PC >> (boos-home)\Desktop\dennis\R.packages\Monte.Carlo.se.March.2023/DESCRIPTION' >> ...─ preparing 'Monte.Carlo.se':✔ checking DESCRIPTION >> meta-information ...─ installing the package to build vignettes✔ >> creating vignettes (3.6s)─ checking for LF line-endings in source and >> make files and shell scripts─ checking for empty or unneeded >> directories─ building 'Monte.Carlo.se_0.1.1.tar.gz' >> ══ Checking >> ════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════Setting >> env vars: >> • _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 'C:/Users/boos/Dropbox/My PC >> (boos-home)/Desktop/dennis/R.packages/Monte.Carlo.se.Rcheck' (793ms)─ >> using R version 4.2.3 (2023-03-15 ucrt)─ using platform: >> x86_64-w64-mingw32 (64-bit)─ using session charset: UTF-8─ using >> options '--no-manual --as-cran' (653ms)✔ checking for file >> 'Monte.Carlo.se/DESCRIPTION'─ checking extension type ... Package─ >> this is package 'Monte.Carlo.se' version '0.1.1'─ package encoding: >> UTF-8✔ checking package namespace information✔ checking package >> dependencies (3.2s)✔ checking if this is a source package✔ checking >> if there is a namespace✔ checking for executable files (491ms)✔ >> checking for hidden files and directories ...✔ checking for portable >> file names✔ checking serialization versions✔ checking whether >> package 'Monte.Carlo.se' can be installed (2.9s)✔ 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 ... ✔ checking whether the package >> can be loaded with stated dependencies ... ✔ checking whether the >> package can be unloaded cleanly ... ✔ checking whether the namespace >> can be loaded with stated dependencies ... ✔ checking whether the >> namespace can be unloaded cleanly ... ✔ checking loading without >> being on the library search path ... N checking dependencies in R >> code ... >> Namespace in Imports field not imported from: 'stats' >> All declared Imports should be used.✔ checking S3 generic/method >> consistency (422ms)✔ checking replacement functions ... ✔ checking >> foreign function calls ... N checking R code for possible problems >> (3s) >> boot.se: no visible global function definition for 'sd' >> boot.var: no visible global function definition for 'var' >> corr: no visible global function definition for 'cor' >> cv: no visible global function definition for 'sd' >> ratio.mean.sdhat.sd: no visible global function definition for 'sd' >> ratio.mean.vhat.var: no visible global function definition for 'var' >> ratio.sd: no visible global function definition for 'sd' >> ratio.var: no visible global function definition for 'var' >> varn: no visible global function definition for 'var' >> Undefined global functions or variables: >> cor sd var >> Consider adding >> importFrom("stats", "cor", "sd", "var") >> to your NAMESPACE file.✔ checking Rd files ... ✔ checking Rd >> metadata ... ✔ checking Rd line widths ... ✔ checking Rd >> cross-references ... ✔ checking for missing documentation entries ... >> ✔ checking for code/documentation mismatches (562ms)✔ checking Rd >> \usage sections (661ms)✔ checking Rd contents ... ✔ checking for >> unstated dependencies in examples ... ✔ checking installed files from >> 'inst/doc'W checking files in 'vignettes' ... >> Files in the 'vignettes' directory newer than same file in 'inst/doc': >> 'Brief-Overview.Rmd'✔ checking examples (573ms)─ checking >> examples with --run-donttest ... [24s] OK (24.7s)✔ checking for >> unstated dependencies in vignettes ... ✔ checking package vignettes >> in 'inst/doc' ...✔ checking re-building of vignette outputs (6.8s)✔ >> checking for non-standard things in the check directory ...✔ checking >> for detritus in the temp directory >> >> See >> 'C:/Users/boos/Dropbox/My PC >> (boos-home)/Desktop/dennis/R.packages/Monte.Carlo.se.Rcheck/00check.log' >> for details. >> >> ── R CMD check results >> ─────────────────────────────────────────────────────────────────────────────────── >> Monte.Carlo.se 0.1.1 ──── >> Duration: 51.5s >> ❯ checking files in 'vignettes' ... WARNING >> Files in the 'vignettes' directory newer than same file in 'inst/doc': >> 'Brief-Overview.Rmd' >> ❯ checking dependencies in R code ... NOTE >> Namespace in Imports field not imported from: 'stats' >> All declared Imports should be used. >> ❯ checking R code for possible problems ... NOTE >> boot.se: no visible global function definition for 'sd' >> boot.var: no visible global function definition for 'var' >> corr: no visible global function definition for 'cor' >> cv: no visible global function definition for 'sd' >> ratio.mean.sdhat.sd: no visible global function definition for 'sd' >> ratio.mean.vhat.var: no visible global function definition for 'var' >> ratio.sd: no visible global function definition for 'sd' >> ratio.var: no visible global function definition for 'var' >> varn: no visible global function definition for 'var' >> Undefined global functions or variables: >> cor sd var >> Consider adding >> importFrom("stats", "cor", "sd", "var") >> to your NAMESPACE file. >> 0 errors ✔ | 1 warning ✖ | 2 notes ✖ >> Error: R CMD check found WARNINGs >> Execution halted >> >> Exited with status 1. >> >> >> >> >> >> On Sat, Apr 1, 2023 at 5:34 PM Duncan Murdoch <murdoch.dun...@gmail.com> >> wrote: >> >>> On 31/03/2023 4:51 p.m., Dennis Boos wrote: >>> > Recently I got a message from CRAN that my package Monte.Carlo.se (on >>> CRAN >>> > for the last few years) does not pass current testing. There seemed >>> > to >>> be >>> > 2 problems: >>> > >>> > >>> *************************************************************************************************************** >>> > >>> > 1. * checking LazyData ... NOTE >>> > 'LazyData' is specified without a 'data' directory >>> > >>> > I have this line in my DESCRIPTION file: >>> > >>> > LazyData: true >>> > >>> > Should I remove that? >>> > >>> > >>> ***************************************************************************************************************** >>> > >>> > 2. * checking examples with --run-donttest ... [42s/42s] ERROR >>> > Running examples in ‘Monte.Carlo.se-Ex.R’ failed >>> > The error most likely occurred in: >>> > >>> >> pairwise.se(hold,xcol=10:12,summary.f=cv) >>> > Error: object 'hold' not found >>> > Execution halted >>> > >>> > >>> *************************************************************************************** >>> > >>> > So, I put in the R code to generate the data matrix *hold. *But that >>> > brought a host of other errors when checking in Rstudio with >>> > >>> >> >>> devtools::check("S:/Documents/srcis/a.projects/Monte.Carlo.isr.and.package/Monte.Carlo.se.March.2023") >>> > >>> > I started seeing the following list about standard functions like sd. >>> > >>> > N checking R code for possible problems (3.4s) >>> > boot.se: no visible global function definition for 'sd' >>> > boot.var: no visible global function definition for 'var' >>> > corr: no visible global function definition for 'cor' >>> > cv: no visible global function definition for 'sd' >>> > ratio.mean.sdhat.sd: no visible global function definition for >>> > 'sd' >>> > ratio.mean.vhat.var: no visible global function definition for >>> > 'var' >>> > ratio.sd: no visible global function definition for 'sd' >>> > ratio.var: no visible global function definition for 'var' >>> > varn: no visible global function definition for 'var' >>> > Undefined global functions or variables: >>> > cor sd var >>> > Consider adding >>> > importFrom("stats", "cor", "sd", "var") >>> > to your NAMESPACE file. >>> > >>> > But you can't add those functions to NAMESPACE. Well I did but >>> > >>> > devtools::build() >>> > >>> > >>> > gets rid of it. Also, I keep getting the message in the Rstudio check >>> > >>> > WARNING >>> > 'qpdf' is needed for checks on size reduction of PDFs >>> > >>> > >>> > but I got the latest versions of R and Rstudio and was able to get >>> > qpdf to install and loaded with library(qpdf), but Rstudio still gives >>> > that message. >>> > >>> >>> It sounds as though you're using Roxygen2 to generate your NAMESPACE >>> file. If so, you need @imports directives in the comments >>> (conventionally before the function that uses the import, but I think it >>> doesn't really matter where). >>> >>> Duncan Murdoch >>> >>> >> >> -- >> Dennis Boos email: dennis_b...@ncsu.edu >> Department of Statistics Phone: 919-515-1918 >> NC State University Fax: 919-515-1169 >> Raleigh, NC 27695-8203 http://www4.stat.ncsu.edu/~boos >> >> Aim for kindness, tolerance, and humility. >> >> [[alternative HTML version deleted]] >> >> ______________________________________________ >> R-package-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-package-devel >> > ______________________________________________ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel